bims-pimaco 2023-03-19 papers

on PI3K and MAPK signalling in colorectal cancer

Issue of 2023–03–19
seven papers selected by
Lucas B. Zeiger, CRUK Scotland Institute, Beatson Institute for Cancer Research

PI3K-alpha translocation mediates nuclear PtdIns(3,4,5)P3 effector signaling in colorectal cancer.
The emerging role of PI3K inhibitors for solid tumour treatment and beyond.
Phospho PTEN mediated dephosphorylation of mitotic kinase PLK1 and Aurora Kinase A prevents aneuploidy and preserves genomic stability.
Fibroblast-derived EGF ligand Neuregulin-1 induces fetal-like reprogramming of the intestinal epithelium without supporting tumorigenic growth.
Precision oncology for KRASG12C-mutant colorectal cancer.
First passage time analysis of spatial mutation patterns reveals sub-clonal evolutionary dynamics in colorectal cancer.
Emulator-based Bayesian calibration of the CISNET colorectal cancer models.

Mol Cell Proteomics. 2023 Mar 15. pii: S1535-9476(23)00039-7. [Epub ahead of print] 100529

PI3K-alpha translocation mediates nuclear PtdIns(3,4,5)P3 effector signaling in colorectal cancer.

Michelle Palmieri, Bruno Catimel, Dmitri Mouradov, Anuratha Sakthianandeswaren, Eugene Kapp, Ching-Seng Ang, Nicholas A Williamson, Cameron J Nowell, Michael Christie, Jayesh Desai, Peter Gibbs, Antony W Burgess, Oliver M Sieber.

  The canonical view of phosphatidylinositol 3-kinase alpha (PI3Kα) signaling describes PtdIns(3,4,5)P3 generation and activation of downstream effectors at the plasma membrane or at microtubule-bound endosomes. Here, we show that colorectal cancer (CRC) cell lines exhibit a diverse plasma membrane-nuclear distribution of PI3Kα, controlling corresponding levels of subcellular PtdIns(3,4,5)P3 pools. PI3Kα nuclear translocation was mediated by the importin β-dependent nuclear import pathway. By PtdIns(3,4,5)P3 affinity capture mass spectrometry done in the presence of SDS on CRC cell lines with PI3Kα nuclear localization, we identified 867 potential nuclear PtdIns(3,4,5)P3 effector proteins. Nuclear PtdIns(3,4,5)P3 interactome proteins were characterized by non-canonical PtdIns(3,4,5)P3 binding domains and showed overrepresentation for nuclear membrane, nucleolus and nuclear speckles. The nuclear PtdIns(3,4,5)P3 interactome was enriched for proteins related to RNA metabolism, with splicing reporter assays and SC-35 foci staining suggesting a role of EGF-stimulated nuclear PI3Kα signaling in modulating pre-mRNA splicing. In patient tumors, nuclear p110α staining was associated with lower T stage and mucinous histology. These results indicate that PI3Kα translocation mediates nuclear PtdIns(3,4,5)P3 effector signaling in human CRC, modulating signaling responses.

Keywords:  PtdIns(3,4,5)P(3) interactome; colorectal cancer; nuclear import pathway; phosphatidylinositol 3-kinase alpha; pre-mRNA splicing

DOI:  https://doi.org/10.1016/j.mcpro.2023.100529
Br J Cancer. 2023 Mar 13.

The emerging role of PI3K inhibitors for solid tumour treatment and beyond.

Carmen Belli, Matteo Repetto, Santosh Anand, Camillo Porta, Vivek Subbiah, Giuseppe Curigliano.

Phosphoinositide 3-kinases (PI3Ks) play a central role in tumourigenesis with recurrent activating mutations of its p110α subunit (PIK3CA) identified in several tumours. Although several PI3K inhibitors are approved for haematological malignancies, only alpelisib was approved in solid tumours and for the treatment of PIK3CA-related overgrowth spectrum (PROS) syndrome. Traditional PI3K inhibitors inhibit both wild-type and mutant PI3K with almost equal potency, thus limiting their efficacy due to on-target toxicity. Since the initiation of phase I clinical trials investigating next generation allosteric mutant and isoform selective PIK3CA inhibitors, there has been a surge in interest in PIK3CA targeting in solid tumours. Preclinical characterisation of these compounds showed that maximal mutant protein inhibition fails to elicit metabolic and glucose homoeostasis dysregulation, one of the dose limiting toxicities of both selective and pan PI3K inhibitors. While extreme selectivity can be hypothesised to grant activity and safety advantage to these novel agents, on the other hand reduced benefit can be speculated for patients harbouring multiple or rare PIK3CA mutations. This review summarises the current understanding of PI3K alterations and the state-of-the-art treatment strategies in PI3K driven solid tumours, while also exploring the potential intrinsic and acquired resistance mechanisms to these agents, and the emerging role of mutant selective PIK3CA inhibitors.

