bims-pimaco 2022-02-06 papers

on PI3K and MAPK signalling in colorectal cancer

Issue of 2022–02–06
sixteen papers selected by
Lucas B. Zeiger, CRUK Scotland Institute, Beatson Institute for Cancer Research

Single cell imaging of ERK and Akt activation dynamics and heterogeneity induced by G protein-coupled receptors.
A brief history of RAS and the RAS Initiative.
Targeting RAS oncogenesis with SOS1 inhibitors.
Recapitulation of cell-like KRAS4b membrane dynamics on complex biomimetic membranes.
Targeting the ERK mitogen-activated protein kinase cascade for the treatment of KRAS-mutant pancreatic cancer.
Pan-RAS inhibitors: Hitting multiple RAS isozymes with one stone.
E3 ligase RNF167 and deubiquitinase STAMBPL1 modulate mTOR and cancer progression.
Not all RAS mutations are equal: A detailed review of the functional diversity of RAS hot spot mutations.
Inhibition of SHP2 as an approach to block RAS-driven cancers.
Interplay between K-RAS and miRNAs.
Drug targeting opportunities en route to Ras nanoclusters.
Targeting the "undruggable" RAS with biologics.
The present and future of PI3K inhibitors for cancer therapy.
Stabilization of the RAS:PDE6D Complex Is a Novel Strategy to Inhibit RAS Signaling.
Dysregulated lipid metabolism in colorectal cancer.
Recent Advances of PI3 Kinase Inhibitors: Structure Anticancer Activity Relationship Studies.

J Cell Sci. 2022 Feb 02. pii: jcs.259685. [Epub ahead of print]

Single cell imaging of ERK and Akt activation dynamics and heterogeneity induced by G protein-coupled receptors.

Sergei Chavez-Abiega, Max L B Grönloh, T W J Gadella, Frank J Bruggeman, J Goedhart.

  Kinases play key roles in signaling networks that are activated by G protein-coupled receptors (GPCRs). Kinase activities are generally inferred from cell lysates, hiding cell-to-cell variability. To study the dynamics and heterogeneity of ERK and Akt, we employed high-content biosensor imaging with kinase translocation reporters. The kinases were activated with GPCR ligands. We observed ligand-concentration dependent response kinetics to histamine, α2-adrenergic, and S1P receptor stimulation. By using G protein inhibitors, we observed that Gq mediated the ERK and Akt responses to histamine. In contrast, Gi was necessary for ERK and Akt activation in response to α2-adrenergic receptor activation. ERK and Akt were also strongly activated by S1P, showing high heterogeneity at the single cell level, especially for ERK. Cluster analysis of time-series derived from 68,000 cells obtained under the different conditions revealed several distinct populations of cells that display similar response dynamics. ERK response dynamics to S1P showed high heterogeneity, which was reduced by the inhibition of Gi. To conclude, we have set up an imaging and analysis strategy that reveals substantial cell-to-cell heterogeneity in kinase activity driven by GPCRs.

Keywords:  Biosensor; Fluorescence imaging; GPCR; Image analysis; Kinase; Signaling

DOI:  https://doi.org/10.1242/jcs.259685
Adv Cancer Res. 2022 ;pii: S0065-230X(21)00065-8. [Epub ahead of print]153 1-27

A brief history of RAS and the RAS Initiative.

Frank McCormick.

  In this review, I provide a brief history of the discovery of RAS and the GAPs and GEFs that regulate its activity from a personal perspective. Much of this history has been driven by technological breakthroughs that occurred concurrently, such as molecular cloning, cDNA expression to analyze RAS proteins and their structures, and application of PCR to detect mutations. I discuss the RAS superfamily and RAS proteins as therapeutic targets, including recent advances in developing RAS inhibitors. I also describe the role of the RAS Initiative at Frederick National Laboratory for Cancer Research in advancing development of RAS inhibitors and providing new insights into signaling complexes and interaction of RAS proteins with the plasma membrane.

Keywords:  GAP; HRAS; KRAS; NRAS; RAS superfamily; SOS

DOI:  https://doi.org/10.1016/bs.acr.2021.07.003
Adv Cancer Res. 2022 ;pii: S0065-230X(21)00063-4. [Epub ahead of print]153 169-203

Targeting RAS oncogenesis with SOS1 inhibitors.

