- F. Ramírezet al., deepTools2: A next generation web server for
deep-sequencing data analysis.Nucleic Acids Res. 44 ,
W160–W165 (2016). doi:10.1093/nar/gkw257; pmid: 27079975 - J. T. Robinsonet al., Integrative genomics viewer.Nat. Biotechnol.
29 , 24–26 (2011). doi:10.1038/nbt.1754; pmid: 21221095 - T. L. Baileyet al., MEME SUITE: Tools for motif discovery and
searching.Nucleic Acids Res. 37 , W202–W208 (2009).
doi:10.1093/nar/gkp335; pmid: 19458158 - V. Kulakovskiyet al., HOCOMOCO: Towards a complete collection
of transcription factor binding models for human and mouse
via large-scale ChIP-Seq analysis.Nucleic Acids Res. 46 ,
D252–D259 (2018). doi:10.1093/nar/gkx1106; pmid: 29140464 - C. E. Grant, T. L. Bailey, W. S. Noble, FIMO: Scanning for
occurrences of a given motif.Bioinformatics 27 , 1017– 1018
(2011). doi:10.1093/bioinformatics/btr064; pmid: 21330290 - B. Langmead, S. L. Salzberg, Fast gapped-read alignment with
Bowtie 2.Nat. Methods 9 , 357–359 (2012). doi:10.1038/
nmeth.1923; pmid: 22388286 - D. Kimet al., TopHat2: Accurate alignment of transcriptomes
in the presence of insertions, deletions and gene fusions.
Genome Biol. 14 , R36 (2013). doi:10.1186/gb-2013-14-4-r36;
pmid: 23618408 - Y. Liao, G. K. Smyth, W. Shi, The Subread aligner: Fast, accurate
and scalable read mapping by seed-and-vote.Nucleic Acids Res.
41 , e108–e108 (2013). doi:10.1093/nar/gkt214; pmid: 23558742 - A. Subramanianet al., Gene set enrichment analysis:
A knowledge-based approach for interpreting genome-wide
expression profiles.Proc. Natl. Acad. Sci. U.S.A. 102 ,
15545 – 15550 (2005). doi:10.1073/pnas.0506580102;
pmid: 16199517 - D. Merico, R. Isserlin, O. Stueker, A. Emili, G. D. Bader, Enrichment
map: A network-based method for gene-set enrichment
visualization and interpretation.PLOS ONE 5 , e13984 (2010).
doi:10.1371/journal.pone.0013984; pmid: 21085593 - D. Szklarczyket al., STRING v11: Protein-protein association
networks with increased coverage, supporting functional
discovery in genome-wide experimental datasets.Nucleic Acids
Res. 47 (D1), D607–D613 (2019). doi:10.1093/nar/gky1131;
pmid: 30476243 - A. Liberzonet al., Molecular signatures database (MSigDB) 3.0.
Bioinformatics 27 , 1739–1740 (2011). doi:10.1093/
bioinformatics/btr260; pmid: 21546393 - M. Ashburneret al., Gene ontology: Tool for the unification of
biology.Nat. Genet. 25 , 25–29 (2000). doi:10.1038/75556;
pmid: 10802651 - The Gene Ontology Consortium, Expansion of the Gene Ontology
knowledgebase and resources.Nucleic Acids Res. 45 , D331–D338
(2017). doi:10.1093/nar/gkw1108; pmid: 27899567 - D. Binnset al., QuickGO: A web-based tool for Gene Ontology
searching.Bioinformatics 25 , 3045–3046 (2009).
doi:10.1093/bioinformatics/btp536; pmid: 19744993
63. A. Kahramanet al., TRAIL mediates liver injury by the innate
immune system in the bile duct-ligated mouse.Hepatology 47 ,
1317 – 1330 (2008). doi:10.1002/hep.22136; pmid: 18220275
64. K. Azizet al., Ccne1 Overexpression Causes Chromosome
Instability in Liver Cells and Liver Tumor Development in Mice.
Gastroenterology 157 , 210–226.e12 (2019). doi:10.1053/
j.gastro.2019.03.016; pmid: 30878468
65. C. N. Mayhewet al., Liver-specific pRB loss results in ectopic
cell cycle entry and aberrant ploidy.Cancer Res. 65 ,
4568 – 4577 (2005). doi:10.1158/0008-5472.CAN-04-4221;
pmid: 15930274
66. J. Moffatet al., A lentiviral RNAi library for human and mouse
genes applied to an arrayed viral high-content screen.Cell 124 ,
1283 – 1298 (2006). doi:10.1016/j.cell.2006.01.040;
pmid: 16564017
67. T. Miest, D. Saenz, A. Meehan, M. Llano, E. M. Poeschla,
Intensive RNAi with lentiviral vectors in mammalian cells.
