bims-pimaco 2022-07-24 papers

on PI3K and MAPK signalling in colorectal cancer

Issue of 2022–07–24
eight papers selected by
Lucas B. Zeiger, CRUK Scotland Institute, Beatson Institute for Cancer Research

Comparative molecular dynamics analyses on PIK3CA hotspot mutations with PI3Kα specific inhibitors and ATP.
Chemical acylation of an acquired serine suppresses oncogenic signaling of K-Ras(G12S).
KRAS Mutation: Characterization and Its Impact on Survival Outcome of Patients with Metastatic Colorectal Cancer.
Activating mTOR mutations are detrimental in nutrient-poor conditions.
Sestrin mediates detection of and adaptation to low-leucine diets in Drosophila.
Structure of the metastatic factor P-Rex1 reveals a two-layered autoinhibitory mechanism.
Patient Derived Organoids Confirm That PI3K/AKT Signalling Is an Escape Pathway for Radioresistance and a Target for Therapy in Rectal Cancer.
PI3K/Akt/mTOR signaling pathway in cancer stem cells.

Comput Biol Chem. 2022 Jul 08. pii: S1476-9271(22)00106-2. [Epub ahead of print]99 107726

Comparative molecular dynamics analyses on PIK3CA hotspot mutations with PI3Kα specific inhibitors and ATP.

Muratcan Menteş, Başak Buse Karakuzulu, Gönlüm Bahar Uçar, Cihangir Yandım.

  PI3K pathway is heavily emphasized in cancer where PIK3CA, which encodes for the p110α subunit of PI3Kα, presents itself as the second most common mutated gene. A lot of effort has been put in developing PI3K inhibitors, opening promising avenues for the treatment of cancer. Among these, PI3Kα specific inhibitor alpelisib was approved by FDA for breast cancer and other α-isoform specific inhibitors such as inavolisib and serabelisib reached clinical trials. However, the mode of action of these inhibitors on mutated PI3Kα and how they interact with mutant structures has not been fully elucidated yet. In this study, we are revealing the calculated interactions and binding affinities of these inhibitors within the context of PIK3CA hotspot mutations (E542K, E545K and H1047R) by employing molecular dynamics (MD) simulations. We performed principal component analysis to understand the motions of the protein complex during our simulations and also checked the correlated motions of all amino acids. Binding affinity calculations with MM-PBSA confirmed the consistent binding of alpelisib across mutations and revealed relatively higher affinities for inavolisib towards wild-type and H1047R mutant structures in comparison to other inhibitors. On the other hand, E542K mutation significantly impaired the interaction of inavolisib and serabelisib with PI3Kα. We also investigated the structural relationship of the natural ligand ATP with PI3Kα, and interestingly realized a significant reduction in binding affinity for the mutants, with potentially unexpected implications on the mechanisms that render these mutations oncogenic. Moreover, correlated motions of all residues were generally higher for ATP except the H1047R mutation which exhibited a distinguishable reduction. The results presented here could be guiding for pre-clinical and clinical studies of personalized medicine where individual mutations are a strong consideration point.

Keywords:  ATP; Alpelisib; E542K; E545K; H1047R; Inavolisib; Molecular dynamics; PI3K; PIK3CA; Serabelisib

DOI:  https://doi.org/10.1016/j.compbiolchem.2022.107726
Nat Chem Biol. 2022 Jul 21.

Chemical acylation of an acquired serine suppresses oncogenic signaling of K-Ras(G12S).

Ziyang Zhang, Keelan Z Guiley, Kevan M Shokat.

