@article{pmid39348450,

title = {A preliminary indication that HLA-A*03:01 may be associated with visceral leishmaniasis development in people living with HIV in Ethiopia},

author = {Nicky de Vrij and Romi Vandoren and Kadrie Ramadan and Anke Van Hul and Ann Ceulemans and Mekibib Kassa and Roma Melkamu and Arega Yeshanew and Tadfe Bogale and Hailemariam Beyene and Kasaye Sisay and Aderajew Kibret and Dagnew Mersha and Wim L Cuypers and Florian Vogt and Saskia van Henten and Koert Ritmeijer and Thao-Thy Pham and Pieter Meysman and Kris Laukens and Bart Cuypers and Ermias Diro and Rezika Mohammed and Johan van Griensven and Wim Adriaensen},

doi = {10.1371/journal.pntd.0012000},

issn = {1935-2735},

year  = {2024},

date = {2024-09-01},

urldate = {2024-09-01},

journal = {PLoS Negl Trop Dis},

volume = {18},

number = {9},

pages = {e0012000},

abstract = {Human immunodeficiency virus (HIV) co-infection is a major challenge for visceral leishmaniasis (VL) control, particularly in Ethiopia where the incidence of both pathogens is high. VL-HIV often leads to high rates of antileishmanial treatment failure and recurrent VL disease relapses. Considering the high prevalence of HIV and Leishmania in the Ethiopian population, preventing the progression of asymptomatic Leishmania infection to disease would be a valuable asset to VL disease control and to the clinical management of people living with HIV (PLWH). However, such a strategy requires good understanding of risk factors for VL development. In immunocompetent individuals living in Brazil, India, or Iran, the Human Leukocyte Antigen (HLA) gene region has been associated with VL development. We used NanoTYPE, an Oxford Nanopore Technologies sequencing-based HLA genotyping method, to detect associations between HLA genotype and VL development by comparing 78 PLWH with VL history and 46 PLWH that controlled a Leishmania infection, all living in a VL endemic region of North-West Ethiopia. We identified an association between HLA-A*03:01 and increased risk of VL development (OR = 3.89). These data provide candidate HLA alleles that can be further explored for inclusion in a potential Leishmania screen-and-treat strategy in VL endemic regions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38702419,

title = {Persistent T cell unresponsiveness associated with chronic visceral leishmaniasis in HIV-coinfected patients},

author = {Nicky de Vrij and Julia Pollmann and Antonio M Rezende and Ana V Ibarra-Meneses and Thao-Thy Pham and Wasihun Hailemichael and Mekibib Kassa and Tadfe Bogale and Roma Melkamu and Arega Yeshanew and Rezika Mohammed and Ermias Diro and Ilse Maes and Malgorzata A Domagalska and Hanne Landuyt and Florian Vogt and Saskia van Henten and Kris Laukens and Bart Cuypers and Pieter Meysman and Hailemariam Beyene and Kasaye Sisay and Aderajew Kibret and Dagnew Mersha and Koert Ritmeijer and Johan van Griensven and Wim Adriaensen},

doi = {10.1038/s42003-024-06225-2},

issn = {2399-3642},

year  = {2024},

date = {2024-05-01},

journal = {Commun Biol},

volume = {7},

number = {1},

pages = {524},

abstract = {A large proportion of HIV-coinfected visceral leishmaniasis (VL-HIV) patients exhibit chronic disease with frequent VL recurrence. However, knowledge on immunological determinants underlying the disease course is scarce. We longitudinally profiled the circulatory cellular immunity of an Ethiopian HIV cohort that included VL developers. We show that chronic VL-HIV patients exhibit high and persistent levels of TIGIT and PD-1 on CD8/CD8 T cells, in addition to a lower frequency of IFN-γ TIGIT CD8/CD8 T cells, suggestive of impaired T cell functionality. At single T cell transcriptome and clonal resolution, the patients show CD4 T cell anergy, characterised by a lack of T cell activation and lymphoproliferative response. These findings suggest that PD-1 and TIGIT play a pivotal role in VL-HIV chronicity, and may be further explored for patient risk stratification. Our findings provide a strong rationale for adjunctive immunotherapy for the treatment of chronic VL-HIV patients to break the recurrent disease cycle.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37976853,

