5,252
Views
98
CrossRef citations to date
0
Altmetric
Resource

Cross-cancer profiling of molecular alterations within the human autophagy interaction network

, , , , , & show all
Pages 1668-1687 | Received 02 Sep 2014, Accepted 24 Jun 2015, Published online: 18 Sep 2015

References

  • Leone RD, Amaravadi RK. Autophagy: a targetable linchpin of cancer cell metabolism. Trends Endocrinol Metab 2013; 24:209-17; PMID:23474062; http://dx.doi.org/10.1016/j.tem.2013.01.008
  • Yang ZJ, Chee CE, Huang S, Sinicrope FA. The role of autophagy in cancer: therapeutic implications. Mol Cancer Ther 2011; 10:1533-41; PMID:21878654; http://dx.doi.org/10.1158/1535-7163.MCT-11-0047
  • Lebovitz CB, Bortnik SB, Gorski SM. Here, there be dragons: charting autophagy-related alterations in human tumors. Clin Cancer Res Off J Am Assoc Cancer Res 2012; 18:1214-26; PMID:22253413; http://dx.doi.org/10.1158/1078-0432.CCR-11-2465
  • Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz LA, Kinzler KW. Cancer genome landscapes. Science 2013; 339:1546-58; PMID:23539594; http://dx.doi.org/10.1126/science.1235122
  • Rung J, Brazma A. Reuse of public genome-wide gene expression data. Nat Rev Genet 2013; 14:89-99; PMID:23269463; http://dx.doi.org/10.1038/nrg3394
  • Mwenifumbo JC, Marra MA. Cancer genome-sequencing study design. Nat Rev Genet 2013; 14:321-32; PMID:23594910; http://dx.doi.org/10.1038/nrg3445
  • Behrends C, Sowa ME, Gygi SP, Harper JW. Network organization of the human autophagy system. Nature 2010; 466:68-76; PMID:20562859; http://dx.doi.org/10.1038/nature09204
  • Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, de Bono B, Garapati P, Hemish J, Hermjakob H, Jassal B, et al. Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res 2009; 37:D619-22; PMID:18981052; http://dx.doi.org/10.1093/nar/gkn863
  • Newman MEJ. Modularity and community structure in networks. Proc Natl Acad Sci U S A 2006; 103:8577-82; PMID:16723398; http://dx.doi.org/10.1073/pnas.0601602103
  • Greenman C, Stephens P, Smith R, Dalgliesh GL, Hunter C, Bignell G, Davies H, Teague J, Butler A, Stevens C, et al. Patterns of somatic mutation in human cancer genomes. Nature 2007; 446:153-8; PMID:17344846; http://dx.doi.org/10.1038/nature05610
  • TCGA Research Network. Comprehensive genomic characterization of squamous cell lung cancers. Nature 2012; 489:519-25; PMID:22960745; http://dx.doi.org/10.1038/nature11404
  • TCGA Sees Heterogeneity in Head and Neck Cancers. Cancer Discov 2013; 3:475-6; http://dx.doi.org/10.1158/2159-8290.CD-NB2013-049
  • The Cancer Genome Atlas Research Network. Integrated genomic characterization of endometrial carcinoma. Nature 2013; 497:67-73; PMID:23636398; http://dx.doi.org/10.1038/nature12113
  • The Cancer Genome Atlas Research Network. Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature 2013; 499:43-9; PMID:23792563; http://dx.doi.org/10.1038/nature12222
  • Spaans VM, Trietsch MD, Crobach S, Stelloo E, Kremer D, Osse EM, Haar NT, van Eijk R, Muller S, van Wezel T, et al. Designing a high-throughput somatic mutation profiling panel specifically for gynaecological cancers. PLoS ONE 2014; 9:e93451; PMID:24671188; http://dx.doi.org/10.1371/journal.pone.0093451
  • Gao Y-B, Chen Z-L, Li J-G, Hu X-D, Shi X-J, Sun Z-M, Zhang F, Zhao Z-R, Li Z-T, Liu Z-Y, et al. Genetic landscape of esophageal squamous cell carcinoma. Nat Genet 2014; 46:1097-102; PMID:25151357; http://dx.doi.org/10.1038/ng.3076
