bims-pimaco 2023-08-13 papers

on PI3K and MAPK signalling in colorectal cancer

Issue of 2023–08–13
twelve papers selected by
Lucas B. Zeiger, CRUK Scotland Institute, Beatson Institute for Cancer Research

The Axin scaffold protects the kinase GSK3β from cross-pathway inhibition.
Combined blockade of mTOR and p21-activated kinases pathways prevents tumour growth in KRAS-mutated colorectal cancer.
PLEKHS1 drives PI3Ks and remodels pathway homeostasis in PTEN-null prostate.
Targeting KRAS in Colorectal Cancer: A Bench to Bedside Review.
Malonyl-CoA is a conserved endogenous ATP-competitive mTORC1 inhibitor.
The road less traveled: activating an oncogenic kinase.
Recent advances in the development of inhibitors targeting KRAS-G12C and its related pathways.
Allosteric regulation of switch-II domain controls KRAS oncogenicity.
First-line durvalumab and tremelimumab with chemotherapy in RAS-mutated metastatic colorectal cancer: a phase 1b/2 trial.
PTEN in triple-negative breast carcinoma: protein expression and genomic alteration in pretreatment and posttreatment specimens.
Structure-based drug design, synthesis, and biological evaluation of novel 1,3,5-triazine or pyrimidine derivatives containing benzoyl hydrazine moiety as PI3Kα selective inhibitors.
TET2 is required to suppress mTORC1 signaling through urea cycle with therapeutic potential.

Elife. 2023 Aug 07. pii: e85444. [Epub ahead of print]12

The Axin scaffold protects the kinase GSK3β from cross-pathway inhibition.

Maire Gavagan, Noel Jameson, Jesse G Zalatan.

  Multiple signaling pathways regulate the kinase GSK3β by inhibitory phosphorylation at Ser9, which then occupies the GSK3β priming pocket and blocks substrate binding. Since this mechanism should affect GSK3β activity towards all primed substrates, it is unclear why Ser9 phosphorylation does not affect other GSK3β-dependent pathways, such as Wnt signaling. We used biochemical reconstitution and cell culture assays to evaluate how Wnt-associated GSK3β is insulated from cross-activation by other signals. We found that the Wnt-specific scaffold protein Axin allosterically protects GSK3β from phosphorylation at Ser9 by upstream kinases, which prevents accumulation of pS9-GSK3β in the Axin-GSK3β complex. Scaffold proteins that protect bound proteins from alternative pathway reactions could provide a general mechanism to insulate signaling pathways from improper crosstalk.

Keywords:  biochemistry; cell biology; chemical biology; human

DOI:  https://doi.org/10.7554/eLife.85444
Br J Cancer. 2023 Aug 11.

Combined blockade of mTOR and p21-activated kinases pathways prevents tumour growth in KRAS-mutated colorectal cancer.

Stefania Belli, Ada Pesapane, Alberto Servetto, Daniela Esposito, Fabiana Napolitano, Claudia Maria Ascione, Alessandra Allotta, Nicola Zambrano, Federica Zito Marino, Renato Franco, Teresa Troiani, Luigi Formisano, Roberto Bianco.

BACKGROUND: The identification of novel therapeutic strategies for metastatic colorectal cancer (mCRC) patients harbouring KRAS mutations represents an unmet clinical need. In this study, we aimed to clarify the role of p21-activated kinases (Paks) as therapeutic target for KRAS-mutated CRC.
METHODS: Paks expression and activation levels were evaluated in a cohort of KRAS-WT or -mutated CRC patients by immunohistochemistry. The effects of Paks inhibition on tumour cell proliferation and signal transduction were assayed by RNAi and by the use of three pan-Paks inhibitors (PF-3758309, FRAX1036, GNE-2861), evaluating CRC cells, spheroids and tumour xenografts' growth.
RESULTS: Paks activation positively correlated with KRAS mutational status in both patients and cell lines. Moreover, genetic modulation or pharmacological inhibition of Paks led to a robust impairment of KRAS-mut CRC cell proliferation. However, Paks prolonged blockade induced a rapid tumour adaptation through the hyper-activation of the mTOR/p70S6K pathway. The addition of everolimus (mTOR inhibitor) prevented the growth of KRAS-mut CRC tumours in vitro and in vivo, reverting the adaptive tumour resistance to Paks targeting.
CONCLUSIONS: In conclusion, our results suggest the simultaneous blockade of mTOR and Pak pathways as a promising alternative therapeutic strategy for patients affected by KRAS-mut colorectal cancer.

