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Prof. PhD B. Berkhout

Position
Full Professor
Main activities
Research
Specialisation
Virology
Focus of research
  • Mechanism of HIV-1 gene expression and latency
  • Structure and function of the HIV-1 RNA genome
  • Virus evolution and drug-resistance
  • Novel vaccine strategies
  • RNA interference as antiviral therapy
  • Patient-related virus studies
Key publications
  • Liu Ying Poi, Schopman Nick C. T., Berkhout Ben Dicer-independent processing of short hairpin RNAs Nucleic acids research 2013;41 (6):3723-3733 [PubMed]
  • Herrera-Carrillo Elena, Liu Ying Poi, Berkhout Ben The impact of unprotected T cells in RNAi-based gene therapy for HIV-AIDS Molecular therapy 2014;22 (3):596-606 [PubMed]
  • Harwig Alex, Das Atze T., Berkhout Ben Retroviral microRNAs Current opinion in virology 2014;7:47-54 [PubMed]
  • Pasternak Alexander O., Berkhout Ben HIV Reservoir: Finding the Right Needles in a Needlestack Cell host & microbe 2016;20 (3):280-282 [PubMed]
  • Herrera-Carrillo Elena, Gao Zong-Liang, Harwig Alex, Heemskerk Matthias T., Berkhout Ben The influence of the 5΄-terminal nucleotide on AgoshRNA activity and biogenesis: importance of the polymerase III transcription initiation site Nucleic acids research 2017;45 (7):4036-4050 [PubMed]
All Publications
Curriculum Vitae
Personal data

Name: Benjamin Berkhout

Date of Birth: June 18, 1958

Nationality: Dutch

Sex: male

Office address: Laboratory of Experimental Virology
Department of Medical Microbiology
Center for Infection and Immunity Amsterdam (CINIMA)
Academic Medical Center of the University of Amsterdam
Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands
tel. +31-20-5664822
fax +31-20-6916531
b.berkhout@amc.uva.nl

Education

1979 B.Sc. University of Leiden (Chemistry)

1981 M.Sc. University of Leiden (Chemistry, Biochemistry,
Organic Chemistry and Bio-Inorganic Chemistry)
judicium: cum laude

1986 PhD University of Leiden (Molecular Biology and Biochemistry)
Thesis: Translational control mechanisms in bacteriophage MS2

Research and Professional Experience

1977-1981 Teaching Fellow, Department of Biochemistry
University of Leiden

1981-1986 Scientific Officer, Department of Biochemistry
University of Leiden

1986-1988 Research Fellow in Pathology, Harvard Medical School
Dana-Farber Cancer Institute, Boston, MA, USA

1988-1991 Visiting Research Associate, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD, USA

1991-1993 Assistant Professor, Department of Virology
Academic Medical Center, University of Amsterdam

1994-2002 Associate Professor, Department of Human Retrovirology
Academic Medical Center, University of Amsterdam

2002-2006 Head a.i. of the Department of Human Retrovirology
Academic Medical Center, University of Amsterdam

2002-present Professor of Human Retrovirology
Academic Medical Center, University of Amsterdam

2006-present Head of the Laboratory of Experimental Virology
Academic Medical Center, University of Amsterdam

Discoveries, contributions to science

- Novel mechanism for translational coupling in E. coli

- HIV-1 TAR RNA as transcriptional enhancer

- Virus competition assays to monitor fitness

- Concept of genetic barrier in evolution of drug-resistance

- HIV-1 fitness loss due to drug-resistance mutations

- Description of A-rich HIV-1 genome and G-to-A hypermutation

- Modulation of polyadenylation by RNA structure

- First description of a drug-dependent clinical HIV-1 variant (T20)

- Biological differences among HIV-1 subtypes due to LTR promoter variation

- Mechanism of initiation of reverse transcription (tRNA primer selection, PAS motif)

- Identification of new HIV-1 RNA motifs (polyA hairpin, PAS, AUG-U5 interaction)

- HIV-1 RNA functions regulated by a riboswitch mechanism

- Forced evolution approach to study RNA structure, drug-resistance etc

- RNAi gene therapy as antiviral approach

- RNAi-resistance through target RNA structure motifs

- Construction of drug-dependent HIV-1 vaccine candidate (dox)

- Improvement of the Tet-system for inducible gene expression

- Virus discovery, the human coronavirus HCoV-NL63

- First selection of T1249-resistant HIV-1 viruses

- Regulation of splicing by RNA structure

- New tRNA-mediated HIV-1 recombination mechanism

- HIV-1 RNA circularization

- Implementation of the humanized mouse for safety testing of lentiviral RNAi gene therapy

