bims-pimaco 2021-07-11 papers

on PI3K and MAPK signalling in colorectal cancer

Issue of 2021–07–11
eleven papers selected by
Lucas B. Zeiger, CRUK Scotland Institute, Beatson Institute for Cancer Research

Oncogenic KRAS creates an aspartate metabolism signature in colorectal cancer cells.
Blocking K-Ras Interaction With the Plasma Membrane Is a Tractable Therapeutic Approach to Inhibit Oncogenic K-Ras Activity.
Common and mutation specific phenotypes of KRAS and BRAF mutations in colorectal cancer cells revealed by integrative -omics analysis.
The INPP4B paradox: Like PTEN, but different.
The Prognostic Impact of KRAS G12C Mutation in Patients with Metastatic Colorectal Cancer: A Multicenter Retrospective Observational Study.
RAS Nanoclusters Selectively Sort Distinct Lipid Headgroups and Acyl Chains.
Tracking Cell Competition in Colorectal Cancer.
Active elimination of intestinal cells drives oncogenic growth in organoids.
A review of mechanisms of disease across PIK3CA-related disorders with vascular manifestations.
The RAS GTPase RIT1 compromises mitotic fidelity through spindle assembly checkpoint suppression.
Reactivating PTEN promotes antitumour immunity.

FEBS J. 2021 Jul 06.

Oncogenic KRAS creates an aspartate metabolism signature in colorectal cancer cells.

Peter F Doubleday, Luca Fornelli, Ioanna Ntai, Neil L Kelleher.

  Oncogenic mutations in the KRAS gene are found in 30-50% of colorectal cancers (CRC) and recent findings have demonstrated independent and non-redundant roles for wild-type and mutant KRAS alleles in governing signaling and metabolism. Here, we quantify proteomic changes manifested by KRAS mutation and KRAS allele loss in isogenic cell lines. We show that expression of KRASG13D upregulates aspartate metabolizing proteins including PCK1, PCK2, ASNS and ASS1. Furthermore, differential expression analyses of transcript-level data from CRC tumors identified the upregulation of urea cycle enzymes in CRC. We find that expression of ASS1, supports colorectal cancer cell proliferation and promotes tumor formation in vitro. We show that loss of ASS1 can be rescued with high levels of several metabolites.

Keywords:  Quantitative proteomics; aspartate; colorectal cancer; metabolomics; mutant KRAS; urea cycle

DOI:  https://doi.org/10.1111/febs.16111
Front Mol Biosci. 2021 ;8 673096

Blocking K-Ras Interaction With the Plasma Membrane Is a Tractable Therapeutic Approach to Inhibit Oncogenic K-Ras Activity.

Karen M Henkels, Kristen M Rehl, Kwang-Jin Cho.

  Ras proteins are membrane-bound small GTPases that promote cell proliferation, differentiation, and apoptosis. Consistent with this key regulatory role, activating mutations of Ras are present in ∼19% of new cancer cases in the United States per year. K-Ras is one of the three ubiquitously expressed isoforms in mammalian cells, and oncogenic mutations in this isoform account for ∼75% of Ras-driven cancers. Therefore, pharmacological agents that block oncogenic K-Ras activity would have great clinical utility. Most efforts to block oncogenic Ras activity have focused on Ras downstream effectors, but these inhibitors only show limited clinical benefits in Ras-driven cancers due to the highly divergent signals arising from Ras activation. Currently, four major approaches are being extensively studied to target K-Ras-driven cancers. One strategy is to block K-Ras binding to the plasma membrane (PM) since K-Ras requires the PM binding for its signal transduction. Here, we summarize recently identified molecular mechanisms that regulate K-Ras-PM interaction. Perturbing these mechanisms using pharmacological agents blocks K-Ras-PM binding and inhibits K-Ras signaling and growth of K-Ras-driven cancer cells. Together, these studies propose that blocking K-Ras-PM binding is a tractable strategy for developing anti-K-Ras therapies.

Keywords:  K-Ras; cancer; mislocalization; phosphatidylinositol; phosphatidylserine; plasma membrane; recycing endosome; sphingomyelin

DOI:  https://doi.org/10.3389/fmolb.2021.673096
J Exp Clin Cancer Res. 2021 Jul 07. 40(1): 225

Common and mutation specific phenotypes of KRAS and BRAF mutations in colorectal cancer cells revealed by integrative -omics analysis.