  • Shibata T, Kokubu A, Saito S, Narisawa-Saito M, Sasaki H, Aoyagi K, Yoshimatsu Y, Tachimori Y, Kushima R, Kiyono T, et al. NRF2 Mutation Confers Malignant Potential and Resistance to Chemoradiation Therapy in Advanced Esophageal Squamous Cancer. Neoplasia 2011; 13:864-73; PMID:21969819; http://dx.doi.org/10.1593/neo.11750
  • Sato T, Nakashima A, Guo L, Coffman K, Tamanoi F. Single amino-acid changes that confer constitutive activation of mTOR are discovered in human cancer. Oncogene 2010; 29:2746-52; PMID:20190810; http://dx.doi.org/10.1038/onc.2010.28
  • Grabiner BC, Nardi V, Birsoy K, Possemato R, Shen K, Sinha S, Jordan A, Beck AH, Sabatini DM. A diverse array of cancer-associated MTOR mutations are hyperactivating and can predict rapamycin sensitivity. Cancer Discov 2014; 4:554-63; PMID:24631838; http://dx.doi.org/10.1158/2159-8290.CD-13-0929
  • Hast BE, Cloer EW, Goldfarb D, Li H, Siesser PF, Yan F, Walter V, Zheng N, Hayes DN, Major MB. Cancer-derived mutations in KEAP1 impair NRF2 degradation but not ubiquitination. Cancer Res 2014; 74:808-17; PMID:24322982; http://dx.doi.org/10.1158/0008-5472.CAN-13-1655
  • Lo S-C, Li X, Henzl MT, Beamer LJ, Hannink M. Structure of the Keap1:Nrf2 interface provides mechanistic insight into Nrf2 signaling. EMBO J 2006; 25:3605-17; PMID:16888629; http://dx.doi.org/10.1038/sj.emboj.7601243
  • Brunet J-P, Tamayo P, Golub TR, Mesirov JP. Metagenes and molecular pattern discovery using matrix factorization. Proc Natl Acad Sci U S A 2004; 101:4164-9; PMID:15016911; http://dx.doi.org/10.1073/pnas.0308531101
  • Payton JE, Grieselhuber NR, Chang L-W, Murakami M, Geiss GK, Link DC, Nagarajan R, Watson MA, Ley TJ. High throughput digital quantification of mRNA abundance in primary human acute myeloid leukemia samples. J Clin Invest 2009; 119:1714-26; PMID:19451695; http://dx.doi.org/10.1172/JCI38248
  • Liu EY, Ryan KM. Autophagy and cancer – issues we need to digest. J Cell Sci 2012; 125:2349-58; PMID:22641689; http://dx.doi.org/10.1242/jcs.093708
  • Chandra V, Bhagyaraj E, Parkesh R, Gupta P. Transcription factors and cognate signalling cascades in the regulation of autophagy. Biol Rev 2015; PMID:25651938; http://dx.doi.org/10.1111/brv.12177
  • Macneil LT, Walhout AJM. Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression. Genome Res 2011; 21:645-57; PMID:21324878; http://dx.doi.org/10.1101/gr.097378.109
  • Guo JY, Karsli-Uzunbas G, Mathew R, Aisner SC, Kamphorst JJ, Strohecker AM, Chen G, Price S, Lu W, Teng X, et al. Autophagy suppresses progression of K-ras-induced lung tumors to oncocytomas and maintains lipid homeostasis. Genes Dev 2013; 27:1447-61; PMID:23824538; http://dx.doi.org/10.1101/gad.219642.113
  • Rao S, Tortola L, Perlot T, Wirnsberger G, Novatchkova M, Nitsch R, Sykacek P, Frank L, Schramek D, Komnenovic V, et al. A dual role for autophagy in a murine model of lung cancer. Nat Commun 2014; 5:3056; PMID:24445999; http://dx.doi.org/10.1038/ncomms4056
  • Vernier-Magnin S, Nemos C, Mansuy V, Tolle F, Guichard L, Delage-Mourroux R, Jouvenot M, Fraichard A. Analysis of the guinea-pig estrogen-regulated gec1/GABARAPL1 gene promoter and identification of a functional ERE in the first exon. Biochim Biophys Acta 2005; 1731:23-31; PMID:16153720; http://dx.doi.org/10.1016/j.bbaexp.2005.05.002
