BRAF
Journal
Communications biology
ISSN: 2399-3642
Titre abrégé: Commun Biol
Pays: England
ID NLM: 101719179
Informations de publication
Date de publication:
21 09 2023
21 09 2023
Historique:
received:
23
03
2023
accepted:
07
09
2023
medline:
25
9
2023
pubmed:
22
9
2023
entrez:
22
9
2023
Statut:
epublish
Résumé
BRAF mutations occur early in serrated colorectal cancers, but their long-term influence on tissue homeostasis is poorly characterized. We investigated the impact of short-term (3 days) and long-term (6 months) expression of Braf
Identifiants
pubmed: 37735514
doi: 10.1038/s42003-023-05331-x
pii: 10.1038/s42003-023-05331-x
pmc: PMC10514332
doi:
Substances chimiques
BRAF protein, human
EC 2.7.11.1
Cholesterol
97C5T2UQ7J
Proto-Oncogene Proteins B-raf
EC 2.7.11.1
Braf protein, mouse
EC 2.7.11.1
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
962Subventions
Organisme : Cancer Research UK
ID : C325/A15575
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 210911/Z/18/Z
Pays : United Kingdom
Informations de copyright
© 2023. Springer Nature Limited.
Références
Santos, A. J. M., Lo, Y. H., Mah, A. T. & Kuo, C. J. The intestinal stem cell niche: homeostasis and adaptations. Trends Cell Biol. 28, 1062–1078 (2018).
pubmed: 30195922
pmcid: 6338454
doi: 10.1016/j.tcb.2018.08.001
van der Flier, L. G., Haegebarth, A., Stange, D. E., van de Wetering, M. & Clevers, H. OLFM4 is a robust marker for stem cells in human intestine and marks a subset of colorectal cancer cells. Gastroenterology 137, 15–17 (2009).
pubmed: 19450592
doi: 10.1053/j.gastro.2009.05.035
Barker, N. et al. Identification of stem cells in small intestine and colon by marker gene Lgr5. Nature 449, 1003–1007 (2007).
pubmed: 17934449
doi: 10.1038/nature06196
Minoo, P., Zlobec, I., Peterson, M., Terracciano, L. & Lugli, A. Characterization of rectal, proximal and distal colon cancers based on clinicopathological, molecular and protein profiles. Int. J. Oncol. 37, 707–718 (2010).
pubmed: 20664940
doi: 10.3892/ijo_00000720
Stintzing, S., Tejpar, S., Gibbs, P., Thiebach, L. & Lenz, H. J. Understanding the role of primary tumour localisation in colorectal cancer treatment and outcomes. Eur. J. Cancer 84, 69–80 (2017).
pubmed: 28787661
pmcid: 7505124
doi: 10.1016/j.ejca.2017.07.016
Chen, B. et al. Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polyps. Cell 184, 6262–6280.e6226 (2021).
pubmed: 34910928
pmcid: 8941949
doi: 10.1016/j.cell.2021.11.031
Joanito, I. et al. Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer. Nat. Genet. 54, 963–975 (2022).
pubmed: 35773407
pmcid: 9279158
doi: 10.1038/s41588-022-01100-4
Muzny, D. M. et al. Comprehensive molecular characterization of human colon and rectal cancer. Nature 487, 330–337 (2012).
doi: 10.1038/nature11252
Fearon, E. R. & Vogelstein, B. A genetic model for colorectal tumorigenesis. Cell 61, 759–767 (1990).
pubmed: 2188735
doi: 10.1016/0092-8674(90)90186-I
Missiaglia, E. et al. Distal and proximal colon cancers differ in terms of molecular, pathological, and clinical features. Ann. Oncol. 25, 1995–2001 (2014).
pubmed: 25057166
doi: 10.1093/annonc/mdu275
Leach, J. D. G. et al. Oncogenic BRAF, unrestrained by TGFβ-receptor signalling, drives right-sided colonic tumorigenesis. Nat. Commun. 12, 3464 (2021).
pubmed: 34103493
pmcid: 8187652
doi: 10.1038/s41467-021-23717-5
Weisenberger, D. J. et al. CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer. Nat. Genet. 38, 787–793 (2006).
pubmed: 16804544
doi: 10.1038/ng1834
Davies, H. et al. Mutations of the BRAF gene in human cancer. Nature 417, 949–954 (2002).
