bims-pimaco 2023-04-16 papers

on PI3K and MAPK signalling in colorectal cancer

Issue of 2023–04–16
nine papers selected by
Lucas B. Zeiger, CRUK Scotland Institute, Beatson Institute for Cancer Research

KRAS mutated colorectal cancers with or without PIK3CA mutations: Clinical and molecular profiles inform current and future therapeutics.
Translational relevance of SOS1 targeting for KRAS-mutant colorectal cancer.
Genome-wide CRISPR screens identify ILF3 as a mediator of mTORC1-dependent amino acid sensing.
KRAS pathways: A Potential Gateway for Cancer Therapeutics and Diagnostics.
An ERK1/2-driven RNA-binding switch in nucleolin drives ribosome biogenesis and pancreatic tumorigenesis downstream of RAS oncogene.
KRAS-specific antibody binds to KRAS protein inside colorectal adenocarcinoma cells and inhibits its localization to the plasma membrane.
N-acetylcysteine overcomes NF1 loss-driven resistance to PI3Kα inhibition in breast cancer.
PTEN-induced kinase PINK1 supports colorectal cancer growth by regulating the labile iron pool.
The Role of WNT Pathway Mutations in Cancer Development and an Overview of Therapeutic Options.

Crit Rev Oncol Hematol. 2023 Apr 12. pii: S1040-8428(23)00075-6. [Epub ahead of print] 103987

KRAS mutated colorectal cancers with or without PIK3CA mutations: Clinical and molecular profiles inform current and future therapeutics.

Ioannis A Voutsadakis.

   BACKGROUND: Colorectal cancer is one of the most prevalent malignancies and its molecular pathogenesis has been intensely investigated for several decades. As a result, great progress has been made and targeted therapies have been introduced in the clinic. This paper examines colorectal cancers based on two of the most common molecular alterations, KRAS and PIK3CA mutations as a basis for therapeutic targeting.
METHODS: Two publicly available genomic series with clinical data were evaluated for prevalence and characteristics of cases with and without KRAS and PIK3CA mutations and the literature was reviewed for relevant information on the therapeutic implication of these alterations as well as other coincident alterations to derive therapeutic individualized options of targeted treatments.
RESULTS: Colorectal cancers without KRAS and PIK3CA mutations represent the most prevalent group (48% to 58% of patients) and present therapeutic targeted opportunities with BRAF inhibitors and immune checkpoint inhibitors in the subsets with BRAF mutations (15% to 22%) and Microsatellite Instability (MSI, 14% to 16%), respectively. The second most prevalent sub-set, with KRAS mutations and PIK3CA wild type, representing 20% to 25% of patients, has currently few targeted options, besides specific KRAS G12C inhibitors for the small percentage of cases (9%-10%) that bear this mutation. Cancers with KRAS wild type and PIK3CA mutations are observed in 12% to 14% of colorectal cancer patients, harbor the highest percentage of cases with BRAF mutations and Microsatellite Instability (MSI), and are candidates for the respective targeted therapies. New targeted therapies in development, such as ATR inhibitors could be effective in cases with ATM mutations and ARID1A mutations that are also most prevalent in this sub-group (14% to 22% and 30%, respectively). KRAS and PIK3CA double mutant cancers have also few targeted options currently and could benefit from combination therapies with PI3K inhibitors and new KRAS inhibitors in development.
CONCLUSION: The backbone of common KRAS and PIK3CA mutations is a rational frame for development of therapeutic algorithms in colorectal cancer and can help guide new drug therapies development. In addition, the prevalence of different molecular groups presented here may help with planning of combination clinical trials by providing estimations of sub-sets with more than one alteration.

Keywords:  Colon cancer; KRAS; molecular alterations; oncogenic mutations; targeted therapeutics

DOI:  https://doi.org/10.1016/j.critrevonc.2023.103987
Mol Carcinog. 2023 Apr 12.

Translational relevance of SOS1 targeting for KRAS-mutant colorectal cancer.