DOI: https://doi.org/10.1038/s41416-023-02221-1
Med Oncol. 2023 Mar 17. 40(4): 119

Phospho PTEN mediated dephosphorylation of mitotic kinase PLK1 and Aurora Kinase A prevents aneuploidy and preserves genomic stability.

Ginia Ghosh, Sandip Misra, Rachayeeta Ray, Sougata Ghosh Chowdhury, Parimal Karmakar.

  PTEN, dual phosphatase tumor suppressor protein, is found to be frequently mutated in various cancers. Post-translational modification of PTEN is important for its sub-cellular localization and catalytic functions. But how these modifications affect cytological damage and aneuploidy is not studied in detail. We focus on the role of phosphatase activity along with C-terminal phosphorylation of PTEN in perspective of cytological damage like micronucleus, nuclear bud, and nuclear bridge formation. Our data suggest that wild-type PTEN, but not phospho-mutant PTEN significantly reduces cytological damage in PTEN null PC3 cells. In case of phosphatase-dead PTEN, cytological damage markers are increased during 24 h recovery after DNA damage. When we use phosphorylation and phosphatase-dead dual mutant PTEN, the extent of different cytological DNA damage parameters are similar to phosphatase-dead PTEN. We also find that both of those activities are essential for maintaining chromosome numbers. PTEN null cells exhibit significantly aberrant γ-tubulin pole formation during metaphase. Interestingly, we observed that p-PTEN localized to spindle poles along with PLK1 and Aurora Kinase A. Further depletion of phosphorylation and phosphatase activity of PTEN increases the expression of p-Aurora Kinase A (T288) and p-PLK1 (T210), compared to cells expressing wild-type PTEN. Again, wild-type PTEN but not phosphorylation-dead mutant is able to physically interact with PLK1 and Aurora Kinase A. Thus, our study suggests that the phosphorylation-dependent interaction of PTEN with PLK1 and Aurora Kinase A causes dephosphorylation of those mitotic kinases and by lowering their hyperphosphorylation status, PTEN prevents aberrant chromosome segregation in metaphase.

Keywords:  Aneuploidy; Aurora Kinase; Micronucleus; PTEN; Polo-like kinase; Spindle pole

DOI:  https://doi.org/10.1007/s12032-023-01985-z
Dis Model Mech. 2023 Mar 13. pii: dmm.049692. [Epub ahead of print]

Fibroblast-derived EGF ligand Neuregulin-1 induces fetal-like reprogramming of the intestinal epithelium without supporting tumorigenic growth.

Toni T Lemmetyinen, Emma W Viitala, Linnea Wartiovaara, Tuomas Kaprio, Jaana Hagström, Caj Haglund, Pekka Katajisto, Timothy C Wang, Eva Domènech-Moreno, Saara Ollila.

  Growth factors secreted by stromal fibroblasts regulate the intestinal epithelium. Stroma-derived Epidermal growth factor (EGF) family ligands are implicated in epithelial regeneration and tumorigenesis, but their specific contributions and associated mechanisms remain unclear. Here, we use primary intestinal organoids modeling homeostatic, injured, and tumorigenic epithelium to assess how fibroblast-derived EGF family ligands Neuregulin-1 (NRG1) and Epiregulin (EREG) regulate the intestinal epithelium. NRG1 was expressed exclusively in the stroma, robustly increased crypt budding and protected intestinal epithelial organoids from radiation-induced damage. NRG1 also induced regenerative features in the epithelium including a fetal-like transcriptome, suppression of the Lgr5+ stem cell pool, and remodeling of the epithelial actin cytoskeleton. Intriguingly, unlike EGF and EREG, NRG1 failed to support the growth of pre-tumorigenic intestinal organoids lacking the tumor suppressor Apc, commonly mutated in human colorectal cancer (CRC). Interestingly, high expression of stromal NRG1 was associated with improved survival in CRC cohorts, suggesting a tumor suppressive function. Our results highlight the power of stromal NRG1 in transcriptional reprogramming and protection of the intestinal epithelium from radiation injury without promoting tumorigenesis.

Keywords:  Colorectal cancer; EGF; EREG; Intestinal regeneration; NRG1

DOI:  https://doi.org/10.1242/dmm.049692
Nat Rev Clin Oncol. 2023 Mar 13.