Snehangshu Kundu, Muhammad Akhtar Ali, Niklas Handin, Louis P Conway, Veronica Rendo, Per Artursson, Liqun He, Daniel Globisch, Tobias Sjöblom.

   BACKGROUND: Genes in the Ras pathway have somatic mutations in at least 60 % of colorectal cancers. Despite activating the same pathway, the BRAF V600E mutation and the prevalent mutations in codon 12 and 13 of KRAS have all been linked to different clinical outcomes, but the molecular mechanisms behind these differences largely remain to be clarified.
METHODS: To characterize the similarities and differences between common activating KRAS mutations and between KRAS and BRAF mutations, we used genome editing to engineer KRAS G12C/D/V and G13D mutations in colorectal cancer cells that had their mutant BRAF V600E allele removed and subjected them to transcriptome sequencing, global proteomics and metabolomics analyses.
RESULTS: By intersecting differentially expressed genes, proteins and metabolites, we uncovered (i) two-fold more regulated genes and proteins when comparing KRAS to BRAF mutant cells to those lacking Ras pathway mutation, (ii) five differentially expressed proteins in KRAS mutants compared to cells lacking Ras pathway mutation (IFI16, S100A10, CD44, GLRX and AHNAK2) and 6 (CRABP2, FLNA, NXN, LCP1, S100A10 and S100A2) compared to BRAF mutant cells, (iii) 19 proteins expressed differentially in a KRAS mutation specific manner versus BRAF V600E cells, (iv) regulation of the Integrin Linked Kinase pathway by KRAS but not BRAF mutation, (v) regulation of amino acid metabolism, particularly of the tyrosine, histidine, arginine and proline pathways, the urea cycle and purine metabolism by Ras pathway mutations, (vi) increased free carnitine in KRAS and BRAF mutant RKO cells.
CONCLUSIONS: This comprehensive integrative -omics analysis confirms known and adds novel genes, proteins and metabolic pathways regulated by mutant KRAS and BRAF signaling in colorectal cancer. The results from the new model systems presented here can inform future development of diagnostic and therapeutic approaches targeting tumors with KRAS and BRAF mutations.

Keywords:  BRAF; Colorectal cancer; Integrative -omics analysis; Isogenic cell models; KRAS; Ras pathway

DOI:  https://doi.org/10.1186/s13046-021-02025-2
Adv Biol Regul. 2021 Jun 16. pii: S2212-4926(21)00033-6. [Epub ahead of print]82 100817

The INPP4B paradox: Like PTEN, but different.

Sabryn A Hamila, Lisa M Ooms, Samuel J Rodgers, Christina A Mitchell.

  Cancer is a complex and heterogeneous disease marked by the dysregulation of cancer driver genes historically classified as oncogenes or tumour suppressors according to their ability to promote or inhibit tumour development and growth, respectively. Certain genes display both oncogenic and tumour suppressor functions depending on the biological context, and as such have been termed dual-role cancer driver genes. However, because of their context-dependent behaviour, the tumourigenic mechanism of many dual-role genes is elusive and remains a significant knowledge gap in our effort to understand and treat cancer. Inositol polyphosphate 4-phosphatase type II (INPP4B) is an emerging dual-role cancer driver gene, primarily known for its role as a negative regulator of the phosphoinositide 3-kinase (PI3K)/AKT signalling pathway. In response to growth factor stimulation, class I PI3K generates PtdIns(3,4,5)P3 at the plasma membrane. PtdIns(3,4,5)P3 can be hydrolysed by inositol polyphosphate 5-phosphatases to generate PtdIns(3,4)P2, which, together with PtdIns(3,4,5)P3, facilitates the activation of AKT to promote cell proliferation, survival, migration, and metabolism. Phosphatase and tensin homology on chromosome 10 (PTEN) and INPP4B are dual-specificity phosphatases that hydrolyse PtdIns(3,4,5)P3 and PtdIns(3,4)P2, respectively, and thus negatively regulate PI3K/AKT signalling. PTEN is a bona fide tumour suppressor that is frequently lost in human tumours. INPP4B was initially characterised as a tumour suppressor akin to PTEN, and has been implicated as such in a number of cancers, including prostate, thyroid, and basal-like breast cancers. However, evidence has since emerged revealing INPP4B as a paradoxical oncogene in several malignancies, with increased INPP4B expression reported in AML, melanoma and colon cancers among others. Although the tumour suppressive function of INPP4B has been mostly ascribed to its ability to negatively regulate PI3K/AKT signalling, its oncogenic function remains less clear, with proposed mechanisms including promotion of PtdIns(3)P-dependent SGK3 signalling, inhibition of PTEN-dependent AKT activation, and enhancing DNA repair mechanisms to confer chemoresistance. Nevertheless, research is ongoing to identify the factors that dictate the tumourigenic output of INPP4B in different human cancers. In this review we discuss the dualistic role that INPP4B plays in the context of cancer development, progression and treatment, drawing comparisons to PTEN to explore how their similarities and, importantly, their differences may account for their diverging roles in tumourigenesis.

