A.O. Pasternak PhD publications

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Publications PhD A.O. Pasternak

Position
Research Associate
Main activities
Research
Specialisation
Molecular Virology
Focus of research

During my postdoctoral training in the Academic Medical Center of the University of Amsterdam, I have developed an ultra-sensitive HIV-1 detection assay, based on an innovative semi-nested qPCR of my own design (Pasternak, J Clin Microbiol 2008; Kiselinova, Pasternak, PLoS One 2014). This assay is extremely sensitive and robust, allowing to detect the virus in >90% of patient samples that are undetectable by conventional viral load measurements. This assay allowed us to identify cell-associated HIV RNA as a viral marker that predicts disease progression and therapy response, and we have demonstrated the clinical value of this biomarker in several publications. In particular, we have shown that cell-associated HIV RNA predicts antiretroviral therapy (ART) failure and correlates with subtle changes in patients’ adherence to ART in the absence of virological rebound in plasma (Pasternak, PLoS One 2009; J Infect Dis 2012). This pioneering work opened the door for a wider use of HIV biomarkers for monitoring ART response and studying HIV persistence, and the assays I developed are now used in a number of research laboratories worldwide, including those at the forefront of HIV cure research (Rasmussen, Lancet HIV 2014; Elliott, PLoS Pathogens 2014). More recently, I received two prestigious research grants from the Dutch AIDS Fonds as a Principal Investigator, allowing me to start an independent research group within the department. My current scientific interests are focused on persistence and dynamics of HIV reservoir. The ongoing research projects of my group deal with HIV reservoir and viral diversity in patients treated with ART during primary infection, viral and host factors determining immunological failure on ART, and virological correlates of co-morbidities in HIV-infected patients.

2020

  • Darcis Gilles, Kootstra Neeltje A., Hooibrink Berend, van Montfort Thijs, Maurer Irma, Groen Kevin, Jurriaans Suzanne, Bakker Margreet, van Lint Carine, Berkhout Ben, Pasternak Alexander O. CD32+CD4+ T Cells Are Highly Enriched for HIV DNA and Can Support Transcriptional Latency Cell reports 2020;30 (7):2284-2296.e3 [PubMed]
  • Pasternak Alexander O., Grijsen Marlous L., Wit Ferdinand W., Bakker Margreet, Jurriaans Suzanne, Prins Jan M., Berkhout Ben Cell-associated HIV-1 RNA predicts viral rebound and disease progression after discontinuation of temporary early ART JCI insight 2020;5 (6) [PubMed]
  • Darcis Gilles, Maes Nathalie, Pasternak Alexander O., Sauvage Anne-Sophie, Frippiat Frédéric, Meuris Christelle, Uurlings Françoise, Lecomte Marianne, Léonard Philippe, Elmoussaoui Majdouline, Fombellida Karine, Vaira Dolores, Moutschen Michel Detectability of HIV residual Viremia despite therapy is highly associated with treatment with a protease inhibitor-based combination antiretroviral therapy Antimicrobial agents and chemotherapy 2020;64 (3) [PubMed]
  • Darcis Gilles, Berkhout Ben, Pasternak Alexander O. Differences in HIV markers between infected individuals treated with different ART regimens: Implications for the persistence of viral reservoirs Viruses 2020;12 (5) [PubMed]

2019

  • van Montfort Thijs, van der Sluis Renée, Darcis Gilles, Beaty Doyle, Groen Kevin, Pasternak Alexander O., Pollakis Georgios, Vink Monique, Westerhout Ellen M., Hamdi Mohamed, Bakker Margreet, van der Putten Boas, Jurriaans Suzanne, Prins Jan H., Jeeninga Rienk, Thomas Adri A.M., Speijer Dave, Berkhout Ben Dendritic cells potently purge latent HIV-1 beyond TCR-stimulation, activating the PI3K-Akt-mTOR pathway EBioMedicine 2019;42:97-108 [PubMed]
  • Pinzone Marilia Rita, VanBelzen D. Jake, Weissman Sam, Bertuccio Maria Paola, Cannon LaMont, Venanzi-Rullo Emmanuele, Migueles Stephen, Jones R. Brad, Mota Talia, Joseph Sarah B., Groen Kevin, Pasternak Alexander O., Hwang Wei-Ting, Sherman Brad, Vourekas Anastasios, Nunnari Giuseppe, O’Doherty Una Longitudinal HIV sequencing reveals reservoir expression leading to decay which is obscured by clonal expansion Nature communications 2019;10 (1) [PubMed]
  • Das Atze T., Pasternak Alexander O., Berkhout Ben On the generation of the MSD class of defective HIV proviruses Retrovirology 2019;16 (1) [PubMed]
  • Darcis Gilles, Berkhout Ben, Pasternak Alexander O. The quest for cellular markers of HIV reservoirs: Any color you like Frontiers in immunology 2019;10 [PubMed]

