bims-pimaco 2021-02-28 papers

J Cell Biol. 2021 May 03. pii: e202004010. [Epub ahead of print]220(5):

mTORC1 activity is supported by spatial association with focal adhesions.

Yoana Rabanal-Ruiz, Adam Byron, Alexander Wirth, Ralitsa Madsen, Lucia Sedlackova, Graeme Hewitt, Glyn Nelson, Julian Stingele, Jimi C Wills, Tong Zhang, André Zeug, Reinhard Fässler, Bart Vanhaesebroeck, Oliver D K Maddocks, Evgeni Ponimaskin, Bernadette Carroll, Viktor I Korolchuk.

The mammalian target of rapamycin complex 1 (mTORC1) integrates mitogenic and stress signals to control growth and metabolism. Activation of mTORC1 by amino acids and growth factors involves recruitment of the complex to the lysosomal membrane and is further supported by lysosome distribution to the cell periphery. Here, we show that translocation of lysosomes toward the cell periphery brings mTORC1 into proximity with focal adhesions (FAs). We demonstrate that FAs constitute discrete plasma membrane hubs mediating growth factor signaling and amino acid input into the cell. FAs, as well as the translocation of lysosome-bound mTORC1 to their vicinity, contribute to both peripheral and intracellular mTORC1 activity. Conversely, lysosomal distribution to the cell periphery is dispensable for the activation of mTORC1 constitutively targeted to FAs. This study advances our understanding of spatial mTORC1 regulation by demonstrating that the localization of mTORC1 to FAs is both necessary and sufficient for its activation by growth-promoting stimuli.

DOI: https://doi.org/10.1083/jcb.202004010

Cancer Res. 2021 Feb 25. pii: canres.2929.2020. [Epub ahead of print]

Targeting eIF4A Dependent Translation of KRAS Signaling Molecules.

Pancreatic adenocarcinoma (PDAC) epitomizes a deadly cancer driven by abnormal KRAS signalling. Here we show that the eIF4A RNA helicase is required for translation of key KRAS signaling molecules and that pharmacological inhibition of eIF4A has single-agent activity against murine and human PDAC models at safe dose levels. EIF4A was uniquely required for the translation of mRNAs with long and highly structured 5'UTRs including those with multiple G-quadruplex (GQ) elements. Computational analyses identified these features in mRNAs encoding KRAS and key downstream molecules. Transcriptome-scale ribosome footprinting accurately identified eIF4A-dependent mRNAs in PDAC including critical KRAS signaling molecules such as PI3K, RALA, RAC2, MET, MYC, and YAP1. These findings contrast with a recent study that relied on an older method, polysome fractionation, and implicated redox-related genes as eIF4A clients. Together, our findings highlight the power of ribosome footprinting in conjunction with deep RNA sequencing in accurately decoding translational control mechanisms and define the therapeutic mechanism of eIF4A inhibitors in PDAC.

DOI: https://doi.org/10.1158/0008-5472.CAN-20-2929

BMC Cancer. 2021 Feb 25. 21(1): 193

Molecular profile of KRAS G12C-mutant colorectal and non-small-cell lung cancer.

Luiz Henrique Araujo, Bianca Mendes Souza, Laura Rabelo Leite, Sabrina A F Parma, Natália P Lopes, Frederico S V Malta, Maíra C M Freire.

