Matthew Hirsch, PhD

Research Interests

The DNA packaging capacity of the Adeno-Associated Vectors (AAV) is relatively small, currently rendering it deficient for the treatment of diseases requiring large gene transfer (>4.7kb). To overcome this size limitation, we have developed a novel technique (OAGR) and characterized existing approaches that exploit host DNA repair pathways for intracellular large transgene reconstruction. During this work we have identified host DNA repair proteins and pathways necessary for episomal genetic engineering with the understanding that enhancements at the basic science level will aid in the generation of a safer and more efficient clinical reagent. Towards disease therapy, we have evaluated different AAV large gene delivery contexts in disease models of dysferlinopathy and hemophilia A.

Our lab has also been focused on emerging technologies using DNA endonucleases to genetically engineer human and mouse chromosomes. These efforts use AAV vectors for gene delivery of both an endonuclease that creates a precise double-strand break that stimulates homologous recombination, and a DNA repair substrate containing the desired modification. Importantly, we have defined the role of duplexed AAV genomes to enhance the targeted repair process and were the first to engineer and validate a universal AAV context which allows the delivery of 2 zinc-finger nucleases, as well as a repair substrate, in a single AAV vector (in collaboration with Dr. M. Porteus). Additionally, we have demonstrated the stimulation of gene editing using FDA approved drugs while providing mechanistic insights into this process. Currently we are characterizing structured DNA elements, implicated in genome instability and cancer, as targets for genetic engineering.

Consistent with my interest in AAV-mediated gene delivery, the DNA damage response, and genetic engineering, we have also focused on the AAV vector transduction of different types of stem cells. Stems cell are known to be intolerant of DNA damage and often prefer apoptotic induction instead of cell cycle arrests. Initial interests in AAV-mediated gene delivery to human embryonic stem cells (hESCs) resulted in an AAV-induced DNA damage response culminating in apoptosis. A tedious evaluation of this phenomenon indicated that a sequence in the inverted terminal repeat of the AAV vector was acting like an uncapped telomere to induce apoptosis during S-phase. Interestingly, investigations since that time demonstrated that adult human cells that are considered multi-potent (hMAPCs), are efficiently and safely transduced by AAV vectors. The collective analyses demonstrate the burgeoning concept of “stemness” and suggests that AAV vector transduction may be used to distinguish different cell populations based on this attribute.

Publications

Hirsch ML, Li C, Bellon I, Yin C, Chavala S, Pryadkina M, Richard I, Samulski RJ. Oversized AAV Transduction is Mediated by Fragmented Genomes via a DNA-PKcs Independent, Rad51c-dependent Repair Pathway. Molecular Therapy. 2013 21(12):2205-16. PMID: 23939025. PMC3863795

Ellis B, Barker J, Hirsch ML, Connelly JP, Steininger RJ, Porteus MH. A Survey of ex vivoTransduction Efficiency of Mammalian Primary Cells and Cell Lines with Nine Natural (AAV1-9) and One Engineered AAV Serotype. Virology 2013 10:74. PMID: 23497173. PMC3607841.

Li C, He Y, Nicolson S, Hirsch ML, Weinberg M, Zhang P, Kafri T, and R.J. Samulski. AAV Capsid Antigen Presentation from Transduced Cells Is Dependent on Endosomal Escape but not AAV Nuclear Uncoating. JCI 2012 123(3):1390-401. PMID: 23454772. PMC3582142

Li C, Diprimio N, Bowles DE, Hirsch ML, Monahan PE, Asokan A, Rabinowitz J, Agbandje-McKenna M, Samulski RJ. Single Amino Acid Modification of Adeno-Associated Virus Capsid Changes Transduction and Humoral Immune Profiles. J Virol. 2012 6(15):7752-9.. PMID:2259315. PMC3421647

Ferreira JR, Hirsch ML, Zhang L, Park Y, Samulski RJ, Hu W, Ko C. Three-dimensional multipotent progenitor cell aggregates for the expansion, osteogenic differentiation and in vivo tracing with AAV vector 6. Gene Ther. 2012 20(2):158-68. PMID:22402320. PMC3374053

Ellis BL^Δ, Hirsch ML^Δ, Porter SN, Samulski RJ, Porteus MH. Zinc-finger nuclease-mediated gene correction using single AAV vector transduction and enhancement by Food and Drug Administration-approved drugs. Gene Ther. 2012 Jan 19. PMID:22257934.

