Koenraad Van Doorslaer

Koenraad Van Doorslaer
The University of Arizona | UA · BIO5 Institute

Ph.D.

About

96
Publications
10,406
Reads
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3,230
Citations
Additional affiliations
January 2010 - present
National Institute of Allergy and Infectious Diseases
Position
  • PostDoc Position
August 2005 - January 2010
Albert Einstein College of Medicine
Position
  • PhD Student

Publications

Publications (96)
Article
Full-text available
Upon infection, DNA viruses can be sensed by pattern recognition receptors (PRRs), leading to the activation of type I and III interferons to block infection. Therefore, viruses must inhibit these signaling pathways, avoid being detected, or both. Papillomavirus virions are trafficked from early endosomes to the Golgi apparatus and wait for the ons...
Article
Full-text available
Following the results of the International Committee on Taxonomy of Viruses (ICTV) Ratification Vote held in March 2021, a standard two-part "binomial nomenclature" is now the norm for naming virus species. Adoption of the new nomenclature is still in its infancy; thus, it is timely to reiterate the distinction between "virus" and "virus species" a...
Article
Fish papillomaviruses form a newly discovered group broadly recognized as the Secondpapillomavirinae subfamily. This study expands the documented genomes of the fish papillomaviruses from six to 16, including one from the Antarctic emerald notothen, seven from commercial market fishes, one from data mining of sea bream sequence data, and one from a...
Article
Polyomaviruses are non–enveloped viruses with circular double-stranded DNA genomes (∼4–7 kb). Initially identified in mammals, polyomaviruses have now been identified in birds and a few fish species. Although fragmentary polyomavirus-like sequences have been detected as apparent ‘hitchhikers’ in shotgun genomics datasets for various arthropods, the...
Article
During persistent human papillomavirus infection, the viral genome replicates as an extrachromosomal plasmid that is efficiently partitioned to daughter cells during cell division. We have previously shown that an element which overlaps the HPV18 transcriptional enhancer promotes stable DNA replication of replicons containing the viral replication...
Article
Anellovirus infections are highly prevalent in mammals but prior to this study only a handful of anellovirus genomes had been identified in members of the Felidae family. Here characterise anelloviruses in pumas (Puma concolor), bobcats (Lynx rufus), Canada lynx (Lynx canadensis), caracals (Caracal caracal) and domestic cats (Felis catus). The comp...
Preprint
Full-text available
Polyomaviruses are nonenveloped viruses with circular double stranded DNA genomes that range in size from ~4 to 7 kilobasepairs. Initially identified in mammals, polyomaviruses have now been identified in birds and a few fish species. Although fragmentary polyomavirus-like sequences have been detected as apparent 'hitchhikers' in shotgun genomics d...
Preprint
Full-text available
CD4+ T cells use T cell receptor (TCR)-CD3 complexes, and CD4, to respond to peptide antigens within MHCII molecules (pMHCII). We report here that, through ~435 million years of evolution in jawed vertebrates, purifying selection has shaped motifs in the extracellular, transmembrane, and intracellular domains of eutherian CD4 that both enhance pMHC...
Article
Full-text available
We recently identified and treated a rare case of oral focal epithelial hyperplasia (FEH) in an adult patient with chronic graft‐vs‐host disease. This is the first report linking KTP laser therapy to successful long‐term treatment HPV32 FEH.
Preprint
Full-text available
Upon infection, DNA viruses can be sensed by pattern recognition receptors (PRRs) leading to the activation of type I and III interferons, aimed at blocking infection. Therefore, viruses must inhibit these signaling pathways, avoid being detected, or both. Papillomavirus virions are trafficked from early endosomes to the Golgi apparatus and wait fo...
Article
Full-text available
The family Cactaceae comprises a diverse group of typically succulent plants that are native to the American continent but have been introduced to nearly all other continents, predominantly for ornamental purposes. Despite their economic, cultural, and ecological importance, very little research has been conducted on the viral community that infect...
Preprint
Full-text available
During persistent human papillomavirus infection, the viral genome replicates as an extrachromosomal plasmid that is efficiently partitioned to daughter cells during cell division. We have previously shown that an element which overlaps the HPV18 transcriptional enhancer promotes stable DNA replication of replicons containing the viral replication...
Article
Human papillomavirus (HPV) infection occurs in differentiating epithelial tissues. Cancers caused by high‐risk types (e.g., HPV16 and HPV18) typically occur at oropharyngeal and anogenital anatomical sites. The HPV life cycle is differentiation‐dependent, requiring tissue culture methodology that is able to recapitulate the three‐dimensional (3D) s...
Article
Full-text available
Oncogenic human papillomaviruses (HPVs) replicate in differentiating epithelium, causing 5% of cancers worldwide. Like most other DNA viruses, HPV infection initiates after trafficking viral genome (vDNA) to host cell nuclei. Cells possess innate surveillance pathways to detect microbial components or physiological stresses often associated with mi...
