Therapeutic targeting of TFE3/IRS-1/PI3K/mTOR axis in translocation renal cell carcinoma

Nur P. Damayanti, Justin A. Budka, Heba W.Z. Khella, Mary W. Ferris, Sheng Yu Ku, Eric Kauffman, Anthony C. Wood, Khunsha Ahmed, Venkata Nithinsai Chintala, Remi Adelaiye-Ogala, May Elbanna, Ashley Orillion, Sreenivasulu Chintala, Chinghai Kao, W. Marston Linehan, George M. Yousef, Peter Hollenhorst, Roberto Pili

Research output: Contribution to journalArticle

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Abstract

Purpose: Translocation renal cell carcinoma (tRCC) represents a rare subtype of kidney cancer associated with various TFE3, TFEB, or MITF gene fusions that are not responsive to standard treatments for RCC. Therefore, the identification of new therapeutic targets represents an unmet need for this disease. Experimental Design: We have established and characterized a tRCC patient-derived xenograft, RP-R07, as a novel preclinical model for drug development by using next-generation sequencing and bioinformatics analysis. We then assessed the therapeutic potential of inhibiting the identified pathway using in vitro and in vivo models. Results: The presence of a SFPQ-TFE3 fusion [t(X;1) (p11.2; p34)] with chromosomal break-points was identified by RNA-seq and validated by RT-PCR. TFE3 chromatin immunoprecipitation followed by deep sequencing analysis indicated a strong enrichment for the PI3K/AKT/mTOR pathway. Consistently, miRNA microarray analysis also identified PI3K/AKT/mTOR as a highly enriched pathway in RP-R07. Upregulation of PI3/AKT/mTOR pathway in additional TFE3–tRCC models was confirmed by significantly higher expression of phospho-S6 (P < 0.0001) and phospho-4EBP1 (P < 0.0001) in established tRCC cell lines compared with clear cell RCC cells. Simultaneous vertical targeting of both PI3K/AKT and mTOR axis provided a greater antiproliferative effect both in vitro (P < 0.0001) and in vivo (P < 0.01) compared with single-node inhibition. Knockdown of TFE3 in RP-R07 resulted in decreased expression of IRS-1 and inhibited cell proliferation. Conclusions: These results identify TFE3/IRS-1/PI3K/AKT/ mTOR as a potential dysregulated pathway in TFE3–tRCC, and suggest a therapeutic potential of vertical inhibition of this axis by using a dual PI3K/mTOR inhibitor for patients with TFE3–tRCC.

Original languageEnglish (US)
Pages (from-to)5977-5989
Number of pages13
JournalClinical Cancer Research
Volume24
Issue number23
DOIs
StatePublished - Dec 1 2018

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Phosphatidylinositol 3-Kinases
Renal Cell Carcinoma
Therapeutics
S 6
High-Throughput Nucleotide Sequencing
Chromosome Breakage
Kidney Neoplasms
Chromatin Immunoprecipitation
Gene Fusion
Microarray Analysis
Computational Biology
MicroRNAs
Heterografts
Research Design
Up-Regulation
Cell Proliferation
RNA
Cell Line
Polymerase Chain Reaction
Pharmaceutical Preparations

ASJC Scopus subject areas

  • Oncology
  • Cancer Research

Cite this

Damayanti, N. P., Budka, J. A., Khella, H. W. Z., Ferris, M. W., Ku, S. Y., Kauffman, E., ... Pili, R. (2018). Therapeutic targeting of TFE3/IRS-1/PI3K/mTOR axis in translocation renal cell carcinoma. Clinical Cancer Research, 24(23), 5977-5989. https://doi.org/10.1158/1078-0432.CCR-18-0269

Therapeutic targeting of TFE3/IRS-1/PI3K/mTOR axis in translocation renal cell carcinoma. / Damayanti, Nur P.; Budka, Justin A.; Khella, Heba W.Z.; Ferris, Mary W.; Ku, Sheng Yu; Kauffman, Eric; Wood, Anthony C.; Ahmed, Khunsha; Chintala, Venkata Nithinsai; Adelaiye-Ogala, Remi; Elbanna, May; Orillion, Ashley; Chintala, Sreenivasulu; Kao, Chinghai; Marston Linehan, W.; Yousef, George M.; Hollenhorst, Peter; Pili, Roberto.

In: Clinical Cancer Research, Vol. 24, No. 23, 01.12.2018, p. 5977-5989.