pubmed: 12068308
doi: 10.1038/nature00766
Rajagopalan, H. et al. RAF/RAS oncogenes and mismatch-repair status. Nature 418, 934–934 (2002).
pubmed: 12198537
doi: 10.1038/418934a
Dhillon, A. S., Hagan, S., Rath, O. & Kolch, W. MAP kinase signalling pathways in cancer. Oncogene 26, 3279–3290 (2007).
pubmed: 17496922
doi: 10.1038/sj.onc.1210421
Parsons, R. et al. Microsatellite instability and mutations of the transforming growth factor beta type II receptor gene in colorectal cancer. Cancer Res. 55, 5548–5550 (1995).
pubmed: 7585632
Barras, D. et al. BRAF V600E mutant colorectal cancer subtypes based on gene expression. Clin. Cancer Res. 23, 104–115 (2017).
pubmed: 27354468
doi: 10.1158/1078-0432.CCR-16-0140
Tong, K. et al. Degree of tissue differentiation dictates susceptibility to BRAF-driven colorectal cancer. Cell Rep. 21, 3833–3845 (2017).
pubmed: 29281831
pmcid: 5747303
doi: 10.1016/j.celrep.2017.11.104
Rad, R. et al. A genetic progression model of Braf(V600E)-induced intestinal tumorigenesis reveals targets for therapeutic intervention. Cancer Cell 24, 15–29 (2013).
pubmed: 23845441
pmcid: 3706745
doi: 10.1016/j.ccr.2013.05.014
Carragher, L. A. et al. V600EBraf induces gastrointestinal crypt senescence and promotes tumour progression through enhanced CpG methylation of p16INK4a. EMBO Mol. Med. 2, 458–471 (2010).
pubmed: 20941790
pmcid: 3394506
doi: 10.1002/emmm.201000099
Jänne, P. A. & Mayer, R. J. Chemoprevention of colorectal cancer. N. Engl. J. Med. 342, 1960–1968 (2000).
pubmed: 10874065
doi: 10.1056/NEJM200006293422606
Riemer, P. et al. Transgenic expression of oncogenic BRAF induces loss of stem cells in the mouse intestine, which is antagonized by β-catenin activity. Oncogene 34, 3164–3175 (2015).
pubmed: 25109331
doi: 10.1038/onc.2014.247
Feng, Y. et al. Mutant KRAS promotes hyperplasia and alters differentiation in the colon epithelium but does not expand the presumptive stem cell pool. Gastroenterology 141, 1003–1013.e1010 (2011).
pubmed: 21699772
doi: 10.1053/j.gastro.2011.05.007
Liberzon, A. et al. Molecular signatures database (MSigDB) 3.0. Bioinformatics 27, 1739–1740 (2011).
pubmed: 21546393
pmcid: 3106198
doi: 10.1093/bioinformatics/btr260
Popovici, V. et al. Identification of a poor-prognosis BRAF-mutant-like population of patients with colon cancer. J. Clin. Oncol. 30, 1288–1295 (2012).
pubmed: 22393095
doi: 10.1200/JCO.2011.39.5814
Tsai, J.-H. et al. Aberrant expression of annexin A10 is closely related to gastric phenotype in serrated pathway to colorectal carcinoma. Mod. Pathol. 28, 268–278 (2015).
pubmed: 25081749
doi: 10.1038/modpathol.2014.96
Gonzalo, D. H. et al. Gene expression profiling of serrated polyps identifies annexin A10 as a marker of a sessile serrated adenoma/polyp. J. Pathol. 230, 420–429 (2013).
pubmed: 23595865
doi: 10.1002/path.4200
Lytras, T., Nikolopoulos, G. & Bonovas, S. Statins and the risk of colorectal cancer: an updated systematic review and meta-analysis of 40 studies. World J. Gastroenterol. 20, 1858–1870 (2014).
pubmed: 24587664
pmcid: 3930985
doi: 10.3748/wjg.v20.i7.1858
Mullen, P. J., Yu, R., Longo, J., Archer, M. C. & Penn, L. Z. The interplay between cell signalling and the mevalonate pathway in cancer. Nat. Rev. Cancer 16, 718–731 (2016).
