bims-pimaco Biomed News
on PI3K and MAPK signalling in colorectal cancer
Issue of 2023–12–10
seven papers selected by
Lucas B. Zeiger, CRUK Scotland Institute, Beatson Institute for Cancer Research



  1. Cell Metab. 2023 Dec 05. pii: S1550-4131(23)00417-5. [Epub ahead of print]35(12): 2097-2099
      Nutrient availability is conveyed to the mechanistic target of rapamycin (mTOR), which couples metabolic processes with cell growth and proliferation. How mTOR itself is modulated by amino acid levels remains poorly understood. Ge and colleagues now demonstrate that broad sensing of uncharged tRNAs by GCN2/FBXO22 inactivates mTOR complex 1 (mTORC1) via mTOR ubiquitination.
    DOI:  https://doi.org/10.1016/j.cmet.2023.11.006
  2. Acta Pharmacol Sin. 2023 Dec 04.
      Kirsten rat sarcoma 2 viral oncogene homolog (KRAS) is the most frequently mutated oncogene in human cancers with mutations predominantly occurring in codon 12. These mutations disrupt the normal function of KRAS by interfering with GTP hydrolysis and nucleotide exchange activity, making it prone to the GTP-bound active state, thus leading to sustained activation of downstream pathways. Despite decades of research, there has been no progress in the KRAS drug discovery until the groundbreaking discovery of covalently targeting the KRASG12C mutation in 2013, which led to revolutionary changes in KRAS-targeted therapy. So far, two small molecule inhibitors sotorasib and adagrasib targeting KRASG12C have received accelerated approval for the treatment of non-small cell lung cancer (NSCLC) harboring KRASG12C mutations. In recent years, rapid progress has been achieved in the KRAS-targeted therapy field, especially the exploration of KRASG12C covalent inhibitors in other KRASG12C-positive malignancies, novel KRAS inhibitors beyond KRASG12C mutation or pan-KRAS inhibitors, and approaches to indirectly targeting KRAS. In this review, we provide a comprehensive overview of the molecular and mutational characteristics of KRAS and summarize the development and current status of covalent inhibitors targeting the KRASG12C mutation. We also discuss emerging promising KRAS-targeted therapeutic strategies, with a focus on mutation-specific and direct pan-KRAS inhibitors and indirect KRAS inhibitors through targeting the RAS activation-associated proteins Src homology-2 domain-containing phosphatase 2 (SHP2) and son of sevenless homolog 1 (SOS1), and shed light on current challenges and opportunities for drug discovery in this field.
    Keywords:  KRAS mutation; KRASG12C inhibitor; Pan-KRAS inhibitor; SHP2 allosteric inhibitor; SOS1 inhibitor; combination therapy
    DOI:  https://doi.org/10.1038/s41401-023-01194-4
  3. Comput Biol Chem. 2023 Nov 30. pii: S1476-9271(23)00185-8. [Epub ahead of print]108 107994
      Phosphoinositide 3-kinases (PI3Ks) are lipid kinases known to regulate important cellular functions by phosphorylating the inositol ring of inositol-phospholipids (PtdIns) at 3' position. The PI3Kα is a heterodimer and the activation of the catalytic subunit (p110α) is regulated by its regulatory subunit (p85α). The current work deals with studying the activation mechanism of the PI3Kα using multi micro-second molecular dynamic simulations. Structural changes involved in activation mechanism is studied by gradually releasing the inhibitory effects of different domains of regulatory subunit namely, n-terminal SH2 (nSH2) and inter SH2 (iSH2). The observation shows that even in the presence of n-terminal and inter SH2 domain (niSH2) of regulatory subunit, the catalytic domain has some intrinsic activation activity and the presence of c-terminal SH2 (cSH2) domain may be required for complete inhibition. The release of nSH2 domain leads to loss of interactions between iSH2 domain (regulatory subunit) and C2 and kinase domain (catalytic subunit). The study shows that early events in the activation mechanism involve the movement of the ABD domain of the catalytic subunit along with the linker region between ABD and RBD region which may lead to movement of ABD closer to the CLobe of the kinase domain. This movement is essentially as it triggers the rearrangement of CLobe especially the catalytic loop and activation loop which bring catalytic important residues closer to ATP and PIP2(phosphatidylinositol-4,5-bisphosphate). Water mediated interaction analysis reveal that water may be playing an important role in the transfer of phosphate from ATP to PIP2. The study shows that initial signal for release of inhibitory effect of the regulatory subunit might be propagated through the linker region between ABD and RBD through allosteric effect to different regions of the protein. These understanding of early events during the activation mechanism may help in the design of better therapeutic targeting PI3K.