Hirsch ML*, Fagan BM, Dumitru R., Bower J, Yadav S, Porteus M, Pevny L, Samulski, RJ. Viral single-strand DNA induces p53-dependent Apoptosis of Human Embryonic Stem Cells. PloS ONE. 2011 6(11):e27520. PMID:22114676. PMC3219675

Ke L, He M, Li C, Liu Y, Gao L, Yao F, Li J, Bi X, Lv Y, Wang J, Hirsch ML*, Li W. The prevalence of human parvovirus B19 DNA and antibodies in blood donors from four Chinese blood centers. Transfusion. 2011 51(9):1909-18. PMID: 21382040.

Monahan P, Lothrop CD, Sun J, Hirsch ML, Kafri T, Kantor B, Tillson DM, Elia J, Samulski RJ. Proteasome inhibitors enhance gene delivery by AAV virus vectors expressing large genomes in hemophilia mouse and dog models: a strategy for broad clinical application.Mol Ther. 2010 18(11):1907-16. PMID: 20700109. PMC2990516

Hirsch ML, Green L, Porteus M, Samulski RJ. Self-Complementary AAV Mediates Gene Targeting and Enhances Endonuclease Delivery for Double-Strand Break Repair. Gene Ther. 2010 17(9):1175-80. PMID: 20463753. PMC3152950

Hirsch ML, Agbandje-McKenna, M, Samulski RJ. Little Vector, Big Gene Transduction: fragmented genome re-assembly of AAV. Mol Ther 2010 18(1):6-8. PMID: 20048740. PMC2839225

Hirsch ML, Storici F, Li C, Choi VW, Samulski RJ. AAV recombineering with single strand oligonucleotides. PLoS One. 2009 4(11):e7705. PMID: 19888330. PMC2765622

Li C, Goudy K, Hirsch ML, Fan Y, Alexander J, Asokan A, Sun J, Monahan P, Seiber D, Tisch R, Frelinger J, Samulski RJ. Cellular Immun Response to Cryptic Epitopes during Therapeutic Gene Transfer. PNAS. 2009 106; 10770-4. PMID: 19541644. PMC2705599

Li C, Hirsch ML, DiPrimio N, Asokan A, Goudy K, Tisch R, Samulski RJ. Cytotoxic T-Lymphocyte-Mediated Elimination of Target Cells Transduced with Engineered AAV Type 2 Vector In Vivo. J Virol. 2009 83:6817-24. PMID: 19369348. PMC2698563

Li C, Hirsch ML, Carter P, Asokan A, Zhou X, Wu Z, Samulski RJ. A Small Regulatory Element from Chromosome 19 Enhances Liver Specific Gene Expression. Gene Ther. 2009 16:43-51. PMID: 18701910

Hollis ER 2nd, Kadoya K, Hirsch ML, Samulski RJ, Tuszynski MH. Efficient retrograde neuronal transduction utilizing self-complementary AAV1. Mol Ther. 2008 16(2):296-301. PMID: 18223548

Li C, Hirsch ML, Asokan A, Zeithaml B, Ma H, Kafri T, Samulski RJ. AAV2 capsid specific CTLs eliminate target cells that express AAV capsid but not those transduced by AAV.Journal of Virology. 2007 81(14):7540-7. PMID: 17475652. PMC1933335

Hirsch M, Elliott T. Stationary Phase Induction of RpoS in Escherichia coli. Journal of Bacteriology. 2005 187(21):7204-13. PMID: 16237004. PMC1272984

Hirsch M, Elliott T. Fis regulates transcriptional induction of RpoS in Salmonella enterica. Journal of Bacteriology. 2005 187(5):1568-80. PMID: 15716427. PMC1064004

Hirsch M, Elliott T. Role of ppGpp in rpoS stationary-phase regulation in Escherichia coli. Journal of Bacteriology. 2002 184(18):5077-87. PMID: 12193624. PMC135317

Book Chapters

Hirsch ML. Gene Correction using AAV. Methods in Molecular Biology. 2014 1114:291-307. PMID: 24557911 (invited chapter).

Hirsch ML, Samulski RJ. Transgenes. Encyclopedia of Genetics. 2^nd Edition. (in press).

Li C, Hirsch ML, Samulski RJ. Development of AAV Vectors for the Therapy of Autoimmune and Inflammatory Disease. Milestones in Gene Therapy. Springer Publishing. 161-180. 2010.

Dismuke DJ, Gray SJ, Hirsch ML, Samulski RJ, Muzkya N. Viral Vectors for Gene Delivery.Structural Virology. M. Agbandje-McKenna and R. McKenna. Cambridge, Royal Society of Chemistry Publishing. 2010