Oncoscience

Next generation sequencing of carcinoma of unknown primary reveals novel combinatorial strategies in a heterogeneous mutational landscape

Ishwaria M. Subbiah1, Apostolia Tsimberidou2, Vivek Subbiah2, Filip Janku2, Sinchita Roy-Chowdhuri3 and David S. Hong2

1Department of Palliative, Rehabilitation, and Integrative Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA

2Department of Investigational Cancer Therapeutics, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA

3Department of Pathology, all at the University of Texas MD Anderson Cancer Center, Houston, TX, USA

Correspondence to:

David S. Hong, email: dshong@mdanderson.org

Keywords: carcinoma of unknown primary, next generation sequencing

Received: March 24, 2017    Accepted: May 02, 2017    Published: June 23, 2017

ABSTRACT

Background: Advanced carcinoma of unknown primary (CUP) has limited effective therapeutic options given the phenotypic and genotypic diversity. To identify future novel therapeutic strategies we conducted an exploratory analysis of next-generation sequencing (NGS) of relapsed, refractory CUP.

Methods: We identified patients in our phase I clinic where archival tissue was available for a targeted NGS CLIA-certified assay.

Results: Of 17 patients tested, 15 (88%) demonstrated genomic alterations (median 2 aberrations; range 0–8, total 59 alterations). Nine (53%) patients had altered cell signaling including the PI3K/AKT/MTOR (n=5, 29%) and MAPK pathways (n=3,18%); 7 (41%) patients demonstrated ≥1 alterations in tumor suppressor genes (TP53 in 5 patients), 8 (47%) had impaired epigenetic regulation and DNA methylation, 8 (47%) had aberrant cell cycle regulation, commonly in the cyclin dependent kinases. Ten (59%) patients had alterations in transcriptional regulators. Concurrent mutations affecting cell cycle regulation were noted to occur with aberrant epigenetic regulation (n=6, 35%) and MAPK/PI3K pathway (n=5, 29%).

Conclusion: Every patient had a unique molecular profile with no two patients demonstrating an identical panel of mutations. We identify two emerging novel combinatorial strategies targeting impaired cell cycle arrest, first with epigenetic modifiers and, second, with MAPK/PI3K pathway inhibition.


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