pubmed: 27562463
doi: 10.1038/nrc.2016.76
De Sousa, E. M. F. et al. Poor-prognosis colon cancer is defined by a molecularly distinct subtype and develops from serrated precursor lesions. Nat. Med. 19, 614–618 (2013).
doi: 10.1038/nm.3174
Delker, D. A. et al. RNA sequencing of sessile serrated colon polyps identifies differentially expressed genes and immunohistochemical markers. PLoS ONE 9, e88367 (2014).
pubmed: 24533081
pmcid: 3922809
doi: 10.1371/journal.pone.0088367
Parker, H. R. et al. The proto CpG island methylator phenotype of sessile serrated adenomas/polyps. Epigenetics 13, 1088–1105 (2018).
pubmed: 30398409
pmcid: 6342079
doi: 10.1080/15592294.2018.1543504
Andreatta, M. & Carmona, S. J. UCell: Robust and scalable single-cell gene signature scoring. Comput. Struct. Biotechnol. J. 19, 3796–3798 (2021).
pubmed: 34285779
pmcid: 8271111
doi: 10.1016/j.csbj.2021.06.043
Aibar, S. et al. SCENIC: single-cell regulatory network inference and clustering. Nat. Methods 14, 1083–1086 (2017).
pubmed: 28991892
pmcid: 5937676
doi: 10.1038/nmeth.4463
Suo, S. et al. Revealing the critical regulators of cell identity in the mouse cell atlas. Cell Rep. 25, 1436–1445.e1433 (2018).
pubmed: 30404000
pmcid: 6281296
doi: 10.1016/j.celrep.2018.10.045
Janky, R. et al. iRegulon: from a gene list to a gene regulatory network using large motif and track collections. PLoS Comput. Biol. 10, e1003731 (2014).
pubmed: 25058159
pmcid: 4109854
doi: 10.1371/journal.pcbi.1003731
Beumer, J. & Clevers, H. Regulation and plasticity of intestinal stem cells during homeostasis and regeneration. Development 143, 3639–3649 (2016).
pubmed: 27802133
doi: 10.1242/dev.133132
de Jong, P. R. et al. ERK5 signalling rescues intestinal epithelial turnover and tumour cell proliferation upon ERK1/2 abrogation. Nat. Commun. 7, 11551 (2016).
pubmed: 27187615
pmcid: 4873670
doi: 10.1038/ncomms11551
Miller, S. A. et al. LSD1 and aberrant DNA methylation mediate persistence of enteroendocrine progenitors that support BRAF-mutant colorectal cancer. Cancer Res. 81, 3791–3805 (2021).
pubmed: 34035083
pmcid: 8513805
doi: 10.1158/0008-5472.CAN-20-3562
Herr, R. et al. B-Raf inhibitors induce epithelial differentiation in BRAF-mutant colorectal cancer cells. Cancer Res. 75, 216–229 (2015).
pubmed: 25381152
doi: 10.1158/0008-5472.CAN-13-3686
Giannakis, M. et al. RNF43 is frequently mutated in colorectal and endometrial cancers. Nat. Genet. 46, 1264–1266 (2014).
pubmed: 25344691
pmcid: 4283570
doi: 10.1038/ng.3127
Borowsky, J. et al. The role of APC in WNT pathway activation in serrated neoplasia. Mod. Pathol. 31, 495–504 (2018).
pubmed: 29148535
doi: 10.1038/modpathol.2017.150
Panarelli, N. C., Vaughn, C. P., Samowitz, W. S. & Yantiss, R. K. Sporadic microsatellite instability-high colon cancers rarely display immunohistochemical evidence of Wnt signaling activation. Am. J. Surg. Pathol. 39, 313–317 (2015).
pubmed: 25602793
doi: 10.1097/PAS.0000000000000380
Yachida, S., Mudali, S., Martin, S. A., Montgomery, E. A. & Iacobuzio-Donahue, C. A. Beta-catenin nuclear labeling is a common feature of sessile serrated adenomas and correlates with early neoplastic progression after BRAF activation. Am. J. Surg. Pathol. 33, 1823–1832 (2009).
pubmed: 19745699
pmcid: 2788075
doi: 10.1097/PAS.0b013e3181b6da19
Cairns, R. A., Harris, I. S. & Mak, T. W. Regulation of cancer cell metabolism. Nat. Rev. Cancer 11, 85–95 (2011).
