I am interested in the establishment and maintenance of cellular identity. These processes depend on correctly controlled access to biologic information by creating, remodeling or removing genetic and epigenetic barriers that modulate access to the information stored in the DNA sequence. A deep understanding of how these mechanisms regulate development and terminal differentiation are essential in order to understand diseases such as cancer and natural processes such as aging and for the development of treatments for many of the health issues impacting modern society.

We are using the recent development of in vitro cellular reprogramming (iPSC) and differentiation of these cells into hepatocytes (iHeps) to facilitate liver repair via cellular transplantation. Both of these processes are heavily dependent on modulation of genetic and epigenetic mechanisms that control access to information in the DNA sequence. Our three main focuses are 1. The development of a clinically safe and feasible reprogramming system suitable for large-scale clinical applications. 2. The development of a clinically safe and feasible hepatocyte differentiation system suitable for large-scale clinical applications. 3. The development of a clinically relevant cellular transplantation regimen that allows efficient re-population of a host liver using targeted radiation therapy.

A practical system of quickly and safely generating patient derived iPSCs in the clinic coupled with in vitro differentiation of these cells into specific cells and tissues is needed in order for this to become a real treatment option and not only a research tool.

Kelly Stanton, Fabio Parisi, Francesco Strino, Neta Rabin, Patrik Asp and Yuval Kluger. Arpeggio: harmonic compression of ChIP-seq data reveals protein-chromatin interaction signatures. Nucleic Acids Research 2013, Sept 1;41:e161 

Patrice Nancy, Elisa Tagliani, Chin-Siean Tay, Patrik Asp, David E. Levy and Adrian Erlebacher. Chemokine gene silencing in decidual stromal cells limits T cell access to the maternal-fetal interface. Science 2012, Jun 8;336(6086): 1317-21.

Micsinai, Mariann; Parisi, Fabio; Strino, Francesco; Asp, Patrik; Dynlacht, Brian; Kluger, Yuval. Picking ChIP-Seq Peak Detectors for Analyzing Chromatin Modification Experiments. Nucleic Acids Res 2012, May;40(9): e70.

Panagiotis Ntziachristos, Aristotelis Tsirigos, Pieter Van Vlierberghe, Jelena Nedjic, Thomas Trimarchi, Maria Sol Flaherty, Dolors Ferres-Marco, Vanina da Ros, Zuojian Tang, Jasmin Siegle, Patrik Asp, Michael Hadler, Isaura Rigo, Kim De Keersmaecker, Jay Patel, Tien Huynh, Filippo Utro, Sandrine Poglio, Jeremy B Samon, Elisabeth Paietta, Janis Racevskis, Jacob M Rowe, Raul Rabadan, Ross L Levine, Stuart Brown, Francoise Pflumio, Maria Dominguez, Adolfo Ferrando & Iannis Aifantis. Genetic inactivation of the polycomb repressive complex 2 in T cell acute lymphoblastic leukemia. Nat Med 2012, Feb 6 ;18(2):298-301.

Asp P, Blum R, Vethantham V, Parisi F, Micsiani M, Cheng J, Bowman C, Kluger Y, Dynlacht BD. Genome-wide remodeling of the epigenetic landscape during myogenic differentiation. Proc Natl Acad Sci U S A, 2011 108(22): E149-158.

Patrik Asp, Diego Acosta-Alvear, Mary Tsikitis, Chris van Oevelen and Brian David Dynlacht (2009) E2f3b plays an essential role in myogenic differentiation through isoform specific gene regulation. Genes Dev 2009. 23:37-53.

Van Oevelen C, Wang J, Asp P, Yan Q, Kaelin WG Jr, Kluger Y, Dynlacht BD. (2008) A role for mammalian Sin3 in permanent gene silencing. Mol Cell. 2008 Nov 7;32 (3):359-70.

Erica Cavellán, Patrik Asp, Piergiorgio Percipalle and Ann-Kristin Östlund-Farrants (2006)The WSTF-SNF2h chromatin remodeling complex interacts with several nuclear proteins in transcription. J Biol Chem. 2006 Jun 16;281(24):16264-71.