Diego Alem, Xinrui Yang, Francisca Beato, Bhaswati Sarcar, Alexandra F Tassielli, Ruifan Dai, Tara L Hogenson, Margaret A Park, Kun Jiang, Jianfeng Cai, Yu Yuan, Martin E Fernandez-Zapico, Aik Choon Tan, Jason B Fleming, Hao Xie.

  It has been challenging to target mutant KRAS (mKRAS) in colorectal cancer (CRC) and other malignancies. Recent efforts have focused on developing inhibitors blocking molecules essential for KRAS activity. In this regard, SOS1 inhibition has arisen as an attractive approach for mKRAS CRC given its essential role as a guanine nucleotide exchange factor for this GTPase. Here, we demonstrated the translational value of SOS1 blockade in mKRAS CRC. We used CRC patient-derived organoids (PDOs) as preclinical models to evaluate their sensitivity to SOS1 inhibitor BI3406. A combination of in silico analyses and wet lab techniques was utilized to define potential predictive markers for SOS1 sensitivity and potential mechanisms of resistance in CRC. RNA-seq analysis of CRC PDOs revealed two groups of CRC PDOs with differential sensitivities to SOS1 inhibitor BI3406. The resistant group was enriched in gene sets involving cholesterol homeostasis, epithelial-mesenchymal transition, and TNF-α/NFκB signaling. Expression analysis identified a significant correlation between SOS1 and SOS2 mRNA levels (Spearman's ρ 0.56, p < 0.001). SOS1/2 protein expression was universally present with heterogeneous patterns in CRC cells but only minimal to none in surrounding nonmalignant cells. Only SOS1 protein expression was associated with worse survival in patients with RAS/RAF mutant CRC (p = 0.04). We also found that SOS1/SOS2 protein expression ratio >1 by immunohistochemistry (p = 0.03) instead of KRAS mutation (p = 1) was a better predictive marker to BI3406 sensitivity of CRC PDOs, concordant with the significant positive correlation between SOS1/SOS2 protein expression ratio and SOS1 dependency. Finally, we showed that GTP-bound RAS level underwent rebound even in BI3406-sensitive PDOs with no change of KRAS downstream effector genes, thus suggesting upregulation of guanine nucleotide exchange factor as potential cellular adaptation mechanisms to SOS1 inhibition. Taken together, our results show that high SOS1/SOS2 protein expression ratio predicts sensitivity to SOS1 inhibition and support further clinical development of SOS1-targeting agents in CRC.

Keywords:  KRAS; SOS1; SOS2; colorectal cancer; therapeutics

DOI:  https://doi.org/10.1002/mc.23543
Nat Cell Biol. 2023 Apr 10.

Genome-wide CRISPR screens identify ILF3 as a mediator of mTORC1-dependent amino acid sensing.

Guokai Yan, Jinxin Yang, Wen Li, Ao Guo, Jialiang Guan, Ying Liu.

The mechanistic target of rapamycin complex 1 (mTORC1) is an essential hub that integrates nutrient signals and coordinates metabolism to control cell growth. Amino acid signals are detected by sensor proteins and relayed to the GATOR2 and GATOR1 complexes to control mTORC1 activity. Here we perform genome-wide CRISPR/Cas9 screens, coupled with an assay for mTORC1 activity based on fluorescence-activated cell sorting analysis of pS6, to identify potential regulators of mTORC1-dependent amino acid sensing. We then focus on interleukin enhancer binding factor 3 (ILF3), one of the candidate genes from the screen. ILF3 tethers the GATOR complexes to lysosomes to control mTORC1. Adding a lysosome-targeting sequence to the GATOR2 component WDR24 bypasses the requirement for ILF3 to modulate amino-acid-dependent mTORC1 signalling. ILF3 plays an evolutionarily conserved role in human and mouse cells, and in worms to regulate the mTORC1 pathway, control autophagy activity and modulate the ageing process.

DOI: https://doi.org/10.1038/s41556-023-01123-x
Recent Pat Anticancer Drug Discov. 2023 Apr 06.

KRAS pathways: A Potential Gateway for Cancer Therapeutics and Diagnostics.

