bims-pimaco 2023-07-23 papers

on PI3K and MAPK signalling in colorectal cancer

Issue of 2023–07–23
nine papers selected by
Lucas B. Zeiger, CRUK Scotland Institute, Beatson Institute for Cancer Research

The mechanisms of class 1A PI3K and Wnt/β-catenin coupled signaling in breast cancer.
RAS GTPases and Interleaflet Coupling in the Plasma Membrane.
Characterization of Lipid Alterations by Oncogenic PIK3CA Mutations Using Untargeted Lipidomics in Breast Cancer.
KRAS regulation of miRNA: Stepping on the brake to go faster.
Mutant APC reshapes Wnt signaling plasma membrane nanodomains by altering cholesterol levels via oncogenic β-catenin.
Structure-based pharmacophore modeling and DFT studies of Indian Ocean-derived red algal compounds as PI3Kα inhibitors.
The effect of the alpha-specific PI3K inhibitor alpelisib combined with anti-HER2 therapy in HER2+/PIK3CA mutant breast cancer.
NADPH oxidase promotes glioblastoma radiation resistance in a PTEN-dependent manner.
Diverse clonal fates emerge upon drug treatment of homogeneous cancer cells.

Biochem Soc Trans. 2023 Jul 20. pii: BST20220866. [Epub ahead of print]

The mechanisms of class 1A PI3K and Wnt/β-catenin coupled signaling in breast cancer.

Samuel J Rodgers, Christina A Mitchell, Lisa M Ooms.

  The class IA PI3K signaling pathway is activated by growth factor stimulation and regulates a signaling cascade that promotes diverse events including cell growth, proliferation, migration and metabolism. PI3K signaling is one of the most commonly hyperactivated pathways in breast cancer, leading to increased tumor growth and progression. PI3K hyperactivation occurs via a number of genetic and epigenetic mechanisms including mutation or amplification of PIK3CA, the gene encoding the p110α subunit of PI3Kα, as well as via dysregulation of the upstream growth factor receptors or downstream signaling effectors. Over the past decade, extensive efforts to develop therapeutics that suppress oncogenic PI3K signaling have been undertaken. Although FDA-approved PI3K inhibitors are now emerging, their clinical success remains limited due to adverse effects and negative feedback mechanisms which contribute to their reduced efficacy. There is an emerging body of evidence demonstrating crosstalk between the PI3K and Wnt/β-catenin pathways in breast cancer. However, PI3K exhibits opposing effects on Wnt/β-catenin signaling in distinct tumor subsets, whereby PI3K promotes Wnt/β-catenin activation in ER+ cancers, but paradoxically suppresses this pathway in ER- breast cancers. This review discusses the molecular mechanisms for PI3K-Wnt crosstalk in breast cancer, and how Wnt-targeted therapies have the potential to contribute to treatment regimens for breast cancers with PI3K dysregulation.

Keywords:  INPP4B; Wnt/β-catenin; breast cancer; phosphoinositide; phosphoinositide 3-kinase

DOI:  https://doi.org/10.1042/BST20220866
Cold Spring Harb Perspect Biol. 2023 Jul 18. pii: a041414. [Epub ahead of print]

RAS GTPases and Interleaflet Coupling in the Plasma Membrane.

Junchen Liu, Neha Arora, Yong Zhou.

RAS genes are frequently mutated in cancer. The primary signaling compartment of wild-type and constitutively active oncogenic mutant RAS proteins is the inner leaflet of the plasma membrane (PM). Thus, a better understanding of the unique environment of the PM inner leaflet is important to shed further light on RAS function. Over the past few decades, an integrated approach of superresolution imaging, molecular dynamic simulations, and biophysical assays has yielded new insights into the capacity of RAS proteins to sort lipids with specific headgroups and acyl chains, to assemble signaling nanoclusters on the inner PM. RAS proteins also sense and respond to changes in components of the outer PM leaflet, including glycophosphatidylinositol-anchored proteins, sphingophospholipids, glycosphingolipids, and galectins, as well as cholesterol that translocates between the two leaflets. Such communication between the inner and outer leaflets of the PM, called interleaflet coupling, allows RAS to potentially integrate extracellular mechanical and electrostatic information with intracellular biochemical signaling events, and reciprocally allows mutant RAS-transformed tumor cells to modify tumor microenvironments. Here, we review RAS-lipid interactions and speculate on potential mechanisms that allow communication between the opposing leaflets of the PM.

