bims-pimaco 2023-07-02 papers

on PI3K and MAPK signalling in colorectal cancer

Issue of 2023–07–02
thirteen papers selected by
Lucas B. Zeiger, CRUK Scotland Institute, Beatson Institute for Cancer Research

mTORC2-NDRG1-CDC42 axis couples fasting to mitochondrial fission.
PDE4DIP contributes to colorectal cancer growth and chemoresistance through modulation of the NF1/RAS signaling axis.
K-Ras Binds Calmodulin-Related Centrin1 with Potential Implications for K-Ras Driven Cancer Cell Stemness.
CRISPR prime editing for unconstrained correction of oncogenic KRAS variants.
KRAS and NRAS Translation Is Increased upon MEK Inhibitors-Induced Processing Bodies Dissolution.
An optogenetic-phosphoproteomic study reveals dynamic Akt1 signaling profiles in endothelial cells.
Multiple Inositol Polyphosphate Phosphatase Compartmentalization Separates Inositol Phosphate Metabolism from Inositol Lipid Signaling.
A PI(3,5)P2 reporter reveals PIKfyve activity and dynamics on macropinosomes and phagosomes.
Kinase-targeted therapy in subsets of colorectal cancer.
Rapamycin improves social and stereotypic behavior abnormalities induced by pre-mitotic neuronal subset specific Pten deletion.
The bidirectional relationship between metabolism and cell cycle control.
YAP and TAZ orchestrate adaptive resistance to KRAS inhibitors.
Identification of XAF1 as an endogenous AKT inhibitor.

Nat Cell Biol. 2023 Jun 29.

mTORC2-NDRG1-CDC42 axis couples fasting to mitochondrial fission.

Nuria Martinez-Lopez, Pamela Mattar, Miriam Toledo, Henrietta Bains, Manu Kalyani, Marie Louise Aoun, Mridul Sharma, Laura Beth J McIntire, Leslie Gunther-Cummins, Frank P Macaluso, Jennifer T Aguilan, Simone Sidoli, Mathieu Bourdenx, Rajat Singh.

Fasting triggers diverse physiological adaptations including increases in circulating fatty acids and mitochondrial respiration to facilitate organismal survival. The mechanisms driving mitochondrial adaptations and respiratory sufficiency during fasting remain incompletely understood. Here we show that fasting or lipid availability stimulates mTORC2 activity. Activation of mTORC2 and phosphorylation of its downstream target NDRG1 at serine 336 sustains mitochondrial fission and respiratory sufficiency. Time-lapse imaging shows that NDRG1, but not the phosphorylation-deficient NDRG1Ser336Ala mutant, engages with mitochondria to facilitate fission in control cells, as well as in those lacking DRP1. Using proteomics, a small interfering RNA screen, and epistasis experiments, we show that mTORC2-phosphorylated NDRG1 cooperates with small GTPase CDC42 and effectors and regulators of CDC42 to orchestrate fission. Accordingly, RictorKO, NDRG1Ser336Ala mutants and Cdc42-deficient cells each display mitochondrial phenotypes reminiscent of fission failure. During nutrient surplus, mTOR complexes perform anabolic functions; however, paradoxical reactivation of mTORC2 during fasting unexpectedly drives mitochondrial fission and respiration.

DOI: https://doi.org/10.1038/s41556-023-01163-3
Cell Death Dis. 2023 Jun 24. 14(6): 373

PDE4DIP contributes to colorectal cancer growth and chemoresistance through modulation of the NF1/RAS signaling axis.

Rulu Pan, Juji Dai, Weicheng Liang, Hongxiao Wang, Lin Ye, Siqi Ye, Ziqi Lin, Shishun Huang, Yan Xiong, Li Zhang, Liting Lu, Ouchen Wang, Xian Shen, Wanqin Liao, Xincheng Lu.