    Keywords:  Cancer; Catalytic subunit; Molecular Simulations; PCA; PI3Kα
    DOI:  https://doi.org/10.1016/j.compbiolchem.2023.107994
  4. Nat Med. 2023 Dec 05.
    GO42144 Investigator and Study Group
      KRAS G12C mutation is prevalent in ~4% of colorectal cancer (CRC) and is associated with poor prognosis. Divarasib, a KRAS G12C inhibitor, has shown modest activity as a single agent in KRAS G12C-positive CRC at 400 mg. Epidermal growth factor receptor has been recognized as a major upstream activator of RAS-MAPK signaling, a proposed key mechanism of resistance to KRAS G12C inhibition in CRC. Here, we report on divarasib plus cetuximab (epidermal growth factor receptor inhibitor) in patients with KRAS G12C-positive CRC (n = 29) from arm C of an ongoing phase 1b trial. The primary objective was to evaluate safety. Secondary objectives included preliminary antitumor activity. The safety profile of this combination was consistent with those of single-agent divarasib and cetuximab. Treatment-related adverse events led to divarasib dose reductions in four patients (13.8%); there were no treatment withdrawals. The objective response rate was 62.5% (95% confidence interval: 40.6%, 81.2%) in KRAS G12C inhibitor-naive patients (n = 24). The median duration of response was 6.9 months. The median progression-free survival was 8.1 months (95% confidence interval: 5.5, 12.3). As an exploratory objective, we observed a decline in KRAS G12C variant allele frequency associated with response and identified acquired genomic alterations at disease progression that may be associated with resistance. The manageable safety profile and encouraging antitumor activity of divarasib plus cetuximab support the further investigation of this combination in KRAS G12C-positive CRC.ClinicalTrials.gov identifier: NCT04449874.
    DOI:  https://doi.org/10.1038/s41591-023-02696-8
  5. iScience. 2023 Dec 15. 26(12): 108399
      Precision oncology approaches for patients with colorectal cancer (CRC) continue to lag behind other solid cancers. Functional precision oncology-a strategy that is based on perturbing primary tumor cells from cancer patients-could provide a road forward to personalize treatment. We extend this paradigm to measuring proteome activity landscapes by acquiring quantitative phosphoproteomic data from patient-derived organoids (PDOs). We show that kinase inhibitors induce inhibitor- and patient-specific off-target effects and pathway crosstalk. Reconstruction of the kinase networks revealed that the signaling rewiring is modestly affected by mutations. We show non-genetic heterogeneity of the PDOs and upregulation of stemness and differentiation genes by kinase inhibitors. Using imaging mass-cytometry-based profiling of the primary tumors, we characterize the tumor microenvironment (TME) and determine spatial heterocellular crosstalk and tumor-immune cell interactions. Collectively, we provide a framework for inferring tumor cell intrinsic signaling and external signaling from the TME to inform precision (immuno-) oncology in CRC.
    Keywords:  Cancer; Cancer systems biology; Proteomics
    DOI:  https://doi.org/10.1016/j.isci.2023.108399
  6. STAR Protoc. 2023 Oct 27. pii: S2666-1667(23)00589-0. [Epub ahead of print]4(4): 102622
      PI3K signaling elicits distinct outputs in response to different patterns of extracellular stimulation. Here, we present a protocol for screening cellular outputs activated by optogenetically controlled temporal PI3K signaling activation patterns in 96-well plates. We describe steps for establishing PPAP2-stable cells, probe expression, and blue light irradiation. We then detail procedures for analysis of translation activity. This protocol can be applied for purposes, such as examining the effect of PI3K signaling on the efficacy of anticancer drugs. For complete details on the use and execution of this protocol, please refer to Ueda et al. (2022).1.
    Keywords:  Cancer; Cell Biology; Cell Membrane
    DOI:  https://doi.org/10.1016/j.xpro.2023.102622
  7. Math Biosci. 2023 Dec 04. pii: S0025-5564(23)00153-0. [Epub ahead of print] 109113
      The periodic secretion of insulin is a salient feature of the blood glucose control system in vivo. Insulin levels in the blood exhibit oscillations on multiple time scales-rapid, ultradian, and circadian-and the improved metabolic regulation resulting from pulsatile insulin release has been well established. Although numerous mathematical models investigating the causal mechanisms of insulin oscillations have appeared in the literature, to date there has been comparatively little attention given to the influence of periodic insulin stimulation on downstream components of the insulin signalling pathway. In this paper, we explore the effect of high frequency periodic insulin stimulation on Akt (also known as PKB), a crucial crosstalk node in the insulin signalling pathway that coordinates metabolic and mitogenic processes in the cell. We analyse a mathematical model of Akt translocation to the plasma membrane under both single step insulin perturbations and periodic insulin stimulation with an emphasis on-but not limited to-the physiological range of parameter values. It was shown that the system rapidly attains a robust dynamic steady state entrained to the periodic insulin stimulation. Moreover, the translocation of Akt to the plasma membrane in the model permits a sufficient level of phosphorylation to trigger downstream metabolic regulators. However, the modelling also indicated that further investigation of this activation process is required to determine whether the response of Akt is a key determinant of the enhanced metabolic control observed under periodic insulin stimulation.
    Keywords:  Akt/PKB; Insulin signaling; ODE model; Periodic stimulation; Signalling
    DOI:  https://doi.org/10.1016/j.mbs.2023.109113