DOI: https://doi.org/10.1038/s41416-023-02390-z
Mol Cell. 2023 Aug 08. pii: S1097-2765(23)00558-0. [Epub ahead of print]

PLEKHS1 drives PI3Ks and remodels pathway homeostasis in PTEN-null prostate.

Tamara A M Chessa, Piotr Jung, Arqum Anwar, Sabine Suire, Karen E Anderson, David Barneda, Anna Kielkowska, Barzan A Sadiq, Ieng Wai Lai, Sergio Felisbino, Daniel J Turnham, Helen B Pearson, Wayne A Phillips, Junko Sasaki, Takehiko Sasaki, David Oxley, Dominik Spensberger, Anne Segonds-Pichon, Michael Wilson, Simon Walker, Hanneke Okkenhaug, Sabina Cosulich, Phillip T Hawkins, Len R Stephens.

  The PIP3/PI3K network is a central regulator of metabolism and is frequently activated in cancer, commonly by loss of the PIP3/PI(3,4)P2 phosphatase, PTEN. Despite huge research investment, the drivers of the PI3K network in normal tissues and how they adapt to overactivation are unclear. We find that in healthy mouse prostate PI3K activity is driven by RTK/IRS signaling and constrained by pathway feedback. In the absence of PTEN, the network is dramatically remodeled. A poorly understood YXXM- and PIP3/PI(3,4)P2-binding PH domain-containing adaptor, PLEKHS1, became the dominant activator and was required to sustain PIP3, AKT phosphorylation, and growth in PTEN-null prostate. This was because PLEKHS1 evaded pathway-feedback and experienced enhanced PI3K- and Src-family kinase-dependent phosphorylation of Y258XXM, eliciting PI3K activation. hPLEKHS1 mRNA and activating Y419 phosphorylation of hSrc correlated with PI3K pathway activity in human prostate cancers. We propose that in PTEN-null cells receptor-independent, Src-dependent tyrosine phosphorylation of PLEKHS1 creates positive feedback that escapes homeostasis, drives PIP3 signaling, and supports tumor progression.

Keywords:  IRS1; PI3K; PLEKHS1; PTEN; Src-family kinase; prostate

DOI:  https://doi.org/10.1016/j.molcel.2023.07.015
Int J Mol Sci. 2023 Jul 27. pii: 12030. [Epub ahead of print]24(15):

Targeting KRAS in Colorectal Cancer: A Bench to Bedside Review.

Fernand Bteich, Mahshid Mohammadi, Terence Li, Muzaffer Ahmed Bhat, Amalia Sofianidi, Ning Wei, Chaoyuan Kuang.

  Colorectal cancer (CRC) is a heterogeneous disease with a myriad of alterations at the cellular and molecular levels. Kristen rat sarcoma (KRAS) mutations occur in up to 40% of CRCs and serve as both a prognostic and predictive biomarker. Oncogenic mutations in the KRAS protein affect cellular proliferation and survival, leading to tumorigenesis through RAS/MAPK pathways. Until recently, only indirect targeting of the pathway had been investigated. There are now several KRAS allele-specific inhibitors in late-phase clinical trials, and many newer agents and targeting strategies undergoing preclinical and early-phase clinical testing. The adequate treatment of KRAS-mutated CRC will inevitably involve combination therapies due to the existence of robust adaptive resistance mechanisms in these tumors. In this article, we review the most recent understanding and findings related to targeting KRAS mutations in CRC, mechanisms of resistance to KRAS inhibitors, as well as evolving treatment strategies for KRAS-mutated CRC patients.