  • Nemos C, Mansuy V, Vernier-Magnin S, Fraichard A, Jouvenot M, Delage-Mourroux R. Expression of gec1/GABARAPL1 versus GABARAP mRNAs in human: predominance of gec1/GABARAPL1 in the central nervous system. Mol Brain Res 2003; 119:216-9; PMID:14625090; http://dx.doi.org/10.1016/j.molbrainres.2003.09.011
  • Berthier A, Seguin S, Sasco AJ, Bobin JY, De Laroche G, Datchary J, Saez S, Rodriguez-Lafrasse C, Tolle F, Fraichard A, et al. High expression of gabarapl1 is associated with a better outcome for patients with lymph node-positive breast cancer. Br J Cancer 2010; 102:1024-31; PMID:20197771; http://dx.doi.org/10.1038/sj.bjc.6605568
  • Kroemer G, Jäättelä M. Lysosomes and autophagy in cell death control. Nat Rev Cancer 2005; 5:886-97; PMID:16239905; http://dx.doi.org/10.1038/nrc1738
  • Mathew R, White E. Autophagy, stress, and cancer metabolism: what doesn't kill you makes you stronger. Cold Spring Harb Symp Quant Biol 2011; 76:389-96; PMID:22442109; http://dx.doi.org/10.1101/sqb.2012.76.011015
  • Lee J, Giordano S, Zhang J. Autophagy, mitochondria and oxidative stress: cross-talk and redox signalling. Biochem J 2012; 441:523-40; PMID:22187934; http://dx.doi.org/10.1042/BJ20111451
  • Li L, Wei XH, Pan YP, Li HC, Yang H, He QH, Pang Y, Shan Y, Xiong FX, Shao GZ, et al. LAPTM4B: A novel cancer-associated gene motivates multidrug resistance through efflux and activating PI3K/AKT signaling. Oncogene 2010; 29:5785-95; PMID:20711237; http://dx.doi.org/10.1038/onc.2010.303
  • Li Y, Zhang Q, Tian R, Wang Q, Zhao JJ, Iglehart JD, Wang ZC, Richardson AL. Lysosomal transmembrane protein LAPTM4B promotes autophagy and tolerance to metabolic stress in cancer cells. Cancer Res 2011; 71:7481-9; PMID:22037872; http://dx.doi.org/10.1158/0008-5472.CAN-11-0940
  • Zhang J, Ney PA. Role of BNIP3 and NIX in cell death, autophagy, and mitophagy. Cell Death Differ 2009; 16:939-46; PMID:19229244; http://dx.doi.org/10.1038/cdd.2009.16
  • Karpathiou G, Sivridis E, Koukourakis M, Mikroulis D, Bouros D, Froudarakis M, Bougioukas G, Maltezos E, Giatromanolaki A. Autophagy and Bcl-2/BNIP3 death regulatory pathway in non-small cell lung carcinomas. APMIS Acta Pathol Microbiol Immunol Scand 2013; 121:592-604; PMID:23216071; http://dx.doi.org/10.1111/apm.12026
  • Vijayalingam S, Pillai SG, Rashmi R, Subramanian T, Sagartz JE, Chinnadurai G. Overexpression of BH3-Only protein BNIP3 leads to enhanced tumor growth. Genes Cancer 2010; 1:964-71; PMID:21779475; http://dx.doi.org/10.1177/1947601910386110
  • Blum R, Kloog Y. Metabolism addiction in pancreatic cancer. Cell Death Dis 2014; 5:e1065; PMID:24556680; http://dx.doi.org/10.1038/cddis.2014.38
  • Rosenfeldt MT, O'Prey J, Morton JP, Nixon C, MacKay G, Mrowinska A, Au A, Rai TS, Zheng L, Ridgway R, et al. p53 status determines the role of autophagy in pancreatic tumour development. Nature 2013; 504:296-300; PMID:24305049; http://dx.doi.org/10.1038/nature12865
  • An H-J, Maeng O, Kang K-H, Lee J-O, Kim Y-S, Paik S-G, Lee H. Activation of Ras Up-regulates Pro-apoptotic BNIP3 in Nitric Oxide-induced Cell Death. J Biol Chem 2006; 281:33939-48; PMID:16954213; http://dx.doi.org/10.1074/jbc.M605819200
  • Cheng H, Liu P, Zhang F, Xu E, Symonds L, Ohlson CE, Bronson RT, Maira S-M, Di Tomaso E, Li J, et al. A genetic mouse model of invasive endometrial cancer driven by concurrent loss of pten and Lkb1 is highly responsive to mtor inhibition. Cancer Res 2013; 74:15-23.
