Single-cell trajectories of melanoma cell resistance to targeted treatment (2024)

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References

1

Cancer Genome Atlas Network. Genomic classification of cutaneous melanoma. Cell. 2015; 161: 1681-96.

2

Schadendorf D, van Akkooi ACJ, Berking C, Griewank KG, Gutzmer R, Hauschild A, et al. Melanoma. Lancet. 2018; 392: 971-84.

3

Robert C, Grob JJ, Stroyakovskiy D, Karaszewska B, Hauschild A, Levchenko E, et al. Five-year outcomes with dabrafenib plus trametinib in metastatic melanoma. N Engl J Med. 2019; 381: 626-36.

4

Eddy K, Shah R, Chen S. Decoding melanoma development and progression: identification of therapeutic vulnerabilities. Front Oncol. 2020; 10: 626129.

5

McGranahan N, Swanton C. Biological and therapeutic impact of intratumor heterogeneity in cancer evolution. Cancer Cell. 2015; 27: 15-26.

6

Hausser J, Alon U. Tumour heterogeneity and the evolutionary trade-offs of cancer. Nat Rev Cancer. 2020; 20: 247-57.

7

Lim B, Lin Y, Navin N. Advancing cancer research and medicine with single-cell genomics. Cancer Cell. 2020; 37: 456-70.

8

Tirosh I, Izar B, Prakadan SM, Wadsworth MH, Treacy D, Trombetta JJ, et al. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science. 2016; 352: 189-96.

9

Gerber T, Willscher E, Loeffler-Wirth H, Hopp L, Schadendorf D, Schartl M, et al. Mapping heterogeneity in patient-derived melanoma cultures by single-cell RNA-seq. Oncotarget. 2017; 8: 846-62.

10

Jönsson G, Busch C, Knappskog S, Geisler J, Miletic H, Ringnér M, et al. Gene expression profiling-based identification of molecular subtypes in stage Ⅳ melanomas with different clinical outcome. Clin Cancer Res. 2010; 16: 3356-67.

11

Harbst K, Staaf J, Lauss M, Karlsson A, Måsbäck A, Johansson I, et al. Molecular profiling reveals low- and high-grade forms of primary melanoma. Clin Cancer Res. 2012; 18: 4026-36.

13

Wirth H, Bergen M von, Binder H. Mining SOM expression portraits: feature selection and integrating concepts of molecular function. BioData Min. 2012; 5: 18.

14

Loeffler-Wirth H, Kreuz M, Hopp L, Arakelyan A, Haake A, Cogliatti SB, et al. A modular transcriptome map of mature B cell lymphomas. Genome Med. 2019; 11: 27.

15

Löffler-Wirth H, Kalcher M, Binder H. oposSOM: R-package for high-dimensional portraying of genome-wide expression landscapes on bioconductor. Bioinformatics. 2015; 31: 3225-7.

16

Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat Biotechnol. 2014; 32: 381-6.

17

Farrell JA, Wang Y, Riesenfeld SJ, Shekhar K, Regev A, Schier AF. Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis. Science. 2018; 360: eaar3131.

18

La Manno G, Soldatov R, Zeisel A, Braun E, Hochgerner H, Petukhov V, et al. RNA velocity of single cells. Nature. 2018; 560: 494-8.

19

Bergen V, Lange M, Peidli S, Wolf FA, Theis FJ. Generalizing RNA velocity to transient cell states through dynamical modeling. Nat Biotechnol. 2020; 38: 1408-14.

20

Schmidt M, Loeffler-Wirth H, Binder H. Developmental scRNAseq trajectories in gene- and cell- state space-the flatworm example. Genes (Basel). 2020; 11: 1214.

21

Fattore L, Ruggiero CF, Liguoro D, Mancini R, Ciliberto G. Single cell analysis to dissect molecular heterogeneity and disease evolution in metastatic melanoma. Cell Death Dis. 2019; 10: 827.

22

Jost L. Partitioning diversity into independent alpha and beta components. Ecology. 2007; 88: 2427-39.

23

Liberzon A, Birger C, Thorvaldsdóttir H, Ghandi M, Mesirov JP, Tamayo P. The Molecular Signatures Database (MSigDB) hallmark gene set collection. Cell Syst. 2015; 1: 417-25.

24

Roesch A, Vultur A, Bogeski I, Wang H, Zimmermann KM, Speicher D, et al. Overcoming intrinsic multidrug resistance in melanoma by blocking the mitochondrial respiratory chain of slow-cycling JARID1B(high) cells. Cancer Cell. 2013; 23: 811-25.

25

Liu X, Zhang S-M, McGeary MK, Krykbaeva I, Lai L, Jansen DJ, et al. KDM5B promotes drug resistance by regulating melanoma-propagating cell subpopulations. Mol Cancer Ther. 2019; 18: 706-17.

26

Riverso M, Montagnani V, Stecca B. KLF4 is regulated by RAS/RAF/MEK/ERK signaling through E2F1 and promotes melanoma cell growth. Oncogene. 2017; 36: 3322-33.

