Arnes Group: Pancreas development and pancreatic cancer

Our aim is to understand the molecular regulation of cellular identity in pancreas development and cancer and translate this knowledge into better diagnosis and treatment of pancreatic ductal adenocarcinoma. 

Cancer is a disease of differentiation, and molecular regulators of cellular identity are potent tumor suppressors in pancreatic cancer. We are interested in understanding how long non-coding RNAs interact with transcription factors and chromatin modifiers to regulate gene expression and cellular plasticity in development and disease. We are particularly interested in long non-coding RNAs located in the genomic vicinity of lineage-specific transcription factors that we and others defined as positionally-conserved lncRNAs. We employ a multidisciplinary approach using techniques in molecular biology, high throughput screening, systems biology and laboratory models of pancreas development and pancreatic cancer. These studies are intended to discover novel molecular markers of tumor progression and targetable molecular mediators of cellular identity to prevent the initiation and progression of pancreatic cancer.

Ongoing Projects

Pancreatic ductal adenocarcinoma (PDAC) is a particularly lethal form of cancer due to the lack of effective screening tests and resistance to conventional anti-tumor therapies; more than 80% of patients have untreatable disease by the time of diagnosis. Although the molecular characterization of pancreatic tumors has provided important clues about causative genetic abnormalities and disease progression, advances in diagnostics and treatments remain elusive. Recently, long non-coding RNAs (lncRNAs) have been identified as a new class of RNA transcripts deregulated in cancer and associated with malignancy progression; however, very little is known in the context of pancreatic cancer. In my postdoctoral work, in collaboration with the laboratory of Dr. Raul Rabadan and Dr. Ken Olive at Columbia University, we developed a computational resource (NORI: NOn-coding Rna Identification) to annotate the non-coding transcriptome of pancreatic cancer, which has laid the foundation for three main lines of investigation on lncRNAs in pancreatic cancer:

Identifying molecular determinants of cellular identity in PDAC. Cancer is intimately linked to cellular differentiation; indeed, loss of differentiation is one of the cardinal features of the disease, both at the point of initiation and during tumor progression through the process of epithelial-to-mesenchymal transition. We have determined that lncRNAs segregate tumor samples into subgroups distinguished by differentiation status and associated with clinical prognosis. Furthermore, we have shown that lncRNAs are not just readouts of cellular differentiation but rather active modulators of cellular states. We are using mouse genetics, high throughput screening and molecular biology to identify key non-coding determinants of cellular identity necessary for the progression of pancreatic cancer.

LncRNA mode of action. Here, we are interested in the characterization of a novel layer of gene regulation mediated by positionally-conserved lncRNAs. Our data indicate that positionally-conserved lncRNAs are molecular “tools” that the associated transcription factor utilize to remodel the transcriptional and epigenetic landscape during pancreas development and tumor progression. We use genome editing (CRISPR-Cas9), unbiased mass-spectrophotometry protein analysis and systems biology to define lncRNAs mode of action. These studies are performed in experimental models of pancreatic cancer and pancreas development (differentiation of human embryonic stem cells and mouse models). We expect to uncover a cell-type specific role of positionally-conserved lncRNAs in the local regulation of chromatin conformation, recruitment of chromatin modifiers and/or scaffolds of regulatory proteins. This information will aid in the design of therapeutic targets to modulate the plasticity of the pancreatic epithelium and prevent pancreatic tumor progression.

Exploring the therapeutic potential of lncRNAs on pre-clinical models. The ability to provide effective therapies to treat patients with pancreatic cancer relies on the capacity to identify the tumor at the early stages of development and/or identification of tumor-specific targets.

LncRNAs as biomarkers detectable in circulating fluids. Circulating free nucleic acids (cfNA) from primary solid tumors can be detected in plasma, and although its translation to the clinic is still on its early days, the results are very promising. These cfNA originate from exosome secretion, apoptosis of the tumor cells or circulating tumor cells. LncRNAs are among the species of cfNA that has been identified in circulating fluids from patients of pancreatic cancer, and circulating pancreatic tumor cells have been identified in a murine model of PDAC even before the development of frank carcinoma. We have determined that lncRNAs associated with PDAC are tumor-specific compared to an array of normal tissues (GTEX portal), making lncRNAs ideal biomarkers. We apply NORI to identify lncRNAs from the stroma and epithelium of low- grade neoplastic lesions and primary carcinoma to generate a catalogue of compartment- and stage-specific lncRNAs in PDAC. We are assessing the translational potential of lncRNAs that being expressed in PDAC can also be detected in blood from GEMMs and/or PDXs of pancreatic cancer.

RNA-based therapeutics in preclinical models of PDAC. Most of the work on tumor progression has been focused on identifying driver somatic mutations. It is becoming evident that non-genetic events, such us epigenetics and transcriptome reprogramming, play significant roles in tumor progression and resistance to therapies. We have shown that lncRNAs are expressed specifically in PDAC and that lncRNAs regulate the proliferation of pancreatic cancer cells, making lncRNAs ideal targets of PDAC. We are designing antisense oligonucleotides targeting PDAC-associated lncRNAs in mouse models of PDAC and PDXs derived from tumor samples. We anticipate that the collection of PDAC-associated lncRNAs will aid in the design of targeted therapies and may contribute to the development of improved diagnostic tools for PDAC. The recent clinical approval of antisense therapy for human disease provides a viable, practical approach for leveraging this new understanding of cancer biology.

Selected Publications

Arnes, L.*#, Liu, Z.#, Wang, J.#, Carlo Maurer, H., Sagalovskiy, I., Sanchez-Martin, M., Bommakanti, N., Garofalo, D. C., Balderes, D. B., Sussel, L., Olive, K. P.*, Rabadan, R*. (2018). Comprehensive characterisation of compartment-specific long non-coding RNAs associated with pancreatic ductal adenocarcinoma. Gut. doi:10.1136/gutjnl-2017-314353. *joint senior author #joint first author

Arnes, L., Akerman, I., Balderes, D. A., Ferrer, J., & Sussel, L. (2016). betalinc1 encodes a long noncoding RNA that regulates islet beta-cell formation and function. Genes Dev, 30(5), 502-507. doi:10.1101/gad.273821.115

Arnes, L., & Sussel, L. (2015). Epigenetic modifications and long noncoding RNAs influence pancreas development and function. Trends Genet, 31(6), 290-299. doi:10.1016/j.tig.2015.02.008

Arnes, L., Hill, J. T., Gross, S., Magnuson, M. A., & Sussel, L. (2012). Ghrelin expression in the mouse pancreas defines a unique multipotent progenitor population. PLoS One, 7(12), e52026. doi:10.1371/journal.pone.0052026

Arnes, L., Leclerc, K., Friel, J. M., Hipkens, S. B., Magnuson, M. A., & Sussel, L. (2012). Generation of Nkx2.2:lacZ mice using recombination-mediated cassette exchange technology. Genesis, 50(8), 612-624. doi:10.1002/dvg.22037