Methods 47 , 298–303 (2009). doi:10.1016/
j.ymeth.2008.11.001; pmid: 19041944
68. R. L. Weaveret al., BubR1 alterations that reinforce mitotic
surveillance act against aneuploidy and cancer.eLife 5 , e16620
(2016). doi:10.7554/eLife.16620; pmid: 27528194
69. M. J. Wanget al., Reversal of hepatocyte senescence after
continuous in vivo cell proliferation.Hepatology 60 , 349– 361
(2014). doi:10.1002/hep.27094; pmid: 24711261
70. X. Chenet al., Endogenous expression of Hras(G12V) induces
developmental defects and neoplasms with copy number
imbalances of the oncogene.Proc. Natl. Acad. Sci. U.S.A. 106 ,
7979 – 7984 (2009). doi:10.1073/pnas.0900343106;
pmid: 19416908
71. L. H. Kasperet al., CREB binding protein interacts with
nucleoporin-specific FG repeats that activate transcription and
mediate NUP98-HOXA9 oncogenicity.Mol. Cell. Biol. 19 ,
764 – 776 (1999). doi:10.1128/MCB.19.1.764; pmid: 9858599
72. A. Ray, B. N. Dittel, Isolation of mouse peritoneal cavity cells.
J. Vis. Exp.(35): 1488 (2010). doi:10.3791/1488; pmid: 20110936
73. J. Luet al., IRX1 hypomethylation promotes osteosarcoma
metastasis via induction of CXCL14/NF-kB signaling.J. Clin.
Invest. 125 , 1839–1856 (2015). doi:10.1172/JCI78437;
pmid: 25822025
ACKNOWLEDGMENTS
We thank B. G. Childs, J. F. Limzerwala, C. J. Sieben, R. Bram,
J. Elisseeff, and B. van de Sluis for helpful and stimulating
discussions and/or careful evaluation of the manuscript. We also
thank R. Velasco Fierro for valuable technical assistance. We
are grateful to C. Ross for his work on the identification of
super-enhancers and the genes they control, M. H. Hofker for
conceptual discussions, and R. Thaler for assistance in generating
heatmaps. Flow cytometry was performed by the Mayo Clinic
Microscopy and Cell Analysis Core, sequencing by Mayo Clinic
Medical Genomics Facility Sequencing Core, and ChIP in the
Epigenomics Core of the Mayo Clinic Center for Cell Signaling in
Gastroenterology.Funding:This work was supported by grants
from Mayo Clinic’s Center for Biomedical Discovery, the Paul F. Glenn
Foundation for Medical Research, the Keck Foundation, the US
National Institutes of Health (grants R01 AG057493, P30 DK084567
and R01 AG056318), the Mayo Clinic Cancer Center, and the David F.
and Margaret T. Grohne Cancer Immunology and Immunotherapy
Program.Author contributions:J.M.v.D. conceived the project. I.S.
and J.M.v.D. designed most experiments. I.S. performed most
experiments. J.-H.L. and T.O. performed ChIP-related experiments,
and C.Z., I.S., and H.L. conducted super-enhancer–related studies.
C.Z. and I.S. performed bioinformatic analyses. I.S., C.C.S., I.C.,
E.J.v.D., and J.T.S. conducted knockdown experiments, and K.B.J.
coimmunoprecipitation experiments. N.H., J.G., M.H., and D.Y.L.
generated and validated transgenic strains. R.M.L. helped with
experimental design and data interpretation. D.F. and V.S.
designed and executed neutralizing antibody experiments in mice
with I.S. and helped with interpretation of immunosurveillance
data. All authors contributed to data acquisition, analysis and
interpretation. J.M.v.D. and I.S. wrote the paper and all authors
edited the manuscript. D.J.B. helped supervise and interpret
experiments pertaining to the physiological relevance of the PASP.
H.L. directed, supervised, and helped interpret all bioinformatics
analyses and J.M.v.D. directed and supervised all other aspects of
the study.Competing interests:J.M.v.D. is a cofounder of Unity
Biotechnology. J.M.v.D., D.J.B., and R.M.L. are coinventors on
patents licensed to or filed by Unity Biotechnology. I.S., H.L., and
J.M.v.D. are listed as inventors on provisional patent application
U.S. 63/224,177 filed by Mayo Clinic that encompasses aspects of
this publication. J.M.v.D., H.L., R.M.L., and D.J.B. are current Unity
Biotechnology shareholders. This research has been reviewed
by the Mayo Clinic Conflict of Interest Review Board and is being
conducted in compliance with Mayo Clinic conflict of interest
policies.Data and materials availability:ChIP-seq and RNA-seq
data sets have been deposited in the Gene Expression Omnibus
(GSE117278). Mouse strainsL-p21,L-KRASG12V,L-p16andp21floxed
mice are available from Mayo Clinic upon completion of a
material transfer agreement.
SUPPLEMENTARY MATERIALS
science.org/doi/10.1126/science.abb3420
Figs. S1 to S20
Tables S1 to S9
MDAR Reproducibility Checklist
23 February 2020; resubmitted 7 April 2021
Accepted 3 September 2021
10.1126/science.abb3420
Sturmlechneret al.,Science 374 , eabb3420 (2021) 29 October 2021 15 of 15
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