Hi, my name is

Anna Ponomarenko

Research Scientist: Virology, Gene Therapy, Cell Biology

Multidisciplinary and collaborative scientist with deep expertise in virology, gene therapy, cell and molecular biology. Industry experience in gene therapy and cell based disease model development.

About Me

Highly interdisciplinary, results-driven and detail-oriented scientist with extensive experience in virology, gene therapy, cell and molecular biology.

Team-oriented and organized, capable of managing multiple projects and establishing cross-functional collaborations to solve complex research problems.

Excellent written and oral communication skills, as exemplified by multiple publications, internal presentations and participation in research conferences.

Experience

Scientist II - Ultragenyx
Sep 2022 - present
I am currently working in Vector Engineering Team, part of Ultragenyx Gene Therapy Research in Somerville MA. Together with my Scientist and Research Associates teammates we bring our virology subteam to advance Ultragenyx Pinnacle rAAV production system for delivering high quality gene therapy treatment to rare disease patients.

  • Provided scientific leadership and defined experimental strategy for advancing the Pinnacle rAAV production platform
  • Provided virology expertise within a crossfunctional collaboration for evaluating novel rAAV production approaches
  • Investigated viral and cellular processes affecting AAV production and quality
  • Performed in-depth characterization of rAAV genome replication and packaging using ddPCR, CsCl fractionation, Southern blotting and Nanopore sequencing
  • Supervised and supported a Senior Research Associate I
Scientist I - Ultragenyx
Sep 2020 - Aug 2022
I joined Vector Engineering team of Ultragenyx Gene Therapy Research to implement cutting-edge AAV technology to improve efficacy, potency, safety and production of rAAV vectors. My role placed special emphasis on the design, production and evaluation of novel AAV genetic elements and mutant adenoviruses.

  • Executed rAAV and rAd5 studies that drive company research and development goals
  • Collaborated internaly across Gene Therapy teams (Producer Cell Line, Nonclinical, Research Analytica Development), Pharmaceutical Development team and externally with CROs
  • Developed an alternative potency assay for one of Ultragenyx gene therapy programs
  • Applied CRISPR mediated gene up/down regulation for advancing existing cell-based assays
Research Specialist - MIT
Sept 2020
I stayed at the Shoulders Lab at MIT for a month after graduation to finish my investigation of virus-cell interactome

  • Investigated influenza nucleoprotein host cell interactome to elucidate individual factors required for stabilization of biophysically defective but innate immune escape Pro283 variant
Graduate Research Assistant - MIT
June 2016 - Aug 2020
Ph.D. research conducted in Prof. Matthew D. Shoulders lab at MIT Chemistry Department

  • Discovered the critical role of host chaperones in potentiating influenza immune escape
  • Developed cell-based assays in BSL-2+ environment to elucidate the molecular mechanisms of mutant viral proteins dependence on the host protein folding network
  • Established external collaborations for biophysical investigation of influenza nucleoprotein
  • Communicated research at international conferences (EMBO 2019, FASEB 2018, ACS 2018)
Summer Intern - Vertex
July 2019 - Aug 2019
  • Developed human cell-based disease models and characterized using fluorescent microscopy
  • Maintained primary human cells
  • Synthesized, modified and purified RNA in vitro