- Identification of a non-canonical Dicer-independent shRNA processing pathway
- Description of the novel AgoshRNA design

- Regulated expression of the SIV Rev and Env proteins via translational control

- Novel HIV-1 latency mechanism via cellular antisense transcription

- Description of HIV-1 latency in activated T cells

- Natural way to purge the HIV reservoir in activated T cells by dendritic cells

Publications:
> 469 peer-reviewed articles
> 13,700 citations
ISI H-index 61

Research programmes

Prof. PhD B. Berkhout (Virology)

Mechanism of HIV-1 gene expression.  We study the mechanism of LTR-mediated viral transcription. Appropriate in vitro and in vivo assay systems have been developed for these studies, including the evolutionary analysis of mutated viruses. We analyzed the LTR promoter activity for the different HIV-1 subtypes. The mechanism of transcriptional activation by the viral Tat protein through the TAR hairpin motif has been addressed at the molecular level by different approaches. More recently, we have initiated studies on the mechanism of proviral latency. Other aspects of viral gene expression, such as the regulation of mRNA splicing and polyadenylation are also being addressed. 

HIV-1 RNA structure and function. Studies have focused on the untranslated leader that contains many replication signals, e.g. for RNA dimerization and RNA packaging. A riboswitch model was proposed to differentiate between the gene expression (translation) and virus-specific activities (virion packaging) of the HIV-1 RNA genome. We reported that the 9kb HIV-1 RNA circularizes by means of a 5'-3' basepairing interaction. We also have a special interest in the nucleotide-composition and codon usage of retroviruses. We also study the initiation process of HIV-1 reverse transcription, which requires the interaction between the primer-binding site (PBS) and the cellular tRNAlys3 primer and the Reverse Transcriptase enzyme.

Virus evolution and drug-resistance.  We study virus evolution in diverse settings, e.g. the selection of drug-resistant virus variants and the selection of revertant viruses from replication-impaired HIV-1 mutants. Drug resistance was studied for the RT inhibitor 3TC (lamivudine) and we describede for the first time a fitness loss of the mutated RT enzyme and virus. Other studies focus on the mechanism that provides resistance to the entry inhibitor T20 (Fuzeon), we e.g. reported the first drug-dependent HIV-1 variant and RNAi-resistance (see below).

RNA interference as antiviral therapy.  HIV-1 replication in cell culture can be effectively blocked by intracellular expresion of a single shRNA inhibitor that induces RNA interference (RNAi) against HIV-1 or a critical cellular co-factor. However, the virus can escape as was demonstrated in massive evolution studies that described different escape routes. We have succesfully blocked viral escape by a combinatorial RNAi approach that is now being tested in a humanized mouse model as pre-clinical test system. A lentivirus-mediated gene therapy is being developed based on this system. Basic aspects of the virus-RNAi interaction, e.g. the presence of viral RNAi suppressors, are also being studied. We recently described a novel Dicer-independent RNAi pathway.

Novel vaccine strategies.  Live-attenuated virus vaccines have shown to be much more effective than any other AIDS vaccine approach. However, the attenuated virus may revert over time to a virulent and pathogenic phenotype, and live attenuated HIV vaccines are therefore considered to be unsafe. To improve the safety, we have constructed a conditional-live virus in which the doxycycline (dox)-controlled gene expression system (Tet-On system) was incorporated. Upon vaccination, replication of this virus can be limited to the time required to induce a protective immune response by transient administration of dox, which will prevent the evolution of a more pathogenic virus. Promising results have recently been obtained in the SIV-macaque model. Spin-off is formed by the evolution of imporved Tet-On systems (collaboration with dr. A.T. Das).

Patient related virus studies. Based on the availability of relevant patient samples, e.g. as member of the Amsterdam Cohort Studies on HIV-AIDS, we are performing several clinically relevant virology studies. This includes the description of HIV-1 superinfections, novel HIV-1 subtype variants, HBV double infections, and the development of ultra-sensitive intracellular HIV-1 RNA detection assays. 

Faculty
PhD M.T.E. Cornelissen
PhD A.C. van der Kuyl

Postdocs
PhD E. Herrera Carrillo
PhD A.O. Pasternak
PhD Y.U. van der Velden
PhD F.J. van Hemert
PhD T. van Montfort
PhD J.C. Villaudy

Others
E. Frankin
G.P.M. Klaver
E. Siteur-van Rijnstra
M.A. Vink
N. Zhao
F.K. Zorgdrager

Current research funding
  • AMC
  • NWO (Vrijgesteld)
  • National Institutes of Health
  • Stichting Aidsfonds/SOA AIDS Nederland
  • Vrije Universiteit Brussel