  • Bartosch C, Manuel Lopes J, Oliva E. Endometrial carcinomas: a review emphasizing overlapping and distinctive morphological and immunohistochemical features. Adv Anat Pathol 2011; 18:415-37; PMID:21993268; http://dx.doi.org/10.1097/PAP.0b013e318234ab18
  • Jung A, Schrauder M, Oswald U, Knoll C, Sellberg P, Palmqvist R, Niedobitek G, Brabletz T, Kirchner T. The invasion front of human colorectal adenocarcinomas shows co-localization of nuclear beta-catenin, cyclin D1, and p16INK4A and is a region of low proliferation. Am J Pathol 2001; 159:1613-7; PMID:11696421; http://dx.doi.org/10.1016/S0002-9440(10)63007-6
  • Budina-Kolomets A, Hontz RD, Pimkina J, Murphy ME. A conserved domain in exon 2 coding for the human and murine ARF tumor suppressor protein is required for autophagy induction. Autophagy 2013; 9; PMID:23939042; http://dx.doi.org/10.4161/auto.25831
  • Jiang H, Martin V, Gomez-Manzano C, Johnson DG, Alonso M, White E, Xu J, McDonnell TJ, Shinojima N, Fueyo J. The RB-E2F1 pathway regulates autophagy. Cancer Res 2010; 70:7882-93; PMID:20807803; http://dx.doi.org/10.1158/0008-5472.CAN-10-1604
  • Sivridis E, Giatromanolaki A, Liberis V, Koukourakis MI. Autophagy in endometrial carcinomas and prognostic relevance of “stone-like” structures (SLS): What is destined for the atypical endometrial hyperplasia? Autophagy 7:74-82; PMID:21099253; http://dx.doi.org/10.4161/auto.7.1.13947
  • Kimple RJ, Smith MA, Blitzer GC, Torres AD, Martin JA, Yang RZ, Peet CR, Lorenz LD, Nickel KP, Klingelhutz AJ, et al. Enhanced radiation sensitivity in HPV-positive head and neck cancer. Cancer Res 2013; 73:4791-800; PMID:23749640; http://dx.doi.org/10.1158/0008-5472.CAN-13-0587
  • Lechner M, Frampton G, Fenton T, Feber A, Palmer G, Jay A, Pillay N, Forster M, Cronin MT, Lipson D. Targeted next-generation sequencing of head and neck squamous cell carcinoma identifies novel genetic alterations in HPV+ and HPV-tumors. Genome Med 2013; 5:49; PMID:23718828; http://dx.doi.org/10.1186/gm453
  • Taguchi K, Fujikawa N, Komatsu M, Ishii T, Unno M, Akaike T, Motohashi H, Yamamoto M. Keap1 degradation by autophagy for the maintenance of redox homeostasis. Proc Natl Acad Sci U S A 2012; 109:13561-6; PMID:22872865; http://dx.doi.org/10.1073/pnas.1121572109
  • He W, Wang Q, Xu J, Xu X, Padilla MT, Ren G, Gou X, Lin Y. Attenuation of TNFSF10/TRAIL-induced apoptosis by an autophagic survival pathway involving TRAF2- and RIPK1/RIP1-mediated MAPK8/JNK activation. Autophagy 2012; 8:1811-21; PMID:23051914; http://dx.doi.org/10.4161/auto.22145
  • The Cancer Genome Atlas Research Network. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med 2013; 368:2059-74; PMID:23634996; http://dx.doi.org/10.1056/NEJMoa1301689
  • Marchesi F, Annibali O, Cerchiara E, Tirindelli MC, Avvisati G. Cytogenetic abnormalities in adult non-promyelocytic acute myeloid leukemia: A concise review. Crit Rev Oncol Hematol 2011; 80:331-46; PMID:21123080; http://dx.doi.org/10.1016/j.critrevonc.2010.11.006
