Prasad Konkalmatt, PhD

AAV Vector Development and Gene Therapy

Cell:434-245-1635 | pkonkalmatt@gmail.com | linkedin.com/in/pkonkalmatt

Summary

Accomplished scientist with over 20 years of academic research experience and 5 years in the biotech and pharmaceutical industry, specializing in AAV gene therapy and engineering. Expertise spans the full spectrum of AAV therapeutic development, including designing AAV expression cassettes, developing targeted capsids, and optimizing vector cargo for enhanced gene expression.

Proven ability to design and execute in vitro and in vivo preclinical studies, analyze data, and report findings to advance gene therapy programs. Developed novel compact promoters and miniaturized genes to maximize the packaging capacity of AAV vectors, ensuring efficient gene delivery to cardiomyocytes.

Experienced in producing and purifying R&D-grade AAV vectors, adhering to high-quality standards for preclinical research. Strong communicator with a record of publishing in peer-reviewed journals, delivering impactful presentations, and securing grant funding.

A collaborative leader and mentor, fostering innovation and guiding junior scientists to achieve research and project milestones. Dedicated to advancing the field of gene therapy through a combination of technical expertise, innovative solutions, and teamwork.

Accomplishments

  • Discovered AAV Rep78 protein is covalently linked to the 5’ end of the viral genome and it is essential for terminal resolution of the AAV ITR and packaging of AAV DNA into virus particles.

  • Introduced TNNT2 promoter, a gold standard for cardio-myocyte specific gene expression, to the AAV gene therapy community.

  • Demonstrated the preservation of cardiac function against myocardial infarction and subsequent left ventricular remodeling following systemic administration of AAV9 carrying TNNT2 for the expression of extracellular superoxide dismutase (EcSOD) or inducible nitric oxide synthase (iNOS) in a mouse model of ischemia-reperfusion injury.

  • Discovered AAV9 delivered early after cardiac MI preferentially transduces CM bordering the infarct zone and can attenuate LV remodeling.

  • Developed a method of AAV administration—retrograde infusion via the ureter—for enhanced gene transfer to the renal nephron.

  • Designed AAV vector promoter constructs for nephron segment-specific gene expression in the kidney.

  • Discovered G-Protein Coupled Receptor 37L1 (GPR37L1) expressed in the apical membrane/brush border of the mouse kidney proximal tubule and regulates renal sodium transport and blood pressure.

  • Developed rationally designed AAV capsid for targeted gene expression in the pancreatic tumor cells.

  • Led capsid engineering projects using a directed evolution approach, which involved employing shuffled DNA library of AAV capsids and rationally designed AAV capsid libraries via random peptide insertion. The aim was to isolate novel AAV variants with enhanced tropism to cardiomyocytes and lung tissues.

  • Engineered a compact mini gene tailored to fit within the packaging constraints of the AAV genome by understanding protein structure-function relationships.

  • Developed compact cardiomyocyte specific promoters to enhance cargo for therapeutic genes in the AAV genome.

Education

Ph.D. (Biochemistry and Molecular Biology), 01/1990 – 03/1996, University of Toledo College of Medicine and Health Sciences, Toledo, OH. 

Discovered adeno-associated virus (AAV) Rep78 protein is covalently linked to the 5’ end of the viral genome and it is essential for terminal resolution of the AAV ITR and packaging of AAV DNA into virus particles.

Professional Experience

Associate Director - Capsid Engineering, 05/2022 – 05/2024, Tenaya Therapeutics, South San Franscisco, CA

  • Designed novel AAV capsid libraries and screened in mouse and primates to identify capsids with cardiotropic profiles.     

  • Developed compact cardiomyocyte specific promoters to enhance space for therapeutic genes in the AAV genome.

  • Engineered a mini gene to fit within the packaging capacity of the AAV genome via understanding protein structure function relationships.

  • Provided AAV and molecular biology expertise to several Research Associates and scientists.             

Associate Principal Scientist - AAV Technology, 02/2020 - 01/2022, AstraZeneca, Gaithersburg, MD.

  • Led a capsid engineering team with 3 direct reports, tasked with isolating lung-tropic AAV capsids.

  • Utilized a directed evolution approach, employing shuffled AAV capsid libraries and rationally designed AAV capsid libraries via random peptide insertion. Successfully isolated novel AAV variants with enhanced tropism to organs of interest, particularly the lungs.

  • Evaluated the biodistribution of gene transfer from novel capsids in the mouse and primate models.

  • Served as a co-lead, offering AAV expertise on a Gene therapy pipeline project.

Assistant Professor – Hypertension and Renal Physiology (under same PI in two institutions)

George Washington University, Washington DC. , 09/2015 - 02/2020

University of Maryland School of Medicine, Baltimore MD, 02/2012 - 09/2015

  • Employed retrograde ureteral infusion, a novel mode of administration, to transduce renal epithelial cells.

  • Designed AAV vectors with panel of kidney specific promoters and demonstrated targeted expression within the desired segment of the renal nephron.

