Genomic analysis of 220 CTCLs identifies a novel recurrent gain-of-function alteration in RLTPR (p.Q575E)

Joonhee Park, Jingyi Yang, Alexander T. Wenzel, Akshaya Ramachandran, Wung J. Lee, Jay C. Daniels, Juhyun Kim, Estela Martinez-Escala, Nduka Amankulor, Barbara Pro, Joan Guitart, Marc Laurence Mendillo, Jeffrey Nicholas Savas, Titus J. Boggon, Jaehyuk Choi*

*Corresponding author for this work

Research output: Contribution to journalArticle

22 Citations (Scopus)

Abstract

Cutaneous T-cell lymphoma (CTCL) is an incurable non-Hodgkin lymphoma of the skin-homing T cell. In early-stage disease, lesions are limited to the skin, but in later-stage disease, the tumor cells can escape into the blood, the lymph nodes, and at times the visceral organs. To clarify the genomic basis of CTCL, we performed genomic analysis of 220 CTCLs. Our analyses identify 55 putative driver genes, including 17 genes not previously implicated in CTCL. These novel mutations are predicted to affect chromatin (BCOR, KDM6A, SMARCB1, TRRAP), immune surveillance (CD58, RFXAP), MAPK signaling (MAP2K1, NF1), NF-kB signaling (PRKCB, CSNK1A1), PI-3-kinase signaling (PIK3R1, VAV1), RHOA/cytoskeleton remodeling (ARHGEF3), RNA splicing (U2AF1), T-cell receptor signaling (PTPRN2, RLTPR), and T-cell differentiation (RARA). Our analyses identify recurrent mutations in 4 genes not previously identified in cancer. These include CK1a (encoded by CSNK1A1) (p.S27F; p.S27C), PTPRN2 (p.G526E), RARA (p.G303S), and RLTPR (p.Q575E). Last, we functionally validate CSNK1A1 and RLTPR as putative oncogenes. RLTPR encodes a recently described scaffolding protein in the T-cell receptor signaling pathway. We show that RLTPR (p.Q575E) increases binding of RLTPR to downstream components of the NF-kB signaling pathway, selectively upregulates the NF-kB pathway in activated T cells, and ultimately augments T-cell-receptor-dependent production of interleukin 2 by 34-fold. Collectively, our analysis provides novel insights into CTCL pathogenesis and elucidates the landscape of potentially targetable gene mutations.

Original languageEnglish (US)
Pages (from-to)1430-1440
Number of pages11
JournalBlood
Volume130
Issue number12
DOIs
StatePublished - Sep 21 2017

Fingerprint

Cutaneous T-Cell Lymphoma
T-cells
NF-kappa B
T-Cell Antigen Receptor
T-Lymphocytes
Mutation
Genes
RNA Splicing
Skin
Cytoskeleton
Phosphatidylinositol 3-Kinases
Oncogenes
Non-Hodgkin's Lymphoma
Chromatin
Interleukin-2
Cell Differentiation
Neoplasms
Up-Regulation
Lymph Nodes
Tumors