pubmed: 21258394
doi: 10.1038/nrc2981
Vander Heiden, M. G. et al. Metabolic pathway alterations that support cell proliferation. Cold Spring Harb. Symp. Quant. Biol. 76, 325–334 (2011).
doi: 10.1101/sqb.2012.76.010900
Satoh, K. et al. Global metabolic reprogramming of colorectal cancer occurs at adenoma stage and is induced by MYC. Proc. Natl. Acad. Sci. USA 114, E7697–e7706 (2017).
pubmed: 28847964
pmcid: 5604037
doi: 10.1073/pnas.1710366114
Alaqbi, S. S. et al. Increased mitochondrial proline metabolism sustains proliferation and survival of colorectal cancer cells. PLoS ONE 17, e0262364 (2022).
pubmed: 35130302
pmcid: 8820619
doi: 10.1371/journal.pone.0262364
Alexandrou, C. et al. Sensitivity of colorectal cancer to arginine deprivation therapy is shaped by differential expression of urea cycle enzymes. Sci. Rep. 8, 12096 (2018).
pubmed: 30108309
pmcid: 6092409
doi: 10.1038/s41598-018-30591-7
Ying, Z. et al. The unfolded protein response and cholesterol biosynthesis link luman/CREB3 to regenerative axon growth in sensory neurons. J. Neurosci. 35, 14557–14570 (2015).
pubmed: 26511246
pmcid: 6605466
doi: 10.1523/JNEUROSCI.0012-15.2015
Myers, S. A., Wang, S. C. & Muscat, G. E. The chicken ovalbumin upstream promoter-transcription factors modulate genes and pathways involved in skeletal muscle cell metabolism. J. Biol. Chem. 281, 24149–24160 (2006).
pubmed: 16803904
doi: 10.1074/jbc.M601941200
Rodríguez, J. C., Ortiz, J. A., Hegardt, F. G. & Haro, D. Chicken ovalbumin upstream-promoter transcription factor (COUP-TF) could act as a transcriptional activator or repressor of the mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase gene. Biochem. J. 326, 587–592 (1997).
pubmed: 9291136
pmcid: 1218709
doi: 10.1042/bj3260587
Yamazaki, T. et al. The COUP-TFII variant lacking a DNA-binding domain inhibits the activation of the Cyp7a1 promoter through physical interaction with COUP-TFII. Biochem. J. 452, 345–357 (2013).
pubmed: 23458092
doi: 10.1042/BJ20121200
Vallejo, A. et al. FOSL1 promotes cholangiocarcinoma via transcriptional effectors that could be therapeutically targeted. J. Hepatol. 75, 363–376 (2021).
pubmed: 33887357
doi: 10.1016/j.jhep.2021.03.028
Bardou, M., Barkun, A. & Martel, M. Effect of statin therapy on colorectal cancer. Gut 59, 1572 (2010).
pubmed: 20660702
doi: 10.1136/gut.2009.190900
Jung, Y. S., Park, C. H., Eun, C. S., Park, D. I. & Han, D. S. Statin use and the risk of colorectal adenoma: A meta-analysis. J. Gastroenterol. Hepatol. 31, 1823–1830 (2016).
pubmed: 27043957
doi: 10.1111/jgh.13393
Wei, J. T., Mott, L. A., Baron, J. A. & Sandler, R. S. Reported use of 3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitors was not associated with reduced recurrence of colorectal adenomas. Cancer Epidemiol. Biomark. Prev. 14, 1026–1027 (2005).
doi: 10.1158/1055-9965.EPI-03-0080
Lee, J. E. et al. Statin use and colorectal cancer risk according to molecular subtypes in two large prospective cohort studies. Cancer Prev. Res. 4, 1808–1815 (2011).
doi: 10.1158/1940-6207.CAPR-11-0113
Mo, H. & Elson, C. E. Studies of the isoprenoid-mediated inhibition of mevalonate synthesis applied to cancer chemotherapy and chemoprevention. Exp. Biol. Med. 229, 567–585 (2004).
doi: 10.1177/153537020422900701
Wong, W. W., Dimitroulakos, J., Minden, M. D. & Penn, L. Z. HMG-CoA reductase inhibitors and the malignant cell: the statin family of drugs as triggers of tumor-specific apoptosis. Leukemia 16, 508–519 (2002).