  • Employed AAV vectors for kidney specific gene rescue experiments in renal hypertension studies. Demonstrated renal specific rescue of D2R in the global knockout mice results in the reversal of renal injury and high blood pressure.

  • Discovered G-Protein Coupled Receptor 37L1 (GPR37L1) expressed in the apical membrane/brush border of the mouse kidney proximal tubule and regulates renal sodium transport and blood pressure.

  • Renal hydrogen peroxide production prevents salt‐sensitive hypertension

Assistant Professor; Instructor; Research Associate - AAV vector development and Gene Therapy,

University of Virginia, Charlottesville, VA. 08/1999 - 02/2012

  • Identified the TNNT2 promoter from a panel of cardiac specific promoters for designing AAV cargo tailored for robust cardiac-specific gene expression.

  • Demonstrated the preservation of cardiac function against myocardial infarction (MI) and subsequent left ventricular (LV) remodeling following systemic administration of AAV9 carrying TNNT2 for the expression of EcSOD (extracellular superoxide dismutase) or inducible nitric oxide synthase (iNOS) in a mouse model of ischemia-reperfusion injury.

  • Discovered AAV9 delivered early after cardiac MI preferentially transduces CM bordering the infarct zone.

  • Demonstrated AAV vector carrying a therapeutic gene specifically targeted to and expressed in skeletal muscle decreased necrosis in peripheral arterial disease model. 

  • Developed rationally designed AAV capsid for targeted gene expression in the pancreatic tumor cells.

  • Demonstrated increased 12-lipoxygenase expression impairs pancreatic beta cell function and viability.

  • Demonstrated AAV vectors gene transfer efficacies to pancreatic beta cells in diabetes-related studies.

Postdoctoral Research Fellow - AAV vector development and Gene Therapy,

City of Hope National Medical Center, Duarte, CA. 03/1996 - 07/1999

  • Developed AAV vectors for gene transfer to pancreatic beta cells to study the role of 12-Lipoxygenase in insulin secretion. 

Patents

  • Use of Adeno-associated virus (AAV) to deliver genes (US Patent Number 6,485,976)         

  • Cardiac-Specific Promoters for Gene Therapy (Pending: Application No. 63/609,724, filed on Dec 13, 2023

Publications Selected

(2011 and before: Prasad KMR, 2012-present Konkalmatt P)

  • Prasad, KMR. and Trempe, J.P. The adeno‑associated virus Rep78 protein is covalently linked to viral DNA in a preformed virion. Virology, 1995;214: 360‑370.

  • Prasad, KMR., Studies on the adeno-associated virus Rep protein-viral DNA covalent complex. PhD Thesis;1996.

  • Collaco, R*, Prasad, KMR*, and Trempe, J.P. Phosphorylation of adeno‑associated virus replication proteins. Virology, 1997;232: 332-336.  *Both authors contributed equally to this work.

  • Prasad, KMR., Zhou, C. and Trempe, J.P. Characterization of the infectious Rep78/adeno‑associated virus complex. Virology, 1997;229: 183-192.

  • Prasad, KMR., Yang Z.D., Bleich, D.M., Nadler, J. L. Adeno-associated virus vector mediated gene transfer to pancreatic Beta cells. Gene Therapy, 2000;7:1553-1561.

  • Prasad KMR, Xu Y, Yang ZQ, Toufektsian MC, Berr  SS, French BA. Topoisomerase Inhibition Accelerates the Onset of Gene Expression after Adeno-Associated Virus-Mediated Direct Gene Transfer to the Mammalian Heart. Mol. Therapy. 2007;15:764-771.

  • Saqib A, Prasad KMR, Katwal AB, Sanders JM, Lye RJ, French BA, Annex BH. AAV9-Mediated Overexpression of Extracellular Superoxide Dismutase Improves Recovery from Hind-limb Ischemia in BALB/c Mice. J Vasc Surg. 2011;54:810-8.

  • Prasad KMR, Xu Y, Yang ZQ, Acton ST, Berr SS, French BA. Robust, Cardiac-Specific Gene Expression from a Single Systemic Injection of AAV: In Vivo Gene Transfer Follows a Poisson Distribution. Gene Therapy, 2011;18:43-52.

  • Prasad KMR, Robert SS, Xu Y, French BA. A Single Direct Injection into the Left Ventricular Wall of an AAV9 Vector Expressing EcSOD from the Cardiac Troponin-T Promoter Protects Mice Against Myocardial Infarction. J. Gene Med. 2011, 13:333-4.

  • Konkalmatt P, Wang F, Xu Y, Piras BA, Beyers RJ, O’Conner DM, Annex BH, Hossack JA, French BA. AAV9 preferentially targets cardiomyocytes in the infarct border zone after systemic administration: A robust system for the genetic reprogramming of LV remodeling. J Gene Med. 2012;14:609-20.

  • Katwal AB, Konkalmatt P, Piras BA, Hazarika S, Li SS, John Lye R, Sanders JM, Ferrante EA, Yan Z, Annex BH, French BA. Adeno-associated virus serotype 9 efficiently targets ischemic skeletal muscle following systemic delivery. Gene Ther. 2013; 20(9):930-8.