Education

2015 - 2020
Ph.D. in Chemistry
Massachusetts Institute of Technology

Cambridge MA, USA

Prof. Matthew D. Shoulders Lab of Protein Folding

Thesis: The host heat shock response, viral immune escape and viral replication

2009 - 2014
M.Sc. in Chemistry
Lomonosov Moscow State University

Moscow, Russia

Thesis: Functionalization of CdTe quantum dots with biomolecules

Publications

The endoplasmic reticulum proteostasis network profoundly shapes the protein sequence space accessible to HIV envelope
HIV HSF1 Viral Evolution
The endoplasmic reticulum proteostasis network profoundly shapes the protein sequence space accessible to HIV envelope
Yoon, J.; Nekongo,E.E.; Patrick, J.E.; Hui, T.; Phillips, A.M.; Ponomarenko, A.I.; Hendel, S.J.; Sebastian, R.M.; Zhang, Y.M.; Butty, V.L.; Ogbunugafor C.B.; Lin, Y.-S.; Shoulders, M.D. PLoS Biol., 20(2), e3001569 (2022)
HSF1 Activation Can Restrict HIV Replication
HIV HSF1 Viral Evolution
HSF1 Activation Can Restrict HIV Replication
Nekongo, E.E.; Ponomarenko, A.I.; Dewal, M.B.; Butty, V.L.; Browne, E.P.; Shoulders, M.D. ACS Infect. Dis., 6, 1659-66 (2020)
*These authors contributed equally.
Destabilized adaptive influenza variants critical for innate immune system escape are potentiated by host chaperones
Influenza HSF1 Viral Evolution
Destabilized adaptive influenza variants critical for innate immune system escape are potentiated by host chaperones

Phillips, A.M.; Ponomarenko, A.I.; Chen, K.; Ashenberg, O.; Miao, J.; McHugh, S.M.; Butty, V.L.; Whittaker, C.A.; Moore, C.L.; Bloom, J.D.; Lin, Y.-S.; Shoulders, M.D. PLoS Biol., 16, e3000008 (2018)

*These authors contributed equally, the listed order was determined by a random coin flip.

Host proteostasis modulates influenza evolution
Influenza HSF1 Viral Evolution
Host proteostasis modulates influenza evolution
Phillips, A.M.; Gonzalez, L.O.; Nekongo, E.E.; Ponomarenko, A.I.; McHugh, S.M.; Butty, V.L.; Levine, S.L.; Lin, Y.-S.; Mirny, L.A.; Shoulders, M.D. eLife, 6, e28652 (2017)
Tetrahedral DNA conjugates from pentaerythritol-based polyazides
DNA nanostructures Click chemistry
Tetrahedral DNA conjugates from pentaerythritol-based polyazides
Ponomarenko, A.I.; Brylev, V.A.; Sapozhnikova, K.A.; Ustinov, A.V.; Prokhorenko, I.A.; Zatsepin, T.S.; Korshun, V.A. Tetrahedron, 72(19), 2386-91 (2016)
Recent advances in self-assembled fluorescent DNA structures and probes
DNA nanostructures Click chemistry
Recent advances in self-assembled fluorescent DNA structures and probes
Ponomarenko, A.I.; Brylev, V.A.; Nozhevnikova, E.V.; Korshun, V.A. Curr. Top. Med. Chem., 15(13), 1162-1178 (2015)

Skills

Virology
  • Virus (rAAV, adenovirus, lentivirus, influenza A) generation, propagation, titer
  • Small scale rAAV and Ad5 purification
  • Infectivity assays (plaque assay, TCID50)
  • CsCl gradient virus purification
Cell Biology
  • Mammalian cell culture (adherent and suspension)
  • Primary human cells (fibroblasts, NHBE)
  • Transient transfection (DNA, RNA)
  • Lentiviral transduction
  • Cell-based assays
  • Confocal microscopy
Biochemistry
  • Protein SDS-PAGE (Western blotting, Silver stain, Coumassie)
  • DNA PAGE and agarose gel electrophoresis
  • RT-qPCR, ddPCR
  • Southern blotting
  • ELISA
Molecular Biology
  • Restriction cloning
  • Illumina, 10x Genomics and Nanopore sequencing sample prep
  • Nucleic acid isolation from bacteria, mammalian cells and viruses
Data Analysis
  • NGS (Illumina and ONT) data analysis using Python and Bash script (beginner)
  • IGV
  • GraphPad Prism

Get in Touch

My inbox is always open. Whether you have a question or just want to say hi, I’ll try my best to get back to you!