In situ mutation detection and visualization of intratumor heterogeneity for cancer research and diagnostics

Oncotarget

Volumn 4, Issue 12, 2013, Pages 2407-2418

  Grundberg, Ida ^a,b   Kiflemariam, Sara ^a   Mignardi, Marco ^a,c   Imgenberg Kreuz, Juliana ^a,d   Edlund, Karolina ^a,e   Micke, Patrick ^a   Sundström, Magnus ^a   Sjöblom, Tobias ^a   Botling, Johan ^a   Nilsson, Mats ^a,c  

^a UPPSALA UNIVERSITY   (Sweden)

^b OLINK BIOSCIENCE   (Sweden)

^c STOCKHOLM UNIVERSITY   (Sweden)

^d UPPSALA UNIVERSITY   (Sweden)

^e LEIBNIZ RESEARCH CENTRE FOR WORKING ENVIRONMENT AND HUMAN FACTORS   (Germany)

Author keywords

Cancer diagnostics; In situ; KRAS; Padlock probes; RCA

Indexed keywords

ANTINEOPLASTIC AGENT; EPIDERMAL GROWTH FACTOR RECEPTOR; EPIDERMAL GROWTH FACTOR RECEPTOR KINASE INHIBITOR; K RAS PROTEIN; PROTEIN P53; RNA;

ALLELE; ARTICLE; CANCER PROGNOSIS; CANCER RESEARCH; CELL HETEROGENEITY; CODON; COLON CANCER; DRUG TARGETING; FLUORESCENCE IN SITU HYBRIDIZATION; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN CELL; HUMAN TISSUE; LUNG CANCER; MOLECULAR DIAGNOSIS; MUTATIONAL ANALYSIS; NUCLEOTIDE SEQUENCE; PROTEIN EXPRESSION; RNA ANALYSIS; SOMATIC MUTATION; TISSUE MICROARRAY; TISSUE SECTION; TREATMENT RESPONSE; TUMOR GROWTH; WILD TYPE;

CODON; COLONIC NEOPLASMS; DNA MUTATIONAL ANALYSIS; GENES, ERBB-1; GENES, P53; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; LUNG NEOPLASMS; NEOPLASMS; POINT MUTATION; PROTO-ONCOGENE PROTEINS; RAS PROTEINS;

EID: 84891909573     PISSN: None     EISSN: 19492553     Source Type: Journal    
DOI: 10.18632/oncotarget.1527     Document Type: Article

References (25)