Drugs that directly impede the function of driver oncogenes offer exceptional efficacy and a therapeutic window. The recently approved mutant selective small-molecule cysteine-reactive covalent inhibitor of the G12C mutant of K-Ras, sotorasib, provides a case in point. KRAS is the most frequently mutated proto-oncogene in human cancer, yet despite success targeting the G12C allele, targeted therapy for other hotspot mutants of KRAS has not been described. Here we report the discovery of small molecules that covalently target a G12S somatic mutation in K-Ras and suppress its oncogenic signaling. We show that these molecules are active in cells expressing K-Ras(G12S) but spare the wild-type protein. Our results provide a path to targeting a second somatic mutation in the oncogene KRAS by overcoming the weak nucleophilicity of an acquired serine residue. The chemistry we describe may serve as a basis for the selective targeting of other unactivated serines.

DOI: https://doi.org/10.1038/s41589-022-01065-9
Front Biosci (Landmark Ed). 2022 Jul 07. 27(7): 213

KRAS Mutation: Characterization and Its Impact on Survival Outcome of Patients with Metastatic Colorectal Cancer.

Datul Damit, Ravi Patnaik, Li Ling Chaw, Shir Kiong Lu, Pemasiri Upali Telisinghe, Zen Huat Lu, Kenneth Kok, Long Chiau Ming, Ya Chee Lim.

   INTRODUCTION: Colorectal cancer (CRC) is one of the most common cancer types, with rising incidence due to imbalanced lifestyle and dietary habit. Association between CRC cases and KRAS mutation has been established recently. Brunei Darussalam, located within the Borneo island, is of diverse ethnicity which could represent the genome of Southeast Asia population. Our study, for the first time, determined the survival outcome of metastatic colorectal cancer (mCRC) and established the link with KRAS mutation by modelling the population in Brunei Darussalam.
METHODS: We collected data of 76 metastatic CRC (mCRC) patients undergoing treatment at The Brunei Cancer Centre, the national centre for cancer treatment in Brunei. These patients were diagnosed with Stage 4 CRC between 1 January 2013 and 31 December 2017. Age, gender, ethnicity, date of diagnosis, site of primary tumour, metastatic sites and molecular analysis of KRAS mutation status (either KRAS mutated or KRAS wild-type) of tumour were recorded. The survival outcomes of these mCRC patients were analysed.
RESULTS: The end of this study period recorded 73.1% deceased mutant KRAS mCRC patients and 46.0% deceased wild-type KRAS mCRC patients, contributing to death rates of 45.2% and 54.8%, correspondingly. Chi-squared analysis showed a significant difference between the survival outcomes of wild-type KRAS and mutant KRAS mCRC patients (p-value = 0.024).
CONCLUSIONS: There is a significant difference between the survival outcomes of wild-type KRAS and mutant KRAS mCRC patients in the Brunei population. In addition, we found that mutations in codon 12 of KRAS gene on mutant KRAS mCRC patients have shorter survival median periods than those with mutations within codon 13 of KRAS gene. This is the first study in Brunei Darussalam to analyse both the survival outcomes of mCRC patients and those of mutant KRAS mCRC patients.

Keywords:  KRAS; codon; colorectal cancer; median; metastasis; sided; survival; tumour

DOI:  https://doi.org/10.31083/j.fbl2707213
Cancer Res. 2022 Jul 22. pii: CAN-22-0121. [Epub ahead of print]

Activating mTOR mutations are detrimental in nutrient-poor conditions.

Agata A Bielska, Caitlin F Harrigan, Yeon Ju Kyung, Quaid Morris, Wilhelm Palm, Craig B Thompson.

The mechanistic target of rapamycin (mTOR) is a key regulator of cell growth that integrates growth factor signaling and nutrient availability and is a downstream effector of oncogenic receptor tyrosine kinases (RTKs) and PI3K/Akt signaling. Thus, activating mTOR mutations would be expected to enhance growth in many tumor types. However, tumor sequencing data has shown that mTOR mutations are enriched only in renal clear cell carcinoma, a clinically hypervascular tumor unlikely to be constrained by nutrient availability. To further define this cancer type-specific restriction, we studied activating mutations in mTOR. All mTOR mutants tested enhanced growth in a cell type agnostic manner under nutrient-replete conditions but were detrimental to cell survival in nutrient-poor conditions. Consistently, analysis of tumor data demonstrated that oncogenic mutations in the nutrient-sensing arm of the mTOR pathway display a similar phenotype and were exceedingly rare in human cancers of all types. Together, these data suggest that maintaining the ability to turn off mTOR signaling in response to changing nutrient availability is retained in most naturally occurring tumors.