Phosphodiesterase 4D interacting protein (PDE4DIP) is a centrosome/Golgi protein associated with cyclic nucleotide phosphodiesterases. PDE4DIP is commonly mutated in human cancers, and its alteration in mice leads to a predisposition to intestinal cancer. However, the biological function of PDE4DIP in human cancer remains obscure. Here, we report for the first time the oncogenic role of PDE4DIP in colorectal cancer (CRC) growth and adaptive MEK inhibitor (MEKi) resistance. We show that the expression of PDE4DIP is upregulated in CRC tissues and associated with the clinical characteristics and poor prognosis of CRC patients. Knockdown of PDE4DIP impairs the growth of KRAS-mutant CRC cells by inhibiting the core RAS signaling pathway. PDE4DIP plays an essential role in the full activation of oncogenic RAS/ERK signaling by suppressing the expression of the RAS GTPase-activating protein (RasGAP) neurofibromin (NF1). Mechanistically, PDE4DIP promotes the recruitment of PLCγ/PKCε to the Golgi apparatus, leading to constitutive activation of PKCε, which triggers the degradation of NF1. Upregulation of PDE4DIP results in adaptive MEKi resistance in KRAS-mutant CRC by reactivating the RAS/ERK pathway. Our work reveals a novel functional link between PDE4DIP and NF1/RAS signal transduction and suggests that targeting PDE4DIP is a promising therapeutic strategy for KRAS-mutant CRC.

DOI: https://doi.org/10.1038/s41419-023-05885-y
Cancers (Basel). 2023 Jun 07. pii: 3087. [Epub ahead of print]15(12):

K-Ras Binds Calmodulin-Related Centrin1 with Potential Implications for K-Ras Driven Cancer Cell Stemness.

Ganesh Babu Manoharan, Christina Laurini, Sara Bottone, Nesrine Ben Fredj, Daniel Kwaku Abankwa.

  Recent data suggest that K-Ras4B (hereafter K-Ras) can drive cancer cell stemness via calmodulin (CaM)-dependent, non-canonical Wnt-signalling. Here we examined whether another Ca2+-binding protein, the CaM-related centrin1, binds to K-Ras and could mediate some K-Ras functions that were previously ascribed to CaM. While CaM and centrin1 appear to distinguish between peptides that were derived from their classical targets, they both bind to K-Ras in cells. Cellular BRET- and immunoprecipitation data suggest that CaM engages more with K-Ras than centrin1 and that the interaction with the C-terminal membrane anchor of K-Ras is sufficient for this. Surprisingly, binding of neither K-Ras nor its membrane anchor alone to CaM or centrin1 is sensitive to inhibition of prenylation. In support of an involvement of the G-domain of K-Ras in cellular complexes with these Ca2+-binding proteins, we find that oncogenic K-RasG12V displays increased engagement with both CaM and centrin1. This is abrogated by addition of the D38A effector-site mutation, suggesting that K-RasG12V is held together with CaM or centrin1 in complexes with effectors. When treated with CaM inhibitors, the BRET-interaction of K-RasG12V with centrin1 was also disrupted in the low micromolar range, comparable to that with CaM. While CaM predominates in regulating functional membrane anchorage of K-Ras, it has a very similar co-distribution with centrin1 on mitotic organelles. Given these results, a significant overlap of the CaM- and centrin1-dependent functions of K-Ras is suggested.

Keywords:  BRET; K-Ras; calmodulin; centrin; centrosome; mitosis

DOI:  https://doi.org/10.3390/cancers15123087
Commun Biol. 2023 Jun 30. 6(1): 681

CRISPR prime editing for unconstrained correction of oncogenic KRAS variants.

Gayoung Jang, Jiyeon Kweon, Yongsub Kim.

KRAS is the most commonly mutated RAS family gene and is a primary cause of the occurrence of several types of cancer. However, KRAS mutations have several unique and diverse molecular identities, making it difficult to find specific treatments. Here, we developed universal pegRNAs which can correct all types of G12 and G13 oncogenic KRAS mutations with CRISPR-mediated prime editors (PEs). The universal pegRNA successfully corrected 12 types of KRAS mutations, accounting for 94% of all known KRAS mutations, by up to 54.8% correction frequency in HEK293T/17 cells. We also applied the universal pegRNA to correct endogenous KRAS mutations in human cancer cells and found that G13D KRAS mutation was successfully corrected to wild-type KRAS sequences with up to 40.6% correction frequency without indel mutations. We propose prime editing with the universal pegRNA as a 'one-to-many' potential therapeutic strategy for KRAS oncogene variants.

