bims-pimaco 2021-07-18 papers

on PI3K and MAPK signalling in colorectal cancer

Issue of 2021–07–18
eleven papers selected by
Lucas B. Zeiger, CRUK Scotland Institute, Beatson Institute for Cancer Research

A Platform for Validating Colorectal Cancer Driver Genes Using Mouse Organoids.
The innate immune kinase TBK1 directly increases mTORC2 activity and downstream signaling to Akt.
Comprehensive Clinical and Molecular Characterization of KRAS G12C-Mutant Colorectal Cancer.
Identification and prognostic analysis of the cetuximab resistance-related gene REV1 in RAS wild-type metastatic colorectal cancer.
Akt phosphorylates insulin receptor substrate to limit PI3K-mediated PIP3 synthesis.
Metabolic networks in mutant KRAS-driven tumours: tissue specificities and the microenvironment.
mTORC1 activity regulates post-translational modifications of glycine decarboxylase to modulate glycine metabolism and tumorigenesis.
Inhibition of mTORC1 through ATF4-induced REDD1 and Sestrin2 expression by Metformin.
Oncogenic mutations drive intestinal cancer initiation through paracrine remodeling.
mTORC2: The other mTOR in autophagy regulation.
An mTORC1-GRASP55 signaling axis controls unconventional secretion to reshape the extracellular proteome upon stress.

Front Genet. 2021 ;12 698771

A Platform for Validating Colorectal Cancer Driver Genes Using Mouse Organoids.

Haruna Takeda.

  Systematic approaches for functionally validating cancer genes are needed since numerous genes mutated in cancer tissues have been identified from cancer genome sequencing. The mouse organoid culture system has been extensively used in the field of cancer research since mouse organoids can faithfully recapitulate the physiological behavior of the cells. Taking advantage of this, we recently described a platform for functionally validating colorectal cancer (CRC) driver genes that utilized CRISPR-Cas9 in mouse intestinal tumor organoids. In this review, we will describe how mouse organoids have been applied to CRC research and focus on how CRC genes can be validated using mouse organoids.

Keywords:  CRISPR-Cas9; colorectal cancer; mouse organoid; transplantation; validation

DOI:  https://doi.org/10.3389/fgene.2021.698771
J Biol Chem. 2021 Jul 07. pii: S0021-9258(21)00742-0. [Epub ahead of print] 100942

The innate immune kinase TBK1 directly increases mTORC2 activity and downstream signaling to Akt.

Aaron Seth Tooley, Dubek Kazyken, Cagri Bodur, Ian E Gonzalez, Diane C Fingar.

  TBK1 responds to microbes to initiate cellular responses critical for host innate immune defense. We found previously that TBK1 phosphorylates mTOR (mechanistic target of rapamycin) on S2159 to increase mTOR complex 1 (mTORC1) signaling in response to the growth factor EGF and the viral dsRNA mimetic poly(I:C). mTORC1 and the less well studied mTORC2 respond to diverse cues to control cellular metabolism, proliferation, and survival. While TBK1 has been linked to Akt phosphorylation, a direct relationship between TBK1 and mTORC2, an Akt kinase, has not been described. By studying MEFs lacking TBK1, as well as MEFs, macrophages, and mice bearing an Mtor S2159A knock-in allele (MtorA/A) using in vitro kinase assays and cell-based approaches, we demonstrate here that TBK1 activates mTOR complex 2 (mTORC2) directly to increase Akt phosphorylation. We find that TBK1 and mTOR S2159 phosphorylation promote mTOR-dependent phosphorylation of Akt in response to several growth factors and poly(I:C). Mechanistically, TBK1 co-immunoprecipitates with mTORC2 and phosphorylates mTOR S2159 within mTORC2 in cells. Kinase assays demonstrate that TBK1 and mTOR S2159 phosphorylation increase mTORC2 intrinsic catalytic activity. Growth factors failed to activate TBK1 or increase mTOR S2159 phosphorylation in MEFs. Thus, basal TBK1 activity cooperates with growth factors in parallel to increase mTORC2 (and mTORC1) signaling. Collectively, these results reveal crosstalk between TBK1 and mTOR, key regulatory nodes within two major signaling networks. As TBK1 and mTOR contribute to tumorigenesis and metabolic disorders, these kinases may work together in a direct manner in a variety of physiological and pathological settings.

Keywords:  Akt; TBK1; mTOR; mTORC2; phosphorylation

DOI:  https://doi.org/10.1016/j.jbc.2021.100942
JCO Precis Oncol. 2021 ;pii: PO.20.00256. [Epub ahead of print]5

Comprehensive Clinical and Molecular Characterization of KRAS G12C-Mutant Colorectal Cancer.