BACKGROUND: KRAS is the most frequently mutated oncogene in cancer, however efforts to develop targeted therapies have been largely unsuccessful. Recently, two small-molecule inhibitors, AMG 510 and MRTX849, have shown promising activity in KRAS G12C-mutant solid tumors. The current study aims to assess the molecular profile of KRAS G12C in colorectal (CRC) and non-small-cell lung cancer (NSCLC) tested in a clinical certified laboratory.
METHODS: CRC and NSCLC samples submitted for KRAS testing between 2017 and 2019 were reviewed. CRC samples were tested for KRAS and NRAS by pyrosequencing, while NSCLC samples were submitted to next generation sequencing of KRAS, NRAS, EGFR, and BRAF.
RESULTS: The dataset comprised 4897 CRC and 4686 NSCLC samples. Among CRC samples, KRAS was mutated in 2354 (48.1%). Most frequent codon 12 mutations were G12D in 731 samples (14.9%) and G12V in 522 (10.7%), followed by G12C in 167 (3.4%). KRAS mutations were more frequent in females than males (p = 0.003), however this difference was exclusive of non-G12C mutants (p < 0.001). KRAS mutation frequency was lower in the South and North regions (p = 0.003), but again KRAS G12C did not differ significantly (p = 0.80). In NSCLC, KRAS mutations were found in 1004 samples (21.4%). As opposed to CRC samples, G12C was the most common mutation in KRAS, in 346 cases (7.4%). The frequency of KRAS G12C was higher in the South and Southeast regions (p = 0.012), and lower in patients younger than 50 years (p < 0.001). KRAS G12C mutations were largely mutually exclusive with other driver mutations; only 11 NSCLC (3.2%) and 1 CRC (0.6%) cases had relevant co-mutations.
CONCLUSIONS: KRAS G12C presents in frequencies higher than several other driver mutations, and may represent a large volume of patients in absolute numbers. KRAS testing should be considered in all CRC and NSCLC patients, independently of clinical or demographic characteristics.

Keywords: Colorectal neoplasms; KRAS; Lung neoplasms; Molecular diagnostics; Molecular targeted therapy

DOI: https://doi.org/10.1186/s12885-021-07884-8

Gut. 2021 Feb 25. pii: gutjnl-2020-321534. [Epub ahead of print]

Genetic architectures of proximal and distal colorectal cancer are partly distinct.

Jeroen R Huyghe, Tabitha A Harrison, Stephanie A Bien, Heather Hampel, Jane C Figueiredo, Stephanie L Schmit, David V Conti, Sai Chen, Conghui Qu, Yi Lin, Richard Barfield, John A Baron, Amanda J Cross, Brenda Diergaarde, David Duggan, Sophia Harlid, Liher Imaz, Hyun Min Kang, David M Levine, Vittorio Perduca, Aurora Perez-Cornago, Lori C Sakoda, Fredrick R Schumacher, Martha L Slattery, Amanda E Toland, Fränzel J B van Duijnhoven, Bethany Van Guelpen, Antonio Agudo, Demetrius Albanes, M Henar Alonso, Kristin Anderson, Coral Arnau-Collell, Volker Arndt, Barbara L Banbury, Michael C Bassik, Sonja I Berndt, Stéphane Bézieau, D Timothy Bishop, Juergen Boehm, Heiner Boeing, Marie-Christine Boutron-Ruault, Hermann Brenner, Stefanie Brezina, Stephan Buch, Daniel D Buchanan, Andrea Burnett-Hartman, Bette J Caan, Peter T Campbell, Prudence R Carr, Antoni Castells, Sergi Castellví-Bel, Andrew T Chan, Jenny Chang-Claude, Stephen J Chanock, Keith R Curtis, Albert de la Chapelle, Douglas F Easton, Dallas R English, Edith J M Feskens, Manish Gala, Steven J Gallinger, W James Gauderman, Graham G Giles, Phyllis J Goodman, William M Grady, John S Grove, Andrea Gsur, Marc J Gunter, Robert W Haile, Jochen Hampe, Michael Hoffmeister, John L Hopper, Wan-Ling Hsu, Wen-Yi Huang, Thomas J Hudson, Mazda Jenab, Mark A Jenkins, Amit D Joshi, Temitope O Keku, Charles Kooperberg, Tilman Kühn, Sébastien Küry, Loic Le Marchand, Flavio Lejbkowicz, Christopher I Li, Li Li, Wolfgang Lieb, Annika Lindblom, Noralane M Lindor, Satu Männistö, Sanford D Markowitz, Roger L Milne, Lorena Moreno, Neil Murphy, Rami Nassir, Kenneth Offit, Shuji Ogino, Salvatore Panico, Patrick S Parfrey, Rachel Pearlman, Paul D P Pharoah, Amanda I Phipps, Elizabeth A Platz, John D Potter, Ross L Prentice, Lihong Qi, Leon Raskin, Gad Rennert, Hedy S Rennert, Elio Riboli, Clemens Schafmayer, Robert E Schoen, Daniela Seminara, Mingyang Song, Yu-Ru Su, Catherine M Tangen, Stephen N Thibodeau, Duncan C Thomas, Antonia Trichopoulou, Cornelia M Ulrich, Kala Visvanathan, Pavel Vodicka, Ludmila Vodickova, Veronika Vymetalkova, Korbinian Weigl, Stephanie J Weinstein, Emily White, Alicja Wolk, Michael O Woods, Anna H Wu, Goncalo R Abecasis, Deborah A Nickerson, Peter C Scacheri, Anshul Kundaje, Graham Casey, Stephen B Gruber, Li Hsu, Victor Moreno, Richard B Hayes, Polly A Newcomb, Ulrike Peters.