title = {Malate production, sugar metabolism, and redox homeostasis in the leaf growth zone of Rye (Secale cereale) increase stress tolerance to aluminum stress: A biochemical and genome-wide transcriptional study},

author = {Chase P Donnelly and Alexandra De Sousa and Bart Cuypers and Kris Laukens and Asma A Al-Huqail and Han Asard and Gerrit T S Beemster and Hamada AbdElgawad},

doi = {10.1016/j.jhazmat.2023.132956},

issn = {1873-3336},

year  = {2024},

date = {2024-02-01},

journal = {J Hazard Mater},

volume = {464},

pages = {132956},

abstract = {Global soil acidification is increasing, enlarging aluminum (Al) availability in soils, leading to reductions in plant growth. This study investigates the effect of Al stress on the leaf growth zones of Rye (Secale cereale, cv Beira). Kinematic analysis showed that the effect of Al on leaf growth rates was mainly due to a reduced cell production rate in the meristem. Transcriptomic analysis identified 2272 significantly (log2fold > |0.5| FDR < 0.05) differentially expressed genes (DEGs) for Al stress. There was a downregulation in several DEGs associated with photosynthetic processes and an upregulation in genes for heat/light response, and HO production in all leaf zones. DEGs associated with heavy metals and malate transport were increased, particularly, in the meristem. To determine the putative function of these processes in Al tolerance, we performed biochemical analyses comparing the tolerant Beira with an Al sensitive variant RioDeva. Beira showed improved sugar metabolism and redox homeostasis, specifically in the meristem compared to RioDeva. Similarly, a significant increase in malate and citrate production, which are known to aid in Al detoxification in plants, was found in Beira. This suggests that Al tolerance in Rye is linked to its ability for Al exclusion from the leaf meristem.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38054750,

title = {Selective whole-genome sequencing of  parasites directly from blood samples by nanopore adaptive sampling},

author = {Katlijn De Meulenaere and Wim L Cuypers and Julia M Gauglitz and Pieter Guetens and Anna Rosanas-Urgell and Kris Laukens and Bart Cuypers},

doi = {10.1128/mbio.01967-23},

issn = {2150-7511},

year  = {2024},

date = {2024-01-01},

journal = {mBio},

volume = {15},

number = {1},

pages = {e0196723},

abstract = {Malaria is caused by parasites of the genus , and reached a global disease burden of 247 million cases in 2021. To study drug resistance mutations and parasite population dynamics, whole-genome sequencing of patient blood samples is commonly performed. However, the predominance of human DNA in these samples imposes the need for time-consuming laboratory procedures to enrich  DNA. We used the Oxford Nanopore Technologies' adaptive sampling feature to circumvent this problem and enrich  reads directly during the sequencing run. We demonstrate that adaptive nanopore sequencing efficiently enriches  reads, which simplifies and shortens the timeline from blood collection to parasite sequencing. In addition, we show that the obtained data can be used for monitoring genetic markers, or to generate nearly complete genomes. Finally, owing to its inherent mobility, this technology can be easily applied on-site in endemic areas where patients would benefit the most from genomic surveillance.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37821878,

title = {A new Plasmodium vivax reference genome for South American isolates},

author = {Katlijn De Meulenaere and Bart Cuypers and Dionicia Gamboa and Kris Laukens and Anna Rosanas-Urgell},