1. Fisher R, Pusztai L and Swanton C. Cancer heterogeneity: implications for targeted therapeutics. Br J Cancer. 2013; 108(3):479-485.
2. Larsson C, Grundberg I, Soderberg O and Nilsson M. In situ detection and genotyping of individual mRNA molecules. Nat Methods. 2010; 7(5):395-397.
3. Larsson C, Koch J, Nygren A, Janssen G, Raap AK, Landegren U and Nilsson M. In situ genotyping individual DNA molecules by target-primed rolling-circle amplification of padlock probes. Nat Methods. 2004; 1(3):227-232.
4. Luo J, Bergstrom DE and Barany F. Improving the fidelity of Thermus thermophilus DNA ligase. Nucleic Acids Res. 1996; 24(15):3071-3078.
5. Nilsson M, Barbany G, Antson DO, Gertow K and Landegren U. Enhanced detection and distinction of RNA by enzymatic probe ligation. Nat Biotechnol. 2000; 18(7):791-793.
6. Nilsson M, Malmgren H, Samiotaki M, Kwiatkowski M, Chowdhary BP and Landegren U. Padlock probes: circularizing oligonucleotides for localized DNA detection. Science. 1994; 265(5181):2085-2088.
7. Daly TM, Dumaual CM, Miao X, Farmen MW, Njau RK, Fu DJ, Bauer NL, Close S, Watanabe N, Bruckner C, Hardenbol P and Hockett RD. Multiplex assay for comprehensive genotyping of genes involved in drug metabolism, excretion, and transport. Clin Chem. 2007; 53(7):1222-1230.
8. Amado RG, Wolf M, Peeters M, Van Cutsem E, Siena S, Freeman DJ, Juan T, Sikorski R, Suggs S, Radinsky R, Patterson SD and Chang DD. Wild-type KRAS is required for panitumumab efficacy in patients with metastatic colorectal cancer. J Clin Oncol. 2008; 26(10):1626-1634.
9. Sundstrom M, Edlund K, Lindell M, Glimelius B, Birgisson H, Micke P and Botling J. KRAS analysis in colorectal carcinoma: analytical aspects of Pyrosequencing and allele-specific PCR in clinical practice. BMC Cancer. 2010; 10:660.
10. John T, Liu G and Tsao MS. Overview of molecular testing in non-small-cell lung cancer: mutational analysis, gene copy number, protein expression and other biomarkers of EGFR for the prediction of response to tyrosine kinase inhibitors. Oncogene. 2009; 28 Suppl 1:S14-23.
11. Micke P, Edlund K, Holmberg L, Kultima HG, Mansouri L, Ekman S, Bergqvist M, Scheibenflug L, Lamberg K, Myrdal G, Berglund A, Andersson A, Lambe M, Nyberg F, Thomas A, Isaksson A, et al. Gene Copy Number Aberrations Are Associated with Survival in Histologic Subgroups of Non-small Cell Lung Cancer. J Thorac Oncol. 2011; 6(11):1833-1840.
12. Edlund K, Larsson O, Ameur A, Bunikis I, Gyllensten U, Leroy B, Sundstrom M, Micke P, Botling J and Soussi T. Data-driven unbiased curation of the TP53 tumor suppressor gene mutation database and validation by ultradeep sequencing of human tumors. Proc Natl Acad Sci U S A. 2012; 109(24):9551-9556.
13. Landegren U, Kaiser R, Sanders J and Hood L. A ligase-mediated gene detection technique. Science. 1988; 241(4869):1077-1080.
14. Kononen J, Bubendorf L, Kallioniemi A, Barlund M, Schraml P, Leighton S, Torhorst J, Mihatsch MJ, Sauter G and Kallioniemi OP. Tissue microarrays for high-throughput molecular profiling of tumor specimens. Nat Med. 1998; 4(7):844-847.
15. Azuma K, Okamoto I, Kawahara A, Taira T, Nakashima K, Hattori S, Kinoshita T, Takeda M, Nakagawa K, Takamori S, Kuwano M, Ono M and Kage M. Association of the expression of mutant epidermal growth factor receptor protein as determined with mutation-specific antibodies in non-small cell lung cancer with progression-free survival after gefitinib treatment. J Thorac Oncol. 2012; 7(1):122-127.
16. Camp RL, Neumeister V and Rimm DL. A decade of tissue microarrays: progress in the discovery and validation of cancer biomarkers. J Clin Oncol. 2008; 26(34):5630-5637.
17. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP and Burge CB. Alternative isoform regulation in human tissue transcriptomes. Nature. 2008; 456(7221):470-476.
18. Hardenbol P, Baner J, Jain M, Nilsson M, Namsaraev EA, Karlin-Neumann GA, Fakhrai-Rad H, Ronaghi M, Willis TD, Landegren U and Davis RW. Multiplexed genotyping with sequence-tagged molecular inversion probes. Nat Biotechnol. 2003; 21(6):673-678.
19. Goransson J, Wahlby C, Isaksson M, Howell WM, Jarvius J and Nilsson M. A single molecule array for digital targeted molecular analyses. Nucleic Acids Res. 2009; 37(1):e7.
20. Ke R, Mignardi M, Pacureanu A, Svedlund J, Botling J, Wählby C, Nilsson M. In situ sequencing for RNA analysis in preserved tissue and cells. Nat Methods. 2013 Sep;10(9):857-60.
21. Zieba A, Wahlby C, Hjelm F, Jordan L, Berg J, Landegren U and Pardali K. Bright-field microscopy visualization of proteins and protein complexes by in situ proximity ligation with peroxidase detection. Clin Chem. 2010; 56(1):99-110.
22. Pao W and Chmielecki J. Rational, biologically based treatment of EGFR-mutant non-small-cell lung cancer. Nat Rev Cancer. 2010; 10(11):760-774.
23. Diaz LA, Jr., Williams RT, Wu J, Kinde I, Hecht JR, Berlin J, Allen B, Bozic I, Reiter JG, Nowak MA, Kinzler KW, Oliner KS and Vogelstein B. The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. Nature. 2012; 486(7404):537-540.
24. Su KY, Chen HY, Li KC, Kuo ML, Yang JC, Chan WK, Ho BC, Chang GC, Shih JY, Yu SL and Yang PC. Pretreatment epidermal growth factor receptor (EGFR) T790M mutation predicts shorter EGFR tyrosine kinase inhibitor response duration in patients with non-small-cell lung cancer. J Clin Oncol. 2012; 30(4):433-440.
25. Gerlinger M, Rowan AJ, Horswell S, Larkin J, Endesfelder D, Gronroos E, Martinez P, Matthews N, Stewart A, Tarpey P, Varela I, Phillimore B, Begum S, McDonald NQ, Butler A, Jones D, et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med. 2012; 366(10):883-892.