Roman Christian Hillig, Benjamin Bader.

  RAS proteins play major roles in many human cancers, but programs to develop direct RAS inhibitors so far have only been successful for the oncogenic KRAS mutant G12C. As an alternative approach, inhibitors for the RAS guanine nucleotide exchange factor SOS1 have been investigated by several academic groups and companies, and major progress has been achieved in recent years in the optimization of small molecule activators and inhibitors of SOS1. Here, we review the discovery and development of small molecule modulators of SOS1 and their molecular binding modes and modes of action. As targeting the RAS pathway is expected to result in the development of resistance mechanisms, SOS1 inhibitors will most likely be best applied in vertical combination approaches where two nodes of the RAS signaling pathway are hit simultaneously. We summarize the current understanding of which combination partners may be most beneficial for patients with RAS driven tumors.

Keywords:  Activator; Cancer; Combination therapy; GEF; Guanine nucleotide exchange factor; KRAS; RASopathies; SOS1; Small molecule inhibitor; Son of sevenless

DOI:  https://doi.org/10.1016/bs.acr.2021.07.001
iScience. 2022 Jan 21. 25(1): 103608

Recapitulation of cell-like KRAS4b membrane dynamics on complex biomimetic membranes.

Rebika Shrestha, De Chen, Peter Frank, Dwight V Nissley, Thomas J Turbyville.

  Understanding the spatiotemporal distribution and dynamics of RAS on the plasma membrane (PM) is the key for elucidating the molecular mechanisms of the RAS signaling pathway. Single particle tracking (SPT) experiments show that in cells, KRAS diffuses in at least three interchanging states on the cellular PM; however, KRAS remains monomeric and always shows homogeneous diffusion on artificial membranes. Here, we show for the first time on a supported lipid bilayer composed of heterogeneous lipid components that we can recapitulate the three-state diffusion of KRAS seen in cells. The use of a biologically relevant eight-lipid system opens a new frontier in the biophysical studies of RAS and other membrane associated proteins on a biomimetic system that recapitulates the complexity of a cellular PM.

Keywords:  Biomimetics; Biophysics; Biotechnology; Membrane architecture; Molecular biology

DOI:  https://doi.org/10.1016/j.isci.2021.103608
Adv Cancer Res. 2022 ;pii: S0065-230X(21)00079-8. [Epub ahead of print]153 101-130

Targeting the ERK mitogen-activated protein kinase cascade for the treatment of KRAS-mutant pancreatic cancer.

J Nathaniel Diehl, Priya S Hibshman, Irem Ozkan-Dagliyan, Craig M Goodwin, Sarah V Howard, Adrienne D Cox, Channing J Der.

  Mutational activation of the KRAS oncogene is found in ~95% of pancreatic ductal adenocarcinoma (PDAC), the major form of pancreatic cancer. With substantial experimental evidence that continued aberrant KRAS function is essential for the maintenance of PDAC tumorigenic growth, the National Cancer Institute has identified the development of effective anti-KRAS therapies as one of four major initiatives for pancreatic cancer research. The recent clinical success in the development of an anti-KRAS therapy targeting one specific KRAS mutant (G12C) supports the significant potential impact of anti-KRAS therapies. However, KRASG12C mutations comprise only 2% of KRAS mutations in PDAC. Thus, there remains a dire need for additional therapeutic approaches for targeting the majority of KRAS-mutant PDAC. Among the different directions currently being pursued for anti-KRAS drug development, one of the most promising involves inhibitors of the key KRAS effector pathway, the three-tiered RAF-MEK-ERK mitogen-activated protein kinase (MAPK) cascade. We address the promises and challenges of targeting ERK MAPK signaling as an anti-KRAS therapy for PDAC. In particular, we also summarize the key role of the MYC transcription factor and oncoprotein in supporting ERK-dependent growth of KRAS-mutant PDAC.

