Immunology Faculty Member - Carl Novina, MD, PhD

Carl Novina, MD, PhD

Dana Farber Cancer Institute
Dana Building, Room 1420B
450 Brookline Avenue
Boston, MA 02115
Tel: 617-582-7961
Fax: 617-582-7962
Email: carl_novina@dfci.harvard.edu
Visit my lab page here.



The Novina Lab studies the fundamental biology of microRNAs and their dysregulation in disease. We used a reverse genetic screen to identify effectors and regulators of microRNA activity. Surprisingly, we found that reduced expression of ribosomal protein genes selectively increased translation of microRNA-targeted mRNAs by a mechanism involving the p53 pathway (Janas 2012). Our data suggest that RPGs as a class globally regulated microRNA-mediated repression of translation initiation.

A rare group of genetic diseases called ribosomopathies is characterized by reduced ribosome biogenesis and function. Clinically, these patients present with bone marrow failure (lineage-specific aplasias and pan-anemias) and congenital anomalies, and are at increased risk for cancer. It has been a long-standing mystery why these patients present with this constellation of clinical findings. Because microRNAs frequently target body patterning genes, differentiation and developmental genes and oncogenes, we may have identified the molecular pathogenesis of ribosomopathies.

We are currently using single cell RNA-seq of Diamond Blackfan Anemia (DBA) and Shwachman Diamond Syndrome (SDS) patient bone marrows to comprehensively characterize the affected cells and genetic networks that underlie bone marrow failure in these diseases. Projects are available to define disease-promoting DBA and SDS transcriptomes and translatomes using human patient samples, iPS derived from DBA and SDS patients, and mouse models of these diseases.

In another line of investigation, we are studying how microRNA expression is controlled in normal and disease contexts. Many microRNAs demonstrate altered epigenetic marks such as aberrant promoter hypo- and hyper-methylation in cancers. To study the causes and consequences of inappropriate DNA methylation of microRNA and other disease-causing genes, my lab is developing “epigenetic engineering” tools that will enable site-specific addition and removal of methyl groups on DNA.

To accomplish this, we turned to another RNA-directed process, the Cas9-CRISPR system. There are two key components to this system which can be leveraged for epigenetic reprogramming: (1) the Cas9 protein is directed to specific DNA sequences by a complementary guide RNA (gRNA). Introducing multiple gRNAs can direct Cas9 to multiple sites within a promoter or to multiple different promoters simultaneously. (2) Cas9 is normally an endonuclease that cleaves foreign DNA; however, an endonuclease-deficient Cas9 (dCas9) mutant allows localization without cleavage. To methylate or demethylate DNA at precise sites in the genome, we have fused methyltransferases (MTases) or demethylases to dCas9. To avoid deleterious off-target methylation or demethylation, we took a “split-fusion” approach in which the enzyme is split into two inactive halves that only regain functionality when co-recruited to a particular site.

Precise control over DNA methylation will enable specific reprogramming of cell fates for experimental and therapeutic purposes. A major new initiative in my lab is using Cas9-MTases that target genes which repress immune responses. Our goal is to silence repressive protein-coding and non-coding genes to improve the efficacy of T cell-based cancer immunotherapy. I believe that a robust platform for epigenetic engineering will enable novel therapies against cancer, ribosomopathies and other diseases.



Last Update: 10/8/2014



Publications

 

Akt-mediated phosphorylation of argonaute2 downregulates cleavage and upregulates translational repression of microRNA targets. Horman SR, Janas MM, Litterst C, Wang B, MacRae IJ, Sever MJ, Morrissey DV, Graves P, Luo B, Umesalma S, Qi HH, Miraglia LJ, Novina CD, Orth AP. Mol. Cell. 2013; 50: 356-367.

Reduced expression of ribosomal proteins relieves microRNA-mediated repression. Janas MM, Wang E, Love T, Harris AS, Stevenson K, Semmelmann K, Shaffer JM, Chen P-H, Doench JG, Yerramilli SVBK, Neuberg DS, Iliopoulos D, Housman DE, Burge CB, and Novina CD. Mol Cell. 2012; 46: 171-186.

Alternative RISC assembly: binding and repression of microRNA-mRNA duplexes by human Ago proteins. Janas, MM, Wang B, Harris AS, Aguiar M, Shaffer J.M, Yerramilli SVBK, Behlke MA, Wucherpfennig KW, Gygi SP, Gagnon E, and Novina CD. RNA, 2012; 18(11): 2041-2055.

Feed-forward microprocessing and splicing activities at a microRNA-containing intron. Janas MM, Khaled M, Schubert S, Bernstein JG, Golan D, Veguilla RA, Fisher DE, Shomron N, Levy C, and Novina CD. PLoS Genet. 2011. (7)10:e1002330.

microRNA expression profiling identifies activated B cell status in chronic lymphocytic leukemia cells. Li S, Moffett HF, Lu J, Werner L, Zhang H, Ritz J, Neuberg D, Wucherpfennig KW, Brown JR, Novina CD. PLoS ONE. 2011. 2011; Mar 8;6(3):e16956.

Repression of tumor suppressor miR-451 is essential for NOTCH1-induced oncogenesis in T-ALL.
Li X, Sanda T, Look AT, Novina CD, von Boehmer H.
J. Exp. Med. 2011. 208(4):663-75.

Intronic miR-211 assumes the tumor suppressive function of its host gene in melanoma.
Levy C, Khaled M, Iliopoulos D, Janas M, Schubert S, Pinner S, Chen P-H, Li S, Fletcher A, Yokoyama S, Scott KL, Garraway LA, Song JS, Granter SR, Turley SJ, Fisher DE, and Novina CD.
Mol. Cell. 2010. 40(5):841-9.



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