  • Rücker FG, Schlenk RF, Bullinger L, Kayser S, Teleanu V, Kett H, Habdank M, Kugler C-M, Holzmann K, Gaidzik VI, et al. TP53 alterations in acute myeloid leukemia with complex karyotype correlate with specific copy number alterations, monosomal karyotype, and dismal outcome. Blood 2012; 119:2114-21; PMID:22186996; http://dx.doi.org/10.1182/blood-2011-08-375758
  • Sukhai MA, Prabha S, Hurren R, Rutledge AC, Lee AY, Sriskanthadevan S, Sun H, Wang X, Skrtic M, Seneviratne A, et al. Lysosomal disruption preferentially targets acute myeloid leukemia cells and progenitors. J Clin Invest 2013; 123:315-28; PMID:23202731; http://dx.doi.org/10.1172/JCI64180
  • Settembre C, Di Malta C, Polito VA, Arencibia MG, Vetrini F, Erdin S, Erdin SU, Huynh T, Medina D, Colella P, et al. TFEB links autophagy to lysosomal biogenesis. Science 2011; 332:1429-33; PMID:21617040; http://dx.doi.org/10.1126/science.1204592
  • Zhang Y, Morgan MJ, Chen K, Choksi S, Liu Z. Induction of autophagy is essential for monocyte-macrophage differentiation. Blood 2012; 119:2895-905; PMID:22223827; http://dx.doi.org/10.1182/blood-2011-08-372383
  • Mao K, Wang K, Liu X, Klionsky DJ. The scaffold protein Atg11 recruits fission machinery to drive selective mitochondria degradation by autophagy. Dev Cell 2013; 26:9-18; PMID:23810512; http://dx.doi.org/10.1016/j.devcel.2013.05.024
  • Betin VMS, MacVicar TDB, Parsons SF, Anstee DJ, Lane JD. A cryptic mitochondrial targeting motif in Atg4D links caspase cleavage with mitochondrial import and oxidative stress. Autophagy 2012; 8:664-76; PMID:22441018; http://dx.doi.org/10.4161/auto.19227
  • Joo JH, Dorsey FC, Joshi A, Hennessy-Walters KM, Rose KL, McCastlain K, Zhang J, Iyengar R, Jung CH, Suen D-F, et al. Hsp90-Cdc37 chaperone complex regulates Ulk1- and Atg13-mediated mitophagy. Mol Cell 2011; 43:572-85; PMID:21855797; http://dx.doi.org/10.1016/j.molcel.2011.06.018
  • Isakson P, Bjørås M, Bøe SO, Simonsen A. Autophagy contributes to therapy-induced degradation of the PML/RARA oncoprotein. Blood 2010; 116:2324-31; PMID:20574048; http://dx.doi.org/10.1182/blood-2010-01-261040
  • Huang Y, Hou J-K, Chen T-T, Zhao X-Y, Yan Z-W, Zhang J, Yang J, Kogan SC, Chen G-Q. PML-RARα enhances constitutive autophagic activity through inhibiting the Akt/mTOR pathway. Autophagy 2011; 7:1132-44; PMID:21673516; http://dx.doi.org/10.4161/auto.7.10.16636
  • Linehan WM, Srinivasan R, Schmidt LS. The genetic basis of kidney cancer: a metabolic disease. Nat Rev Urol 2010; 7:277-85; PMID:20448661; http://dx.doi.org/10.1038/nrurol.2010.47
  • Parkhitko A, Myachina F, Morrison TA, Hindi KM, Auricchio N, Karbowniczek M, Wu JJ, Finkel T, Kwiatkowski DJ, Yu JJ, et al. Tumorigenesis in tuberous sclerosis complex is autophagy and p62/sequestosome 1 (SQSTM1)-dependent. Proc Natl Acad Sci 2011; 108:12455-60; PMID:21746920; http://dx.doi.org/10.1073/pnas.1104361108
  • Zhang J, Kim J, Alexander A, Cai S, Tripathi DN, Dere R, Tee AR, Tait-Mulder J, Di Nardo A, Han JM, et al. A tuberous sclerosis complex signalling node at the peroxisome regulates mTORC1 and autophagy in response to ROS. Nat Cell Biol 2013; 15:1186-96; PMID:23955302; http://dx.doi.org/10.1038/ncb2822