Pankaj Kumar Tripathi, Khushi R Mittal, Nandini Jain, Naveen Sharma, Chakresh Kumar Jain.

   BACKGROUND: One of the major disturbing pathways within cancer is "The Kirsten rat sarcoma viral oncogene homolog (KRAS) pathway", and it has recently been demonstrated to be the most crucial in therapies and diagnostics. KRAS pathway includes numerous genes. This multi-component signaling system promotes cell growth, division, survival, and death by transferring signals from outside the cell to its interior. KRAS regulates the activation of a variety of signaling molecules. The KRAS oncogene is a key player in advancing a wide range of malignancies, and the mutation rank of this gene is a key feature of several tumors. For some malignancies, the mutation type of the gene may offer information about prognostic, clinical, and predictive. KRAS belongs to the RAS oncogene family, which consists of a compilation of minor GTP-binding proteins that assimilate environmental inputs and trigger internal signaling pathways that control survival, cell differentiation, and proliferation.
OBJECTIVE: This review aims to examine the recent and fascinating breakthroughs in the identification of new therapies that target KRAS, including the ever-expanding experimental approaches for reducing KRAS activity and signaling as well as direct targeting of KRAS.
METHODS: A literature survey was performed. All the relevant articles and patents related to the KRAS pathway, the mutation in the KRAS gene, cancer treatment, and diagnostics were found on PubMed and Google Patents.
RESULTS: One of the most prevalent causes of cancer in humans is a mutation in the K-RAS protein. It is extremely difficult to decipher KRAS-mediated signaling. It allows transducing signals to go from the cell's outer surface to its nucleus, having an influence on a variety of crucial cellular functions including cell chemotaxis, division, dissemination, and cell death. Other involved signaling pathways are RAF, and the phosphatidylinositol 3 kinase also known as AKT. The EGFR pathway is incomplete without KRAS. The activation of PI3K significantly contributes to acquiring resistance to a mixture of MEK inhibitors and anti-EGFR in colorectal cancer cell lines which are mutated by KRAS.
CONCLUSION: A series of recent patent studies towards cancer diagnostics and therapeutics reveals the paramount importance of mutated protein KRAS as an extensive driver in human tumors. For the prognosis, diagnosis, and treatment of colorectal cancer, KRAS plays a critical role. This review concludes the latest and vowing developments in the discovery of novel techniques for diagnosis and drugs that target KRAS, the advancements in experimental techniques for signaling and inhibiting KRAS function, and the direct targeting of KRAS for cancer therapeutics.

Keywords:  Colorectal cancer; EGFR pathway; KRAS; anemia; apoptosis.; c-Raf; malignancies

DOI:  https://doi.org/10.2174/1574892818666230406085120
EMBO J. 2023 Apr 11. e110902

An ERK1/2-driven RNA-binding switch in nucleolin drives ribosome biogenesis and pancreatic tumorigenesis downstream of RAS oncogene.

Muhammad S Azman, Emilie L Alard, Martin Dodel, Federica Capraro, Rupert Faraway, Maria Dermit, Wanling Fan, Alina Chakraborty, Jernej Ule, Faraz K Mardakheh.

  Oncogenic RAS signaling reprograms gene expression through both transcriptional and post-transcriptional mechanisms. While transcriptional regulation downstream of RAS is relatively well characterized, how RAS post-transcriptionally modulates gene expression to promote malignancy remains largely unclear. Using quantitative RNA interactome capture analysis, we here reveal that oncogenic RAS signaling reshapes the RNA-bound proteomic landscape of pancreatic cancer cells, with a network of nuclear proteins centered around nucleolin displaying enhanced RNA-binding activity. We show that nucleolin is phosphorylated downstream of RAS, which increases its binding to pre-ribosomal RNA (rRNA), boosts rRNA production, and promotes ribosome biogenesis. This nucleolin-dependent enhancement of ribosome biogenesis is crucial for RAS-induced pancreatic cancer cell proliferation and can be targeted therapeutically to inhibit tumor growth. Our results reveal that oncogenic RAS signaling drives ribosome biogenesis by regulating the RNA-binding activity of nucleolin and highlight a crucial role for this mechanism in RAS-mediated tumorigenesis.

