bims-pimaco 2023-03-26 papers

on PI3K and MAPK signalling in colorectal cancer

Issue of 2023–03–26
nine papers selected by
Lucas B. Zeiger, CRUK Scotland Institute, Beatson Institute for Cancer Research

PIK3CA and PIK3R1 tumor mutational landscape in a pan-cancer patient cohort and its association with pathway activation and treatment efficacy.
Surviving and adapting to stress: Translational control and the integrated stress response.
DAB2IP is a bifunctional tumor suppressor that regulates wildtype RAS and inflammatory cascades in KRAS mutant colon cancer.
RAS Degraders: The New Frontier for RAS Driven Cancers.
KRAS Hijacks the MicroRNA Regulatory Pathway in Cancer.
Structure and RAF-family kinase isoform selectivity of Type II RAF inhibitors tovorafenib and naporafenib.
p85α regulatory subunit isoform controls PI3-kinase and TRPC6 membrane translocation.
Recent progress in targeting KRAS mutant cancers with covalent G12C-specific inhibitors.
Generalizable biomarker prediction from cancer pathology slides with self-supervised deep learning: A retrospective multi-centric study.

Sci Rep. 2023 Mar 18. 13(1): 4467

PIK3CA and PIK3R1 tumor mutational landscape in a pan-cancer patient cohort and its association with pathway activation and treatment efficacy.

Zoé Tharin, Corentin Richard, Valentin Derangère, Alis Ilie, Laurent Arnould, François Ghiringhelli, Romain Boidot, Sylvain Ladoire.

There is little data concerning the implications of PIK3CA mutations outside of the known hotspots described in ER+/HER2- metastatic breast cancer (mBC). Similarly, PIK3R1 mutations could also lead to activation of PI3K pathway, but are poorly described. We determined the incidence and type of all somatic PIK3CA and PIK3R1 mutations by whole exome sequencing (WES) in a pan-cancer cohort of 1200 patients. Activation of the PI3K pathway was studied using phospho-AKT immunohistochemistry. Associations between PIK3CA/PIK3R1 mutations and response to chemotherapy were studied in mBC cases. We found 141 patients (11.8%) with a PIK3CA and/or PIK3R1 mutation across 20 different cancer types. The main cancer subtype was mBC (45.4%). Eighty-four mutations (62.2%) occurred in the three described hotspots; 51 mutations occurred outside of these hotspots. In total, 78.4% were considered activating or probably activating. Among PIK3R1 mutations, 20% were loss of function mutations, leading to a constitutional activation of the pathway. Phospho-AKT quantification in tumor samples was in favor of activation of the PI3K pathway in the majority of mutated tumors, regardless of mutation type. In ER+/HER2- mBC, first line chemotherapy efficacy was similar for PIK3CA-mutated and PIK3CA-WT tumors, whereas in triple negative mBC, chemotherapy appeared to be more effective in PIK3CA-WT tumors. In this large, real-life pan-cancer patient cohort, our results indicate that PIK3CA/PIK3R1 mutations are widely spread, and plead in favour of evaluating the efficacy of PI3K inhibitors outside of ER+/HER2- mBC and outside of hotspot mutations.

DOI: https://doi.org/10.1038/s41598-023-31593-w
Antioxid Redox Signal. 2023 Mar 21.

Surviving and adapting to stress: Translational control and the integrated stress response.

Ronald C Wek, Tracy G Anthony, Kirk A Staschke.