Keywords:  KRAS; cancer therapeutics; colorectal cancer; targeted therapy

DOI:  https://doi.org/10.3390/ijms241512030
Nat Cell Biol. 2023 Aug 10.

Malonyl-CoA is a conserved endogenous ATP-competitive mTORC1 inhibitor.

Raffaele Nicastro, Laura Brohée, Josephine Alba, Julian Nüchel, Gianluca Figlia, Stefanie Kipschull, Peter Gollwitzer, Jesus Romero-Pozuelo, Stephanie A Fernandes, Andreas Lamprakis, Stefano Vanni, Aurelio A Teleman, Claudio De Virgilio, Constantinos Demetriades.

Cell growth is regulated by the mammalian/mechanistic target of rapamycin complex 1 (mTORC1), which functions both as a nutrient sensor and a master controller of virtually all biosynthetic pathways. This ensures that cells are metabolically active only when conditions are optimal for growth. Notably, although mTORC1 is known to regulate fatty acid biosynthesis, how and whether the cellular lipid biosynthetic capacity signals back to fine-tune mTORC1 activity remains poorly understood. Here we show that mTORC1 senses the capacity of a cell to synthesise fatty acids by detecting the levels of malonyl-CoA, an intermediate of this biosynthetic pathway. We find that, in both yeast and mammalian cells, this regulation is direct, with malonyl-CoA binding to the mTOR catalytic pocket and acting as a specific ATP-competitive inhibitor. When fatty acid synthase (FASN) is downregulated/inhibited, elevated malonyl-CoA levels are channelled to proximal mTOR molecules that form direct protein-protein interactions with acetyl-CoA carboxylase 1 (ACC1) and FASN. Our findings represent a conserved and unique homeostatic mechanism whereby impaired fatty acid biogenesis leads to reduced mTORC1 activity to coordinately link this metabolic pathway to the overall cellular biosynthetic output. Moreover, they reveal the existence of a physiological metabolite that directly inhibits the activity of a signalling kinase in mammalian cells by competing with ATP for binding.

DOI: https://doi.org/10.1038/s41556-023-01198-6
Trends Pharmacol Sci. 2023 Aug 07. pii: S0165-6147(23)00167-0. [Epub ahead of print]

The road less traveled: activating an oncogenic kinase.

Madhuri Paul, David A Fruman.

  Elevated phosphoinositide 3-kinase (PI3K) activity in human tumors has prompted widespread efforts to develop chemical PI3K inhibitors for oncology indications. In an innovative new study, Gong et al. report the discovery of a highly selective activator of the PI3Kα isoform, with promising activity in assays of nerve regrowth and cardioprotection from ischemia-reperfusion injury (IRI).

Keywords:  PI3K; kinase; oncogene; targeted therapy

DOI:  https://doi.org/10.1016/j.tips.2023.07.005
Eur J Med Chem. 2023 Aug 01. pii: S0223-5234(23)00665-7. [Epub ahead of print]259 115698

Recent advances in the development of inhibitors targeting KRAS-G12C and its related pathways.

Dongqiang Zhao, Yu Liu, Fengchao Yi, Xia Zhao, Kui Lu.