doi = {10.1186/s12864-023-09707-5},

issn = {1471-2164},

year  = {2023},

date = {2023-10-01},

journal = {BMC Genomics},

volume = {24},

number = {1},

pages = {606},

abstract = {BACKGROUND: Plasmodium vivax is the second most important cause of human malaria worldwide, and accounts for the majority of malaria cases in South America. A high-quality reference genome exists for Papua Indonesia (PvP01) and Thailand (PvW1), but is lacking for South America. A reference genome specifically for South America would be beneficial though, as P. vivax is a genetically diverse parasite with geographical clustering.nnRESULTS: This study presents a new high-quality assembly of a South American P. vivax isolate, referred to as PvPAM (P. vivax Peruvian AMazon). The genome was obtained from a low input patient sample from the Peruvian Amazon and sequenced using PacBio technology, resulting in a highly complete assembly with 6497 functional genes. Telomeric ends were present in 17 out of 28 chromosomal ends, and additional (sub)telomeric regions are present in 12 unassigned contigs. A comparison of multigene families between PvPAM and the PvP01 genome revealed remarkable variation in vir genes, and the presence of merozoite surface proteins (MSP) 3.6 and 3.7. Three dhfr and dhps drug resistance associated mutations are present in PvPAM, similar to those found in other Peruvian isolates. Mapping of publicly available South American whole genome sequencing (WGS) data to PvPAM resulted in significantly fewer variants and truncated reads compared to the use of PvP01 or PvW1 as reference genomes. To minimize the number of core genome variants in non-South American samples, PvW1 is most suited for Southeast Asian isolates, both PvPAM and PvW1 are suited for South Asian isolates, and PvPAM is recommended for African isolates. Interestingly, non-South American samples still contained the least subtelomeric variants when mapped to PvPAM, indicating high quality of the PvPAM subtelomeric regions.nnCONCLUSIONS: Our findings show that the PvPAM reference genome more accurately represents South American P. vivax isolates in comparison to PvP01 and PvW1. In addition, PvPAM has a high level of completeness, and contains a similar number of annotated genes as PvP01 or PvW1. The PvPAM genome therefore will be a valuable resource to improve future genomic analyses on P. vivax isolates from the South American continent.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{cells12091224,

title = {IL-22-Activated MUC13 Impacts on Colonic Barrier Function through JAK1/STAT3, SNAI1/ZEB1 and ROCK2/MAPK Signaling},

author = {Tom Breugelmans and Wout Arras and Baptiste Oosterlinck and Aranzazu Jauregui-Amezaga and Micha\"{e}l Somers and Bart Cuypers and Kris Laukens and Joris G. De Man and Heiko U. De Schepper and Benedicte Y. De Winter and Annemieke Smet},

url = {https://www.mdpi.com/2073-4409/12/9/1224},

doi = {10.3390/cells12091224},

issn = {2073-4409},

year  = {2023},

date = {2023-01-01},

journal = {Cells},

volume = {12},

number = {9},

abstract = {Overexpression of the transmembrane mucin MUC13, as seen in inflammatory bowel diseases (IBD), could potentially impact barrier function. This study aimed to explore how inflammation-induced MUC13 disrupts epithelial barrier integrity by affecting junctional protein expression in IBD, thereby also considering the involvement of MUC1. RNA sequencing and permeability assays were performed using LS513 cells transfected with MUC1 and MUC13 siRNA and subsequently stimulated with IL-22. In vivo intestinal permeability and MUC13-related signaling pathways affecting barrier function were investigated in acute and chronic DSS-induced colitis wildtype and Muc13\−/\− mice. Finally, the expression of MUC13, its regulators and other barrier mediators were studied in IBD and control patients. Mucin knockdown in intestinal epithelial cells affected gene expression of several barrier mediators in the presence/absence of inflammation. IL-22-induced MUC13 expression impacted barrier function by modulating the JAK1/STAT3, SNAI1/ZEB1 and ROCK2/MAPK signaling pathways, with a cooperating role for MUC1. In response to DSS, MUC13 was protective during the acute phase whereas it caused more harm upon chronic colitis. The pathways accounting for the MUC13-mediated barrier dysfunction were also altered upon inflammation in IBD patients. These novel findings indicate an active role for aberrant MUC13 signaling inducing intestinal barrier dysfunction upon inflammation with MUC1 as collaborating partner.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{LIN2023100914,

title = {Acquired non-thermal plasma resistance mediates a shift towards aerobic glycolysis and ferroptotic cell death in melanoma},