Article
Sonoran felids are threatened by drought and habitat fragmentation. Vector range expansion and anthropogenic factors such as habitat encroachment and climate change are altering viral evolutionary dynamics and exposure. However, little is known about the diversity of viruses present in these populations. Small felid populations with lower genetic d...
Article
Full-text available
High-throughput sequencing technologies provide unprecedented power to identify novel viruses from a wide variety of (environmental) samples. The field of ‘viral metagenomics’ has dramatically expanded our understanding of viral diversity. Viral metagenomic approaches imply that many novel viruses will not be described by researchers who are expert...
Preprint
Sonoran felids are threatened by drought and habitat fragmentation. Vector range expansion and anthropogenic factors such as habitat encroachment and climate change are altering viral evolutionary dynamics and exposure. However, little is known about the diversity of viruses present in these populations. Small felid populations with lower genetic d...
Article
Full-text available
Many Gram-positive bacteria respond to copper stress by upregulating a copper export system controlled by a copper-sensitive repressor, CopR-CopY. The previous operator sequence for this family of proteins had been identified as TACANNTGTA. Here, using several recombinant proteins and mutations in various DNA fragments, we define those 10 bases as...
Article
Full-text available
Cactaceae comprise a diverse and iconic group of flowering plants which are almost exclusively indigenous to the New World. The wide variety of growth forms found amongst the cacti have led to the trafficking of many species throughout the world as ornamentals. Despite the evolution and physiological properties of these plants having been extensive...
Preprint
Full-text available
Oncogenic human papillomaviruses (HPVs) replicate in differentiating epithelium, causing 5% of cancers worldwide. Like most other DNA viruses, HPV infection initiates after trafficking viral genome (vDNA) to host cell nuclei. Cells possess innate surveillance pathways to detect microbial components or physiological stresses often associated with mi...
Preprint
Full-text available
High-throughput sequencing technologies provide unprecedented power to identify novel viruses from a wide variety of (environmental) samples. The field of 'viral metagenomics' has dramatically expanded our understanding of viral diversity. Viral metagenomic approaches imply that many novel viruses will not be described by researchers who are expert...
Article
Full-text available
Cervical carcinogenesis, the second leading cause of cancer death in women worldwide, is caused by multiple types of human papillomaviruses (HPVs). To investigate a possible role for HPV in a cervical carcinoma that was HPV‐negative by PCR testing, we performed HPV DNA hybridization capture plus massively parallel sequencing. This detected a subgen...
Preprint
Full-text available
Cervical carcinogenesis, the second leading cause of cancer death in women worldwide, is caused by multiple types of human papillomaviruses (HPVs). To investigate a possible role for HPV in a cervical carcinoma that was HPV-negative by PCR testing, we performed HPV DNA hybridization capture plus massively parallel sequencing. This detected a subgen...
Article
Full-text available
The Gram-negative human pathogen N. gonorrhoeae (Ngo) quickly attaches to epithelial cells, and large numbers of the bacteria remain on the cell surface for prolonged periods. Ngo invades cells but few viable intracellular bacteria are recovered until later stages of infection, leading to the assumption that Ngo is a weak invader. On the cell surfa...
Data
Ngo induces LC3-II in the presence of lysosomal inhibitor. Densitometry quantification of immunoblots in Fig 1G (n = 2). As described, ME180 cells were mock infected, starved (St.), or infected with Ngo for 4 h in the presence of indicated concentrations of CQ. LC3-II levels normalized to internal control GAPDH were compared to those of mock infect...
Data
Ngo infection induces autophagic flux in human endocervical Hec1B epithelial cells via CD46-cyt1. (A) Representative immunoblot showing CD46-cyt1 and GAPDH in cells treated with control (Ctrl) or CD46-cyt1 (Cyt-1) siRNA. GAPDH in each sample was used as the internal control. (B) Representative immunoblot showing LC3-I, LC3-II and GAPDH in cells tre...
Data
Autophagic flux in Ngo infected cells is mediated by Tfp retraction. (A) Representative immunoblot showing LC3-I, LC3-II and GAPDH in ME180 cells that were mock infected or infected with Ngo wt or ΔpilT at MOI of 10 for 4 h GAPDH served as the internal control for each sample. (B) Densitometry quantification of LC3-II levels in immunoblots from 2 i...
Data
Rubicon expression is undetectable in ME180s. (A) Representative immunoblot showing Rubicon and GAPDH in ME180 cells and Bone Marrow Derived Macrophages (BMDM). GAPDH in each sample was used as the internal control. (B) Densitometry quantification of immunoblots from 2 independent experiments described in (A). Rubicon levels in uninfected ME180s an...