OBJECTIVE: An understanding of the etiologic heterogeneity of colorectal cancer (CRC) is critical for improving precision prevention, including individualized screening recommendations and the discovery of novel drug targets and repurposable drug candidates for chemoprevention. Known differences in molecular characteristics and environmental risk factors among tumors arising in different locations of the colorectum suggest partly distinct mechanisms of carcinogenesis. The extent to which the contribution of inherited genetic risk factors for CRC differs by anatomical subsite of the primary tumor has not been examined.
DESIGN: To identify new anatomical subsite-specific risk loci, we performed genome-wide association study (GWAS) meta-analyses including data of 48 214 CRC cases and 64 159 controls of European ancestry. We characterised effect heterogeneity at CRC risk loci using multinomial modelling.
RESULTS: We identified 13 loci that reached genome-wide significance (p<5×10-8) and that were not reported by previous GWASs for overall CRC risk. Multiple lines of evidence support candidate genes at several of these loci. We detected substantial heterogeneity between anatomical subsites. Just over half (61) of 109 known and new risk variants showed no evidence for heterogeneity. In contrast, 22 variants showed association with distal CRC (including rectal cancer), but no evidence for association or an attenuated association with proximal CRC. For two loci, there was strong evidence for effects confined to proximal colon cancer.
CONCLUSION: Genetic architectures of proximal and distal CRC are partly distinct. Studies of risk factors and mechanisms of carcinogenesis, and precision prevention strategies should take into consideration the anatomical subsite of the tumour.

Keywords: cancer genetics; cancer susceptibility; colon carcinogenesis; colorectal cancer; genetic polymorphisms

DOI: https://doi.org/10.1136/gutjnl-2020-321534

Future Oncol. 2021 Feb 25.

An evaluation of RAS testing among metastatic colorectal cancer patients in the USA.

Laura Sangaré, Kimberly Delli-Zotti, Ana Florea, Marko Rehn, Al B Benson, Kimberly A Lowe.

Background: Data on RAS testing practices prior to metastatic colorectal cancer (mCRC) treatment initiation are lacking in the USA. Materials & methods: Flatiron data were utilized for patients diagnosed with mCRC between 2011 and 2017. Flatiron is a longitudinal, demographically and geographically diverse database representing data from over 1.5 million active US patients treated at 255 community and hospital-affiliated oncology clinics. Results: Among 17,387 mCRC patients 69% were RAS tested and 31% were never tested. Timing of RAS testing was as follows: 23% were tested at the time of their initial CRC diagnosis, 60% following mCRC diagnosis but prior to first line of treatment, 3% prior to third line, the remaining 14% were tested following third line. Conclusion: A third (31%) of patients failed to receive RAS testing, therefore all treatment options were unavailable to them. These data highlight how universal testing has not been achieved.

Keywords: KRAS; NRAS; RAS; anti-EGFR; metastatic colorectal cancer; panitumumab

DOI: https://doi.org/10.2217/fon-2020-1075

Cell Metab. 2021 Feb 17. pii: S1550-4131(21)00057-7. [Epub ahead of print]

Asparagine couples mitochondrial respiration to ATF4 activity and tumor growth.