Research output: Contribution to journalArticle

Damayanti, NP, Budka, JA, Khella, HWZ, Ferris, MW, Ku, SY, Kauffman, E, Wood, AC, Ahmed, K, Chintala, VN, Adelaiye-Ogala, R, Elbanna, M, Orillion, A, Chintala, S, Kao, C, Marston Linehan, W, Yousef, GM, Hollenhorst, P & Pili, R 2018, 'Therapeutic targeting of TFE3/IRS-1/PI3K/mTOR axis in translocation renal cell carcinoma', Clinical Cancer Research, vol. 24, no. 23, pp. 5977-5989. https://doi.org/10.1158/1078-0432.CCR-18-0269
Damayanti NP, Budka JA, Khella HWZ, Ferris MW, Ku SY, Kauffman E et al. Therapeutic targeting of TFE3/IRS-1/PI3K/mTOR axis in translocation renal cell carcinoma. Clinical Cancer Research. 2018 Dec 1;24(23):5977-5989. https://doi.org/10.1158/1078-0432.CCR-18-0269
Damayanti, Nur P. ; Budka, Justin A. ; Khella, Heba W.Z. ; Ferris, Mary W. ; Ku, Sheng Yu ; Kauffman, Eric ; Wood, Anthony C. ; Ahmed, Khunsha ; Chintala, Venkata Nithinsai ; Adelaiye-Ogala, Remi ; Elbanna, May ; Orillion, Ashley ; Chintala, Sreenivasulu ; Kao, Chinghai ; Marston Linehan, W. ; Yousef, George M. ; Hollenhorst, Peter ; Pili, Roberto. / Therapeutic targeting of TFE3/IRS-1/PI3K/mTOR axis in translocation renal cell carcinoma. In: Clinical Cancer Research. 2018 ; Vol. 24, No. 23. pp. 5977-5989.
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T1 - Therapeutic targeting of TFE3/IRS-1/PI3K/mTOR axis in translocation renal cell carcinoma

AU - Damayanti, Nur P.

AU - Budka, Justin A.

AU - Khella, Heba W.Z.

AU - Ferris, Mary W.

AU - Ku, Sheng Yu

AU - Kauffman, Eric

AU - Wood, Anthony C.

AU - Ahmed, Khunsha

AU - Chintala, Venkata Nithinsai

AU - Adelaiye-Ogala, Remi

AU - Elbanna, May

AU - Orillion, Ashley

AU - Chintala, Sreenivasulu

AU - Kao, Chinghai

AU - Marston Linehan, W.

AU - Yousef, George M.

AU - Hollenhorst, Peter

AU - Pili, Roberto

PY - 2018/12/1

Y1 - 2018/12/1

N2 - Purpose: Translocation renal cell carcinoma (tRCC) represents a rare subtype of kidney cancer associated with various TFE3, TFEB, or MITF gene fusions that are not responsive to standard treatments for RCC. Therefore, the identification of new therapeutic targets represents an unmet need for this disease. Experimental Design: We have established and characterized a tRCC patient-derived xenograft, RP-R07, as a novel preclinical model for drug development by using next-generation sequencing and bioinformatics analysis. We then assessed the therapeutic potential of inhibiting the identified pathway using in vitro and in vivo models. Results: The presence of a SFPQ-TFE3 fusion [t(X;1) (p11.2; p34)] with chromosomal break-points was identified by RNA-seq and validated by RT-PCR. TFE3 chromatin immunoprecipitation followed by deep sequencing analysis indicated a strong enrichment for the PI3K/AKT/mTOR pathway. Consistently, miRNA microarray analysis also identified PI3K/AKT/mTOR as a highly enriched pathway in RP-R07. Upregulation of PI3/AKT/mTOR pathway in additional TFE3–tRCC models was confirmed by significantly higher expression of phospho-S6 (P < 0.0001) and phospho-4EBP1 (P < 0.0001) in established tRCC cell lines compared with clear cell RCC cells. Simultaneous vertical targeting of both PI3K/AKT and mTOR axis provided a greater antiproliferative effect both in vitro (P < 0.0001) and in vivo (P < 0.01) compared with single-node inhibition. Knockdown of TFE3 in RP-R07 resulted in decreased expression of IRS-1 and inhibited cell proliferation. Conclusions: These results identify TFE3/IRS-1/PI3K/AKT/ mTOR as a potential dysregulated pathway in TFE3–tRCC, and suggest a therapeutic potential of vertical inhibition of this axis by using a dual PI3K/mTOR inhibitor for patients with TFE3–tRCC.

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