bims-pimaco 2023-08-27 papers

on PI3K and MAPK signalling in colorectal cancer

Issue of 2023–08–27
eleven papers selected by
Lucas B. Zeiger, CRUK Scotland Institute, Beatson Institute for Cancer Research

Mutant PIK3CA as a negative predictive biomarker for treatment with a highly selective PIM1 inhibitor in human colon cancer.
Nuclear PTEN Regulates Thymidylate Biosynthesis in Human Prostate Cancer Cell Lines.
Proteomic Mapping of the Interactome of KRAS Mutants Identifies New Features of RAS Signalling Networks and the Mechanism of Action of Sotorasib.
The molecular basis of nutrient sensing and signalling by mTORC1 in metabolism regulation and disease.
A single inhibitor for all KRAS mutations.
The Role of PIK3R1 in Metabolic Function and Insulin Sensitivity.
A Chemically Remodeled Cellular Chaperone Targets Active State Mutant KRAS.
Quantum biochemistry description of PI3Kα enzyme bound to selective inhibitors.
Hydrophobic interactions dominate the recognition of a KRAS G12V neoantigen.
Phase Ib/II Study of the Efficacy and Safety of Binimetinib (MEK162) Plus Panitumumab for Mutant or Wild-Type RAS Metastatic Colorectal Cancer.
PTEN regulates expression of its pseudogene in glioblastoma cells in DNA methylation-dependent manner.

Cancer Biol Ther. 2023 Dec 31. 24(1): 2246208

Mutant PIK3CA as a negative predictive biomarker for treatment with a highly selective PIM1 inhibitor in human colon cancer.

Yoon Sun Park, Joseph Kim, Yea Seong Ryu, Jai-Hee Moon, Yu Jin Shin, Jeong Hee Kim, Seung-Woo Hong, Soo-A Jung, Seul Lee, Seung-Mi Kim, Dae Hee Lee, Do Yeon Kim, Hyeseon Yun, Ji-Eun You, Dong Il Yoon, Chul Hee Kim, Dong-In Koh, Dong-Hoon Jin.

  Significant improvement in targeted therapy for colorectal cancer (CRC) has occurred over the past few decades since the approval of the EGFR inhibitor cetuximab. However, cetuximab is used only for patients possessing the wild-type oncogene KRAS, NRAS, and BRAF, and even most of these eventually acquire therapeutic resistance, via activation of parallel oncogenic pathways such as RAS-MAPK or PI3K/Akt/mTOR. The two aforementioned pathways also contribute to the development of therapeutic resistance in CRC patients, due to compensatory and feedback mechanisms. Therefore, combination drug therapies (versus monotherapy) targeting these multiple pathways may be necessary for further efficacy against CRC. In this study, we identified PIK3CA mutant (PIK3CA MT) as a determinant of resistance to SMI-4a, a highly selective PIM1 kinase inhibitor, in CRC cell lines. In CRC cell lines, SMI-4a showed its effect only in PIK3CA wild type (PIK3CA WT) cell lines, while PIK3CA MT cells did not respond to SMI-4a in cell death assays. In vivo xenograft and PDX experiments confirmed that PIK3CA MT is responsible for the resistance to SMI-4a. Inhibition of PIK3CA MT by PI3K inhibitors restored SMI-4a sensitivity in PIK3CA MT CRC cell lines. Taken together, these results demonstrate that sensitivity to SMI-4a is determined by the PIK3CA genotype and that co-targeting of PI3K and PIM1 in PIK3CA MT CRC patients could be a promising and novel therapeutic approach for refractory CRC patients.

Keywords:  PIK3CA; PIM1; colorectal cancer; mutant KRAS; predictive marker

DOI:  https://doi.org/10.1080/15384047.2023.2246208
Metabolites. 2023 Aug 11. pii: 939. [Epub ahead of print]13(8):

Nuclear PTEN Regulates Thymidylate Biosynthesis in Human Prostate Cancer Cell Lines.