Keywords:  ERK; KRAS; MYC; Mitogen-activated protein kinase; Pancreatic cancer

DOI:  https://doi.org/10.1016/bs.acr.2021.07.008
Adv Cancer Res. 2022 ;pii: S0065-230X(21)00080-4. [Epub ahead of print]153 131-168

Pan-RAS inhibitors: Hitting multiple RAS isozymes with one stone.

Alexander B Coley, Antonio Ward, Adam B Keeton, Xi Chen, Yulia Maxuitenko, Aishwarya Prakash, Feng Li, Jeremy B Foote, Donald J Buchsbaum, Gary A Piazza.

  Mutations in the three RAS oncogenes are present in approximately 30% of all human cancers that drive tumor growth and metastasis by aberrant activation of RAS-mediated signaling. Despite the well-established role of RAS in tumorigenesis, past efforts to develop small molecule inhibitors have failed for various reasons leading many to consider RAS as "undruggable." Advances over the past decade with KRAS(G12C) mutation-specific inhibitors have culminated in the first FDA-approved RAS drug, sotorasib. However, the patient population that stands to benefit from KRAS(G12C) inhibitors is inherently limited to those patients harboring KRAS(G12C) mutations. Additionally, both intrinsic and acquired mechanisms of resistance have been reported that indicate allele-specificity may afford disadvantages. For example, the compensatory activation of uninhibited wild-type (WT) NRAS and HRAS isozymes can rescue cancer cells harboring KRAS(G12C) mutations from allele-specific inhibition or the occurrence of other mutations in KRAS. It is therefore prudent to consider alternative drug discovery strategies that may overcome these potential limitations. One such approach is pan-RAS inhibition, whereby all RAS isozymes co-expressed in the tumor cell population are targeted by a single inhibitor to block constitutively activated RAS regardless of the underlying mutation. This chapter provides a review of past and ongoing strategies to develop pan-RAS inhibitors in detail and seeks to outline the trajectory of this promising strategy of RAS inhibition.

Keywords:  Cancer; Drug discovery; HRAS; KRAS; NRAS; RAS inhibitors; pan-RAS

DOI:  https://doi.org/10.1016/bs.acr.2021.07.009
Mol Cell. 2022 Jan 25. pii: S1097-2765(22)00002-8. [Epub ahead of print]

E3 ligase RNF167 and deubiquitinase STAMBPL1 modulate mTOR and cancer progression.

Dong Wang, Chenchen Xu, Wenyu Yang, Jie Chen, Yuhui Ou, Yuanyuan Guan, Jialiang Guan, Ying Liu.

  The mTOR complex 1 (mTORC1) is an essential metabolic hub that coordinates cellular metabolism with the availability of nutrients, including amino acids. Sestrin2 has been identified as a cytosolic leucine sensor that transmits leucine status signals to mTORC1. In this study, we identify an E3 ubiquitin ligase RING finger protein 167 (RNF167) and a deubiquitinase STAMBPL1 that function in concert to control the polyubiquitination level of Sestrin2 in response to leucine availability. Ubiquitination of Sestrin2 promotes its interaction with GATOR2 and inhibits mTORC1 signaling. Bioinformatic analysis reveals decreased RNF167 expression and increased STAMBPL1 expression in gastric and colorectal tumors. Knockout of STAMBPL1 or correction of the heterozygous STAMBPL1 mutation in a human colon cancer cell line suppresses xenograft tumor growth. Lastly, a cell-permeable peptide that blocks the STAMBPL1-Sestrin2 interaction inhibits mTORC1 and provides a potential option for cancer therapy.

Keywords:  Sestrin2; amino acid sensing; colorectal cancer; mTOR; tumorigenesis; ubiquitination

DOI:  https://doi.org/10.1016/j.molcel.2022.01.002
Adv Cancer Res. 2022 ;pii: S0065-230X(21)00066-X. [Epub ahead of print]153 29-61

Not all RAS mutations are equal: A detailed review of the functional diversity of RAS hot spot mutations.

Rachel A Burge, G Aaron Hobbs.