Keywords:  Nucleolin; RAS; RNA-binding proteins; pancreatic ductal adenocarcinoma; ribosome biogenesis

DOI:  https://doi.org/10.15252/embj.2022110902
Front Oncol. 2023 ;13 1036871

KRAS-specific antibody binds to KRAS protein inside colorectal adenocarcinoma cells and inhibits its localization to the plasma membrane.

Kuen Kuen Lam, Yee Syuen Low, Michelle Lo, Michelle Wong, Choong Leong Tang, Emile Tan, Aik Yong Chok, Isaac Seow-En, Siew Heng Wong, Peh Yean Cheah.

  Colorectal cancer (CRC) is the third highest incidence cancer and a leading cause of cancer mortality worldwide. To date, chemotherapeutic treatment of advanced CRC that has metastasized has a dismayed success rate of less than 30%. Further, most (80%) sporadic CRCs are microsatellite-stable and are refractory to immune checkpoint blockade therapy. KRAS is a gatekeeper gene in colorectal tumorigenesis. Nevertheless, KRAS is 'undruggable' due to its structure. Thus, focus has been diverted to develop small molecule inhibitors for its downstream effector such as ERK/MAPK. Despite intense research efforts for the past few decades, no small molecule inhibitor has been in clinical use for CRC. Antibody targeting KRAS itself is an attractive alternative. We developed a transient ex vivo patient-derived matched mucosa-tumor primary culture to assess whether anti-KRAS antibody can be internalized to bind and inactivate KRAS. We showed that anti-KRAS antibody can enter live mucosa-tumor cells and specifically aggregate KRAS in the cytoplasm, thus hindering its translocation to the inner plasma membrane. The mis-localization of KRAS reduces KRAS dwelling time at the site where it tethers to activate downstream effectors. We previously showed that expression of SOX9 was KRAS-mutation-dependent and possibly a better effector than ERK in CRC. Herein, we showed that anti-KRAS antibody treated tumor cells have less intense SOX9 cytoplasmic and nuclear staining compared to untreated cells. Our results demonstrated that internalized anti-KRAS antibody inhibits KRAS function in tumor. With an efficient intracellular antibody delivery system, this can be further developed as combinatorial therapeutics for CRC and other KRAS-driven cancers.

Keywords:  KRAS; SOX9; antibody therapeutics; ex vivo culture; metastatic colorectal cancer

DOI:  https://doi.org/10.3389/fonc.2023.1036871
Cell Rep Med. 2023 Apr 04. pii: S2666-3791(23)00112-X. [Epub ahead of print] 101002

N-acetylcysteine overcomes NF1 loss-driven resistance to PI3Kα inhibition in breast cancer.

Priska Auf der Maur, Marcel P Trefny, Zora Baumann, Milica Vulin, Ana Luisa Correia, Maren Diepenbruck, Nicolas Kramer, Katrin Volkmann, Bogdan-Tiberius Preca, Pedro Ramos, Cedric Leroy, Tobias Eichlisberger, Katarzyna Buczak, Federica Zilli, Ryoko Okamoto, Roland Rad, Michael Rugaard Jensen, Christine Fritsch, Alfred Zippelius, Michael B Stadler, Mohamed Bentires-Alj.

  A genome-wide PiggyBac transposon-mediated screen and a resistance screen in a PIK3CAH1047R-mutated murine tumor model reveal NF1 loss in mammary tumors resistant to the phosphatidylinositol 3-kinase α (PI3Kα)-selective inhibitor alpelisib. Depletion of NF1 in PIK3CAH1047R breast cancer cell lines and a patient-derived organoid model shows that NF1 loss reduces sensitivity to PI3Kα inhibition and correlates with enhanced glycolysis and lower levels of reactive oxygen species (ROS). Unexpectedly, the antioxidant N-acetylcysteine (NAC) sensitizes NF1 knockout cells to PI3Kα inhibition and reverts their glycolytic phenotype. Global phospho-proteomics indicates that combination with NAC enhances the inhibitory effect of alpelisib on mTOR signaling. In public datasets of human breast cancer, we find that NF1 is frequently mutated and that such mutations are enriched in metastases, an indication for which use of PI3Kα inhibitors has been approved. Our results raise the attractive possibility of combining PI3Kα inhibition with NAC supplementation, especially in patients with drug-resistant metastases associated with NF1 loss.