DOI: https://doi.org/10.1038/s42003-023-05052-1
Cancers (Basel). 2023 Jun 06. pii: 3078. [Epub ahead of print]15(12):

KRAS and NRAS Translation Is Increased upon MEK Inhibitors-Induced Processing Bodies Dissolution.

Olivia Vidal-Cruchez, Victoria J Nicolini, Tifenn Rete, Karine Jacquet, Roger Rezzonico, Caroline Lacoux, Marie-Angela Domdom, Barnabé Roméo, Jérémie Roux, Arnaud Hubstenberger, Bernard Mari, Baharia Mograbi, Paul Hofman, Patrick Brest.

  Overactivation of the mitogen-activated protein kinase (MAPK) pathway is a critical driver of many human cancers. However, therapies directly targeting this pathway lead to cancer drug resistance. Resistance has been linked to compensatory RAS overexpression, but the mechanisms underlying this response remain unclear. Here, we find that MEK inhibitors (MEKi) are associated with an increased translation of the KRAS and NRAS oncogenes through a mechanism involving dissolution of processing body (P-body) biocondensates. This effect is seen across different cell types and is extremely dynamic since removal of MEKi and ERK reactivation result in reappearance of P-bodies and reduced RAS-dependent signaling. Moreover, we find that P-body scaffold protein levels negatively impact RAS expression. Overall, we describe a new feedback loop mechanism involving biocondensates such as P-bodies in the translational regulation of RAS proteins and MAPK signaling.

Keywords:  MEK inhibitors; RAS oncogenic signaling; RNA metabolism; liquid–liquid phase separation; translation regulation

DOI:  https://doi.org/10.3390/cancers15123078
Nat Commun. 2023 06 26. 14(1): 3803

An optogenetic-phosphoproteomic study reveals dynamic Akt1 signaling profiles in endothelial cells.

Wenping Zhou, Wenxue Li, Shisheng Wang, Barbora Salovska, Zhenyi Hu, Bo Tao, Yi Di, Ujwal Punyamurtula, Benjamin E Turk, William C Sessa, Yansheng Liu.

The serine/threonine kinase AKT is a central node in cell signaling. While aberrant AKT activation underlies the development of a variety of human diseases, how different patterns of AKT-dependent phosphorylation dictate downstream signaling and phenotypic outcomes remains largely enigmatic. Herein, we perform a systems-level analysis that integrates methodological advances in optogenetics, mass spectrometry-based phosphoproteomics, and bioinformatics to elucidate how different intensity, duration, and pattern of Akt1 stimulation lead to distinct temporal phosphorylation profiles in vascular endothelial cells. Through the analysis of ~35,000 phosphorylation sites across multiple conditions precisely controlled by light stimulation, we identify a series of signaling circuits activated downstream of Akt1 and interrogate how Akt1 signaling integrates with growth factor signaling in endothelial cells. Furthermore, our results categorize kinase substrates that are preferably activated by oscillating, transient, and sustained Akt1 signals. We validate a list of phosphorylation sites that covaried with Akt1 phosphorylation across experimental conditions as potential Akt1 substrates. Our resulting dataset provides a rich resource for future studies on AKT signaling and dynamics.

DOI: https://doi.org/10.1038/s41467-023-39514-1
Biomolecules. 2023 05 24. pii: 885. [Epub ahead of print]13(6):

Multiple Inositol Polyphosphate Phosphatase Compartmentalization Separates Inositol Phosphate Metabolism from Inositol Lipid Signaling.

Jia Yu, Barbara Leibiger, Shao-Nian Yang, Stephen B Shears, Ingo B Leibiger, Per-Olof Berggren, Christopher J Barker.