Keywords:  Cancer; Inositol polyphosphate 4-phosphatase (INPP4B); Oncogene; Phosphate and tensin homologue deleted on chromosome 10 (PTEN); Phosphoinositide signalling; Tumour suppressor

DOI:  https://doi.org/10.1016/j.jbior.2021.100817
Oncologist. 2021 Jul 07.

The Prognostic Impact of KRAS G12C Mutation in Patients with Metastatic Colorectal Cancer: A Multicenter Retrospective Observational Study.

Keigo Chida, Daisuke Kotani, Toshiki Masuishi, Takeshi Kawakami, Yasuyuki Kawamoto, Kyoko Kato, Kunihiro Fushiki, Kentaro Sawada, Ryosuke Kumanishi, Hiromichi Shirasu, Yuki Matsubara, Satoshi Yuki, Yoshito Komatsu, Kentaro Yamazaki, Takayuki Yoshino.

   BACKGROUND: KRAS is one of the most frequently mutated oncogenes in colorectal cancer (CRC). Recently, a novel therapy targeting KRAS G12C mutation has demonstrated promising activities for corresponding advanced solid tumors, including metastatic CRC (mCRC). However, the prognostic impact of the KRAS G12C mutation remains unclear in patients with mCRC.
MATERIALS AND METHODS: We retrospectively reviewed medical records of patients with mCRC who received first-line chemotherapy between January 2005 and December 2017 at four large oncology facilities in Japan. Survival outcomes were compared between patients with KRAS G12C and those with non-G12C mutations.
RESULTS: Among 2,457 patients with mCRC, 1,632 met selection criteria, and of these, 696 had KRAS exon 2 mutations, including 45 with KRAS G12C mutation tumors. Patient characteristics were not significantly different between the KRAS G12C and non-G12C groups. At a median follow-up of 64.8 months, patients with the KRAS G12C mutation showed significantly shorter first-line progression-free survival (PFS; median, 9.4 vs. 10.8 months; p = .015) and overall survival (OS; median, 21.1 vs. 27.3 months; p = .015) than those with non-G12C mutations. Multivariate analysis also showed that KRAS G12C mutation was significantly associated with shorter PFS (hazard ratio [HR], 1.43; 95% confidence interval [CI], 1.04-1.96, p = .030) and OS (HR, 1.42; 95% CI, 1.01-2.00; p = .044).
CONCLUSION: We demonstrate that, compared with non-G12C mutations, KRAS G12C mutation is significantly correlated with shorter first-line PFS and OS. These findings indicate the relevance of a stratified treatment targeting KRAS G12C mutation in mCRC.
IMPLICATIONS FOR PRACTICE: Among patients with KRAS exon 2 mutated metastatic colorectal cancer (mCRC), median progression-free survival (PFS) and overall survival (OS) were 9.4 and 21.1 months, respectively, for G12C mutation and 10.8 and 27.3 months, respectively, for patients with non-G12C mutations, indicating significantly shorter PFS (hazard ratio [HR], 1.47; 95% confidence interval [CI], 1.08-2.01; p = .015) and OS (HR, 1.50; 95% CI, 1.08-2.08; p = .015) in patients with G12C mutation than in those with non-G12C mutations. Furthermore, multivariate analysis showed that KRAS G12C mutation was independently associated with shorter first-line PFS and OS. Thus, these findings underscore the relevance of a stratified treatment targeting KRAS G12C mutation in mCRC.