Keywords:  PI3K alpha inhibition; breast cancer; combination therapy; resistance; transposon screen

DOI:  https://doi.org/10.1016/j.xcrm.2023.101002
J Biol Chem. 2023 Apr 08. pii: S0021-9258(23)00333-2. [Epub ahead of print] 104691

PTEN-induced kinase PINK1 supports colorectal cancer growth by regulating the labile iron pool.

Brandon Chen, Nupur K Das, Indrani Talukder, Rashi Singhal, Cristina Castillo, Anthony Andren, Joseph D Mancias, Costas A Lyssiotis, Yatrik M Shah.

  Mitophagy is a cargo-specific autophagic process that recycles damaged mitochondria to promote mitochondrial turnover. PTEN-induced putative kinase 1 (PINK1) mediates the canonical mitophagic pathway. However, the role of PINK1 in diseases where mitophagy has been purported to play a role, such as colorectal cancer, in unclear.Our results here demonstrate that higher PINK1 expression is positively correlated with decreased colon cancer survival, and mitophagy is required for colon cancer growth following nutrient stress. We show that doxycycline-inducible knockdown (KD) of PINK1 in a panel of colon cancer cell lines inhibited proliferation, whereas disruption of other mitophagy receptors did not impact cell growth. We observed that PINK KD led to a decrease in mitochondrial respiration, membrane hyperpolarization, accumulation of mitochondrial DNA, and depletion of antioxidant glutathione. In addition, mitochondria are important hubs for the utilization of iron and synthesizing iron-dependent cofactors such as heme and iron sulfur clusters. We observed an increase in the iron storage protein ferritin and a decrease labile iron pool in the PINK1 KD cells, but total cellular iron or markers of iron starvation/overload were not affected. Finally, cellular iron storage and the labile iron pool are maintained via autophagic degradation of ferritin (ferritinophagy). We found overexpressing nuclear receptor coactivator 4, a key adaptor for ferritinophagy, rescued cell growth and the labile iron pool in PINK1 KD cells. These results indicate that PINK1 integrates mitophagy and ferritinophagy to regulate intracellular iron availability and is essential for maintaining intracellular iron homeostasis to support survival and growth in colorectal cancer cells.

Keywords:  colon cancer; ferritinophagy; iron; mitochondria; mitophagy

DOI:  https://doi.org/10.1016/j.jbc.2023.104691
Cells. 2023 Mar 24. pii: 990. [Epub ahead of print]12(7):

The Role of WNT Pathway Mutations in Cancer Development and an Overview of Therapeutic Options.

Wibke Groenewald, Anders H Lund, David Michael Gay.

  It is well established that mutations in the canonical WNT-signalling pathway play a major role in various cancers. Critical to developing new therapeutic strategies is understanding which cancers are driven by WNT pathway activation and at what level these mutations occur within the pathway. Some cancers harbour mutations in genes whose protein products operate at the receptor level of the WNT pathway. For instance, tumours with RNF43 or RSPO mutations, still require exogenous WNT ligands to drive WNT signalling (ligand-dependent mutations). Conversely, mutations within the cytoplasmic segment of the Wnt pathway, such as in APC and CTNNB1, lead to constitutive WNT pathway activation even in the absence of WNT ligands (ligand-independent). Here, we review the predominant driving mutations found in cancer that lead to WNT pathway activation, as well as explore some of the therapeutic interventions currently available against tumours harbouring either ligand-dependent or ligand-independent mutations. Finally, we discuss a potentially new therapeutic avenue by targeting the translational apparatus downstream from WNT signalling.

Keywords:  APC; WNT; colon cancer; endometrial cancer; ligand-dependent; β-catenin

DOI:  https://doi.org/10.3390/cells12070990