  The RAS family of small GTPases are among the most frequently mutated oncogenes in human cancer. Approximately 20% of cancers harbor a RAS mutation, and >150 different missense mutations have been detected. Many of these mutations have mutant-specific biochemical defects that alter nucleotide binding and hydrolysis, effector interactions and cell signaling, prompting renewed efforts in the development of anti-RAS therapies, including the mutation-specific strategies. Previously viewed as undruggable, the recent FDA approval of a KRASG12C-selective inhibitor has offered real promise to the development of allele-specific RAS therapies. A broader understanding of the mutational consequences on RAS function must be developed to exploit additional allele-specific vulnerabilities. Approximately 94% of RAS mutations occur at one of three mutational "hot spots" at Gly12, Gly13 and Gln61. Further, the single-nucleotide substitutions represent >99% of these mutations. Within this scope, we discuss the mutational frequencies of RAS isoforms in cancer, mutant-specific effector interactions and biochemical properties. By limiting our analysis to this mutational subset, we simplify the analysis while only excluding a small percentage of total mutations. Combined, these data suggest that the presence or absence of select RAS mutations in human cancers can be linked to their biochemical properties. Continuing to examine the biochemical differences in each RAS-mutant protein will continue to provide additional breakthroughs in allele-specific therapeutic strategies.

Keywords:  Allele-specific signaling; GDP exchange; GTP hydrolysis; Isoform-specific mutation frequencies; RAS GTPases

DOI:  https://doi.org/10.1016/bs.acr.2021.07.004
Adv Cancer Res. 2022 ;pii: S0065-230X(21)00064-6. [Epub ahead of print]153 205-236

Inhibition of SHP2 as an approach to block RAS-driven cancers.

Yu-Ting Chou, Trever G Bivona.

  The non-receptor protein tyrosine phosphatase SHP2 (encoded by PTPN11) is a critical component of RAS/MAPK signaling by acting upstream of RAS to promote oncogenic signaling and tumor growth. Over three decades, SHP2 was considered "undruggable" because enzymatic active-site inhibitors generally showed off-target inhibition of other proteins and low membrane permeability. More recently, allosteric SHP2 inhibitors with striking inhibitory potency have been developed. These small molecules effectively block the signal transduction between receptor tyrosine kinases (RTKs) and RAS/MAPK signaling and show efficacy in preclinical cancer models. Moreover, clinical evaluation of these allosteric SHP2 inhibitors is ongoing. RAS proteins which harbor transforming properties by gain-of-function mutations are present in various cancer types. While inhibitors of KRASG12C show early clinical promise, resistance remains a challenge and other forms of oncogenic RAS remain to be selectively inhibited. Here, we summarize the role of SHP2 in RAS-driven cancers and the therapeutic potential of allosteric SHP2 inhibitors as a strategy to block RAS-driven cancers.

Keywords:  Allosteric SHP2 inhibitor; Combination therapy; PTP; PTPN11; RAS; SHP2

DOI:  https://doi.org/10.1016/bs.acr.2021.07.002
Trends Cancer. 2022 Jan 26. pii: S2405-8033(22)00002-4. [Epub ahead of print]

Interplay between K-RAS and miRNAs.

Bing Shui, Gaspare La Rocca, Andrea Ventura, Kevin M Haigis.

  K-RAS is frequently mutated in cancers, and its overactivation can lead to oncogene-induced senescence (OIS), a barrier to cellular transformation. Feedback onto K-RAS limits its signaling to avoid senescence while achieving the appropriate level of activation that promotes proliferation and survival. Such regulation could be mediated by miRNAs, as aberrant RAS signaling and miRNA activity coexist in several cancers, with miRNAs acting both up- and downstream of K-RAS. Several miRNAs both regulate and are regulated by K-RAS, suggesting a noncoding RNA-based feedback mechanism. Functional interactions between K-RAS and the miRNA machinery have also begun to unfold. This review comprehensively surveys the state of knowledge connecting K-RAS to miRNA function and proposes a model for the regulation of K-RAS signaling by noncoding RNAs.

Keywords:  K-RAS; cancer; feedback regulation; miRNA

DOI:  https://doi.org/10.1016/j.trecan.2022.01.002
Adv Cancer Res. 2022 ;pii: S0065-230X(21)00067-1. [Epub ahead of print]153 63-99

Drug targeting opportunities en route to Ras nanoclusters.

Karolina Pavic, Rohan Chippalkatti, Daniel Abankwa.

