Wong, H.K., Mishra, A., Hake, T. & Porcu, P. Evolving insights in the pathogenesis and therapy of cutaneous T-cell lymphoma (mycosis fungoides and Sezary syndrome). Br. J. Haematol. 155, 150–166 (2011).
Kiessling, M.K. et al. High-throughput mutation profiling of CTCL samples reveals KRAS and NRAS mutations sensitizing tumors toward inhibition of the RAS/RAF/MEK signaling cascade. Blood 117, 2433–2440 (2011).
Vaqué, J.P. et al. PLCG1 mutations in cutaneous T-cell lymphomas. Blood 123, 2034–2043 (2014).
So, T. & Croft, M. Regulation of PI-3-kinase and Akt signaling in T lymphocytes and other cells by TNFR family molecules. Front. Immunol. 4, 139 (2013).
Lee, C.S. et al. Transcriptome sequencing in Sezary syndrome identifies Sezary cell and mycosis fungoides–associated lncRNAs and novel transcripts. Blood 120, 3288–3297 (2012).
Newman, A.M. et al. FACTERA: a practical method for the discovery of genomic rearrangements at breakpoint resolution. Bioinformatics 30, 3390–3393 (2014).
Migliazza, A. et al. Heterogeneous chromosomal aberrations generate 3′ truncations of the NFKB2/lyt-10 gene in lymphoid malignancies. Blood 84, 3850–3860 (1994).
Zhang, J., Chang, C.C., Lombardi, L. & Dalla-Favera, R. Rearranged NFKB2 gene in the HUT78 T-lymphoma cell line codes for a constitutively nuclear factor lacking transcriptional repressor functions. Oncogene 9, 1931–1937 (1994).
Vasmatzis, G. et al. Genome-wide analysis reveals recurrent structural abnormalities of TP63 and other p53-related genes in peripheral T-cell lymphomas. Blood 120, 2280–2289 (2012).
Nguyen, L.T. & Ohashi, P.S. Clinical blockade of PD1 and LAG3—potential mechanisms of action. Nat. Rev. Immunol. 15, 45–56 (2015).
Ashkenazi, A. & Dixit, V.M. Death receptors: signaling and modulation. Science 281, 1305–1308 (1998).
Shin, J.H. et al. Positive conversion of negative signaling of CTLA4 potentiates antitumor efficacy of adoptive T-cell therapy in murine tumor models. Blood 119, 5678–5687 (2012).
Mellman, I., Coukos, G. & Dranoff, G. Cancer immunotherapy comes of age. Nature 480, 480–489 (2011).
Sekulic, A. et al. Personalized treatment of Sezary syndrome by targeting a novel CTLA4:CD28 fusion. Mol. Genet. Genomic Med. 3, 130–136 (2015).
Cabal-Hierro, L. & Lazo, P.S. Signal transduction by tumor necrosis factor receptors. Cell. Signal. 24, 1297–1305 (2012).
van Doorn, R. et al. Oncogenomic analysis of mycosis fungoides reveals major differences with Sezary syndrome. Blood 113, 127–136 (2009).
Heemann, C. et al. Circulating levels of TNF receptor II are prognostic for patients with peripheral T-cell non-Hodgkin lymphoma. Clin. Cancer Res. 18, 3637–3647 (2012).
Lin, W.M. et al. Characterization of the DNA copy-number genome in the blood of cutaneous T-cell lymphoma patients. J. Invest. Dermatol. 132, 188–197 (2012).
Rodríguez, M. et al. NF-κB signal triggering and termination by tumor necrosis factor receptor 2. J. Biol. Chem. 286, 22814–22824 (2011).
Zinzani, P.L. et al. Phase II trial of proteasome inhibitor bortezomib in patients with relapsed or refractory cutaneous T-cell lymphoma. J. Clin. Oncol. 25, 4293–4297 (2007).
Acuto, O. & Michel, F. CD28-mediated co-stimulation: a quantitative support for TCR signalling. Nat. Rev. Immunol. 3, 939–951 (2003).
Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589–595 (2010).
DePristo, M.A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491–498 (2011).
Koboldt, D.C. et al. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics 25, 2283–2285 (2009).
Deng, X. SeqGene: a comprehensive software solution for mining exome- and transcriptome-sequencing data. BMC Bioinformatics 12, 267 (2011).
Ng, S.B. et al. Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461, 272–276 (2009).
Liu, X., Jian, X. & Boerwinkle, E. dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations. Hum. Mutat. 34, E2393–E2402 (2013).
Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).
Shi, J. & Walker, M.G. Gene set enrichment analysis (GSEA) for interpreting gene expression profiles. Curr. Bioinformatics 2, 133–137 (2007).
Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819–823 (2013).