DOI: https://doi.org/10.1158/0008-5472.CAN-22-0121
Nature. 2022 Jul 20.

Sestrin mediates detection of and adaptation to low-leucine diets in Drosophila.

Xin Gu, Patrick Jouandin, Pranav V Lalgudi, Rich Binari, Max L Valenstein, Michael A Reid, Annamarie E Allen, Nolan Kamitaki, Jason W Locasale, Norbert Perrimon, David M Sabatini.

Mechanistic target of rapamycin complex 1 (mTORC1) regulates cell growth and metabolism in response to multiple nutrients, including the essential amino acid leucine1. Recent work in cultured mammalian cells established the Sestrins as leucine-binding proteins that inhibit mTORC1 signalling during leucine deprivation2,3, but their role in the organismal response to dietary leucine remains elusive. Here we find that Sestrin-null flies (Sesn-/-) fail to inhibit mTORC1 or activate autophagy after acute leucine starvation and have impaired development and a shortened lifespan on a low-leucine diet. Knock-in flies expressing a leucine-binding-deficient Sestrin mutant (SesnL431E) have reduced, leucine-insensitive mTORC1 activity. Notably, we find that flies can discriminate between food with or without leucine, and preferentially feed and lay progeny on leucine-containing food. This preference depends on Sestrin and its capacity to bind leucine. Leucine regulates mTORC1 activity in glial cells, and knockdown of Sesn in these cells reduces the ability of flies to detect leucine-free food. Thus, nutrient sensing by mTORC1 is necessary for flies not only to adapt to, but also to detect, a diet deficient in an essential nutrient.

DOI: https://doi.org/10.1038/s41586-022-04960-2
Nat Struct Mol Biol. 2022 Jul 21.

Structure of the metastatic factor P-Rex1 reveals a two-layered autoinhibitory mechanism.

Yong-Gang Chang, Christopher J Lupton, Charles Bayly-Jones, Alastair C Keen, Laura D'Andrea, Christina M Lucato, Joel R Steele, Hari Venugopal, Ralf B Schittenhelm, James C Whisstock, Michelle L Halls, Andrew M Ellisdon.

P-Rex (PI(3,4,5)P3-dependent Rac exchanger) guanine nucleotide exchange factors potently activate Rho GTPases. P-Rex guanine nucleotide exchange factors are autoinhibited, synergistically activated by Gβγ and PI(3,4,5)P3 binding and dysregulated in cancer. Here, we use X-ray crystallography, cryogenic electron microscopy and crosslinking mass spectrometry to determine the structural basis of human P-Rex1 autoinhibition. P-Rex1 has a bipartite structure of N- and C-terminal modules connected by a C-terminal four-helix bundle that binds the N-terminal Pleckstrin homology (PH) domain. In the N-terminal module, the Dbl homology (DH) domain catalytic surface is occluded by the compact arrangement of the DH-PH-DEP1 domains. Structural analysis reveals a remarkable conformational transition to release autoinhibition, requiring a 126° opening of the DH domain hinge helix. The off-axis position of Gβγ and PI(3,4,5)P3 binding sites further suggests a counter-rotation of the P-Rex1 halves by 90° facilitates PH domain uncoupling from the four-helix bundle, releasing the autoinhibited DH domain to drive Rho GTPase signaling.

DOI: https://doi.org/10.1038/s41594-022-00804-9
Front Oncol. 2022 ;12 920444

Patient Derived Organoids Confirm That PI3K/AKT Signalling Is an Escape Pathway for Radioresistance and a Target for Therapy in Rectal Cancer.