Keywords:  Chemotherapy; Colorectal cancer; G12C; KRAS; Prognosis

DOI:  https://doi.org/10.1002/onco.13870
Front Mol Biosci. 2021 ;8 686338

RAS Nanoclusters Selectively Sort Distinct Lipid Headgroups and Acyl Chains.

Yong Zhou, Alemayehu A Gorfe, John F Hancock.

  RAS proteins are lipid-anchored small GTPases that switch between the GTP-bound active and GDP-bound inactive states. RAS isoforms, including HRAS, NRAS and splice variants KRAS4A and KRAS4B, are some of the most frequently mutated proteins in cancer. In particular, constitutively active mutants of KRAS comprise ∼80% of all RAS oncogenic mutations and are found in 98% of pancreatic, 45% of colorectal and 31% of lung tumors. Plasma membrane (PM) is the primary location of RAS signaling in biology and pathology. Thus, a better understanding of how RAS proteins localize to and distribute on the PM is critical to better comprehend RAS biology and to develop new strategies to treat RAS pathology. In this review, we discuss recent findings on how RAS proteins sort lipids as they undergo macromolecular assembly on the PM. We also discuss how RAS/lipid nanoclusters serve as signaling platforms for the efficient recruitment of effectors and signal transduction, and how perturbing the PM biophysical properties affect the spatial distribution of RAS isoforms and their functions.

Keywords:  RAS nanoclusters; cholesterol; depolarization; electron microscopy; membrane curvature; mitogen-activated protein kinases; phospholipids; polybasic domain

DOI:  https://doi.org/10.3389/fmolb.2021.686338
Cancer Discov. 2021 Jul 07.

Tracking Cell Competition in Colorectal Cancer.

Three recent studies have shed light on the competitive dynamics between intestinal stem cells that harbor tumor-initiating mutations, such as in APC, and their wild-type neighbors. Through active cross-talk mechanisms, mutant cells shape the microenvironment to their benefit, which enables them to eventually outcompete nearby normal cells and drive intestinal crypt colonization.

DOI: https://doi.org/10.1158/2159-8290.CD-ND2021-0110
Cell Rep. 2021 Jul 06. pii: S2211-1247(21)00683-5. [Epub ahead of print]36(1): 109307

Active elimination of intestinal cells drives oncogenic growth in organoids.

Ana Krotenberg Garcia, Arianna Fumagalli, Huy Quang Le, Rene Jackstadt, Tamsin Rosemary Margaret Lannagan, Owen James Sansom, Jacco van Rheenen, Saskia Jacoba Elisabeth Suijkerbuijk.

  Competitive cell interactions play a crucial role in quality control during development and homeostasis. Here, we show that cancer cells use such interactions to actively eliminate wild-type intestine cells in enteroid monolayers and organoids. This apoptosis-dependent process boosts proliferation of intestinal cancer cells. The remaining wild-type population activates markers of primitive epithelia and transits to a fetal-like state. Prevention of this cell-state transition avoids elimination of wild-type cells and, importantly, limits the proliferation of cancer cells. Jun N-terminal kinase (JNK) signaling is activated in competing cells and is required for cell-state change and elimination of wild-type cells. Thus, cell competition drives growth of cancer cells by active out-competition of wild-type cells through forced cell death and cell-state change in a JNK-dependent manner.

Keywords:  JNK; cancer; cell competition; fetal-like; organoids; small intestine

DOI:  https://doi.org/10.1016/j.celrep.2021.109307
Orphanet J Rare Dis. 2021 Jul 08. 16(1): 306

A review of mechanisms of disease across PIK3CA-related disorders with vascular manifestations.

Guillaume Canaud, Adrienne M Hammill, Denise Adams, Miikka Vikkula, Kim M Keppler-Noreuil.