  Multiple inositol polyphosphate phosphatase (MINPP1) is an enigmatic enzyme that is responsible for the metabolism of inositol hexakisphosphate (InsP6) and inositol 1,3,4,5,6 pentakisphosphate (Ins(1,3,4,5,6)P5 in mammalian cells, despite being restricted to the confines of the ER. The reason for this compartmentalization is unclear. In our previous studies in the insulin-secreting HIT cell line, we expressed MINPP1 in the cytosol to artificially reduce the concentration of these higher inositol phosphates. Undocumented at the time, we noted cytosolic MINPP1 expression reduced cell growth. We were struck by the similarities in substrate preference between a number of different enzymes that are able to metabolize both inositol phosphates and lipids, notably IPMK and PTEN. MINPP1 was first characterized as a phosphatase that could remove the 3-phosphate from inositol 1,3,4,5-tetrakisphosphate (Ins(1,3,4,5)P4). This molecule shares strong structural homology with the major product of the growth-promoting Phosphatidyl 3-kinase (PI3K), phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3) and PTEN can degrade both this lipid and Ins(1,3,4,5)P4. Because of this similar substrate preference, we postulated that the cytosolic version of MINPP1 (cyt-MINPP1) may not only attack inositol polyphosphates but also PtdIns(3,4,5)P3, a key signal in mitogenesis. Our experiments show that expression of cyt-MINPP1 in HIT cells lowers the concentration of PtdIns(3,4,5)P3. We conclude this reflects a direct effect of MINPP1 upon the lipid because cyt-MINPP1 actively dephosphorylates synthetic, di(C4:0)PtdIns(3,4,5)P3 in vitro. These data illustrate the importance of MINPP1's confinement to the ER whereby important aspects of inositol phosphate metabolism and inositol lipid signaling can be separately regulated and give one important clarification for MINPP1's ER seclusion.

Keywords:  PIP3; inositol lipid; inositol phosphate; multiple inositol polyphosphate phosphatase (MINPP1); pancreatic beta cell; phosphatidylinositol 3,4,5-trisphosphate

DOI:  https://doi.org/10.3390/biom13060885
J Cell Biol. 2023 Sep 04. pii: e202209077. [Epub ahead of print]222(9):

A PI(3,5)P2 reporter reveals PIKfyve activity and dynamics on macropinosomes and phagosomes.

James H Vines, Hannes Maib, Catherine M Buckley, Aurelie Gueho, Zhou Zhu, Thierry Soldati, David H Murray, Jason S King.

Phosphoinositide signaling lipids (PIPs) are key regulators of membrane identity and trafficking. Of these, PI(3,5)P2 is one of the least well-understood, despite key roles in many endocytic pathways including phagocytosis and macropinocytosis. PI(3,5)P2 is generated by the phosphoinositide 5-kinase PIKfyve, which is critical for phagosomal digestion and antimicrobial activity. However PI(3,5)P2 dynamics and regulation remain unclear due to lack of reliable reporters. Using the amoeba Dictyostelium discoideum, we identify SnxA as a highly selective PI(3,5)P2-binding protein and characterize its use as a reporter for PI(3,5)P2 in both Dictyostelium and mammalian cells. Using GFP-SnxA, we demonstrate that Dictyostelium phagosomes and macropinosomes accumulate PI(3,5)P2 3 min after engulfment but are then retained differently, indicating pathway-specific regulation. We further find that PIKfyve recruitment and activity are separable and that PIKfyve activation stimulates its own dissociation. SnxA is therefore a new tool for reporting PI(3,5)P2 in live cells that reveals key mechanistic details of the role and regulation of PIKfyve/PI(3,5)P2.

DOI: https://doi.org/10.1083/jcb.202209077
Oncoscience. 2023 ;10 24-26

Kinase-targeted therapy in subsets of colorectal cancer.

Patricia M Gomez Barila, Jan Paul Medema.



Keywords:  colorectal cancer; drug resistance; kinase inhibitors; signaling pathways

DOI:  https://doi.org/10.18632/oncoscience.580
Genes Brain Behav. 2023 Jun 28. e12854

Rapamycin improves social and stereotypic behavior abnormalities induced by pre-mitotic neuronal subset specific Pten deletion.

David A Narvaiz, Suzanne O Nolan, Gregory D Smith, Andrew J Holley, Conner D Reynolds, Katherine J Blandin, Phuoc H Nguyen, Doan L K Tran, Joaquin N Lugo.