DOI: https://doi.org/10.1101/cshperspect.a041414
OMICS. 2023 Jul;27(7): 327-335

Characterization of Lipid Alterations by Oncogenic PIK3CA Mutations Using Untargeted Lipidomics in Breast Cancer.

Jae Hun Jung, Da-Qing Yang, Hongming Song, Xiangyu Wang, Xinyan Wu, Kwang Pyo Kim, Akhilesh Pandey, Seul Kee Byeon.

  Lipids play crucial biological roles in health and disease, including in cancers. The phosphatidylinositol 3-kinase (PI3K) signaling pathway is a pivotal promoter of cell growth and proliferation in various types of cancer. The somatic mutations in PIK3CA, the gene coding for the catalytic subunit p110α of PI3K, are frequently present in cancer cells, including breast cancer. Although the most prominent mutants, represented by single amino acid substitutions in the helical domain in exon 9 (E545K) and the kinase domain in exon 20 (H1047R) are known to cause a gain of PI3K function, activate AKT signaling and induce oncogenic transformation, the effect of these mutations on cellular lipid profiles has not been studied. We carried out untargeted lipidomics using liquid chromatography-tandem mass spectrometry to detect the lipid alterations in mammary gland epithelial MCF10A cells with isogenic knockin of these mutations. A total of 536 species of lipids were analyzed. We found that the levels of monosialogangliosides, signaling molecules known to enhance cell motility through PI3K/AKT pathway, were significantly higher in both mutants. In addition, triglycerides and ceramides, lipid molecules known to be involved in promoting lipid droplet production, cancer cell migration and invasion, were increased, whereas lysophosphatidylcholines and phosphatidylcholines that are known to inhibit cancer cell motility were decreased in both mutants. Our results provide novel insights into a potential link between altered lipid profile and carcinogenesis caused by the PIK3CA hotspot mutations. In addition, we suggest untargeted lipidomics offers prospects for precision/personalized medicine by unpacking new molecular substrates of cancer biology.

Keywords:  biomarkers; cancer; integrative biology; lipidomics; mutations; personalized medicine

DOI:  https://doi.org/10.1089/omi.2023.0076
Mol Cell. 2023 Jul 20. pii: S1097-2765(23)00476-8. [Epub ahead of print]83(14): 2390-2392

KRAS regulation of miRNA: Stepping on the brake to go faster.

Clint A Stalnecker, Channing J Der.

In this issue of Molecular Cell, Shui et al.1 use a systems biology approach to unravel a paradoxical role of microRNA in oncogenic KrasG12D regulation of gene and protein expression.

DOI: https://doi.org/10.1016/j.molcel.2023.06.029
Nat Commun. 2023 Jul 19. 14(1): 4342

Mutant APC reshapes Wnt signaling plasma membrane nanodomains by altering cholesterol levels via oncogenic β-catenin.

Alfredo Erazo-Oliveras, Mónica Muñoz-Vega, Mohamed Mlih, Venkataramana Thiriveedi, Michael L Salinas, Jaileen M Rivera-Rodríguez, Eunjoo Kim, Rachel C Wright, Xiaoli Wang, Kerstin K Landrock, Jennifer S Goldsby, Destiny A Mullens, Jatin Roper, Jason Karpac, Robert S Chapkin.

Although the role of the Wnt pathway in colon carcinogenesis has been described previously, it has been recently demonstrated that Wnt signaling originates from highly dynamic nano-assemblies at the plasma membrane. However, little is known regarding the role of oncogenic APC in reshaping Wnt nanodomains. This is noteworthy, because oncogenic APC does not act autonomously and requires activation of Wnt effectors upstream of APC to drive aberrant Wnt signaling. Here, we demonstrate the role of oncogenic APC in increasing plasma membrane free cholesterol and rigidity, thereby modulating Wnt signaling hubs. This results in an overactivation of Wnt signaling in the colon. Finally, using the Drosophila sterol auxotroph model, we demonstrate the unique ability of exogenous free cholesterol to disrupt plasma membrane homeostasis and drive Wnt signaling in a wildtype APC background. Collectively, these findings provide a link between oncogenic APC, loss of plasma membrane homeostasis and CRC development.

DOI: https://doi.org/10.1038/s41467-023-39640-w
Mol Divers. 2023 Jul 19.

Structure-based pharmacophore modeling and DFT studies of Indian Ocean-derived red algal compounds as PI3Kα inhibitors.

Archana Vasuki, H Jemmy Christy, K Renugadevi, Manjunath Dammalli.