ASJC Scopus subject areas

  • Biochemistry
  • Immunology
  • Hematology
  • Cell Biology

Cite this

Park, J., Yang, J., Wenzel, A. T., Ramachandran, A., Lee, W. J., Daniels, J. C., ... Choi, J. (2017). Genomic analysis of 220 CTCLs identifies a novel recurrent gain-of-function alteration in RLTPR (p.Q575E). Blood, 130(12), 1430-1440. https://doi.org/10.1182/blood-2017-02-768234
Park, Joonhee ; Yang, Jingyi ; Wenzel, Alexander T. ; Ramachandran, Akshaya ; Lee, Wung J. ; Daniels, Jay C. ; Kim, Juhyun ; Martinez-Escala, Estela ; Amankulor, Nduka ; Pro, Barbara ; Guitart, Joan ; Mendillo, Marc Laurence ; Savas, Jeffrey Nicholas ; Boggon, Titus J. ; Choi, Jaehyuk. / Genomic analysis of 220 CTCLs identifies a novel recurrent gain-of-function alteration in RLTPR (p.Q575E). In: Blood. 2017 ; Vol. 130, No. 12. pp. 1430-1440.
@article{6d5f5e45780b43b0b9ecf953dc95c4a9,
title = "Genomic analysis of 220 CTCLs identifies a novel recurrent gain-of-function alteration in RLTPR (p.Q575E)",
abstract = "Cutaneous T-cell lymphoma (CTCL) is an incurable non-Hodgkin lymphoma of the skin-homing T cell. In early-stage disease, lesions are limited to the skin, but in later-stage disease, the tumor cells can escape into the blood, the lymph nodes, and at times the visceral organs. To clarify the genomic basis of CTCL, we performed genomic analysis of 220 CTCLs. Our analyses identify 55 putative driver genes, including 17 genes not previously implicated in CTCL. These novel mutations are predicted to affect chromatin (BCOR, KDM6A, SMARCB1, TRRAP), immune surveillance (CD58, RFXAP), MAPK signaling (MAP2K1, NF1), NF-kB signaling (PRKCB, CSNK1A1), PI-3-kinase signaling (PIK3R1, VAV1), RHOA/cytoskeleton remodeling (ARHGEF3), RNA splicing (U2AF1), T-cell receptor signaling (PTPRN2, RLTPR), and T-cell differentiation (RARA). Our analyses identify recurrent mutations in 4 genes not previously identified in cancer. These include CK1a (encoded by CSNK1A1) (p.S27F; p.S27C), PTPRN2 (p.G526E), RARA (p.G303S), and RLTPR (p.Q575E). Last, we functionally validate CSNK1A1 and RLTPR as putative oncogenes. RLTPR encodes a recently described scaffolding protein in the T-cell receptor signaling pathway. We show that RLTPR (p.Q575E) increases binding of RLTPR to downstream components of the NF-kB signaling pathway, selectively upregulates the NF-kB pathway in activated T cells, and ultimately augments T-cell-receptor-dependent production of interleukin 2 by 34-fold. Collectively, our analysis provides novel insights into CTCL pathogenesis and elucidates the landscape of potentially targetable gene mutations.",
author = "Joonhee Park and Jingyi Yang and Wenzel, {Alexander T.} and Akshaya Ramachandran and Lee, {Wung J.} and Daniels, {Jay C.} and Juhyun Kim and Estela Martinez-Escala and Nduka Amankulor and Barbara Pro and Joan Guitart and Mendillo, {Marc Laurence} and Savas, {Jeffrey Nicholas} and Boggon, {Titus J.} and Jaehyuk Choi",
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month = "9",
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doi = "10.1182/blood-2017-02-768234",
language = "English (US)",
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Park, J, Yang, J, Wenzel, AT, Ramachandran, A, Lee, WJ, Daniels, JC, Kim, J, Martinez-Escala, E, Amankulor, N, Pro, B, Guitart, J, Mendillo, ML, Savas, JN, Boggon, TJ & Choi, J 2017, 'Genomic analysis of 220 CTCLs identifies a novel recurrent gain-of-function alteration in RLTPR (p.Q575E)', Blood, vol. 130, no. 12, pp. 1430-1440. https://doi.org/10.1182/blood-2017-02-768234

Genomic analysis of 220 CTCLs identifies a novel recurrent gain-of-function alteration in RLTPR (p.Q575E). / Park, Joonhee; Yang, Jingyi; Wenzel, Alexander T.; Ramachandran, Akshaya; Lee, Wung J.; Daniels, Jay C.; Kim, Juhyun; Martinez-Escala, Estela; Amankulor, Nduka; Pro, Barbara; Guitart, Joan; Mendillo, Marc Laurence; Savas, Jeffrey Nicholas; Boggon, Titus J.; Choi, Jaehyuk.

In: Blood, Vol. 130, No. 12, 21.09.2017, p. 1430-1440.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Genomic analysis of 220 CTCLs identifies a novel recurrent gain-of-function alteration in RLTPR (p.Q575E)

AU - Park, Joonhee

AU - Yang, Jingyi

AU - Wenzel, Alexander T.

AU - Ramachandran, Akshaya

AU - Lee, Wung J.

AU - Daniels, Jay C.