Zoe N Loh, Mu-En Wang, Changxin Wan, John M Asara, Zhicheng Ji, Ming Chen.

  The phosphatase and tensin homologue deleted on chromosome 10 (PTEN) tumor suppressor governs a variety of biological processes, including metabolism, by acting on distinct molecular targets in different subcellular compartments. In the cytosol, inactive PTEN can be recruited to the plasma membrane where it dimerizes and functions as a lipid phosphatase to regulate metabolic processes mediated by the phosphatidylinositol 3-kinase (PI3K)/AKT/mammalian target of rapamycin complex 1 (mTORC1) pathway. However, the metabolic regulation of PTEN in the nucleus remains undefined. Here, using a gain-of-function approach to targeting PTEN to the plasma membrane and nucleus, we show that nuclear PTEN contributes to pyrimidine metabolism, in particular de novo thymidylate (dTMP) biosynthesis. PTEN appears to regulate dTMP biosynthesis through interaction with methylenetetrahydrofolate dehydrogenase 1 (MTHFD1), a key enzyme that generates 5,10-methylenetetrahydrofolate, a cofactor required for thymidylate synthase (TYMS) to catalyze deoxyuridylate (dUMP) into dTMP. Our findings reveal a nuclear function for PTEN in controlling dTMP biosynthesis and may also have implications for targeting nuclear-excluded PTEN prostate cancer cells with antifolate drugs.

Keywords:  cancer; metabolic compartmentalization; nuclear PTEN; thymidylate biosynthesis

DOI:  https://doi.org/10.3390/metabo13080939
Cancers (Basel). 2023 Aug 17. pii: 4141. [Epub ahead of print]15(16):

Proteomic Mapping of the Interactome of KRAS Mutants Identifies New Features of RAS Signalling Networks and the Mechanism of Action of Sotorasib.

Aoife Nolan, Cinzia Raso, Walter Kolch, Alex von Kriegsheim, Kieran Wynne, David Matallanas.

  RAS proteins are key regulators of cell signalling and control different cell functions including cell proliferation, differentiation, and cell death. Point mutations in the genes of this family are common, particularly in KRAS. These mutations were thought to cause the constitutive activation of KRAS, but recent findings showed that some mutants can cycle between active and inactive states. This observation, together with the development of covalent KRASG12C inhibitors, has led to the arrival of KRAS inhibitors in the clinic. However, most patients develop resistance to these targeted therapies, and we lack effective treatments for other KRAS mutants. To accelerate the development of RAS targeting therapies, we need to fully characterise the molecular mechanisms governing KRAS signalling networks and determine what differentiates the signalling downstream of the KRAS mutants. Here we have used affinity purification mass-spectrometry proteomics to characterise the interactome of KRAS wild-type and three KRAS mutants. Bioinformatic analysis associated with experimental validation allows us to map the signalling network mediated by the different KRAS proteins. Using this approach, we characterised how the interactome of KRAS wild-type and mutants is regulated by the clinically approved KRASG12C inhibitor Sotorasib. In addition, we identified novel crosstalks between KRAS and its effector pathways including the AKT and JAK-STAT signalling modules.

Keywords:  JAK1; KRAS; RADIL; SOS1; Sotorasib; proteomics

DOI:  https://doi.org/10.3390/cancers15164141
Nat Rev Mol Cell Biol. 2023 Aug 23.

The molecular basis of nutrient sensing and signalling by mTORC1 in metabolism regulation and disease.

Claire Goul, Roberta Peruzzo, Roberto Zoncu.