  Phosphoinositide kinases (PIKs) are a type of lipid kinase that acts as an upstream activator of oncogenic signaling. Presently accessible therapeutic compounds have downsides, such as toxicity and dubious efficacy, as well as lengthy treatment durations, which have bred resistance. Here we attempt to screen the Indian Ocean-derived red algal compounds to be used as a promising lead for PI3Kα inhibitor development. Experimental structure of the PI3K alpha Isoform-Specific Inhibitor alpelisib complex-based pharmacophore model was constructed and used as key to mark off the suitable lead compounds from the pool of marine-derived red algal compounds of Indian Ocean. Besides, the study encompasses pharmacophore scaffold screening as well as physicochemical and pharmacokinetic parameter assessment. We employed molecular docking and molecular dynamics simulation to assess the binding type and stability of 21 red algal derivatives. Twelve compounds demonstrated a sustained binding mode within the PI3Kα binding pocket with an optimal protein backbone root-mean-square deviation, also prompted hydrogen bonding throughout the simulations, and also implies that these MNPs have firmly mediated the interaction with prime hinge region residues in the PI3Kα ATP binding pocket. DFT studies revealed that proposed compounds had the greatest occupied molecular orbital electrophilicity index, basicity, and dipole moment, all of which attributed their stability as well as binding affinity at the PI3Kα active site. Our study's findings revealed that CMNPD31054, CMNPD4798, CMNPD27861, CMNPD4799, CMNPD27860, CMNPD9533, CMNPD3732, CMNPD4221, CMNPD31058, CMNPD31052, CMNPD29281, and CMNPD31055 can be used as lead compounds for PI3KΑ isoform inhibitors design.

Keywords:  Cancer; DFT; Docking and simulation; Marine red algal compounds; PI3Kα; Pan PIK Inhibitor

DOI:  https://doi.org/10.1007/s11030-023-10695-7
Front Oncol. 2023 ;13 1108242

The effect of the alpha-specific PI3K inhibitor alpelisib combined with anti-HER2 therapy in HER2+/PIK3CA mutant breast cancer.

Maria Letizia Cataldo, Pietro De Placido, Daniela Esposito, Luigi Formisano, Grazia Arpino, Mario Giuliano, Roberto Bianco, Carmine De Angelis, Bianca Maria Veneziani.

   Background: HER2 is amplified or overexpressed in around 20% of breast cancers (BC). HER2-targeted therapies have significantly improved the prognosis of patients with HER2+ BC, however, de novo and acquired resistance to anti-HER2 treatment is common. Activating mutations in the PIK3CA gene are reported in ∼30% of HER2+ BC and are associated with resistance to anti-HER2 therapies and a poor prognosis. Here, we investigated the in vitro and in vivo antitumor efficacy of the alpha-specific PI3K inhibitor alpelisib alone or in combination with anti-HER2 therapy using a panel of HER2+ BC cell lines. We also generated models of acquired resistance to alpelisib to investigate the mechanisms underlying resistance to alpha-specific PI3K inhibition.
Materials and methods: PIK3CA mutant (HCC1954, KPL4 and JMT1) and wild-type (BT474 and SKBR3) HER2+ BC cell lines were used. The HCC1954 and KPL4 cells were chronically exposed to increasing concentrations of alpelisib or to alpelisib + trastuzumab in order to generate derivatives with acquired resistance to alpelisib (AR) and to alpelisib + trastuzumab (ATR). The transcriptomic profiles of HCC1954, KPL4 and their AR and ATR derivatives were determined by RNA sequencing. Cell growth was assessed by MTT assay. Changes in the protein levels of key PI3K pathway components were assessed by Western blotting. Gene expression, cellular and patients' data from the Cancer Dependency Map (DepMap) and KMPlot datasets were interrogated.
Results: HER2+ BC cell lines harboring activating mutations in PIK3CA were less sensitive to single or dual anti-HER2 blockade compared to PIK3CA wild-type cells. Alpelisib treatment resulted in dose-dependent inhibition of the growth of cells with or without PIK3CA mutations and enhanced the antitumor efficacy of anti-HER2 therapies in vitro. In addition, alpelisib greatly delayed tumor growth of HCC1954 xenografts in vivo. Functional annotation of the significantly differentially expressed genes suggested the common activation of biological processes associated with oxidation reduction, cell proliferation, immune response and RNA synthesis in alpelisib-resistant models compared with native cells. Eight commonly upregulated genes (log2 fold-change >1, False Discovery Rate [FDR] <0.05) in models with acquired resistance to alpelisib or alpelisib + trastuzumab were identified. Among these, AKR1C1 was associated with alpelisib-resistance in vitro and with a poor prognosis in patients with HER2+ BC.
Conclusions: Our findings support the use of an alpha-selective PI3K inhibitor to overcome the therapeutic limitations associated with single or dual HER2 blockade in PIK3CA-mutant HER2+ breast cancer. Future studies are warranted to confirm the potential role of candidate genes/pathways in resistance to alpelisib.