The RAS gene, also known as the mouse sarcoma virus, includes three genes (KRAS, HRAS, and NRAS) that are associated with human tumors. Among them, KRAS has the highest incidence of mutations in cancer, accounting for around 80% of cases. At the molecular level, the RAS gene plays a regulatory role in transcription and translation, while at the cellular level, it affects cell proliferation and migration, making it crucial for cancer development. In 2021, the FDA approved AMG510, the first direct inhibitor targeting the KRAS-G12C mutation, which has shown tumor regression, prolonged survival, and low off-target activity. However, with the increase of drug resistance, a single inhibitor is no longer sufficient to achieve the desired effect on tumors. Therefore, a large number of other highly efficient inhibitors are being developed at different stages. This article provides an overview of the mechanism of action targeting KRAS-G12C in the KRASGTP-KRASGDP cycle pathway, as well as the structure-activity relationship, structure optimization, and biological activity effects of inhibitors that target the upstream and downstream pathways, or combination therapy.

DOI: https://doi.org/10.1016/j.ejmech.2023.115698
Cancer Res. 2023 Aug 09. pii: CAN-22-3210. [Epub ahead of print]

Allosteric regulation of switch-II domain controls KRAS oncogenicity.

Moon Hee Yang, Timothy H Tran, Bethany Hunt, Rebecca Agnor, Christian W Johnson, Bing Shui, Timothy J Waybright, Jonathan A Nowak, Andrew G Stephen, Dhirendra K Simanshu, Kevin M Haigis.

RAS proteins are GTPases that regulate a wide range of cellular processes. RAS activity is dependent on its nucleotide-binding status, which is modulated by guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). KRAS can be acetylated at lysine 104 (K104), and an acetylation-mimetic mutation of K104 to glutamine (K104Q) attenuates the in vitro transforming capacity of oncogenic KRAS by interrupting GEF induced nucleotide exchange. To assess the effect of this mutation in vivo, we used CRISPR-Cas9 to generate mouse models carrying the K104Q point mutation in wild-type and conditional KrasLSL-G12D alleles. Homozygous animals for K104Q were viable, fertile, and arose at the expected Mendelian frequency, indicating that K104Q is not a complete loss of function mutation. Consistent with our previous findings from in vitro studies, however, the oncogenic activity of KRASG12D was significantly attenuated by mutation at K104. Biochemical and structural analysis indicated that the G12D and K104Q mutations cooperate to suppress GEF-mediated nucleotide exchange, explaining the preferential effect of K104Q on oncogenic KRAS. Furthermore, K104 functioned in an allosteric network with M72, R73 and G75 on the α2 helix of the switch-II region. Intriguingly, point mutation of glutamine 75 to alanine (G75A) showed a strong negative regulatory effect on KRASG12D. These data demonstrate that lysine at position 104 is critical for the full oncogenic activity of mutant KRAS and suggest that modulating the sites in its allosteric network may provide a unique therapeutic approach in cancers expressing mutant KRAS.

DOI: https://doi.org/10.1158/0008-5472.CAN-22-3210
Nat Med. 2023 Aug 10.

First-line durvalumab and tremelimumab with chemotherapy in RAS-mutated metastatic colorectal cancer: a phase 1b/2 trial.

Marion Thibaudin, Jean-David Fumet, Benoist Chibaudel, Jaafar Bennouna, Christophe Borg, Jerome Martin-Babau, Romain Cohen, Marianne Fonck, Julien Taieb, Emeric Limagne, Julie Blanc, Elise Ballot, Léa Hampe, Marjorie Bon, Susy Daumoine, Morgane Peroz, Hugo Mananet, Valentin Derangère, Romain Boidot, Henri-Alexandre Michaud, Caroline Laheurte, Olivier Adotevi, Aurélie Bertaut, Caroline Truntzer, François Ghiringhelli.