  The mechanistic target of rapamycin (mTOR) pathway is a signaling system integral to neural growth and migration. In both patients and rodent models, mutations to the phosphatase and tensin homolog gene (PTEN) on chromosome 10 results in hyperactivation of the mTOR pathway, as well as seizures, intellectual disabilities and autistic behaviors. Rapamycin, an inhibitor of mTOR, can reverse the epileptic phenotype of neural subset specific Pten knockout (NS-Pten KO) mice, but its impact on behavior is not known. To determine the behavioral effects of rapamycin, male and female NS-Pten KO and wildtype (WT) mice were assigned as controls or administered 10 mg/kg of rapamycin for 2 weeks followed by behavioral testing. Rapamycin improved social behavior in both genotypes and stereotypic behaviors in NS-Pten KO mice. Rapamycin treatment resulted in a reduction of several measures of activity in the open field test in both genotypes. Rapamycin did not reverse the reduced anxiety behavior in KO mice. These data show the potential clinical use of mTOR inhibitors by showing its administration can reduce the production of autistic-like behaviors in NS-Pten KO mice.

Keywords:  ASD; PI3K; Ps6; autism; comorbidity; cortical dysplasia; epilepsy; mTOR; social behavior; stereotypic behavior

DOI:  https://doi.org/10.1111/gbb.12854
Trends Cell Biol. 2023 Jun 27. pii: S0962-8924(23)00110-1. [Epub ahead of print]

The bidirectional relationship between metabolism and cell cycle control.

Frances F Diehl, Kiera M Sapp, Matthew G Vander Heiden.

  The relationship between metabolism and cell cycle progression is complex and bidirectional. Cells must rewire metabolism to meet changing biosynthetic demands across cell cycle phases. In turn, metabolism can influence cell cycle progression through direct regulation of cell cycle proteins, through nutrient-sensing signaling pathways, and through its impact on cell growth, which is linked to cell division. Furthermore, metabolism is a key player in mediating quiescence-proliferation transitions in physiologically important cell types, such as stem cells. How metabolism impacts cell cycle progression, exit, and re-entry, as well as how these processes impact metabolism, is not fully understood. Recent advances uncovering mechanistic links between cell cycle regulators and metabolic processes demonstrate a complex relationship between metabolism and cell cycle control, with many questions remaining.

Keywords:  cell growth; mitochondria; mitosis; proliferation; quiescence; translation

DOI:  https://doi.org/10.1016/j.tcb.2023.05.012
Nat Cancer. 2023 Jun;4(6): 784-786

YAP and TAZ orchestrate adaptive resistance to KRAS inhibitors.

Alessia Mira, Chiara Ambrogio.

DOI: https://doi.org/10.1038/s43018-023-00580-5
Cell Rep. 2023 Jun 27. pii: S2211-1247(23)00701-5. [Epub ahead of print]42(7): 112690

Identification of XAF1 as an endogenous AKT inhibitor.

Min Chen, Kangjunjie Wang, Ying Han, Shukun Yan, Huairui Yuan, Qiuli Liu, Long Li, Ni Li, Hongwen Zhu, Dayun Lu, Kaihua Wang, Fen Liu, Dakui Luo, Yuxue Zhang, Jun Jiang, Dali Li, Lei Zhang, Hongbin Ji, Hu Zhou, Yong Chen, Jun Qin, Daming Gao.

  AKT kinase is a key regulator in cell metabolism and survival, and its activation is strictly modulated. Herein, we identify XAF1 (XIAP-associated factor) as a direct interacting protein of AKT1, which strongly binds the N-terminal region of AKT1 to block its K63-linked poly-ubiquitination and subsequent activation. Consistently, Xaf1 knockout causes AKT activation in mouse muscle and fat tissues and reduces body weight gain and insulin resistance induced by high-fat diet. Pathologically, XAF1 expression is low and anti-correlated with the phosphorylated p-T308-AKT signal in prostate cancer samples, and Xaf1 knockout stimulates the p-T308-AKT signal to accelerate spontaneous prostate tumorigenesis in mice with Pten heterozygous loss. And ectopic expression of wild-type XAF1, but not the cancer-derived P277L mutant, inhibits orthotopic tumorigenesis. We further identify Forkhead box O 1 (FOXO1) as a transcriptional regulator of XAF1, thus forming a negative feedback loop between AKT1 and XAF1. These results reveal an important intrinsic regulatory mechanism of AKT signaling.

Keywords:  AKT; CP: Cell biology; FOXO1; XAF1; metabolism; phosphorylation; prostate cancer; ubiquitination

DOI:  https://doi.org/10.1016/j.celrep.2023.112690