Kasun Wanigasooriya, Joao D Barros-Silva, Louise Tee, Mohammed E El-Asrag, Agata Stodolna, Oliver J Pickles, Joanne Stockton, Claire Bryer, Rachel Hoare, Celina M Whalley, Robert Tyler, Toritseju Sillo, Christopher Yau, Tariq Ismail, Andrew D Beggs.

   Objectives: Partial or total resistance to preoperative chemoradiotherapy occurs in more than half of locally advanced rectal cancer patients. Several novel or repurposed drugs have been trialled to improve cancer cell sensitivity to radiotherapy, with limited success. We aimed to understand the mechanisms of resistance to chemoradiotherapy in rectal cancer using patient derived organoid models.
Design: To understand the mechanisms underlying this resistance, we compared the pre-treatment transcriptomes of patient-derived organoids (PDO) with measured radiotherapy sensitivity to identify biological pathways involved in radiation resistance coupled with single cell sequencing, genome wide CRISPR-Cas9 and targeted drug screens.
Results: RNA sequencing enrichment analysis revealed upregulation of PI3K/AKT/mTOR and epithelial mesenchymal transition pathway genes in radioresistant PDOs. Single-cell sequencing of pre & post-irradiation PDOs showed mTORC1 and PI3K/AKT upregulation, which was confirmed by a genome-wide CRSIPR-Cas9 knockout screen using irradiated colorectal cancer (CRC) cell lines. We then tested the efficiency of dual PI3K/mTOR inhibitors in improving cancer cell sensitivity to radiotherapy. After irradiation, significant AKT phosphorylation was detected (p=0.027) which was abrogated with dual PI3K/mTOR inhibitors and lead to significant radiosensitisation of the HCT116 cell line and radiation resistant PDO lines.
Conclusions: The PI3K/AKT/mTOR pathway upregulation contributes to radioresistance and its targeted pharmacological inhibition leads to significant radiosensitisation in CRC organoids, making it a potential target for clinical trials.

Keywords:  PI3K - AKT pathway; colorectal cancer; mTOR; organoid; radiotherapy

DOI:  https://doi.org/10.3389/fonc.2022.920444
Pathol Res Pract. 2022 Jul 03. pii: S0344-0338(22)00254-0. [Epub ahead of print]237 154010

PI3K/Akt/mTOR signaling pathway in cancer stem cells.

Mohsen Karami Fath, Menooa Ebrahimi, Ehsan Nourbakhsh, Ahmad Zia Hazara, Ali Mirzaei, Saba Shafieyari, Azadeh Salehi, Mahsa Hoseinzadeh, Zahra Payandeh, Ghasem Barati.

  Cancer stem cells (CSCs) as a small subpopulation in tumor bulk are believed to initiate tumor formation and are responsible for the resistance to cancer therapy. The proliferation and differentiation of CSCs result in heterogeneity in a tumor which increases the chance of tumor survival and invasion. Many signaling pathways are abnormally activated or repressed in CSCs. Understanding these pathways and the metabolisms in CSCs may help targeted therapy in drug-resistant tumors. The PI3K/Akt/mTOR pathway is one of the major signaling pathways in CSCs involved in the maintenance of stemness, proliferation, differentiation, epithelial to mesenchymal transition (EMT), migration, and autophagy. Thus, suppressing the PI3K/Akt/mTOR pathway with inhibitors might be a promising strategy for targeted cancer therapy. Although the pathway is well-recognized and reviewed in tumor bulks, the functions in CSCs have not been well focused. Here, we reviewed the PI3K/Akt/mTOR signaling pathway and its functions in CSCs and addressed the potential therapeutic applications in drug-resistant tumors.

Keywords:  Cancer stem cell; PI3K/Akt/mTOR pathway; Pathogenesis; Targeted cancer therapy

DOI:  https://doi.org/10.1016/j.prp.2022.154010