AU - Kim, Juhyun

AU - Martinez-Escala, Estela

AU - Amankulor, Nduka

AU - Pro, Barbara

AU - Guitart, Joan

AU - Mendillo, Marc Laurence

AU - Savas, Jeffrey Nicholas

AU - Boggon, Titus J.

AU - Choi, Jaehyuk

PY - 2017/9/21

Y1 - 2017/9/21

N2 - Cutaneous T-cell lymphoma (CTCL) is an incurable non-Hodgkin lymphoma of the skin-homing T cell. In early-stage disease, lesions are limited to the skin, but in later-stage disease, the tumor cells can escape into the blood, the lymph nodes, and at times the visceral organs. To clarify the genomic basis of CTCL, we performed genomic analysis of 220 CTCLs. Our analyses identify 55 putative driver genes, including 17 genes not previously implicated in CTCL. These novel mutations are predicted to affect chromatin (BCOR, KDM6A, SMARCB1, TRRAP), immune surveillance (CD58, RFXAP), MAPK signaling (MAP2K1, NF1), NF-kB signaling (PRKCB, CSNK1A1), PI-3-kinase signaling (PIK3R1, VAV1), RHOA/cytoskeleton remodeling (ARHGEF3), RNA splicing (U2AF1), T-cell receptor signaling (PTPRN2, RLTPR), and T-cell differentiation (RARA). Our analyses identify recurrent mutations in 4 genes not previously identified in cancer. These include CK1a (encoded by CSNK1A1) (p.S27F; p.S27C), PTPRN2 (p.G526E), RARA (p.G303S), and RLTPR (p.Q575E). Last, we functionally validate CSNK1A1 and RLTPR as putative oncogenes. RLTPR encodes a recently described scaffolding protein in the T-cell receptor signaling pathway. We show that RLTPR (p.Q575E) increases binding of RLTPR to downstream components of the NF-kB signaling pathway, selectively upregulates the NF-kB pathway in activated T cells, and ultimately augments T-cell-receptor-dependent production of interleukin 2 by 34-fold. Collectively, our analysis provides novel insights into CTCL pathogenesis and elucidates the landscape of potentially targetable gene mutations.

AB - Cutaneous T-cell lymphoma (CTCL) is an incurable non-Hodgkin lymphoma of the skin-homing T cell. In early-stage disease, lesions are limited to the skin, but in later-stage disease, the tumor cells can escape into the blood, the lymph nodes, and at times the visceral organs. To clarify the genomic basis of CTCL, we performed genomic analysis of 220 CTCLs. Our analyses identify 55 putative driver genes, including 17 genes not previously implicated in CTCL. These novel mutations are predicted to affect chromatin (BCOR, KDM6A, SMARCB1, TRRAP), immune surveillance (CD58, RFXAP), MAPK signaling (MAP2K1, NF1), NF-kB signaling (PRKCB, CSNK1A1), PI-3-kinase signaling (PIK3R1, VAV1), RHOA/cytoskeleton remodeling (ARHGEF3), RNA splicing (U2AF1), T-cell receptor signaling (PTPRN2, RLTPR), and T-cell differentiation (RARA). Our analyses identify recurrent mutations in 4 genes not previously identified in cancer. These include CK1a (encoded by CSNK1A1) (p.S27F; p.S27C), PTPRN2 (p.G526E), RARA (p.G303S), and RLTPR (p.Q575E). Last, we functionally validate CSNK1A1 and RLTPR as putative oncogenes. RLTPR encodes a recently described scaffolding protein in the T-cell receptor signaling pathway. We show that RLTPR (p.Q575E) increases binding of RLTPR to downstream components of the NF-kB signaling pathway, selectively upregulates the NF-kB pathway in activated T cells, and ultimately augments T-cell-receptor-dependent production of interleukin 2 by 34-fold. Collectively, our analysis provides novel insights into CTCL pathogenesis and elucidates the landscape of potentially targetable gene mutations.

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Park J, Yang J, Wenzel AT, Ramachandran A, Lee WJ, Daniels JC et al. Genomic analysis of 220 CTCLs identifies a novel recurrent gain-of-function alteration in RLTPR (p.Q575E). Blood. 2017 Sep 21;130(12):1430-1440. https://doi.org/10.1182/blood-2017-02-768234