The Ser/Thr kinase mechanistic target of rapamycin (mTOR) is a central regulator of cellular metabolism. As part of mTOR complex 1 (mTORC1), mTOR integrates signals such as the levels of nutrients, growth factors, energy sources and oxygen, and triggers responses that either boost anabolism or suppress catabolism. mTORC1 signalling has wide-ranging consequences for the growth and homeostasis of key tissues and organs, and its dysregulated activity promotes cancer, type 2 diabetes, neurodegeneration and other age-related disorders. How mTORC1 integrates numerous upstream cues and translates them into specific downstream responses is an outstanding question with major implications for our understanding of physiology and disease mechanisms. In this Review, we discuss recent structural and functional insights into the molecular architecture of mTORC1 and its lysosomal partners, which have greatly increased our mechanistic understanding of nutrient-dependent mTORC1 regulation. We also discuss the emerging involvement of aberrant nutrient-mTORC1 signalling in multiple diseases.

DOI: https://doi.org/10.1038/s41580-023-00641-8
Nat Cancer. 2023 Aug;4(8): 1060-1062

A single inhibitor for all KRAS mutations.

Ryan B Corcoran.

DOI: https://doi.org/10.1038/s43018-023-00615-x
Int J Mol Sci. 2023 Aug 11. pii: 12665. [Epub ahead of print]24(16):

The Role of PIK3R1 in Metabolic Function and Insulin Sensitivity.

Ariel Tsay, Jen-Chywan Wang.

  PIK3R1 (also known as p85α) is a regulatory subunit of phosphoinositide 3-kinases (PI3Ks). PI3K, a heterodimer of a regulatory subunit and a catalytic subunit, phosphorylates phosphatidylinositol into secondary signaling molecules involved in regulating metabolic homeostasis. PI3K converts phosphatidylinositol 4,5-bisphosphate (PIP2) to phosphatidylinositol 3,4,5-triphosphate (PIP3), which recruits protein kinase AKT to the inner leaflet of the cell membrane to be activated and to participate in various metabolic functions. PIK3R1 stabilizes and inhibits p110 catalytic activity and serves as an adaptor to interact with insulin receptor substrate (IRS) proteins and growth factor receptors. Thus, mutations in PIK3R1 or altered expression of PIK3R1 could modulate the activity of PI3K and result in significant metabolic outcomes. Interestingly, recent studies also found PI3K-independent functions of PIK3R1. Overall, in this article, we will provide an updated review of the metabolic functions of PIK3R1 that includes studies of PIK3R1 in various metabolic tissues using animal models, the mechanisms modulating PIK3R1 activity, and studies on the mutations of human PIK3R1 gene.

Keywords:  PIK3R1; insulin resistance; metabolic disorders; p85α, insulin signaling; phosphoinositide 3-kinases (PI3K); type 2 diabetes

DOI:  https://doi.org/10.3390/ijms241612665
Cancer Discov. 2023 Aug 25. OF1

A Chemically Remodeled Cellular Chaperone Targets Active State Mutant KRAS.

Formation of the CYPA:compound:KRASG12C tricomplex inhibits oncogenic signaling and tumor progression.

DOI: https://doi.org/10.1158/2159-8290.CD-RW2023-134
J Biomol Struct Dyn. 2023 Aug 26. 1-11

Quantum biochemistry description of PI3Kα enzyme bound to selective inhibitors.

Francisca Joseli Freitas de Sousa, Francisca Fernanda Nunes Azevedo, Francisco Lucas Santos de Oliveira, Jaqueline Vieira Carletti, Valder Nogueira Freire, Geancarlo Zanatta.