   BACKGROUND: PIK3CA-related disorders include vascular malformations and overgrowth of various tissues that are caused by postzygotic, somatic variants in the gene encoding phosphatidylinositol-3-kinase (PI3K) catalytic subunit alpha. These mutations result in activation of the PI3K/AKT/mTOR signaling pathway. The goals of this review are to provide education on the underlying mechanism of disease for this group of rare conditions and to summarize recent advancements in the understanding of, as well as current and emerging treatment options for PIK3CA-related disorders.
MAIN BODY: PIK3CA-related disorders include PIK3CA-related overgrowth spectrum (PROS), PIK3CA-related vascular malformations, and PIK3CA-related nonvascular lesions. Somatic activating mutations (predominantly in hotspots in the helical and kinase domains of PIK3CA, but also in other domains), lead to hyperactivation of the PI3K signaling pathway, which results in abnormal tissue growth. Diagnosis is complicated by the variability and overlap in phenotypes associated with PIK3CA-related disorders and should be performed by clinicians with the required expertise along with coordinated care from a multidisciplinary team. Although tissue mosaicism presents challenges for confirmation of PIK3CA mutations, next-generation sequencing and tissue selection have improved detection. Clinical improvement, radiological response, and patient-reported outcomes are typically used to assess treatment response in clinical studies of patients with PIK3CA-related disorders, but objective assessment of treatment response is difficult using imaging (due to the heterogeneous nature of these disorders, superimposed upon patient growth and development). Despite their limitations, patient-reported outcome tools may be best suited to gauge patient improvement. New therapeutic options are needed to provide an alternative or supplement to standard approaches such as surgery and sclerotherapy. Currently, there are no systemic agents that have regulatory approval for these disorders, but the mTOR inhibitor sirolimus has been used for several years in clinical trials and off label to address symptoms. There are also other agents under investigation for PIK3CA-related disorders that act as inhibitors to target different components of the PI3K signaling pathway including AKT (miransertib) and PI3K alpha (alpelisib).
CONCLUSION: Management of patients with PIK3CA-related disorders requires a multidisciplinary approach. Further results from ongoing clinical studies of agents targeting the PI3K pathway are highly anticipated.

Keywords:  Alpelisib; Miransertib; PI3K; PIK3CA; PROS; Sirolimus; Vascular malformation

DOI:  https://doi.org/10.1186/s13023-021-01929-8
Curr Biol. 2021 Jun 30. pii: S0960-9822(21)00825-3. [Epub ahead of print]

The RAS GTPase RIT1 compromises mitotic fidelity through spindle assembly checkpoint suppression.

Antonio Cuevas-Navarro, Richard Van, Alice Cheng, Anatoly Urisman, Pau Castel, Frank McCormick.

  The spindle assembly checkpoint (SAC) functions as a sensor of unattached kinetochores that delays mitotic progression into anaphase until proper chromosome segregation is guaranteed.1,2 Disruptions to this safety mechanism lead to genomic instability and aneuploidy, which serve as the genetic cause of embryonic demise, congenital birth defects, intellectual disability, and cancer.3,4 However, despite the understanding of the fundamental mechanisms that control the SAC, it remains unknown how signaling pathways directly interact with and regulate the mitotic checkpoint activity. In response to extracellular stimuli, a diverse network of signaling pathways involved in cell growth, survival, and differentiation are activated, and this process is prominently regulated by the Ras family of small guanosine triphosphatases (GTPases).5 Here we show that RIT1, a Ras-related GTPase that regulates cell survival and stress response,6 is essential for timely progression through mitosis and proper chromosome segregation. RIT1 dissociates from the plasma membrane (PM) during mitosis and interacts directly with SAC proteins MAD2 and p31comet in a process that is regulated by cyclin-dependent kinase 1 (CDK1) activity. Furthermore, pathogenic levels of RIT1 silence the SAC and accelerate transit through mitosis by sequestering MAD2 from the mitotic checkpoint complex (MCC). Moreover, SAC suppression by pathogenic RIT1 promotes chromosome segregation errors and aneuploidy. Our results highlight a unique function of RIT1 compared to other Ras GTPases and elucidate a direct link between a signaling pathway and the SAC through a novel regulatory mechanism.

Keywords:  GTPase; LZTR1; MAD2; RAS; RIT1; aneuploidy; chromosome segregation; mitotic checkpoint; p31comet

DOI:  https://doi.org/10.1016/j.cub.2021.06.030
Nat Rev Drug Discov. 2021 Jul 07.

Reactivating PTEN promotes antitumour immunity.

Sarah Crunkhorn.

DOI: https://doi.org/10.1038/d41573-021-00119-2