εβOrganisms adapt to changing environments by engaging cellular stress response pathways that serve to restore proteostasis and enhance survival. A primary adaptive mechanism is the Integrated stress response (ISR), which features phosphorylation of the α subunit of eukaryotic initiation factor 2 (eIF2). Four eIF2α kinases respond to different stresses, enabling cells to rapidly control translation to optimize management of resources and reprogram gene expression for stress adaptation. Phosphorylation of eIF2α blocks its guanine nucleotide exchange factor, eIF2B, thus lowering the levels of eIF2•GTP required to deliver initiator tRNA to ribosomes. While bulk mRNA translation can be sharply lowered by heightened phosphorylation of eIF2α, there are other gene transcripts whose translation is unchanged or preferentially translated. Among the preferentially translated genes is ATF4, which directs transcription of adaptive genes in the ISR. This review focuses on how eIF2α kinases function as first responders of stress, the mechanisms by which eIF2α phosphorylation and other stress signals regulate the exchange activity of eIF2B, and the processes by which the ISR triggers differential mRNA translation. The ISR is tunable and integrates with other stress pathways to optimize adaptation. To illustrate the synergy between stress pathways, we describe the mechanisms and functional significance of communication between the ISR and another key regulator of translation, mTORC1, during acute and chronic amino acid insufficiency. Finally, we discuss the pathological conditions that stem from aberrant regulation of the ISR, as well as therapeutic strategies targeting the ISR to alleviate disease.

DOI: https://doi.org/10.1089/ars.2022.0123
Cancer Res. 2023 Mar 20. pii: CAN-22-0370. [Epub ahead of print]

DAB2IP is a bifunctional tumor suppressor that regulates wildtype RAS and inflammatory cascades in KRAS mutant colon cancer.

Abigail L Miller, Naiara Perurena, Alycia Gardner, Toshinori Hinoue, Patrick Loi, Peter W Laird, Karen Cichowski.

The DAB2IP tumor suppressor encodes a RAS GTPase-activating protein (RASGAP). Accordingly, DAB2IP has been shown to be mutated or suppressed in tumor types that typically lack RAS mutations. However, here we report that DAB2IP is mutated or selectively silenced in the vast majority of KRAS and BRAF mutant CRCs. In this setting, DAB2IP loss promoted tumor development by activating wild-type H- and NRAS proteins, which was surprisingly required to achieve robust activation of RAS effector pathways in KRAS-mutant tumors. DAB2IP loss also triggered production of inflammatory mediators and the recruitment of pro-tumorigenic macrophages in vivo. Importantly, tumor growth was suppressed by depleting macrophages or inhibiting cytokine/inflammatory mediator expression with a JAK/TBK1 inhibitor. In human tumors DAB2IP was lost at early stages of tumor development, and its depletion was associated with an enrichment of macrophage and inflammatory signatures. Together, these findings demonstrate that DAB2IP restrains the activation of the RAS pathway and inflammatory cascades in the colon and that its loss represents a common and unappreciated mechanism for amplifying these two critical oncogenic signals in colorectal cancer.

DOI: https://doi.org/10.1158/0008-5472.CAN-22-0370
Mol Ther. 2023 Mar 21. pii: S1525-0016(23)00138-7. [Epub ahead of print]

RAS Degraders: The New Frontier for RAS Driven Cancers.

Taylor E Escher, Karla J F Satchell.

The function and significance of RAS proteins in cancer have been widely studied for decades. In 2013, the National Cancer Institute (NCI) established the RAS Initiative to explore innovative approaches for attacking the proteins encoded by mutant forms ofRAS genes and to create effective therapies for RAS-driven cancers. This initiative spurred researchers to develop novel approaches and to discover small molecules targeting this protein that was at one time termed "undruggable". More recently, advanced efforts in RAS degraders including PROTACs, linker-based degraders, and direct proteolysis degraders have been explored as novel strategies to target RAS for cancer treatment. These RAS degraders present new opportunities for RAS therapies and may prove fruitful in understanding basic cell biology. Novel delivery strategies will further enhance the efficacy of these therapeutics. In this review, we summarize recent efforts to develop RAS degraders, including PROTACs and E3 adaptor and ligase fusions as cancer therapies. This review also details the direct RAS protease degrader, RAS/RAP1-specific endopeptidase (RRSP) that directly and specifically cleaves RAS.

DOI: https://doi.org/10.1016/j.ymthe.2023.03.017
Cancer Res. 2023 Mar 22. pii: CAN-23-0296. [Epub ahead of print]

KRAS Hijacks the MicroRNA Regulatory Pathway in Cancer.

Angelina S Bortoletto, Ronald J Parchem.