Jason T Henry, Oluwadara Coker, Saikat Chowdhury, John Paul Shen, Van K Morris, Arvind Dasari, Kanwal Raghav, Maliha Nusrat, Bryan Kee, Christine Parseghian, Shubham Pant, Nikeshan Jeyakumar, Limin Zhu, Yujiro Nishioka, David Fogelman, Robert A Wolff, David Hong, Michael J Overman, JeanNicolas Vauthey, Scott Kopetz, Benny Johnson.

PURPOSE: KRAS p.G12C mutations occur in approximately 3% of metastatic colorectal cancers (mCRC). Recently, two allosteric inhibitors of KRAS p.G12C have demonstrated activity in early phase clinical trials. There are no robust studies examining the behavior of this newly targetable population.
METHODS: We queried the MD Anderson Cancer Center data set for patients with colorectal cancer who harbored KRAS p.G12C mutations between January 2003 and September 2019. Patients were analyzed for clinical characteristics, overall survival (OS), and progression-free survival (PFS) and compared against KRAS nonG12C. Next, we analyzed several internal and external data sets to assess immune signatures, gene expression profiles, hypermethylation, co-occurring mutations, and proteomics.
RESULTS: Among the 4,632 patients with comprehensive molecular profiling, 134 (2.9%) were found to have KRAS p.G12C mutations. An additional 53 patients with single gene sequencing were included in clinical data but excluded from prevalence analysis allowing for 187 total patients. Sixty-five patients had de novo metastatic disease and received a median of two lines of chemotherapy without surgical intervention. For the first three lines of chemotherapy, the median PFS was 6.4 months (n = 65; 95% CI, 5.0 to 7.4 months), 3.9 months (n = 47; 95% CI, 2.9 to 5.9 months), and 3.0 months (n = 21; 95% CI, 2.0 to 3.4 months), respectively. KRAS p.G12C demonstrated higher rates of basal EGFR activation compared with KRAS nonG12C. When compared with an internal cohort of KRAS nonG12C, KRAS p.G12C patients had worse OS.
CONCLUSION: PFS is poor for patients with KRAS p.G12C metastatic colorectal cancer. OS was worse in KRAS p.G12C compared with KRAS nonG12C patients. Our data highlight the innate resistance to chemotherapy for KRAS p.G12C patients and serve as a historical comparator for future clinical trials.

DOI: https://doi.org/10.1200/PO.20.00256
Am J Cancer Res. 2021 ;11(6): 2769-2781

Identification and prognostic analysis of the cetuximab resistance-related gene REV1 in RAS wild-type metastatic colorectal cancer.

Ning Zhu, Xuefeng Fang, Dan Li, Mengyuan Yang, Lizhen Zhu, Liping Zhong, Shanshan Weng, Juan Wang, Ying Yuan.

The survival of patients with RAS wild-type metastatic colorectal cancer (mCRC) has improved markedly since the introduction of cetuximab, which is an anti-epidermal growth factor receptor monoclonal antibody. However, not all RAS wild-type patients respond to cetuximab treatment. Although some genetic alterations associated with cetuximab resistance have been identified, they cannot fully explain all cases of cetuximab resistance. Thus, in this research, we aimed to identify new genetic alterations associated with resistance to this treatment. The study retrospectively analyzed 70 patients diagnosed with RAS wild-type mCRC at our hospital between November 2009 and July 2018. First, five progression-free survival (PFS)-longest and 5 PFS-shortest tumor deoxyribonucleic acid were analyzed by whole-exome sequencing (WES) to identify differentially mutated genes. Then, PFS analysis of the 70 patients was used to verify the correlation between the candidate gene and cetuximab sensitivity. Finally, data from public databases were used to further verify the relationship between the mRNA expression level of the candidate gene and cetuximab responsiveness. The WES results indicated REV1: c.2108G > A was a candidate gene mutation related to the effectiveness of cetuximab. Survival analysis suggested REV1: c.2108G > A was associated with rapid disease progression (median PFS time, REV1 mutant vs. REV1 wild-type: 4.4 months vs. 8.7 months, P = 0.034). Data from the Genomics of Drug Sensitivity in Cancer and the Gene Expression Omnibus databases suggested low REV1 mRNA levels might be related to the poor response of CRC cells and reduced cetuximab efficacy among mCRC patients. In conclusion, REV1 expression levels and the REV1: c.2108G > A mutation may be related to cetuximab resistance in RAS wild-type mCRC.

Keywords: Colorectal cancer; REV1; cetuximab; resistance; whole-exome sequencing
Elife. 2021 Jul 13. pii: e66942. [Epub ahead of print]10

Akt phosphorylates insulin receptor substrate to limit PI3K-mediated PIP3 synthesis.

Alison L Kearney, Dougall M Norris, Milad Ghomlaghi, Martin Kin Lok Wong, Sean J Humphrey, Luke Carroll, Guang Yang, Kristen C Cooke, Pengyi Yang, Thomas A Geddes, Sungyoung Shin, Daniel J Fazakerley, Lan K Nguyen, David E James, James G Burchfield.