2018

  • Sarracino Ambra, Gharu Lavina, Kula Anna, Pasternak Alexander O., Avettand-Fenoel Veronique, Rouzioux Christine, Bardina Maryana, de Wit Stéphane, Benkirane Monsef, Berkhout Ben, van Lint Carine, Marcello Alessandro Posttranscriptional Regulation of HIV-1 Gene Expression during Replication and Reactivation from Latency by Nuclear Matrix Protein MATR3 mBio 2018;9 (6) [PubMed]
  • Mueller Nancy, Pasternak Alexander O., Klaver Bep, Cornelissen Marion, Berkhout Ben, Das Atze T. The HIV-1 tat protein enhances splicing at the major splice donor site Journal of virology 2018;92 (14) [PubMed]
  • Pasternak Alexander O., Berkhout Ben What do we measure when we measure cell-associated HIV RNA Retrovirology 2018;15 (1):13 [PubMed]

2017

  • Bartelsman M., Joore I. K., van Bergen J. E., Hogewoning A. A., Zuure F. R., van Veen M. G., Deug F., Heidenrijk M., Prins J. M., Prins M. [= Maria], Smit P. J., van der Valk M., Reiss P., de Bree G. J., Hoornenborg E., Davidovich U., Geerlings S. E., Oomen A., van sighem A., Zuilhof W., Achterbergh R. C. A., van Agtmael M., Ananworanich J., van de Beek D., van den Berk G. E. L., Berkhout B., Berretty B., Bezemer D., Blok W. L., Bomers M., Boucher C. A. B., Brokking W., Burger D., Brinkman K., de Bruin M., Geijtenbeek T. B. H., Godfried M. H., Goorhuis A., van der Helm J. J., Hovius J. W., Kootstra N. A., van der Meer J. T., Nellen F. J., Pasternak A. O., van der Poll T., van Rooijen M. S., de Vries H. J., van Vugt M., Wiersinga W. J., Wit F. W. HIV testing week 2015: lowering barriers for HIV testing among high-risk groups in Amsterdam BMC infectious diseases 2017;17 (1):529 [PubMed]

2016

  • DeMaster Laura K., Liu Xiaohe, VanBelzen D. Jake, Trinité Benjamin, Zheng Lingjie, Agosto Luis M., Migueles Stephen A., Connors Mark, Sambucetti Lidia, Levy David N., Pasternak Alexander O., O'Doherty Una A Subset of CD4/CD8 Double-Negative T Cells Expresses HIV Proteins in Patients on Antiretroviral Therapy Journal of virology 2016;90 (5):2165-2179 [PubMed]
  • Pasternak Alexander O., Berkhout Ben HIV Reservoir: Finding the Right Needles in a Needlestack Cell host & microbe 2016;20 (3):280-282 [PubMed]
  • Pasternak Alexander O., DeMaster Laura K., Kootstra Neeltje A., Reiss Peter, O'Doherty Una, Berkhout Ben Minor Contribution of Chimeric Host-HIV Readthrough Transcripts to the Level of HIV Cell-Associated gag RNA Journal of virology 2016;90 (2):1148-1151 [PubMed]
  • Mann Jaclyn, Pasternak Alexander O., Chahroudi Ann, Singh Jerome A., Ross Anna Laura The latest science from the IAS Towards an HIV Cure Symposium: 16-17 July 2016, Durban, South Africa Journal of virus eradication 2016;2 (4):235-241 [PubMed]

2015

  • Pasternak Alexander O., de Bruin Marijn, Bakker Margreet, Berkhout Ben, Prins Jan M. High Current CD4+ T Cell Count Predicts Suboptimal Adherence to Antiretroviral Therapy PLoS ONE 2015;10 (10):e0140791 [PubMed]

2014

  • Kiselinova Maja, Pasternak Alexander O., de Spiegelaere Ward, Vogelaers Dirk, Berkhout Ben, Vandekerckhove Linos Comparison of droplet digital PCR and seminested real-time PCR for quantification of cell-associated HIV-1 RNA PLoS ONE 2014;9 (1):e85999 [PubMed]

2013

  • Pasternak Alexander O., Lukashov Vladimir V., Berkhout Ben Cell-associated HIV RNA: a dynamic biomarker of viral persistence Retrovirology 2013;10 (1):41 [PubMed]
  • van der Kuyl Antoinette C., Bakker Margreet, Jurriaans Suzanne, Back Nicole K. T., Pasternak Alexander O., Cornelissen Marion, Berkhout Ben Translational HIV-1 research: from routine diagnostics to new virology insights in Amsterdam, the Netherlands during 1983-2013 Retrovirology 2013;10 (1):93 [PubMed]