  Disruption of the native membrane organization of Ras by the farnesyltransferase inhibitor tipifarnib in the late 1990s constituted the first indirect approach to drug target Ras. Since then, our understanding of how dynamically Ras shuttles between subcellular locations has changed significantly. Ras proteins have to arrive at the plasma membrane for efficient MAPK-signal propagation. On the plasma membrane Ras proteins are organized into isoform specific proteo-lipid assemblies called nanocluster. Recent evidence suggests that Ras nanocluster have a specific lipid composition, which supports the recruitment of effectors such as Raf. Conversely, effectors possess lipid-recognition motifs, which appear to serve as co-incidence detectors for the lipid domain of a given Ras isoform. Evidence suggests that dimeric Raf proteins then co-assemble dimeric Ras in an immobile complex, thus forming the minimal unit of an active nanocluster. Here we review established and novel trafficking chaperones and trafficking factors of Ras, along with the set of lipid and protein modulators of Ras nanoclustering. We highlight drug targeting approaches and opportunities against these determinants of functional Ras membrane organization. Finally, we reflect on implications for Ras signaling in polarized cells, such as epithelia, which are a common origin of tumorigenesis.

Keywords:  Drug development; Nanocluster; Polarized cell; Ras; Trafficking chaperones

DOI:  https://doi.org/10.1016/bs.acr.2021.07.005
Adv Cancer Res. 2022 ;pii: S0065-230X(21)00068-3. [Epub ahead of print]153 237-266

Targeting the "undruggable" RAS with biologics.

Michael Whaby, Imran Khan, John P O'Bryan.

  RAS proteins represent critical drivers of tumor development and thus are the focus of intense efforts to pharmacologically inhibit these proteins in human cancer. Although recent success has been attained in developing clinically efficacious inhibitors to KRASG12C, there remains a critical need for developing approaches to inhibit additional mutant RAS proteins. A number of anti-RAS biologics have been developed which reveal novel and potentially therapeutically targetable vulnerabilities in oncogenic RAS. This review will discuss the growing field of anti-RAS biologics and potential development of these reagents into new anti-RAS therapies.

Keywords:  Antibodies; Cyclic peptides; DARPins; Intrabodies; Miniproteins; Monobodies; PROTACs; Sso7d; Stapled peptides; Toxin peptidases; cancer therapeutics

DOI:  https://doi.org/10.1016/bs.acr.2021.07.006
Nat Cancer. 2021 Jun;2(6): 587-597

The present and future of PI3K inhibitors for cancer therapy.

Pau Castel, Eneda Toska, Jeffrey A Engelman, Maurizio Scaltriti.

Phosphoinositide-3- kinase (PI3K) signaling regulates cellular proliferation, survival and metabolism, and its aberrant activation is one of the most frequent oncogenic events across human cancers. In the last few decades, research focused on the development of PI3K inhibitors, from preclinical tool compounds to the highly specific medicines approved to treat patients with cancer. Herein we discuss current paradigms for PI3K inhibitors in cancer therapy, focusing on clinical data and mechanisms of action. We also discuss current limitations in the use of PI3K inhibitors including toxicities and mechanisms of resistance, with specific emphasis on approaches aimed to improve their efficacy.

DOI: https://doi.org/10.1038/s43018-021-00218-4
J Med Chem. 2022 Feb 01.

Stabilization of the RAS:PDE6D Complex Is a Novel Strategy to Inhibit RAS Signaling.

Tamas Yelland, Esther Garcia, Charles Parry, Dominika Kowalczyk, Marta Wojnowska, Andrea Gohlke, Matja Zalar, Kenneth Cameron, Gillian Goodwin, Qing Yu, Peng-Cheng Zhu, Yasmin ElMaghloob, Angelo Pugliese, Lewis Archibald, Andrew Jamieson, Yong Xiang Chen, Duncan McArthur, Justin Bower, Shehab Ismail.