  • Konkalmatt P, Beyers RJ, O'Connor DM, Xu Y, Seaman ME, French BA. Cardiac-Selective Overexpression of EcSOD Following a Single Intravenous Injection of AAV9 Protects the Heart Against both Myocardial Infarction and Subsequent LV Remodeling Circulation: Cardiovascular Imaging. 2013;1;6(3):478-86.

  • Konkalmatt P, Deng D, Thomas S, Wu MT, Logsdon CD, French BA, Kelly KA. Plectin-1 Targeted AAV Vector for the Molecular Imaging of Pancreatic Cancer.Front Oncol. 2013; 3:84.

  • Asico LD, Cuevas S, Ma X, Jose PA, Armando I, Konkalmatt P. Nephron segment-specific gene expression using AAV vectors. BBRC 2018;497(1):19-24. 

Link to complete list of publications.

https://www.ncbi.nlm.nih.gov/myncbi/prasad.konkalmatt.1/bibliography/public/

Recent Abstracts Presented at the 2024 ASGCT Annual Meeting 

  1. Konkalmatt P, Shenwai R, Ivey K. AAV DNA Shuffle Library of GH Loop Regions for Directed Evolution of Cardiotropic Capsids. Mol Thera Suppl. 464, 2024, Vol 32, No 4S1:249.

    https://www.tenayatherapeutics.com/wp-content/uploads/ASGCT-2024-DNA-Shuflle-Library-Capsids.pdf

  2. Konkalmatt P, Reid CA, Van Pell M, Jones S, Cheng Z, Woods J, Budan A, Aycinena A, Mandegar M, Ivey K, Chimeric and Rationally Designed Compact Promoters for Cardiomyocyte-Specific Gene Expression. Mol Thera Suppl. 482, 2024, Vol 32, No 4S1:257.

    https://www.tenayatherapeutics.com/wp-content/uploads/ASGCT-2024-Promoter-Engineering.pdf

  3. Highlighted Contribution: Abstracts presented at the ASGCT 2024 meeting in Baltimore were recognized by Faraz Ali, CEO of Tenaya Therapeutics, in a video interview (timestamp 1:42 – 3:20 minutes).

    https://www.cgtlive.com/view/ali-continued-innovation-cardiovascular-targeted-aav-gene-therapy

Grants and Awards

  1. R56 DK116828: NIH/NIDDK (PI: Prasad Konkalmatt) 08/21/2018 - 08/31/2020, Renal G Protein-Coupled Receptor 37L1 Regulates Blood Pressure.

  2. NKF-Mini: NKF-Maryland, (PI: Prasad Konkalmatt) 07/01/14-06/30/15, Development of AAV vectors for Nephron Segment-Specific Gene Expression and Silencing.

Major Invited presentations

Invited to present at “the 22nd US-Japan Cellular and Gene Therapy Conference.” Organized by the US Food and Drug administration. March 17, 2019.

https://www.fda.gov/vaccines-blood-biologics/workshops-meetings-conferences-biologics/22nd-us-japan-cellular-and-gene-therapy-conference-03072019-03072019

Technical skills

Special skills:

  • Hands-on and supervisory experience in the discovery and development of AAV-based gene therapies from designing, executing, analyzing, and reporting proof of concept in vitro and in vivo pre-clinical studies.

  • AAV capsid engineering for targeted gene delivery: AAV capsid library design (DNA shuffle and rational design). Library preparation, screening and biodistribution study in mice and primates.

  • AAV cargo design for optimum gene expression.

  • Promoter engineering for tissue specific gene expression.

  • Protein engineering and expression; miniaturizing the genes to fit within packaging capacity of AAV.

  • AAV vector production, purification, titer determination and use for in vivo gene transfer in the mouse model, gene expression analyses.

Laboratory skills: Molecular cloning, Gibson assembly, Plasmid DNA preparation, DNA agarose gel analyses, mammalian cell culture, transfection, AAV transduction, siRNA transfection, gene expression analysis, SDS-PAGE and immunoblotting, RNA preparation, gDNA preparation, qPCR (dye binding and taqman probe), familiar with ddPCR technology, RT-qPCR, ELISA, Bioluminescence imaging (IVIS, PerkinElmer), Tissue processing, immunohistochemistry (IHC), immunofluorescence (IF), Confocal microscopy, AAV production and purification, large scale transfection, Affinity chromatography, gradient ultracentrifugation, familiar with CRIPR-Cas9 technology, preparation of stable cell lines.

Writing and communication: Prepared and published several research articles as first, senior and/or corresponding author. Successfully wrote research grant applications and received research funds. Delivered several oral presentations at the international scientific meetings: Scientific Sessions of the AHA, Experimental Biology Annual Meeting, Council of Hypertension, American Society of Cell and Gene Therapy.

Basic computer skills: MS Word, Excel, GraphPad Prism, Power Point, Adobe Photoshop. SnapGene, familiar with various online Bioinformatics tools.