  The PI3K class I is composed of four PI3K isoforms that serve as regulatory enzymes governing cellular metabolism, proliferation, and survival. The hyperactivation of PI3Kα is observed in various types of cancer and is linked to poor prognosis. Unfortunately, the development inhibitors selectively targeting one of the isoforms remains challenging, with only few agents in clinical use. The main difficulty arises from the high conservation among residues at the ATP-binding pocket across isoforms, which also serves as target pocket for inhibitors. In this work, molecular dynamics and quantum calculations were performed to investigate the molecular features guiding the binding of selective inhibitors, alpelisib and GDC-0326, into the ATP-binding pocket of PI3Kα. While molecular dynamics allowed crystallographic coordinates to relax, the interaction eergy between each amino acid residues and inhibitors was obtained by combining the Molecular Fractionation with Conjugated Caps scheme with Density Functional Theory calculations. In addition, the atomic charge of ligands in the bound and unbound (free) was calculated. Results indicated that the most relevant residues for the binding of alpelisib are Ile932, Glu859, Val851, Val850, Tyr836, Met922, Ile800, and Ile848, while the most important residues for the binding of GDC-0326 are Ile848, Ile800, Ile932, Gln859, Glu849, and Met922. In addition, residues Trp780, Ile800, Tyr836, Ile848, Gln859 Val850, Val851, Ile932 and Met922 are common hotspots for both inhibitors. Overall, the results from this work contribute to improving the understanding of the molecular mechanisms controlling selectivity and highlight important interactions to be considered during the rational design of new agents.Communicated by Ramaswamy H. Sarma.

Keywords:  Alpelisib; GDC-0326; PI3Kα-inhibitors; molecular fragmentation with conjugated caps; phosphoinositide-3-kinase; quantum calculation

DOI:  https://doi.org/10.1080/07391102.2023.2251063
Nat Commun. 2023 Aug 21. 14(1): 5063

Hydrophobic interactions dominate the recognition of a KRAS G12V neoantigen.

Katharine M Wright, Sarah R DiNapoli, Michelle S Miller, P Aitana Azurmendi, Xiaowei Zhao, Zhiheng Yu, Mayukh Chakrabarti, WuXian Shi, Jacqueline Douglass, Michael S Hwang, Emily Han-Chung Hsiue, Brian J Mog, Alexander H Pearlman, Suman Paul, Maximilian F Konig, Drew M Pardoll, Chetan Bettegowda, Nickolas Papadopoulos, Kenneth W Kinzler, Bert Vogelstein, Shibin Zhou, Sandra B Gabelli.

Specificity remains a major challenge to current therapeutic strategies for cancer. Mutation associated neoantigens (MANAs) are products of genetic alterations, making them highly specific therapeutic targets. MANAs are HLA-presented (pHLA) peptides derived from intracellular mutant proteins that are otherwise inaccessible to antibody-based therapeutics. Here, we describe the cryo-EM structure of an antibody-MANA pHLA complex. Specifically, we determine a TCR mimic (TCRm) antibody bound to its MANA target, the KRASG12V peptide presented by HLA-A*03:01. Hydrophobic residues appear to account for the specificity of the mutant G12V residue. We also determine the structure of the wild-type G12 peptide bound to HLA-A*03:01, using X-ray crystallography. Based on these structures, we perform screens to validate the key residues required for peptide specificity. These experiments led us to a model for discrimination between the mutant and the wild-type peptides presented on HLA-A*03:01 based exclusively on hydrophobic interactions.

DOI: https://doi.org/10.1038/s41467-023-40821-w
Oncologist. 2023 Aug 19. pii: oyad210. [Epub ahead of print]

Phase Ib/II Study of the Efficacy and Safety of Binimetinib (MEK162) Plus Panitumumab for Mutant or Wild-Type RAS Metastatic Colorectal Cancer.

Eric Van Cutsem, Rona Yaeger, Jean-Pierre Delord, Josep Tabernero, Lillian L Siu, Michel Ducreux, Salvatore Siena, Elena Elez, Stefan Kasper, Thomas Zander, Neeltje Steeghs, Danielle Murphy, Michelle Edwards, Zev A Wainberg.