Abigail S Krall, Peter J Mullen, Felicia Surjono, Milica Momcilovic, Ernst W Schmid, Christopher J Halbrook, Apisadaporn Thambundit, Steven D Mittelman, Costas A Lyssiotis, David B Shackelford, Simon R V Knott, Heather R Christofk.

Mitochondrial respiration is critical for cell proliferation. In addition to producing ATP, respiration generates biosynthetic precursors, such as aspartate, an essential substrate for nucleotide synthesis. Here, we show that in addition to depleting intracellular aspartate, electron transport chain (ETC) inhibition depletes aspartate-derived asparagine, increases ATF4 levels, and impairs mTOR complex I (mTORC1) activity. Exogenous asparagine restores proliferation, ATF4 and mTORC1 activities, and mTORC1-dependent nucleotide synthesis in the context of ETC inhibition, suggesting that asparagine communicates active respiration to ATF4 and mTORC1. Finally, we show that combination of the ETC inhibitor metformin, which limits tumor asparagine synthesis, and either asparaginase or dietary asparagine restriction, which limit tumor asparagine consumption, effectively impairs tumor growth in multiple mouse models of cancer. Because environmental asparagine is sufficient to restore tumor growth in the context of respiration impairment, our findings suggest that asparagine synthesis is a fundamental purpose of tumor mitochondrial respiration, which can be harnessed for therapeutic benefit to cancer patients.

Keywords: asparaginase; asparagine; cancer metabolism; cancer treatment; dietary restriction; metformin; respiration

DOI: https://doi.org/10.1016/j.cmet.2021.02.001

Clin Cancer Res. 2021 Feb 22. pii: clincanres.CCR-20-3872-A.2020. [Epub ahead of print]

Cell-type Specific Adaptive Signaling Responses to KRASG12C inhibition.

Eric B Haura, Hitendra S Solanki, Eric A Welsh, Bin Fang, Victoria Izumi, Lancia N F Darville, Brandon Stone, Ryan Franzese, Sandip Chavan, Fumi Kinose, Denis Imbody, John M Koomen, Uwe Rix.

PURPOSE: Covalent inhibitors of KRASG12C specifically target tumors driven by this form of mutant KRAS, yet early studies show that bypass signaling drives adaptive resistance. While several combination strategies have been shown to improve efficacy of KRASG12C inhibitors, underlying mechanisms and predictive strategies for patient enrichment are less clear.
EXPERIMENTAL DESIGN: We performed mass spectrometry based phosphoproteomics analysis in KRASG12C cell lines after short term treatment with ARS-1620. To understand signaling diversity and cell-type specific markers, we compared proteome and phosphoproteomes of KRASG12C cells. Gene expression patterns of KRASG12C cell lines and lung tumor tissues were examined.
RESULTS: Our analysis suggests cell-type specific perturbation to ERBB2/3 signaling compensate for repressed ERK and AKT signaling following ARS-1620 treatment in epithelial cell type, and this subtype was also more responsive to co-inhibition of SHP2 and SOS1. Conversely, both high basal and feedback activation of FGFR or AXL signaling was identified in mesenchymal cells. Inhibition of FGFR signaling suppress feedback activation of ERK and mTOR, while AXL inhibition suppress PI3K pathway. In both cell lines and human lung cancer tissues with KRASG12C we observed high basal ERBB2/3 associated with epithelial gene signatures while higher basal FGFR1 and AXL was observed in cells/tumors with mesenchymal gene signatures.
CONCLUSIONS: Our phosphoproteomic study identified cell-type adaptive responses to KRASG12C inhibitors. Markers and targets associated with ERBB2/3 signaling in epithelial subtype and FGFR1/AXL signaling in mesenchymal subtype should be considered in patient enrichment schemes with KRASG12C inhibitors.

DOI: https://doi.org/10.1158/1078-0432.CCR-20-3872

Gut. 2021 Feb 22. pii: gutjnl-2020-323924. [Epub ahead of print]

ERBB2 in anti-EGFR-resistant colorectal cancer: cancer stem cells come into play.

Sophie Mouillet-Richard.

Keywords: colorectal cancer; drug resistance; stem cells

DOI: https://doi.org/10.1136/gutjnl-2020-323924