Keywords:  AK1RC1; HER2; PIK3CA; alpelisib; breast cancer; resistance

DOI:  https://doi.org/10.3389/fonc.2023.1108242
Antioxid Redox Signal. 2023 Jul 20.

NADPH oxidase promotes glioblastoma radiation resistance in a PTEN-dependent manner.

Kirsten Ludwig, Janel E Le Belle, Sree Deepthi Muthukrishnan, Jantzen Sperry, Michael Condro, Erina Vlashi, Frank Pajonk, Harley I Kornblum.

AIMS: The goal of this study was to determine whether NADPH oxidase (NOX)-produced reactive oxygen species enhances brain tumor growth of glioblastoma (GBM) under hypoxic conditions and during radiation treatment.
RESULTS: Exogenous ROS promoted brain tumor growth in gliomasphere cultures that expressed functional PTEN, but not in tumors that were PTEN deficient. Hypoxia induced the production of endogenous cytoplasmic ROS and tumor cell growth via activation of NOX. NOX activation resulted in oxidation of PTEN and downstream Akt activation. Radiation also promoted ROS production via NOX which, in turn, resulted in cellular protection that could be abrogated by knockdown of the key NOX component, p22. Knockdown of p22 also inhibited tumor growth and enhanced the efficacy of radiation in PTEN-expressing GBM cells.
INNOVATION: While other studies have implicated NOX function in GBM models, these studies demonstrate NOX activation and function under physiological hypoxia and following radiation in GBM, two conditions that are seen in patients. NOX plays an important role in a PTEN-expressing GBM model system, but not in PTEN-non-functional systems and provide a potential, patient-specific therapeutic opportunity. Conclusions This study provides a strong basis for pursuing NOX inhibition in PTEN-expressing GBM cells as a possible adjunct to radiation therapy.

DOI: https://doi.org/10.1089/ars.2022.0086
Nature. 2023 Jul 19.

Diverse clonal fates emerge upon drug treatment of homogeneous cancer cells.

Yogesh Goyal, Gianna T Busch, Maalavika Pillai, Jingxin Li, Ryan H Boe, Emanuelle I Grody, Manoj Chelvanambi, Ian P Dardani, Benjamin Emert, Nicholas Bodkin, Jonas Braun, Dylan Fingerman, Amanpreet Kaur, Naveen Jain, Pavithran T Ravindran, Ian A Mellis, Karun Kiani, Gretchen M Alicea, Mitchell E Fane, Syeda Subia Ahmed, Haiyin Li, Yeqing Chen, Cedric Chai, Jessica Kaster, Russell G Witt, Rossana Lazcano, Davis R Ingram, Sarah B Johnson, Khalida Wani, Margaret C Dunagin, Alexander J Lazar, Ashani T Weeraratna, Jennifer A Wargo, Meenhard Herlyn, Arjun Raj.

Even among genetically identical cancer cells, resistance to therapy frequently emerges from a small subset of those cells1-7. Molecular differences in rare individual cells in the initial population enable certain cells to become resistant to therapy7-9; however, comparatively little is known about the variability in the resistance outcomes. Here we develop and apply FateMap, a framework that combines DNA barcoding with single-cell RNA sequencing, to reveal the fates of hundreds of thousands of clones exposed to anti-cancer therapies. We show that resistant clones emerging from single-cell-derived cancer cells adopt molecularly, morphologically and functionally distinct resistant types. These resistant types are largely predetermined by molecular differences between cells before drug addition and not by extrinsic factors. Changes in the dose and type of drug can switch the resistant type of an initial cell, resulting in the generation and elimination of certain resistant types. Samples from patients show evidence for the existence of these resistant types in a clinical context. We observed diversity in resistant types across several single-cell-derived cancer cell lines and cell types treated with a variety of drugs. The diversity of resistant types as a result of the variability in intrinsic cell states may be a generic feature of responses to external cues.

DOI: https://doi.org/10.1038/s41586-023-06342-8