Data
Intracellular Ngo colocalize with autophagolysosomal markers (LC3+LAMP1+) throughout the length of the cell. Successive SIM Z-sections of a field of Ngo-infected ME180 cells. LAMP1, LC3, and DAPI are red, green, and blue, respectively. Bot: bottom-most Z section. Top: Top-most Z seection. Most intracellular Ngo colocalized with LAMP1+, LC3+ compart...
Data
CD46-cyt1 knockdown does not affect Ngo invasion. (A) Flow cytometry analysis of ME180 cells treated with control (Ctrl) or CD46-cyt1 (Cyt-1) siRNA and mock infected or infected with CFSE-labeled Ngo at an MOI of 10, for 4 h (n = 3). Prior to analysis, extracellular CFSE signal was quenched with Trypan Blue (final concentration 0.4%). Live populati...
Data
Lysosomal inhibitors increase the number of viable intracellular Ngo in human primary human endocervical epithelial cells. Quantitation of attached and intracellular Ngo colony forming units (CFU) in primary cells treated with CQ (50 μM) or Bafilomycin (50 nM) followed by infection at an MOI of 10 for 4 h. Attached CFUs were normalized to total inp...
Article
Full-text available
The Papillomaviridae is a family of DNA viruses [...]
Article
Full-text available
Although some members of the viral family Papillomaviridae cause benign skin warts (papillomas), many human papillomavirus (HPV) infections are not associated with visible symptoms. For example, most healthy adults chronically shed Gammapapillomavirus ( Gamma ) virions from apparently healthy skin surfaces. To further explore the diversity of papil...
Article
Phylogenetic analyses allow for inferring a hypothesis about the evolutionary history of a set of homologous molecular sequences. This hypothesis can be used as the basis for further molecular and computational studies. In this unit, we offer one specific method to construct a Maximum Likelihood phylogenetic tree. We outline how to identify homolog...
Article
The Papillomaviridae is a family of small, non-enveloped viruses with double-stranded DNA genomes of 5 748 to 8 607 bp. Their classification is based on pairwise nucleotide sequence identity across the L1 open reading frame. Members of the Papillomaviridae primarily infect mucosal and keratinised epithelia, and have been isolated from fish, reptile...
Article
Full-text available
The Polyomaviridae is a diverse family of circular double-stranded DNA viruses. Polyomaviruses have been isolated from a wide array of animal hosts. An understanding of the evolutionary and ecological dynamics of these viruses is essential to understanding the pathogenicity of polyomaviruses. Using a high throughput sequencing approach, we identifi...
Article
Full-text available
Papillomaviridae is a diverse family of circular, double-stranded DNA (dsDNA) viruses that infect a broad range of mammalian, avian and fish hosts. While papillomaviruses have been characterized most extensively in humans, the study of non-human papillomaviruses has contributed greatly to our understanding of their pathogenicity and evolution. Usin...
Article
Full-text available
Human papillomavirus (HPV) genomes are replicated and maintained as extrachromosomal plasmids during persistent infection. The viral E2 proteins are thought to promote stable maintenance replication by tethering the viral DNA to host chromatin. However, this has been very difficult to prove genetically, as the E2 protein is involved in transcriptio...
Article
The family Papillomaviridae contains more than 320 papillomavirus types, with most having been identified as infecting skin and mucosal epithelium in mammalian hosts. To date, only nine non-mammalian papillomaviruses have been described from birds (n = 5), a fish (n = 1), a snake (n = 1), and turtles (n = 2). The identification of papillomaviruses...
Article
Full-text available
The apolipoprotein B messenger RNA-editing, enzyme-catalytic, polypeptide-like 3 (APOBEC3) family of cytidine deaminases plays an important role in the innate immune response to viral infections by editing viral genomes. However, the cytidine deaminase activity of APOBEC3 enzymes also induces somatic mutations in host genomes, which may drive cance...
Article
Full-text available
Papillomaviruses infect and replicate in keratinocytes, but viral proteins are initially expressed at low levels and there is no effective and quantitative method to determine the efficiency of infection on a cell-to-cell basis. Here we describe human papillomavirus (HPV) genomes that express marker proteins (antibiotic resistance genes and Green F...
Chapter
Pathology departments routinely process and store formalin-fixed, paraffin-embedded (FFPE) tissue samples for clinical diagnosis. These collections often contain decades’ worth of samples and represent a treasure trove of specimens that can be analyzed for retrospective epidemiological studies, diagnostics, and pathogen discovery. Accurate amplific...
Article
Full-text available
The Papillomavirus Episteme (PaVE) is a database of curated papillomavirus genomic sequences, accompanied by web-based sequence analysis tools. This update describes the addition of major new features. The papillomavirus genomes within PaVE have been further annotated, and now includes the major spliced mRNA transcripts. Viral genes and transcripts...