  The phosphoinositide 3-kinase (PI3K)-Akt network is tightly controlled by feedback mechanisms that regulate signal flow and ensure signal fidelity. A rapid overshoot in insulin-stimulated recruitment of Akt to the plasma membrane has previously been reported, which is indicative of negative feedback operating on acute timescales. Here, we show that Akt itself engages this negative feedback by phosphorylating insulin receptor substrate (IRS) 1 and 2 on a number of residues. Phosphorylation results in the depletion of plasma membrane-localised IRS1/2, reducing the pool available for interaction with the insulin receptor. Together these events limit plasma membrane-associated PI3K and phosphatidylinositol (3,4,5)-trisphosphate (PIP3) synthesis. We identified two Akt-dependent phosphorylation sites in IRS2 at S306 (S303 in mouse) and S577 (S573 in mouse) that are key drivers of this negative feedback. These findings establish a novel mechanism by which the kinase Akt acutely controls PIP3 abundance, through post-translational modification of the IRS scaffold.

Keywords:  Akt; PI3K; cell biology; computational biology; human; insulin; mouse; phosphorylation; plasma membrane; signal transduction; systems biology

DOI:  https://doi.org/10.7554/eLife.66942
Nat Rev Cancer. 2021 Jul 09.

Metabolic networks in mutant KRAS-driven tumours: tissue specificities and the microenvironment.

Samuel A Kerk, Thales Papagiannakopoulos, Yatrik M Shah, Costas A Lyssiotis.

Oncogenic mutations in KRAS drive common metabolic programmes that facilitate tumour survival, growth and immune evasion in colorectal carcinoma, non-small-cell lung cancer and pancreatic ductal adenocarcinoma. However, the impacts of mutant KRAS signalling on malignant cell programmes and tumour properties are also dictated by tumour suppressor losses and physiological features specific to the cell and tissue of origin. Here we review convergent and disparate metabolic networks regulated by oncogenic mutant KRAS in colon, lung and pancreas tumours, with an emphasis on co-occurring mutations and the role of the tumour microenvironment. Furthermore, we explore how these networks can be exploited for therapeutic gain.

DOI: https://doi.org/10.1038/s41568-021-00375-9
Nat Commun. 2021 07 09. 12(1): 4227

mTORC1 activity regulates post-translational modifications of glycine decarboxylase to modulate glycine metabolism and tumorigenesis.

Rui Liu, Lin-Wen Zeng, Rong Gong, Fanen Yuan, Hong-Bing Shu, Shu Li.

Glycine decarboxylase (GLDC) is a key enzyme of glycine cleavage system that converts glycine into one-carbon units. GLDC is commonly up-regulated and plays important roles in many human cancers. Whether and how GLDC is regulated by post-translational modifications is unknown. Here we report that mechanistic target of rapamycin complex 1 (mTORC1) signal inhibits GLDC acetylation at lysine (K) 514 by inducing transcription of the deacetylase sirtuin 3 (SIRT3). Upon inhibition of mTORC1, the acetyltransferase acetyl-CoA acetyltransferase 1 (ACAT1) catalyzes GLDC K514 acetylation. This acetylation of GLDC impairs its enzymatic activity. In addition, this acetylation of GLDC primes for its K33-linked polyubiquitination at K544 by the ubiquitin ligase NF-X1, leading to its degradation by the proteasomal pathway. Finally, we find that GLDC K514 acetylation inhibits glycine catabolism, pyrimidines synthesis and glioma tumorigenesis. Our finding reveals critical roles of post-translational modifications of GLDC in regulation of its enzymatic activity, glycine metabolism and tumorigenesis, and provides potential targets for therapeutics of cancers such as glioma.

DOI: https://doi.org/10.1038/s41467-021-24321-3
BMC Cancer. 2021 Jul 12. 21(1): 803

Inhibition of mTORC1 through ATF4-induced REDD1 and Sestrin2 expression by Metformin.

Se-Kyeong Jang, Sung-Eun Hong, Da-Hee Lee, Ji-Young Kim, Ji Yea Kim, Sang-Kyu Ye, Jungil Hong, In-Chul Park, Hyeon-Ok Jin.