  • Ravichandran K, Edelstein CL. Polycystic kidney disease: a case of suppressed autophagy? Semin Nephrol 2014; 34:27-33; PMID:24485027; http://dx.doi.org/10.1016/j.semnephrol.2013.11.005
  • Chen Y-B, Tickoo SK. Spectrum of preneoplastic and neoplastic cystic lesions of the kidney. Arch Pathol Lab Med 2012; 136:400-9; PMID:22458902; http://dx.doi.org/10.5858/arpa.2011-0485-RA
  • Belibi F, Zafar I, Ravichandran K, Segvic AB, Jani A, Ljubanovic DG, Edelstein CL. Hypoxia-inducible factor-1α (HIF-1α) and autophagy in polycystic kidney disease (PKD). Am J Physiol Renal Physiol 2011; 300:F1235-43; PMID:21270095; http://dx.doi.org/10.1152/ajprenal.00348.2010
  • Jiang M, Liu K, Luo J, Dong Z. Autophagy is a renoprotective mechanism during in vitro hypoxia and in vivo ischemia-reperfusion injury. Am J Pathol 2010; 176:1181-92; PMID:20075199; http://dx.doi.org/10.2353/ajpath.2010.090594
  • Rekhtman N, Ang DC, Sima CS, Travis WD, Moreira AL. Immunohistochemical algorithm for differentiation of lung adenocarcinoma and squamous cell carcinoma based on large series of whole-tissue sections with validation in small specimens. Mod Pathol 2011; 24:1348-59; PMID:21623384; http://dx.doi.org/10.1038/modpathol.2011.92
  • Kim YR, Oh JE, Kim MS, Kang MR, Park SW, Han JY, Eom HS, Yoo NJ, Lee SH. Oncogenic NRF2 mutations in squamous cell carcinomas of oesophagus and skin. J Pathol 2010; 220:446-51; PMID:19967722; http://dx.doi.org/10.1002/path.2653
  • Sakuma Y, Matsukuma S, Nakamura Y, Yoshihara M, Koizume S, Sekiguchi H, Saito H, Nakayama H, Kameda Y, Yokose T, et al. Enhanced autophagy is required for survival in EGFR-independent EGFR-mutant lung adenocarcinoma cells. Lab Investig J Tech Methods Pathol 2013; 93:1137-46; PMID:23938604; http://dx.doi.org/10.1038/labinvest.2013.102
  • Guo JY, Chen H-Y, Mathew R, Fan J, Strohecker AM, Karsli-Uzunbas G, Kamphorst JJ, Chen G, Lemons JMS, Karantza V, et al. Activated Ras requires autophagy to maintain oxidative metabolism and tumorigenesis. Genes Dev 2011; 25:460-70; PMID:21317241; http://dx.doi.org/10.1101/gad.2016311
  • Taguchi K, Motohashi H, Yamamoto M. Molecular mechanisms of the Keap1–Nrf2 pathway in stress response and cancer evolution. Genes Cells 2011; 16:123-40; PMID:21251164; http://dx.doi.org/10.1111/j.1365-2443.2010.01473.x
  • Inami Y, Waguri S, Sakamoto A, Kouno T, Nakada K, Hino O, Watanabe S, Ando J, Iwadate M, Yamamoto M, et al. Persistent activation of Nrf2 through p62 in hepatocellular carcinoma cells. J Cell Biol 2011; 193:275-84; PMID:21482715; http://dx.doi.org/10.1083/jcb.201102031
  • Jain A, Lamark T, Sjøttem E, Larsen KB, Awuh JA, Øvervatn A, McMahon M, Hayes JD, Johansen T. p62/SQSTM1 is a target gene for transcription factor NRF2 and creates a positive feedback loop by inducing antioxidant response element-driven gene transcription. J Biol Chem 2010; 285:22576-91; PMID:20452972; http://dx.doi.org/10.1074/jbc.M110.118976
