Anna Ponomarenko, PhD
Research Scientist: Cell Biology & Virology
Industry experience in gene therapy and cell based assay development
Hi, my name is
About Me
Results-oriented and data-driven PhD Scientist with industry experience in cell biology and gene therapy. Proficient in cell culture, cell-based assay development, and a wide range of cell and molecular biology methods.
Excellent organizational skills for managing multiple projects in a fast-paced environment and establishing cross-functional collaborations to solve complex research problems.
Team-oriented and skilled in training and mentoring junior scientists. Experienced in managing a direct report, providing support for professional growth and development.
Excellent written and oral communication skills, as exemplified by multiple publications, internal presentations and participation in research conferences.
Here are a few of my core competencies:- Cell culture
- Cell-based assays
- Virology
- Cell Biology methods
- Next Generation Sequencing (NGS)
- Cross-functional Collaborations
- Mentorship
- Leadership
Experience
Vector Engineering Team of Ultragenyx Gene Therapy Research
- Investigated viral and cellular processes affecting AAV production and genome quality using ELISA, Western Blot, ddPCR, RT-qPCR
- Led Oxford Nanopore sequencing efforts of a 5 people team for characterizing packaged AAV genome quality. Provided training and support for library preparation, QC, sequencing, data analysis and interpretation
- Established numerous cross-functional collaborations and provided virology expertise for advancing AAV gene therapy quality and efficacy
- Collaborated with the Translational Science team to perform evaluation of novel neuromuscular diseases for Ultragenyx portfolio and reported results to senior leadeship
- Provided support and lab-based training to junior scientists. Managed a Senior Research Associate I (direct report)
Vector Engineering team of Ultragenyx Gene Therapy Research
- Collaborated with Analytical Deveoplment team to troubleshoot the existing cell-based potency assay for one of gene therapy programs. Proposed and developed a new functional fluorescence based assay with improved sensitivity and reporoducibility
- Independently designed, executed and analyzed cell based assays and AAV and Ad5 virology experiments driving improvement of AAV gene therapy efficacy and safety
- Applied CRISPR mediated gene up/down regulation for advancing existing cell-based assays
- Collaborated internaly across Gene Therapy teams (Producer Cell Line, Nonclinical, Research Analytica Development), Pharmaceutical Development team and externally with CROs
- Routinely presented research data and results to diverse internal teams
I stayed at the Shoulders Lab at MIT for a month after graduation to finish my investigation of virus-cell interactome
- Performed pull-down assays in collaboration with Mass Spectrometry core facility to elucidate individual host factors required for stabilization of biophysically defective but innate immune escape Pro283 variant
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 study viral evolution. Performed viral infections, titrations and analysis using qPCR, Western Blotting, NGS sequencing
- Applied NGS sequencing for mutrational analysis of viral RNA genome. Performed RNA extraction, NGS library preparation and data analysis using Python.
- Established external collaborations for biophysical characterization of influenza nucleoprotein
- Communicated research at international conferences (EMBO 2019, FASEB 2018, ACS 2018)
- Developed human primary cell based disease models and characterized using fluorescent microscopy
- Maintained and immortalized human primary cells
- Synthesized RNA using in vitro transcription, purified and modified RNA for biophysics collaboration
Education
2015 - 2020
Ph.D. in Biological Chemistry
Massachusetts Institute of TechnologyCambridge 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 UniversityMoscow, Russia
Thesis: Functionalization of CdTe quantum dots with biomolecules
Publications
influenza
Protein Structure
Viral Evolution
The immune-evasive proline-283 substitution in influenza nucleoprotein increases aggregation propensity without altering the native structure
Yoon, J.; Zhang, Y.M.; Her, C.; Grant, R.A.; Ponomarenko, A.I.; Ackermann, B.E.; Hui, T.; Lin, Y.-S.; Debelouchina, G.T.; Shoulders, M.D.
Sci. Adv Biol., 10(16), eadl6144 (2024)
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)
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.
*These authors contributed equally.
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.
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)
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)
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
Cell Culture
- Mammalian cell culture (adherent and suspension)
- Immortalized cells (HeLa, HEK, CHO, A549, CEM, Vero, MDCK, C2C12)
- Primary human cells (fibroblasts, NHBE)
- Transient transfection (DNA, mRNA)
- Lentiviral transduction
- Cell-based assays
- Reporter assays (luminescence, fluorescence)
- High-throughput assays (96-well)
- Cell line development
- CRISPRa/i gene activation/suppression
- Aseptic techniques
- BLS2+ laboratory practices
Virology
- Virus handling: AAV, adenovirus, lentivirus, influenza A
- Virus generation by transfection of producer cells
- Virus DNA/RNA isolation
- Virus titer: ddPCR, dPCR
- Infectivity assays (plaque assay, TCID50)
- Virus antibody neutralization assays
- Viral genome NGS sequencing (Illumina, ONT)
- Virus purification (<1L scale)
- CsCl gradient virus purification
Cell Biology
- Protein expression analysis
- SDS-PAGE (Western blotting, Silver stain, Coumassie)
- ProteinSimple WES, Jess, CE-SDS
- DNA PAGE and agarose gel electrophoresis
- RT-qPCR, ddPCR, dPCR gene expression analysis
- Southern blotting
- Northern blotting
- ELISA
- MSD-ELISA
- fluorescent microscopy
- confocal microscopy
Molecular Biology
- Restriction cloning
- Site-directed mutagenesis
- Probe and primer design
- Next Generation Sequencing (NGS): Illumina and Oxford Nanopore (ONT)
- NSG library preparation and QC
- DNA and RNA isolation
- In vitro transcription
- Nanodrop
- TapeStation
Data Analysis
- NGS data analysis: Illumina, 10x Genomics and Nanopore sequencing
- Python and Bash script (beginner)
- GraphPad Prism
- Microsoft Office
- SnapGene
- IGV
- Technical reports
- SOP drafting
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!