   BACKGROUND: Although the major anticancer effect of metformin involves AMPK-dependent or AMPK-independent mTORC1 inhibition, the mechanisms of action are still not fully understood.
METHODS: To investigate the molecular mechanisms underlying the effect of metformin on the mTORC1 inhibition, MTT assay, RT-PCR, and western blot analysis were performed.
RESULTS: Metformin induced the expression of ATF4, REDD1, and Sestrin2 concomitant with its inhibition of mTORC1 activity. Treatment with REDD1 or Sestrin2 siRNA reversed the mTORC1 inhibition induced by metformin, indicating that REDD1 and Sestrin2 are important for the inhibition of mTORC1 triggered by metformin treatment. Moreover, REDD1- and Sestrin2-mediated mTORC1 inhibition in response to metformin was independent of AMPK activation. Additionally, lapatinib enhances cell sensitivity to metformin, and knockdown of REDD1 and Sestrin2 decreased cell sensitivity to metformin and lapatinib.
CONCLUSIONS: ATF4-induced REDD1 and Sestrin2 expression in response to metformin plays an important role in mTORC1 inhibition independent of AMPK activation, and this signalling pathway could have therapeutic value.

Keywords:  AMPK; Metformin; REDD1; Sestrin2; mTORC1

DOI:  https://doi.org/10.1186/s12885-021-08346-x
Cancer Cell. 2021 Jul 12. pii: S1535-6108(21)00335-4. [Epub ahead of print]39(7): 913-915

Oncogenic mutations drive intestinal cancer initiation through paracrine remodeling.

Helen H N Yan, April S Chan, Suet Yi Leung.

Three articles in Nature show that intestinal stem cells with cancer-promoting mutations could shape the surrounding normal tissue in their favor to promote clonal fixation and field expansion, raising the possibility of developing therapeutic strategies that maintain or enhance the health of normal cells to out-compete the mutant cells.

DOI: https://doi.org/10.1016/j.ccell.2021.06.013
Aging Cell. 2021 Jul 12. e13431

mTORC2: The other mTOR in autophagy regulation.

Josué Ballesteros-Álvarez, Julie K Andersen.

  The mechanistic target of rapamycin (mTOR) has gathered significant attention as a ubiquitously expressed multimeric kinase with key implications for cell growth, proliferation, and survival. This kinase forms the central core of two distinct complexes, mTORC1 and mTORC2, which share the ability of integrating environmental, nutritional, and hormonal cues but which regulate separate molecular pathways that result in different cellular responses. Particularly, mTORC1 has been described as a major negative regulator of endosomal biogenesis and autophagy, a catabolic process that degrades intracellular components and organelles within the lysosomes and is thought to play a key role in human health and disease. In contrast, the role of mTORC2 in the regulation of autophagy has been considerably less studied despite mounting evidence this complex may regulate autophagy in a different and perhaps complementary manner to that of mTORC1. Genetic ablation of unique subunits is currently being utilized to study the differential effects of the two mTOR complexes. RICTOR is the best-described subunit specific to mTORC2 and as such has become a useful tool for investigating the specific actions of this complex. The development of complex-specific inhibitors for mTORC2 is also an area of intense interest. Studies to date have demonstrated that mTORC1/2 complexes each signal to a variety of exclusive downstream molecules with distinct biological roles. Pinpointing the particular effects of these downstream effectors is crucial toward the development of novel therapies aimed at accurately modulating autophagy in the context of human aging and disease.

Keywords:  AKT; FOXOs; SGK-1; autophagy; mTORC2

DOI:  https://doi.org/10.1111/acel.13431
Mol Cell. 2021 Jul 05. pii: S1097-2765(21)00497-4. [Epub ahead of print]

An mTORC1-GRASP55 signaling axis controls unconventional secretion to reshape the extracellular proteome upon stress.

Julian Nüchel, Marina Tauber, Janica L Nolte, Matthias Mörgelin, Clara Türk, Beate Eckes, Constantinos Demetriades, Markus Plomann.

  Cells communicate with their environment via surface proteins and secreted factors. Unconventional protein secretion (UPS) is an evolutionarily conserved process, via which distinct cargo proteins are secreted upon stress. Most UPS types depend upon the Golgi-associated GRASP55 protein. However, its regulation and biological role remain poorly understood. Here, we show that the mechanistic target of rapamycin complex 1 (mTORC1) directly phosphorylates GRASP55 to maintain its Golgi localization, thus revealing a physiological role for mTORC1 at this organelle. Stimuli that inhibit mTORC1 cause GRASP55 dephosphorylation and relocalization to UPS compartments. Through multiple, unbiased, proteomic analyses, we identify numerous cargoes that follow this unconventional secretory route to reshape the cellular secretome and surfactome. Using MMP2 secretion as a proxy for UPS, we provide important insights on its regulation and physiological role. Collectively, our findings reveal the mTORC1-GRASP55 signaling hub as the integration point in stress signaling upstream of UPS and as a key coordinator of the cellular adaptation to stress.

Keywords:  ECM; GORASP2; GRASP55; Golgi; MMP2; Rapamycin; Tuberous Sclerosis Complex (TSC); cellular stress response; mTORC1; unconventional protein secretion (UPS)

DOI:  https://doi.org/10.1016/j.molcel.2021.06.017