author = {Abraham Lin and Maxime Sahun and Eline Biscop and Hanne Verswyvel and Jorrit De Waele and Joey De Backer and Claudia Theys and Bart Cuypers and Kris Laukens and Wim Vanden Berghe and Evelien Smits and Annemie Bogaerts},

url = {https://www.sciencedirect.com/science/article/pii/S1368764622001133},

doi = {https://doi.org/10.1016/j.drup.2022.100914},

issn = {1368-7646},

year  = {2023},

date = {2023-01-01},

journal = {Drug Resistance Updates},

volume = {67},

pages = {100914},

abstract = {Aims 

To gain insights into the underlying mechanisms of NTP therapy sensitivity and resistance, using the first-ever NTP-resistant cell line derived from sensitive melanoma cells (A375). 

Methods 

Melanoma cells were exposed to NTP and re-cultured for 12 consecutive weeks before evaluation against the parental control cells. Whole transcriptome sequencing analysis was performed to identify differentially expressed genes and enriched molecular pathways. Glucose uptake, extracellular lactate, media acidification, and mitochondrial respiration was analyzed to determine metabolic changes. Cell death inhibitors were used to assess the NTP-induced cell death mechanisms, and apoptosis and ferroptosis was further validated via Annexin V, Caspase 3/7, and lipid peroxidation analysis. 

Results 

Cells continuously exposed to NTP became 10 times more resistant to NTP compared to the parental cell line of the same passage, based on their half-maximal inhibitory concentration (IC50). Sequencing and metabolic analysis indicated that NTP-resistant cells had a preference towards aerobic glycolysis, while cell death analysis revealed that NTP-resistant cells exhibited less apoptosis but were more vulnerable to lipid peroxidation and ferroptosis. 

Conclusions 

A preference towards aerobic glycolysis and ferroptotic cell death are key physiological changes in NTP-resistance cells, which opens new avenues for further, in-depth research into other cancer types.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36176603,

title = {The effect of local non-thermal plasma therapy on the cancer-immunity cycle in a melanoma mouse model},

author = {Abraham Lin and Joey De Backer and Delphine Quatannens and Bart Cuypers and Hanne Verswyvel and Edgar Cardenas De La Hoz and Bart Ribbens and Vasiliki Siozopoulou and Jonas Van Audenaerde and Elly Marcq and Filip Lardon and Kris Laukens and Steve Vanlanduit and Evelien Smits and Annemie Bogaerts},

doi = {10.1002/btm2.10314},

issn = {2380-6761},

year  = {2022},

date = {2022-09-01},

journal = {Bioeng Transl Med},

volume = {7},

number = {3},

pages = {e10314},

abstract = {Melanoma remains a deadly cancer despite significant advances in immune checkpoint blockade and targeted therapies. The incidence of melanoma is also growing worldwide, which highlights the need for novel treatment options and strategic combination of therapies. Here, we investigate non-thermal plasma (NTP), an ionized gas, as a promising, therapeutic option. In a melanoma mouse model, direct treatment of tumors with NTP results in reduced tumor burden and prolonged survival. Physical characterization of NTP treatment in situ reveals the deposited NTP energy and temperature associated with therapy response, and whole transcriptome analysis of the tumor identified several modulated pathways. NTP treatment also enhances the cancer-immunity cycle, as immune cells in both the tumor and tumor-draining lymph nodes appear more stimulated to perform their anti-cancer functions. Thus, our data suggest that local NTP therapy stimulates systemic, anti-cancer immunity. We discuss, in detail, how these fundamental insights will help direct the translation of NTP technology into the clinic and inform rational combination strategies to address the challenges in melanoma therapy.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid35758754,

title = {Variants in Bedaquiline-Candidate-Resistance Genes: Prevalence in Bedaquiline-Naive Patients, Effect on MIC, and Association with Mycobacterium tuberculosis Lineage},

author = {Emmanuel Rivi\`{e}re and Lennert Verboven and Anzaan Dippenaar and Sander Goossens and Elise De Vos and Elizabeth Streicher and Bart Cuypers and Kris Laukens and Fathia Ben-Rached and Timothy C Rodwell and Arnab Pain and Robin M Warren and Tim H Heupink and Annelies Van Rie},