   INTRODUCTION: Activating RAS gene mutations occur in approximately 55% of patients with metastatic colorectal cancer (mCRC) and are associated with poorer clinical outcomes due to epidermal growth factor receptor (EGFR) blockade resistance. Combined EGFR and mitogen-activated protein kinase (MEK) inhibition may extend response to EGFR inhibition and overcome acquired resistance. This phase Ib/II dose escalation trial evaluated the safety and activity of dual inhibition with binimetinib (MEK1/2 inhibitor) and panitumumab (EGFR inhibitor [EGFRi]) in patients with RAS mutant or BRAF wild type (WT)/RAS WT mCRC.
METHODS: Phase Ib dose escalation started with binimetinib 45 mg twice daily plus panitumumab 6 mg/kg administered every 2 weeks. In the phase II study, patients with measurable mCRC were enrolled into 4 groups based on previous anti-EGFR monoclonal antibody therapy and RAS mutational status.
RESULTS: No patients in the phase Ib portion (n = 10) had a response; 70% of patients had stable disease. In the phase II portion (n = 43), overall response rate (ORR, confirmed) was 2.3% with one partial response in the RAS WT group, DCR was 30.2%, and median progression-free survival was 1.8 months (95%CI, 1.6-3.3). All patients experienced ≥1 adverse event, with the most common being diarrhea (71.7%), vomiting (52.8%), nausea (50.9%), fatigue (49.1%), dermatitis acneiform (43.4%), and rash (41.5%). Most patients required treatment interruption or dose reduction due to difficulties tolerating treatment.
CONCLUSIONS: The combination of binimetinib and panitumumab had substantial toxicity and limited clinical activity for patients with mutant or WT RAS mCRC, independent of EGFRi treatment history (Trial registration: NCT01927341).

Keywords:   RAS mutation; RAS wild type; binimetinib; colorectal cancer; panitumumab

DOI:  https://doi.org/10.1093/oncolo/oyad210
Biochimie. 2023 Aug 22. pii: S0300-9084(23)00201-8. [Epub ahead of print]

PTEN regulates expression of its pseudogene in glioblastoma cells in DNA methylation-dependent manner.

Tatyana F Kovalenko, Bhupender Yadav, Ksenia S Anufrieva, Tatyana D Larionova, Tatiana E Aksinina, Yaroslav A Latyshev, Soniya Bastola, Michail I Shakhparonov, Amit Kumar Pandey, Marat S Pavlyukov.

  Glioblastoma (GBM) is the most aggressive and frequent type of primary brain cancer in adult patients. One of the key molecular features associated with GBM pathogenesis is the dysfunction of PTEN oncosuppressor. In addition to PTEN gene, humans and several primates possess processed PTEN pseudogene (PTENP1) that gives rise to long non-coding RNA lncPTENP1-S. Regulation and functions of PTEN and PTENP1 are highly interconnected, however, the exact molecular mechanism of how these two genes affect each other remains unclear. Here, we analyzed the methylation level of the CpG islands (CpGIs) in the promoter regions of PTEN and PTENP1 in patient-derived GBM neurospheres. We found that increased PTEN methylation corelates with decreased PTEN mRNA level. Unexpectedly, we showed the opposite trend for PTENP1. Using targeted methylation and demethylation of PTENP1 CpGI, we demonstrated that DNA methylation increases lncPTENP1-S expression in the presence of wild type PTEN protein but decreases lncPTENP1-S expression if PTEN protein is absent. Further experiments revealed that PTEN protein binds to PTENP1 promoter region and inhibits lncPTENP1-S expression if its CpGI is demethylated. Interestingly, we did not detect any effect of lncPTENP1-S on the level of PTEN mRNA, indicating that in GBM cells PTENP1 is a downstream target of PTEN rather than its upstream regulator. Finally, we studied the functions of lncPTENP1-S and demonstrated that it plays a pro-oncogenic role in GBM cells by upregulating the expression of cancer stem cell markers and decreasing cell adhesion.

Keywords:  CpG island; DNA methylation; Glioblastoma; PTEN; PTENP1; lncPTENP1

DOI:  https://doi.org/10.1016/j.biochi.2023.08.010