Extensive studies have focused on the misregulation of individual miRNAs in cancer. More recently, mutations in the miRNA biogenesis and processing machinery have been implicated in several malignancies. Such mutations can lead to global miRNA misregulation, which may promote many of the well-known hallmarks of cancer. Interestingly, recent evidence also suggests that oncogenic KRAS mutations act in part by modulating the activity of members of the miRNA regulatory pathway. Here, we highlight the vital role mutations in the miRNA core machinery play in promoting malignant transformation. Furthermore, we discuss how mutant KRAS can simultaneously impact multiple steps of miRNA processing and function to promote tumorigenesis. Although the ability of KRAS to hijack the miRNA regulatory pathway adds a layer of complexity to its oncogenic nature, it also provides a potential therapeutic avenue that has yet to be exploited in the clinic. Moreover, concurrent targeting of mutant KRAS and members of the miRNA core machinery represents a potential strategy for treating cancer.

DOI: https://doi.org/10.1158/0008-5472.CAN-23-0296
J Biol Chem. 2023 Mar 22. pii: S0021-9258(23)00276-4. [Epub ahead of print] 104634

Structure and RAF-family kinase isoform selectivity of Type II RAF inhibitors tovorafenib and naporafenib.

Emre Tkacik, Kunhua Li, Gonzalo Gonzalez-Del Pino, Byung Hak Ha, Javier Vinals, Eunyoung Park, Tyler S Beyett, Michael J Eck.

  Upon activation by RAS, RAF-family kinases initiate signaling through the MAP kinase cascade to control cell growth, proliferation, and differentiation. Among RAF isoforms (ARAF, BRAF, and CRAF), oncogenic mutations are by far most frequent in BRAF. The BRAFV600E mutation drives more than half of all malignant melanoma and is also found in many other cancers. Selective inhibitors of BRAFV600E (vemurafenib, dabrafenib, encorafenib) are used clinically for these indications, but they are not effective inhibitors in the context of oncogenic RAS, which drives dimerization and activation of RAF, nor for malignancies driven by aberrantly dimerized truncation/fusion variants of BRAF. By contrast, a number of "type II" RAF inhibitors have been developed as potent inhibitors of RAF dimers. Here we compare potency of type II inhibitors tovorafenib (TAK-580) and naporafenib (LHX254) in biochemical assays against the three RAF isoforms, and describe crystal structures of both compounds in complex with BRAF. We find that tovorafenib and naporafenib are most potent against CRAF, but markedly less potent against ARAF. Crystal structures of both compounds with BRAFV600E or WT BRAF reveal the details of their molecular interactions, including the expected type II binding mode, with full occupancy of both subunits of the BRAF dimer. Our findings have important clinical ramifications. Type II RAF inhibitors are generally regarded as Pan-RAF inhibitors, but our studies of these two agents, together with recent work with type II inhibitors belvarafenib and naporafenib, indicate that relative sparing of ARAF may be a property of multiple drugs of this class.

Keywords:  RAF kinase; cooperativity; drug action; fluorescence resonance energy transfer (FRET); inhibitor mechanism; x-ray crystallography

DOI:  https://doi.org/10.1016/j.jbc.2023.104634
Cell Calcium. 2023 Mar 15. pii: S0143-4160(23)00030-1. [Epub ahead of print]111 102718

p85α regulatory subunit isoform controls PI3-kinase and TRPC6 membrane translocation.

Pinaki Chaudhuri, Priya Putta, Linda M Graham, Michael A Rosenbaum.