doi = {10.1128/aac.00322-22},

issn = {1098-6596},

year  = {2022},

date = {2022-07-01},

journal = {Antimicrob Agents Chemother},

volume = {66},

number = {7},

pages = {e0032222},

abstract = {Studies have shown that variants in bedaquiline-resistance genes can occur in isolates from bedaquiline-naive patients. We assessed the prevalence of variants in all bedaquiline-candidate-resistance genes in bedaquiline-naive patients, investigated the association between these variants and lineage, and the effect on phenotype. We used whole-genome sequencing to identify variants in bedaquiline-resistance genes in isolates from 509 bedaquiline treatment naive South African tuberculosis patients. A phylogenetic tree was constructed to investigate the association with the isolate lineage background. Bedaquiline MIC was determined using the UKMYC6 microtiter assay. Variants were identified in 502 of 509 isolates (98.6%), with the highest (85%) prevalence of variants in the  () gene. We identified 36 unique variants, including 19 variants not reported previously. Only four isolates had a bedaquiline MIC equal to or above the epidemiological cut-off value of 0.25 μg/mL. Phylogenetic analysis showed that 14 of the 15 variants observed more than once occurred monophyletically in one Mycobacterium tuberculosis (sub)lineage. The bedaquiline MIC differed between isolates belonging to lineage 2 and 4 (Fisher's exact test,  = 0.0004). The prevalence of variants in bedaquiline-resistance genes in isolates from bedaquiline-naive patients is high, but very few (<2%) isolates were phenotypically resistant. We found an association between variants in bedaquiline resistance genes and Mycobacterium tuberculosis (sub)lineage, resulting in a lineage-dependent difference in bedaquiline phenotype. Future studies should investigate the impact of the presence of variants on bedaquiline-resistance acquisition and treatment outcome.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10.1371/journal.ppat.1010848,

title = {Four layer multi-omics reveals molecular responses to aneuploidy in Leishmania},

author = {Bart Cuypers and Pieter Meysman and Ionas Erb and Wout Bittremieux and Dirk Valkenborg and Geert Baggerman and Inge Mertens and Shyam Sundar and Basudha Khanal and Cedric Notredame and Jean-Claude Dujardin and Malgorzata A. Domagalska and Kris Laukens},

url = {https://doi.org/10.1371/journal.ppat.1010848},

doi = {10.1371/journal.ppat.1010848},

year  = {2022},

date = {2022-01-01},

journal = {PLOS Pathogens},

volume = {18},

number = {9},

pages = {1-23},

publisher = {Public Library of Science},

abstract = {Aneuploidy causes system-wide disruptions in the stochiometric balances of transcripts, proteins, and metabolites, often resulting in detrimental effects for the organism. The protozoan parasite Leishmania has an unusually high tolerance for aneuploidy, but the molecular and functional consequences for the pathogen remain poorly understood. Here, we addressed this question in vitro and present the first integrated analysis of the genome, transcriptome, proteome, and metabolome of highly aneuploid Leishmania donovani strains. Our analyses unambiguously establish that aneuploidy in Leishmania proportionally impacts the average transcript- and protein abundance levels of affected chromosomes, ultimately correlating with the degree of metabolic differences between closely related aneuploid strains. This proportionality was present in both proliferative and non-proliferative in vitro promastigotes. However, as in other Eukaryotes, we observed attenuation of dosage effects for protein complex subunits and in addition, non-cytoplasmic proteins. Differentially expressed transcripts and proteins between aneuploid Leishmania strains also originated from non-aneuploid chromosomes. At protein level, these were enriched for proteins involved in protein metabolism, such as chaperones and chaperonins, peptidases, and heat-shock proteins. In conclusion, our results further support the view that aneuploidy in Leishmania can be adaptive. Additionally, we believe that the high karyotype diversity in vitro and absence of classical transcriptional regulation make Leishmania an attractive model to study processes of protein homeostasis in the context of aneuploidy and beyond.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{https://doi.org/10.1002/1878-0261.13226,