2012

  • Eekels J. J. M., Pasternak A. O., Schut A. M., Geerts D., Jeeninga R. E., Berkhout B. A competitive cell growth assay for the detection of subtle effects of gene transduction on cell proliferation Gene therapy 2012;19 (11):1058-1064 [PubMed]
  • Cornelissen Marion, Pasternak Alexander O., Grijsen Marlous L., Zorgdrager Fokla, Bakker Margreet, Blom Petra, Prins Jan M., Jurriaans Suzanne, van der Kuyl Antoinette C. HIV-1 Dual Infection Is Associated With Faster CD4(+) T-Cell Decline in a Cohort of Men With Primary HIV Infection Clinical infectious diseases 2012;54 (4):539-547 [PubMed]
  • van Gulck Ellen, Bracke Lotte, Heyndrickx Leo, Coppens Sandra, Atkinson Derek, Merlin Céline, Pasternak Alexander, Florence Eric, Vanham Guido Immune and Viral Correlates of "Secondary Viral Control" after Treatment Interruption in Chronically HIV-1 Infected Patients PLoS ONE 2012;7 (5):e37792 [PubMed]
  • Pasternak Alexander O., de Bruin Marijn, Jurriaans Suzanne, Bakker Margreet, Berkhout Ben, Prins Jan M., Lukashov Vladimir V. Modest Nonadherence to Antiretroviral Therapy Promotes Residual HIV-1 Replication in the Absence of Virological Rebound in Plasma Journal of infectious diseases 2012;206 (9):1443-1452 [PubMed]

2010

  • Giliazova A. V., Zenin P. V., Pronin A. Iu, Serkov I. L., Khametova K. M., Orlova-Morozova E. A., Zhukova E. V., Kornilaeva G. V., Pasternak A. O., Lukashov V. V., Karamov E. V. [Molecular epidemiology of HIV-1 strains in the Moscow Region] Voprosy virusologii 2010;55 (5):25-29 [PubMed]
  • Pasternak Alexander O., Jurriaans Suzanne, Bakker Margreet, Berkhout Ben, Lukashov Vladimir V. Steady increase in cellular HIV-1 load during the asymptomatic phase of untreated infection despite stable plasma viremia AIDS (London, England) 2010;24 (11):1641-1649 [PubMed]

2009

  • Pasternak Alexander O., Jurriaans Suzanne, Bakker Margreet, Prins Jan M., Berkhout Ben, Lukashov Vladimir V. Cellular Levels of HIV Unspliced RNA from Patients on Combination Antiretroviral Therapy with Undetectable Plasma Viremia Predict the Therapy Outcome PLoS ONE 2009;4 (12):e8490 [PubMed]

2008

  • Pasternak Alexander O., Adema Karen W., Bakker Margreet, Jurriaans Suzanne, Berkhout Ben, Cornelissen Marion, Lukashov Vladimir V. Highly sensitive methods based on seminested real-time reverse transcription-PCR for quantitation of human immunodeficiency virus type 1 unspliced and multiply spliced RNA and proviral DNA Journal of clinical microbiology 2008;46 (7):2206-2211 [PubMed]

2006

  • Pasternak Alexander O., Spaan Willy J. M., Snijder Eric J. Nidovirus transcription: how to make sense...? Journal of general virology 2006;87 (Part 6):1403-1421 [PubMed]

2004

  • Pasternak Alexander O., Spaan Willy J. M., Snijder Eric J. Regulation of relative abundance of arterivirus subgenomic mRNAs Journal of virology 2004;78 (15):8102-8113 [PubMed]

2003

  • Pasternak Alexander O., van den Born Erwin, Spaan Willy J. M., Snijder Eric J. The stability of the duplex between sense and antisense transcription-regulating sequences is a crucial factor in arterivirus subgenomic mRNA synthesis Journal of virology 2003;77 (2):1175-1183 [PubMed]

2001

  • Pasternak A. O., van den Born E., Spaan W. J., Snijder E. J. Sequence requirements for RNA strand transfer during nidovirus discontinuous subgenomic RNA synthesis EMBO journal 2001;20 (24):7220-7228 [PubMed]

2000

  • Pasternak A. O., Gultyaev A. P., Spaan W. J., Snijder E. J. Genetic manipulation of arterivirus alternative mRNA leader-body junction sites reveals tight regulation of structural protein expression Journal of virology 2000;74 (24):11642-11653 [PubMed]