John A. Pulikkan, PhD

Chromatin dynamics and gene regulation in normal and malignant hematopoiesis

Acute myeloid leukemia (AML) and several hematological malignancies arise from acquisition of multiple stepwise genetic and epigenetic changes in hematopoietic stem and progenitor cells. Understanding the regulatory pathways that are deregulated in hematopoietic stem and progenitor cells is important to better understand the development of leukemia and to design novel therapeutic strategies for the treatment of leukemia. With that broad focus in mind, our lab applies genetic, epigenetic and biochemical approaches in genetically modified mouse models, humanized mouse models and human primary leukemic cells. Our research focuses on three areas:

1. Interplay between transcription factors and chromatin dynamics in normal and malignant hematopoietic stem cells (HSC)

The development of chromosome conformation capture technology has revolutionized our understanding of long-range enhancer-promoter interactions and how these interactions are deregulated in multiple diseases. However, our understanding of chromatin structure and how transcription factors regulate higher-order genome architecture is limited. We are exploring the mechanisms by which transcription factors regulate chromatin dynamics in normal and malignant HSCs, and the implications of chromosomal rearrangements observed in hematological malignancies in topologically associated domains (TAD) architecture and gene expression.

2. Transcriptional deregulation in AML

Mutations in transcription factors have long been shown to be central in tumorigenesis. Our lab is interested in understanding transcriptional regulation of myeloid differentiation and how this is altered in AML. In particular, we are studying deregulation of transcription factors C/EBPα and core-binding factors, CBFs (consisting of RUNX and CBFβ proteins) in AML. We are investigating the preleukemic molecular events in AML with CEBPA mutations and chromosomally rearranged RUNX1/ CBFβ.

3. Non-coding RNA function in hematopoiesis and leukemia

While around 76% of the human genome is transcribed into RNA, only 2% of the genome is translated to proteins. Recent findings in RNA biology made a paradigm shift in our understanding of RNA function beyond acting as templates for protein synthesis. An emerging theme in gene regulation is the central role played by long non-coding RNAs (lncRNAs). We are interested in understanding the functional relevance of deregulated lncRNAs in AML with altered CBF and C/EBPα activity and the therapeutic relevance of targeting lncRNAs in AML treatment.

SMARCA4 as a novel target in Acute Myeloid Leukemia with CEBPA mutations
Source: American Cancer Society – Institutional Research Grant (MCW Cancer Center) 
Role: Principle Investigator 
Dates: 07/01/2021 Ongoing

Philomina Sona Peramangalam
Research Technologist

Sridevi Surapally
Postdoctoral Fellow

1. Surapally S, Tenen DG, Pulikkan JA. Emerging therapies for inv(16) AML. Blood. 2021 May 13;137(19):2579-2584
2. Van der Kouwe E*, Heller G*, Czibere A*, Pulikkan JA*, Agreiter C, Castilla LH, Delwel R, Di Ruscio A, Ebralidze AK, Forte M, Grebien F, Heyes E, Kazianka L, Klinger J, Kornauth C, Le T, Lind K, Barbosa IAM, Pemovska T, Pichler AS, Schmolke AS, Schweicker CM, Sill H, Sperr WR, Spittler A, Surapally S, Trinh BQ, Valent P, Vanura K, Welner RS, Zuber J, Tenen DG, Staber PB. Core binding factor leukemia hijacks T-cell prone PU.1 antisense promoter. Blood. 2021 May 19 (*Co-first author)
3. Heimbruch KE, Fisher JB, Stelloh CT, Phillips E, Reimer MH Jr, Wargolet AJ, Meyer AE, Pulakanti K, Viny AD, Loppnow JJ, Levine RL, Pulikkan JA, Zhu N, Rao S. DOT1L inhibitors block abnormal self-renewal induced by cohesin loss. Sci Rep. 2021 Mar 31;11(1):7288
4. Pulikkan JA, Hegde M, Ahmed H, Belaghzal H, Illendula A, Yu J, O’Hagen K, Ou J, Muller-Tidow C, Wolfe SA, Zhu LJ, Dekker J, Bushweller JH, Castilla LH. CBFβ-SMMHC inhibition triggers apoptosis by disrupting MYC chromatin dynamics in acute myeloid leukemia. Cell 2018 Jun 28;174(1):172-186.
5. Pulikkan JA and Castilla LH. Pre-leukemia in inv(16) acute myeloid leukemia development. Frontiers in Oncology 2018 Apr  26: 8(129): 1-7.
6. Pulikkan JA^†, Tenen DG^†, Behre G^†. C/EBPα deregulation as a paradigm for leukemogenesis. Leukemia 2017 Nov;31(11):2279-2285. (^†Corresponding author)
7. Illendula A*, Pulikkan JA*, Zong H, Grembecka J, Xue L, Sen S, Zhou Y, Boulton A, Kuntimaddi A, Gao Y, Rajewski RA, Guzman ML, Castilla LH^†, Bushweller JH^†. A small-molecule inhibitor of the aberrant transcription factor CBFβ-SMMHC delays leukemia in mice. Science 2015 Feb 13;347(6223):779-84. (*Co-first author) (^†Corresponding author).
8. Pulikkan JA*, Madera D*, Xue L, Bradley P, Landrette SF, Kuo YH, Abbas S, Zhu LJ, Valk P, Castilla LH. Thrombopoietin/MPL participates in initiating and maintaining RUNX1-ETO acute myeloid leukemia via PI3K/AKT signaling. Blood 2012 Jul 26;120(4):868-79
9. Pulikkan JA, Peramangalam PS, Dengler V, Müller-Tidow C, Bohlander SK, Preudhomme C, Tenen DG, Behre G. C/EBPα regulated microRNA-34a targets E2F3 during granulopoiesis and is downregulated in AML with CEBPA mutations. Blood 2010 Dec 16;116(25):5638-49.
10. Pulikkan JA, Dengler V, Peer Zada AA, Kawasaki A, Geletu MH, Pasalic Z, Bohlander SK, Ryo A, Tenen DG, Behre G. Elevated PIN1 expression by C/EBPα-p30 blocks C/EBPα induced granulocytic differentiation via c-Jun in AML. Leukemia 2010 May;24(5):914-23.
11. Pulikkan JA*, Dengler  V*, Peramangalam PS, Peer Zada AA, Müller-Tidow C, Bohlander SK, Tenen DG, Behre G. Cell cycle regulator E2F1 and microRNA-223 comprise an autoregulatory negative feedback loop in acute myeloid leukemia. Blood 2010 Mar 4;115(9):1768-78.