  Activation of phosphatidylinositol 3-kinase (PI3K) by lipid oxidation products, including lysophosphatidylcholine (lysoPC), increases the externalization of canonical transient receptor potential 6 (TRPC6) channels leading to a subsequent increase in intracellular calcium that contributes to cytoskeletal changes which inhibit endothelial cell (EC) migration in vitro and impair EC healing of arterial injuries in vivo. The PI3K p110α and p110δ catalytic subunit isoforms regulate lysoPC-induced TRPC6 externalization in vitro, but have many other functions. The goal of the current study is to identify the PI3K regulatory subunit isoform involved in TRPC6 externalization to potentially identify a more specific treatment regimen to improve EC migration and arterial healing, while minimizing off-target effects. Decreasing the p85α regulatory subunit isoform protein levels, but not the p85β and p55γ regulatory subunit isoforms, with small interfering RNA inhibits lysoPC-induced translocation of the PI3K catalytic subunit to the plasma membrane, dramatically decreased phosphatidylinositol (3,4,5)-trisphosphate (PIP3) production and TRPC6 externalization, and significantly improves EC migration in the presence of lysoPC. These results identify the important and specific role of p85α in controlling translocation of PI3K from the cytosol to the plasma membrane and PI3K-mediated TRPC externalization by oxidized lipids. Current PI3K inhibitors block the catalytic subunit, but our data suggest that the regulatory subunit is a novel therapeutic target to promote EC migration and healing after arterial injuries that occur with angioplasty.

Keywords:  Endothelial cell migration; Phosphatidylinositol 3-kinase; TRPC6; p85α

DOI:  https://doi.org/10.1016/j.ceca.2023.102718
Drug Discov Today. 2023 Mar 17. pii: S1359-6446(23)00073-9. [Epub ahead of print] 103557

Recent progress in targeting KRAS mutant cancers with covalent G12C-specific inhibitors.

Lala S Rathod, Pratap S Dabhade, Santosh N Mokale.

  KRASG12C has been identified as a potential target in the treatment of solid tumors. One of the most often transformed proteins in human cancers is the small Kirsten rat sarcoma homolog (KRAS) subunit of GTPase, which is typically the oncogene driver. KRASG12C is altered to keep the protein in an active GTP-binding form. KRAS has long been considered an 'undrugable' target, but sustained research efforts focusing on the KRASG12C mutant cysteine have achieved promising results. For example, the US Food and Drug Administration (FDA) has passed emergency approval for sotorasib and adagrasib for the treatment of metastatic lung cancer. Such achievements have sparked several original approaches to KRASG12C. In this review, we focus on the design, development, and history of KRASG12C inhibitors.

Keywords:  KRAS mutation; KRAS(G12C); covalent inhibitors; drug design; lung cancer

DOI:  https://doi.org/10.1016/j.drudis.2023.103557
Cell Rep Med. 2023 Mar 14. pii: S2666-3791(23)00086-1. [Epub ahead of print] 100980

Generalizable biomarker prediction from cancer pathology slides with self-supervised deep learning: A retrospective multi-centric study.

Jan Moritz Niehues, Philip Quirke, Nicholas P West, Heike I Grabsch, Marko van Treeck, Yoni Schirris, Gregory P Veldhuizen, Gordon G A Hutchins, Susan D Richman, Sebastian Foersch, Titus J Brinker, Junya Fukuoka, Andrey Bychkov, Wataru Uegami, Daniel Truhn, Hermann Brenner, Alexander Brobeil, Michael Hoffmeister, Jakob Nikolas Kather.

  Deep learning (DL) can predict microsatellite instability (MSI) from routine histopathology slides of colorectal cancer (CRC). However, it is unclear whether DL can also predict other biomarkers with high performance and whether DL predictions generalize to external patient populations. Here, we acquire CRC tissue samples from two large multi-centric studies. We systematically compare six different state-of-the-art DL architectures to predict biomarkers from pathology slides, including MSI and mutations in BRAF, KRAS, NRAS, and PIK3CA. Using a large external validation cohort to provide a realistic evaluation setting, we show that models using self-supervised, attention-based multiple-instance learning consistently outperform previous approaches while offering explainable visualizations of the indicative regions and morphologies. While the prediction of MSI and BRAF mutations reaches a clinical-grade performance, mutation prediction of PIK3CA, KRAS, and NRAS was clinically insufficient.

Keywords:  artificial intelligence; attention heatmaps; attention-based multiple-instance learning; biomarker; colorectal cancer; computational pathology; multi-input models; oncogenic mutation; self-supervised learning

DOI:  https://doi.org/10.1016/j.xcrm.2023.100980