27

Zhang D, Lin J, Chao Y, Zhang L, Jin L, Li N, et al. Regulation of the adaptation to ER stress by KLF4 facilitates melanoma cell metastasis via upregulating NUCB2 expression. J Exp Clin Cancer Res. 2018; 37: 176.

28

Nersisyan L, Löffler-Wirth H, Arakelyan A, Binder H. Gene set- and pathway-centered knowledge discovery assigns transcriptional activation patterns in brain, blood, and colon cancer. IJKDB. 2014; 4: 46-69.

29

Jalili A, Wagner C, Pashenkov M, Pathria G, Mertz KD, Widlund HR, et al. Dual suppression of the cyclin-dependent kinase inhibitors CDKN2C and CDKN1A in human melanoma. J Natl Cancer Inst. 2012; 104: 1673-9.

30

Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, et al. Integrative analysis of 111 reference human epigenomes. Nature. 2015; 518: 317-30.

31

Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011; 473: 43-9.

32

Hebenstreit D, Fang M, Gu M, Charoensawan V, van Oudenaarden A, Teichmann SA. RNA sequencing reveals two major classes of gene expression levels in metazoan cells. Mol Syst Biol. 2011; 7: 497.

33

Tsoi J, Robert L, Paraiso K, Galvan C, Sheu KM, Lay J, et al. Multi-stage differentiation defines melanoma subtypes with differential vulnerability to drug-induced iron-dependent oxidative stress. Cancer Cell. 2018; 33: 890-904.e5.

34

Rambow F, Rogiers A, Marin-Bejar O, Aibar S, Femel J, Dewaele M, et al. Toward minimal residual disease-directed therapy in melanoma. Cell. 2018; 174: 843-55.e19.

35

Wouters J, Kalender-Atak Z, Minnoye L, Spanier KI, De Waegeneer M, Bravo González-Blas C, et al. Robust gene expression programs underlie recurrent cell states and phenotype switching in melanoma. Nat Cell Biol. 2020; 22: 986-98.

36

Su Y, Wei W, Robert L, Xue M, Tsoi J, Garcia-Diaz A, et al. Single-cell analysis resolves the cell state transition and signaling dynamics associated with melanoma drug-induced resistance. Proc Natl Acad Sci USA. 2017; 114: 13679-84.

37

Su Y, Ko ME, Cheng H, Zhu R, Xue M, Wang J, et al. Multi-omic single-cell snapshots reveal multiple independent trajectories to drug tolerance in a melanoma cell line. Nat Commun. 2020; 11: 2345.

38

Belote RL, Le D, Maynard A, Lang UE, Sinclair A, Planells-Palop V, et al. Human melanocyte development and melanoma dedifferentiation at single cell resolution, 2020. bioRxiv preprint. https://doi.org/10.1101/2020.05.25.115287

39

Smalley I, Kim E, Li J, Spence P, Wyatt CJ, Eroglu Z, et al. Leveraging transcriptional dynamics to improve BRAF inhibitor responses in melanoma. EBioMedicine. 2019; 48: 178-90.

40

Shaffer SM, Dunagin MC, Torborg SR, Torre EA, Emert B, Krepler C, et al. Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance. Nature. 2017; 546: 431-5.

41

Thalheim T, Hopp L, Binder H, Aust G, Galle J. On the Cooperation between epigenetics and transcription factor networks in the specification of tissue stem cells. Epigenomes. 2018; 2: 20.

42

Long JE, Wongchenko MJ, Nickles D, Chung W-J, Wang B-E, Riegler J, et al. Therapeutic resistance and susceptibility is shaped by cooperative multi-compartment tumor adaptation. Cell Death Differ. 2019; 26: 2416-29.

43

van Allen EM, Wagle N, Sucker A, Treacy DJ, Johannessen CM, Goetz EM, et al. The genetic landscape of clinical resistance to RAF inhibition in metastatic melanoma. Cancer Discov. 2014; 4: 94-109.

44

Long GV, Fung C, Menzies AM, Pupo GM, Carlino MS, Hyman J, et al. Increased MAPK reactivation in early resistance to dabrafenib/trametinib combination therapy of BRAF-mutant metastatic melanoma. Nat Commun. 2014; 5: 5694.

45

Hugo W, Shi H, Sun L, Piva M, Song C, Kong X, et al. Non-genomic and immune evolution of melanoma acquiring MAPKi resistance. Cell. 2015; 162: 1271-85.

46

Moriceau G, Hugo W, Hong A, Shi H, Kong X, Yu CC, et al. Tunable-combinatorial mechanisms of acquired resistance limit the efficacy of BRAF/MEK cotargeting but result in melanoma drug addiction. Cancer Cell. 2015; 27: 240-56.

47

Granados K, Poelchen J, Novak D, Utikal J. Cellular reprogramming—a model for melanoma cellular plasticity. Int J Mol Sci. 2020; 21: 8274.

48

Rambow F, Marine J-C, Goding CR. Melanoma plasticity and phenotypic diversity: therapeutic barriers and opportunities. Genes Dev. 2019; 33: 1295-18.

Single-cell trajectories of melanoma cell resistance to targeted treatment (2024)
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