Kidney angiomyolipomas are defined by a unique transcriptomic profile and H3K27ac chromatin state

Krinio Giannikou, BSc, MSc, PhD
Department of Medicine
Division of Pulmonary and Critical Care Medicine
Poster Overview

Renal angiomyolipomas are a common kidney tumor in subjects affected with Tuberous Sclerosis Complex (TSC), being seen in up of 80% of those of age >12 years. We have learned a great deal about both the molecular basis and clinical aspects of this rare tumor. However, the role of other driver events beyond genetic alterations in TSC2 or TSC1 gene in angiomyolipoma development are unknown. Epigenetics is the study of the organization of the genome, and how it affects gene expression. Nothing is known regarding the epigenetic changes for this tumor.

We applied cutting-edge approaches including RNA-Seq and ChIP-Seq to study angiomyolipomas (n=30) in an unbiased genome-wide manner. We discovered that angiomyolipomas have a unique pattern of gene expression, different from all known cancers and normal tissues. We found that organization of the genome is distinct in angiomyolipoma compared to multiple normal tissues and that epigenetic alterations in chromatin state influence gene transcription, likely contributing to tumor pathogenesis. Particularly, we found several genes (e.g. MITF) whose expression is critical for angiomyolipoma growth and can become appropriate targets for therapies. Our data provide a deeper understanding of angiomyolipoma development and have the potential to identify novel and more efficient therapeutic interventions.

Scientific Abstract

Kidney angiomyolipomas (AML) are mesenchymal tumors, commonly seen in Tuberous Sclerosis Complex (TSC) and are known to be due to biallelic TSC1/TSC2 loss. We hypothesized that epigenetic events may also drive to AML tumor growth. We performed whole transcriptome RNA-sequencing on 28 angiomyolipomas and ChIP-seq for H3K27ac (a histone modification that marks open chromatin) on 25 angiomyolipomas as well as the human angiomyolipoma derived 621-101 and SK-MEL30 melanoma cell line. MITF (a known driver oncogene in melanoma and other cancers) ChIP-Seq was also performed on 3 angiomyolipomas.

RNA-sequencing analysis revealed a unique gene expression pattern of 347 differentially expressed genes for angiomyolipomas compared to all The Cancer Genome Atlas (TCGA) cancers and multiple normal tissues. H3K27ac ChIP-seq analysis identified a set of tissue-specific regulatory regions known as super-enhancers compared to Roadmap Epigenomics Project dataset. These highly expressed and H3K27ac marked genes include several transcription factors(TFs) (e.g. MITF-A, PPRAG, NR2F2, MEIS2) with pivotal roles in cell growth/proliferation. Functional studies confirmed the oncogenic role of MITF in vitro and in vivo. Also, immunohistochemistry confirmed this specificity in AML sections. Our studies have identified unique chromatin signatures, and several highly-expressed TFs, which likely are essential for angiomyolipoma development, enabling potential novel treatment strategies.

Clinical Implications
Our studies have identified unique epigenetic signatures, and several highly-expressed transcription factors/other genes, including MITF whose expression is critical for angiomyolipoma development. Our results have the potential to identify novel more effective therapeutic targets beyond the current mTORC1 inhibitors/rapalogs.
Research Areas
Authors
Krinio Giannikou, Clemens Probst, Mahsa Zarei, Xintao Qiu, Melissa Duarte, Nikolas Kesten, Zach Hebert, Raga Vadhi, Alba Font-Tello, Paloma Cejas, Charles H. Yoon, Chin-Lee Wu, Myles Brown, Elizabeth Henske, Henry Long, David J. Kwiatkowski
Principal Investigator
David J. Kwiatkowski

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