Article
Full-text available
It is becoming clear that, in addition to gene gain, the loss of genes may be an important evolutionary mechanism for many organisms. However, gene loss is often associated with an increased mutation rate, thus quickly erasing evidence from the genome. The analysis of evolutionarily related sequences can provide empirical evidence for gene loss eve...
Article
Full-text available
Polyomaviruses are a family of DNA tumor viruses that are known to infect mammals and birds. To investigate the deeper evolutionary history of the family, we used a combination of viral metagenomics, bioinformatics, and structural modeling approaches to identify and characterize polyomavirus sequences associated with fish and arthropods. Analyses d...
Article
This article provides information to support the database article titled “UbSRD: The Ubiquitin Structural Relational Database” (Harrison et al., 2015) [1] . The ubiquitin-like homology fold (UBL) represents a large family that encompasses both post-translational modifications, like ubiquitin (UBQ) and SUMO, and functional domains on many biological...
Article
Full-text available
The structurally defined ubiquitin-like homology fold (UBL) can engage in several unique protein-protein interactions (PPI) and many of these complexes have been characterized with high-resolution techniques. Using Rosetta's structural classification tools we have created the Ubiquitin Structural Relational Database (UbSRD), an SQL database of feat...
Article
Full-text available
In order to complete their life cycle, papillomaviruses have evolved to manipulate a plethora of cellular pathways. The products of the human Alphapapillomavirus E6 proteins specifically interact with and target PDZ containing proteins for degradation. This viral phenotype has been suggested to play a role in viral oncogenesis. To analyze the assoc...
Article
Papillomaviruses are a very successful group of viruses that replicate persistently in localized regions of the stratified epithelium of their specific host. Infection results in pathologies ranging from asymptomatic infection, benign warts, to malignant carcinomas. Despite this diversity, papillomavirus genomes are small (7-8 kbp) and contain at m...
Article
Full-text available
More than 270 different types of papillomaviruses have been discovered in a wide array of animal species. Despite the great diversity of papillomaviruses, little is known about the evolutionary processes that drive host tropism and the emergence of oncogenic genotypes. Although host defense mechanisms have evolved to interfere with various aspects...
Article
Viruses belonging to the Papillomaviridae family have been isolated from a variety of mammals, birds and non-avian reptiles. It is likely that most, if not all, amniotes carry a broad array of viral types. To date, the complete genomic sequence of more than 240 distinct viral types has been characterized at the nucleotide level. The analysis of thi...
Article
Full-text available
Genital condyloma-like lesions were observed on male and female cynomolgus macaque monkeys (Macaca fascicularis) originating from the island of Mauritius. Cytobrush and/or biopsy samples were obtained from lesions of 57 affected macaques. Primary histologic features included eosinophilic, neutrophilic, and lymphoplasmacytic penile and vulvar inflam...
Article
Full-text available
The goal of the Papillomavirus Episteme (PaVE) is to provide an integrated resource for the analysis of papillomavirus (PV) genome sequences and related information. The PaVE is a freely accessible, web-based tool (http://pave.niaid.nih.gov) created around a relational database, which enables storage, analysis and exchange of sequence information....
Article
Expression of activated telomerase and subversion of the p16/pRb pathway is sufficient and essential for the in vitro immortalization of primary keratinocytes. Most cancers-including cervical carcinoma-over-express hTERT, the catalytic domain of the telomerase complex. Only a limited set of viruses within the Alphapapillomavirus genus are oncogenic...
Article
Full-text available
The role of caveolin and caveolae in the pathogenesis of infection has only recently been appreciated. In this chapter, we have highlighted some important new data on the role of caveolin in infections due to bacteria, viruses and fungi but with particular emphasis on the protozoan parasites Leishmania spp., Trypanosoma cruzi and Toxoplasma gondii....
Data
Full-text available
Diagnostic single nucleotide polymorphisms (SNPs) for HPV16 lineages. (PDF)
Data
Mathematica 7 code for performing imputation based on BLAST results. A partial sequence of the HPV16 genome was used to search a database of complete genomes using BLAST. The results of the BLAST search were then used to identify the full length genomes that had the highest score and one complete genome sequence was added to a new file that was use...
Data
Full-text available
Mathematica 7 HPV sequence analysis code. Mathematica 7 notebook containing code used for performing sequence analysis on the nucleotide sequences of a reference HPV complete genome sequence library. Analyses include calculating pairwise differences and plotting a heatmap of values, as well as identifying lineage-specific (diagnostic) single nucleo...
Article
Full-text available
Human Papillomavirus type 16 (HPV16) causes over half of all cervical cancer and some HPV16 variants are more oncogenic than others. The genetic basis for the extraordinary oncogenic properties of HPV16 compared to other HPVs is unknown. In addition, we neither know which nucleotides vary across and within HPV types and lineages, nor which of the s...
Article
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