pubmed: 11960327
doi: 10.1038/sj.leu.2402476
Kodach, L. L. et al. The effect of statins in colorectal cancer is mediated through the bone morphogenetic protein pathway. Gastroenterology 133, 1272–1281 (2007).
pubmed: 17919499
doi: 10.1053/j.gastro.2007.08.021
Amirkhah, R. et al. MmCMS: mouse models’ consensus molecular subtypes of colorectal cancer. Br. J. Cancer 128, 1333–1343 (2023).
pubmed: 36717674
pmcid: 10050155
doi: 10.1038/s41416-023-02157-6
Ouahoud, S. et al. Statin use is associated with a reduced incidence of colorectal cancer expressing SMAD4. Br. J. Cancer 126, 297–301 (2022).
pubmed: 34703008
doi: 10.1038/s41416-021-01604-6
DeStefano Shields, C. E. et al. Bacterial-driven inflammation and mutant BRAF expression combine to promote murine colon tumorigenesis that is sensitive to immune checkpoint therapy. Cancer Discov. 11, 1792–1807 (2021).
pubmed: 33632774
pmcid: 8295175
doi: 10.1158/2159-8290.CD-20-0770
Andersen, C. L., Jensen, J. L. & Ørntoft, T. F. Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res. 64, 5245–5250 (2004).
pubmed: 15289330
doi: 10.1158/0008-5472.CAN-04-0496
Bustin, S. A. et al. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin. Chem. 55, 611–622 (2009).
pubmed: 19246619
doi: 10.1373/clinchem.2008.112797
Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890 (2018).
pubmed: 30423086
pmcid: 6129281
doi: 10.1093/bioinformatics/bty560
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
pubmed: 23104886
doi: 10.1093/bioinformatics/bts635
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
pubmed: 25516281
pmcid: 4302049
doi: 10.1186/s13059-014-0550-8
Smedley, D. et al. BioMart—biological queries made easy. BMC Genomics 10, 22 (2009).
pubmed: 19144180
pmcid: 2649164
doi: 10.1186/1471-2164-10-22
Yu, G., Wang, L. G., Han, Y. & He, Q. Y. clusterProfiler: an R package for comparing biological themes among gene clusters. Omics 16, 284–287 (2012).
pubmed: 22455463
pmcid: 3339379
doi: 10.1089/omi.2011.0118
Liberzon, A. et al. The Molecular Signatures Database (MSigDB) hallmark gene set collection. Cell Syst. 1, 417–425 (2015).
pubmed: 26771021
pmcid: 4707969
doi: 10.1016/j.cels.2015.12.004
Gautier, L., Cope, L., Bolstad, B. M. & Irizarry, R. A. affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 20, 307–315 (2004).
pubmed: 14960456
doi: 10.1093/bioinformatics/btg405
Grossman, R. L. et al. Toward a shared vision for cancer genomic data. New Engl. J. Med. 375, 1109–1112 (2016).
pubmed: 27653561
doi: 10.1056/NEJMp1607591
Colaprico, A. et al. TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data. Nucleic Acids Res. 44, e71 (2016).
pubmed: 26704973
doi: 10.1093/nar/gkv1507
Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545–15550 (2005).
pubmed: 16199517
pmcid: 1239896
doi: 10.1073/pnas.0506580102
Wolf, F. A., Angerer, P. & Theis, F. J. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol. 19, 15 (2018).
pubmed: 29409532
pmcid: 5802054
doi: 10.1186/s13059-017-1382-0
Reback, J. et al. pandas-dev/pandas: Pandas 1.3.1 (v1.3.1). Zenodo. https://doi.org/10.5281/zenodo.5136416 . (2021).
Stuart, T. et al. Comprehensive integration of single-cell data. Cell 177, 1888–1902.e1821 (2019).
pubmed: 31178118
pmcid: 6687398
doi: 10.1016/j.cell.2019.05.031
Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587.e3529 (2021).
pubmed: 34062119
pmcid: 8238499
doi: 10.1016/j.cell.2021.04.048
Kassambara A ggpubr: ‘ggplot2’ Based Publication Ready Plots. R package version 0.4.0, https://rpkgs.datanovia.com/ggpubr/ . (2020).
Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504 (2003).
pubmed: 14597658
pmcid: 403769
doi: 10.1101/gr.1239303