Although patients with microsatellite instable metastatic colorectal cancer (CRC) benefit from immune checkpoint blockade, chemotherapy with targeted therapies remains the only therapeutic option for microsatellite stable (MSS) tumors. The single-arm, phase 1b/2 MEDITREME trial evaluated the safety and efficacy of durvalumab plus tremelimumab combined with mFOLFOX6 chemotherapy in first line, in 57 patients with RAS-mutant unresectable metastatic CRC. Safety was the primary objective of phase Ib; no safety issue was observed. The phase 2 primary objective of efficacy in terms of 3-month progression-free survival (PFS) in patients with MSS tumors was met, with 3-month PFS of 90.7% (95% confidence interval (CI): 79.2-96%). For secondary objectives, response rate was 64.5%; median PFS was 8.2 months (95% CI: 5.9-8.6); and overall survival was not reached in patients with MSS tumors. We observed higher tumor mutational burden and lower genomic instability in responders. Integrated transcriptomic analysis underlined that high immune signature and low epithelial-mesenchymal transition were associated with better outcome. Immunomonitoring showed induction of neoantigen and NY-ESO1 and TERT blood tumor-specific T cell response associated with better PFS. The combination of durvalumab-tremelimumab with mFOLFOX6 was tolerable with promising clinical activity in MSS mCRC. Clinicaltrials.gov identifier: NCT03202758 .

DOI: https://doi.org/10.1038/s41591-023-02497-z
Ther Adv Med Oncol. 2023 ;15 17588359231189422

PTEN in triple-negative breast carcinoma: protein expression and genomic alteration in pretreatment and posttreatment specimens.

Hui Chen, Qingqing Ding, Laila Khazai, Li Zhao, Senthil Damodaran, Jennifer K Litton, Gaiane M Rauch, Clinton Yam, Jeffrey T Chang, Sahil Seth, Bora Lim, Alastair M Thompson, Elizabeth A Mittendorf, Beatriz Adrada, Kiran Virani, Jason B White, Elizabeth Ravenberg, Xingzhi Song, Rosalind Candelaria, Banu Arun, Naoto T Ueno, Lumarie Santiago, Sadia Saleem, Sausan Abouharb, Rashmi K Murthy, Nuhad Ibrahim, Mark J Routbort, Aysegul Sahin, Vicente Valero, William Fraser Symmans, Debu Tripathy, Wei-Lien Wang, Stacy Moulder, Lei Huo.

   Background: Recent advances have been made in targeting the phosphoinositide 3-kinase pathway in breast cancer. Phosphatase and tensin homolog (PTEN) is a key component of that pathway.
Objective: To understand the changes in PTEN expression over the course of the disease in patients with triple-negative breast cancer (TNBC) and whether PTEN copy number variation (CNV) by next-generation sequencing (NGS) can serve as an alternative to immunohistochemistry (IHC) to identify PTEN loss.
Methods: We compared PTEN expression by IHC between pretreatment tumors and residual tumors in the breast and lymph nodes after neoadjuvant chemotherapy in 96 patients enrolled in a TNBC clinical trial. A correlative analysis between PTEN protein expression and PTEN CNV by NGS was also performed.
Results: With a stringent cutoff for PTEN IHC scoring, PTEN expression was discordant between pretreatment and posttreatment primary tumors in 5% of patients (n = 96) and between posttreatment primary tumors and lymph node metastases in 9% (n = 33). A less stringent cutoff yielded similar discordance rates. Intratumoral heterogeneity for PTEN loss was observed in 7% of the patients. Among pretreatment tumors, PTEN copy numbers by whole exome sequencing (n = 72) were significantly higher in the PTEN-positive tumors by IHC compared with the IHC PTEN-loss tumors (p < 0.0001). However, PTEN-positive and PTEN-loss tumors by IHC overlapped in copy numbers: 14 of 60 PTEN-positive samples showed decreased copy numbers in the range of those of the PTEN-loss tumors.
Conclusion: Testing various specimens by IHC may generate different PTEN results in a small proportion of patients with TNBC; therefore, the decision of testing one versus multiple specimens in a clinical trial should be defined in the patient inclusion criteria. Although a distinct cutoff by which CNV differentiated PTEN-positive tumors from those with PTEN loss was not identified, higher copy number of PTEN may confer positive PTEN, whereas lower copy number of PTEN would necessitate additional testing by IHC to assess PTEN loss.
Trial registration: NCT02276443.