  • Ji H, Ramsey MR, Hayes DN, Fan C, McNamara K, Kozlowski P, Torrice C, Wu MC, Shimamura T, Perera SA, et al. LKB1 modulates lung cancer differentiation and metastasis. Nature 2007; 448:807-10; PMID:17676035; http://dx.doi.org/10.1038/nature06030
  • Orenstein SJ, Kuo S-H, Tasset I, Arias E, Koga H, Fernandez-Carasa I, Cortes E, Honig LS, Dauer W, Consiglio A, et al. Interplay of LRRK2 with chaperone-mediated autophagy. Nat Neurosci 2013; 16:394-406; PMID:23455607; http://dx.doi.org/10.1038/nn.3350
  • Manzoni C, Mamais A, Dihanich S, Abeti R, Soutar MPM, Plun-Favreau H, Giunti P, Tooze SA, Bandopadhyay R, Lewis PA. Inhibition of LRRK2 kinase activity stimulates macroautophagy. Biochim Biophys Acta 2013; 1833:2900-10; PMID:23916833; http://dx.doi.org/10.1016/j.bbamcr.2013.07.020
  • Pozo K, Castro-Rivera E, Tan C, Plattner F, Schwach G, Siegl V, Meyer D, Guo A, Gundara J, Mettlach G, et al. The role of Cdk5 in neuroendocrine thyroid cancer. Cancer Cell 2013; 24:499-511; PMID:24135281; http://dx.doi.org/10.1016/j.ccr.2013.08.027
  • Liang Q, Li L, Zhang J, Lei Y, Wang L, Liu D-X, Feng J, Hou P, Yao R, Zhang Y, et al. CDK5 is essential for TGF-β1-induced epithelial-mesenchymal transition and breast cancer progression. Sci Rep 2013; 3:2932; PMID:24121667
  • Wong ASL, Lee RHK, Cheung AY, Yeung PK, Chung SK, Cheung ZH, Ip NY. Cdk5-mediated phosphorylation of endophilin B1 is required for induced autophagy in models of Parkinson's disease. Nat Cell Biol 2011; 13:568-79; PMID:21499257; http://dx.doi.org/10.1038/ncb2217
  • Jain K, Paranandi KS, Sridharan S, Basu A. Autophagy in breast cancer and its implications for therapy. Am J Cancer Res 2013; 3:251; PMID:23841025
  • Croft D, O'Kelly G, Wu G, Haw R, Gillespie M, Matthews L, Caudy M, Garapati P, Gopinath G, Jassal B, et al. Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res 2011; 39:D691-7; PMID:21067998; http://dx.doi.org/10.1093/nar/gkq1018
  • Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003; 13:2498-504; PMID:14597658; http://dx.doi.org/10.1101/gr.1239303
  • Greenman C, Wooster R, Futreal PA, Stratton MR, Easton DF. Statistical analysis of pathogenicity of somatic mutations in cancer. Genetics 2006; 173:2187-98; PMID:16783027; http://dx.doi.org/10.1534/genetics.105.044677
  • Law CW, Chen Y, Shi W, Smyth GK. Voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol 2014; 15:R29; PMID:24485249; http://dx.doi.org/10.1186/gb-2014-15-2-r29
  • Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO, Sun Y, Jacobsen A, Sinha R, Larsson E, et al. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal 2013; 6:pl1; PMID:23550210; http://dx.doi.org/10.1126/scisignal.2004088
  • R-Forge: NMF - Nonnegative Matrix Factorization: R Development Page [Internet]. [cited 2012 Mar 1]; Available from: https://r-forge.r-project.org/R/?group_id=649
  • Rousseeuw PJ. Silhouettes: A graphical aid to the interpretation and validation of cluster analysis. J Comput Appl Math 1987; 20:53-65; http://dx.doi.org/10.1016/0377-0427(87)90125-7