RAS is a major anticancer drug target which requires membrane localization to activate downstream signal transduction. The direct inhibition of RAS has proven to be challenging. Here, we present a novel strategy for targeting RAS by stabilizing its interaction with the prenyl-binding protein PDE6D and disrupting its localization. Using rationally designed RAS point mutations, we were able to stabilize the RAS:PDE6D complex by increasing the affinity of RAS for PDE6D, which resulted in the redirection of RAS to the cytoplasm and the primary cilium and inhibition of oncogenic RAS/ERK signaling. We developed an SPR fragment screening and identified fragments that bind at the KRAS:PDE6D interface, as shown through cocrystal structures. Finally, we show that the stoichiometric ratios of KRAS:PDE6D vary in different cell lines, suggesting that the impact of this strategy might be cell-type-dependent. This study forms the foundation from which a potential anticancer small-molecule RAS:PDE6D complex stabilizer could be developed.

DOI: https://doi.org/10.1021/acs.jmedchem.1c01265
Curr Opin Gastroenterol. 2022 Mar 01. 38(2): 162-167

Dysregulated lipid metabolism in colorectal cancer.

Olivia Coleman, Miriam Ecker, Dirk Haller.

PURPOSE OF REVIEW: Lipid metabolism presents a targetable metabolic vulnerability in colorectal cancer (CRC). Lipid signatures and cancer-cell lipid requirements may serve as noninvasive diagnostic and prognostic biomarkers and as a therapeutic target, respectively.
RECENT FINDINGS: A growing body of new studies highlight the complexity of lipid metabolism in CRC. Cancer cells are able to utilize an alternative fatty acid desaturation pathway, underlining the metabolic plasticity of tumors. CRC tissue shows a robust triglyceride-species signature with prognostic value in CRC patients. Lipidomic analyses in germfree and colonized mice identify a unique lipid signature and suggest that bacteria inhibit metabolism of polyunsaturated fatty acids by blocking desaturase and elongase activities. Cellular stress responses, particularly the well characterized unfolded protein response, are involved in regulating lipid synthesis and homeostasis, and contribute to adaptation of the lipid environment. Together, lipid metabolism, the intestinal microbiota and cellular stress responses unarguably play crucial roles in CRC.
SUMMARY: A number of recent advances in our understanding of dysregulated lipid metabolism in CRC underline the importance of this research field. An improved knowledge of the complex interplay between lipid metabolism, cellular stress and the intestinal microbiota in the context of CRC may lead to novel therapeutic strategies.

DOI: https://doi.org/10.1097/MOG.0000000000000811
Mini Rev Med Chem. 2022 Feb 02.

Recent Advances of PI3 Kinase Inhibitors: Structure Anticancer Activity Relationship Studies.

Vivek Asati, Arjun Anant, Debarshi Kar Mahapatra, Sanjay Kumar Bharti.

  Phosphatidyl-inositol-3-kinase (PI3K) has emerged as a potential therapeutic target for the development of novel anticancer drugs. The dysregulation of PI3K has been associated with many human malignancies such as breast, colon, endometrial, brain, and prostate cancers. The PI3K kinases in their different isoforms namely α, β, δ, and γ, encode PIK3CA, PIK3CB, PIK3CD, and PIK3CG genes. Specific gene mutation or overexpression of the protein is responsible for therapeutic failure of current therapeutics. Recently, various PI3K signaling pathway inhibitors have been identified which showed promising therapeutic results by acting on specific isoforms of the kinase too. Several inhibitors containing medicinally privileged scaffolds like oxadiazole, pyrrolotriazine, quinazoline, quinazolinone, quinazoline-chalcone hybrids, quinazoline-sulfonamide, pyrazolochalcone, quinolone hydroxamic acid, benzofuropyridinone, imidazopyridine, benzoxazines, dibenzoxanthene, indoloderivatives, benzimidazole, and benzothiazine derivatives have been developed to target PI3K pathway and/or a specific isoform. The PI3K inhibitors which are under clinical trial studies include GDC-0032, INK1117 for PI3K-α, and AZD8186 for PI3K-β. This review primarily focuses on the structural insights and structure anticancer activity relationship studies of recent PI3K inhibitors including their clinical stages of development and therapeutic values.

Keywords:  PI3K; SAR; anticancer agents; kinase; proliferation; signaling pathways

DOI:  https://doi.org/10.2174/1389450123666220202154757