Precision oncology for KRASG12C-mutant colorectal cancer.

Federica Di Nicolantonio, Alberto Bardelli.

DOI: https://doi.org/10.1038/s41571-023-00748-z
PLoS Comput Biol. 2023 Mar 13. 19(3): e1010952

First passage time analysis of spatial mutation patterns reveals sub-clonal evolutionary dynamics in colorectal cancer.

Magnus J Haughey, Aleix Bassolas, Sandro Sousa, Ann-Marie Baker, Trevor A Graham, Vincenzo Nicosia, Weini Huang.

The signature of early cancer dynamics on the spatial arrangement of tumour cells is poorly understood, and yet could encode information about how sub-clones grew within the expanding tumour. Novel methods of quantifying spatial tumour data at the cellular scale are required to link evolutionary dynamics to the resulting spatial architecture of the tumour. Here, we propose a framework using first passage times of random walks to quantify the complex spatial patterns of tumour cell population mixing. First, using a simple model of cell mixing we demonstrate how first passage time statistics can distinguish between different pattern structures. We then apply our method to simulated patterns of mutated and non-mutated tumour cell population mixing, generated using an agent-based model of expanding tumours, to explore how first passage times reflect mutant cell replicative advantage, time of emergence and strength of cell pushing. Finally, we explore applications to experimentally measured human colorectal cancer, and estimate parameters of early sub-clonal dynamics using our spatial computational model. We infer a wide range of sub-clonal dynamics, with mutant cell division rates varying between 1 and 4 times the rate of non-mutated cells across our sample set. Some mutated sub-clones emerged after as few as 100 non-mutant cell divisions, and others only after 50,000 divisions. The majority were consistent with boundary driven growth or short-range cell pushing. By analysing multiple sub-sampled regions in a small number of samples, we explore how the distribution of inferred dynamics could inform about the initial mutational event. Our results demonstrate the efficacy of first passage time analysis as a new methodology in spatial analysis of solid tumour tissue, and suggest that patterns of sub-clonal mixing can provide insights into early cancer dynamics.

DOI: https://doi.org/10.1371/journal.pcbi.1010952
medRxiv. 2023 Mar 01. pii: 2023.02.27.23286525. [Epub ahead of print]

Emulator-based Bayesian calibration of the CISNET colorectal cancer models.

Carlos Pineda-Antunez, Claudia Seguin, Luuk van Duuren, Amy B Knudsen, Barak Davidi, Pedro Nascimento de Lima, Carolyn Rutter, Karen M Kuntz, Iris Lansdorp-Vogelaar, Nicholson Collier, Jonathan Ozik, Fernando Alarid-Escudero.

Purpose: To calibrate Cancer Intervention and Surveillance Modeling Network (CISNET) 's SimCRC, MISCAN-Colon, and CRC-SPIN simulation models of the natural history colorectal cancer (CRC) with an emulator-based Bayesian algorithm and internally validate the model-predicted outcomes to calibration targets.
Methods: We used Latin hypercube sampling to sample up to 50,000 parameter sets for each CISNET-CRC model and generated the corresponding outputs. We trained multilayer perceptron artificial neural networks (ANN) as emulators using the input and output samples for each CISNET-CRC model. We selected ANN structures with corresponding hyperparameters (i.e., number of hidden layers, nodes, activation functions, epochs, and optimizer) that minimize the predicted mean square error on the validation sample. We implemented the ANN emulators in a probabilistic programming language and calibrated the input parameters with Hamiltonian Monte Carlo-based algorithms to obtain the joint posterior distributions of the CISNET-CRC models' parameters. We internally validated each calibrated emulator by comparing the model-predicted posterior outputs against the calibration targets.
Results: The optimal ANN for SimCRC had four hidden layers and 360 hidden nodes, MISCAN-Colon had 4 hidden layers and 114 hidden nodes, and CRC-SPIN had one hidden layer and 140 hidden nodes. The total time for training and calibrating the emulators was 7.3, 4.0, and 0.66 hours for SimCRC, MISCAN-Colon, and CRC-SPIN, respectively. The mean of the model-predicted outputs fell within the 95% confidence intervals of the calibration targets in 98 of 110 for SimCRC, 65 of 93 for MISCAN, and 31 of 41 targets for CRC-SPIN.
Conclusions: Using ANN emulators is a practical solution to reduce the computational burden and complexity for Bayesian calibration of individual-level simulation models used for policy analysis, like the CISNET CRC models.

DOI: https://doi.org/10.1101/2023.02.27.23286525