Keywords:  ARTEMIS; PTEN; TNBC; copy number; heterogeneity; immunohistochemistry; neoadjuvant chemotherapy; next-generation sequencing

DOI:  https://doi.org/10.1177/17588359231189422
Bioorg Chem. 2023 Jul 18. pii: S0045-2068(23)00399-1. [Epub ahead of print]140 106738

Structure-based drug design, synthesis, and biological evaluation of novel 1,3,5-triazine or pyrimidine derivatives containing benzoyl hydrazine moiety as PI3Kα selective inhibitors.

Siyu Fu, Jiuyu Liu, Chunting Li, Jiakuan Wei, Hao Yue, Ao Yang, Kang Wang, Yongshuo Wu, Yunlei Hou, Yanfang Zhao.

  Phosphoinositide 3-kinase (PI3K) was an important cellular signal transducer, while PI3Kα was the most mutated family member in cancer. Selective PI3Kα inhibitors have become the frequent research in recent years because of their excellent curative effect and reduced side effects. Here, we described a series of PI3Kα inhibitors with 1,3,5-triazine or pyrimidine skeleton containing benzoyl hydrazine based on the pan-PI3K inhibitor ZSTK474 relying on the strategies of structure-based drug discovery (SBDD) and computer-aided drug design (CADD). Among them, compound F8 exhibited improved selective PI3Kα inhibition with an IC50 value of 0.14 nM and more significant anti-proliferative activities against three tumor-derived cell lines (PC-3 IC50 = 0.28 μM, HCT-116 IC50 = 0.57 μM, and U87-MG IC50 = 1.37 μM) than ZSTK-474. Compound F-8 induced a great decrease in mitochondrial membrane which caused cell cycle arrest at G1 phase and apoptosis in U87-MG cells in a dose-dependent manner. Furthermore, compound F8 induced significant tumor regressions in a xenograft mouse model of U87-MG cell line with no clear evidence of toxicity following intraperitoneal injection of 40 mg/kg. Compound F8 may serve as a PI3Kα-selective inhibitor and provided the opportunity to spare patients the side effects associated with broader inhibition of the class I PI3K family.

Keywords:  Antitumor; Benzoyl hydrazine; Kinase selectivity; PI3-kinase; Synthesis

DOI:  https://doi.org/10.1016/j.bioorg.2023.106738
Cell Discov. 2023 Aug 08. 9(1): 84

TET2 is required to suppress mTORC1 signaling through urea cycle with therapeutic potential.

Jing He, Mingen Lin, Xinchao Zhang, Ruonan Zhang, Tongguan Tian, Yuefan Zhou, Wenjing Dong, Yajing Yang, Xue Sun, Yue Dai, Yue Xu, Zhenru Zhang, Ming Xu, Qun-Ying Lei, Yanping Xu, Lei Lv.

Tumor development, involving both cell growth (mass accumulation) and cell proliferation, is a complex process governed by the interplay of multiple signaling pathways. TET2 mainly functions as a DNA dioxygenase, which modulates gene expression and biological functions via oxidation of 5mC in DNA, yet whether it plays a role in regulating cell growth remains unknown. Here we show that TET2 suppresses mTORC1 signaling, a major growth controller, to inhibit cell growth and promote autophagy. Mechanistically, TET2 functions as a 5mC "eraser" by mRNA oxidation, abolishes YBX1-HuR binding and promotes decay of urea cycle enzyme mRNAs, thus negatively regulating urea cycle and arginine production, which suppresses mTORC1 signaling. Therefore, TET2-deficient tumor cells are more sensitive to mTORC1 inhibition. Our results uncover a novel function for TET2 in suppressing mTORC1 signaling and inhibiting cell growth, linking TET2-mediated mRNA oxidation to cell metabolism and cell growth control. These findings demonstrate the potential of mTORC1 inhibition as a possible treatment for TET2-deficient tumors.

DOI: https://doi.org/10.1038/s41421-023-00567-7