title = {Fractionated irradiation of MCF7 breast cancer cells rewires a gene regulatory circuit towards a treatment-resistant stemness phenotype},

author = {Auchi Inalegwu and Bart Cuypers and J\"{u}rgen Claesen and Ann Janssen and Amelie Coolkens and Sarah Baatout and Kris Laukens and Winnok H. De Vos and Roel Quintens},

url = {https://febs.onlinelibrary.wiley.com/doi/abs/10.1002/1878-0261.13226},

doi = {https://doi.org/10.1002/1878-0261.13226},

year  = {2022},

date = {2022-01-01},

journal = {Molecular Oncology},

volume = {16},

number = {19},

pages = {3410-3435},

abstract = {Radiotherapy is the standard of care for breast cancer. However, surviving radioresistant cells can repopulate following treatment and provoke relapse. Better understanding of the molecular mechanisms of radiation resistance may help to improve treatment of radioresistant tumours. To emulate radiation therapy at the cellular level, we exposed MCF7 breast cancer cells to daily radiation doses of 2 Gy up to an accumulated dose of 20 Gy. Fractionally irradiated cells (FIR20) displayed increased clonogenic survival and population doubling time as compared with age-matched sham-irradiated cells and untreated parental MCF7 cells. RNA-sequencing revealed a core signature of 229 mRNAs and 7 circular RNAs of which the expression was significantly altered in FIR20 cells. Dysregulation of several top genes was mirrored at the protein level. The FIR20 cell transcriptome overlapped significantly with canonical radiation response signatures and demonstrated a remarkable commonality with radiation and endocrine therapy resistance expression profiles, suggesting crosstalk between both acquired resistance pathways, as indicated by reduced sensitivity to tamoxifen cytotoxicity of FIR20 cells. Using predictive analyses and functional enrichment, we identified a gene-regulatory network that promotes stemness and inflammatory signalling in FIR20 cells. We propose that these phenotypic traits render breast cancer cells more radioresistant but may at the same time serve as potential targets for combination therapies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36250048,

title = {Band 3-mediated  invasion is associated with transcriptional variation in  genes},

author = {Katlijn De Meulenaere and Surendra Kumar Prajapati and Elizabeth Villasis and Bart Cuypers and Johanna Helena Kattenberg and Bernadine Kasian and Moses Laman and Leanne J Robinson and Dionicia Gamboa and Kris Laukens and Anna Rosanas-Urgell},

doi = {10.3389/fcimb.2022.1011692},

issn = {2235-2988},

year  = {2022},

date = {2022-01-01},

journal = {Front Cell Infect Microbiol},

volume = {12},

pages = {1011692},

abstract = {The  reticulocyte invasion process is still poorly understood, with only a few receptor-ligand interactions identified to date. Individuals with the Southeast Asian ovalocytosis (SAO) phenotype have a deletion in the band 3 protein on the surface of erythrocytes, and are reported to have a lower incidence of clinical  malaria. Based on this observation, band 3 has been put forward as a receptor for  invasion, although direct proof is still lacking. In this study, we combined functional  invasion assays and transcriptome sequencing to uncover a band 3-mediated invasion pathway in  and potential band 3 ligands. Invasion by  field isolates was 67%-71% lower in SAO reticulocytes compared with non-SAO reticulocytes. Reticulocyte invasion was decreased by 40% and 27%-31% when blocking with an anti-band 3 polyclonal antibody and a PvTRAg38 peptide, respectively. To identify new band 3 receptor candidates, we mRNA-sequenced schizont-stage isolates used in the invasion assays, and observed high transcriptional variability in multigene and invasion-related families. Transcriptomes of isolates with low or high dependency on band 3 for invasion were compared by differential expression analysis, which produced a list of band 3 ligand candidates with high representation of  genes. Our  invasion assays have demonstrated that band 3 is a  invasion receptor and confirm previous  studies showing binding between PvTRAg38 and band 3, although the lower and variable inhibition levels observed suggest the involvement of other ligands. By coupling transcriptomes and invasion phenotypes from the same isolates, we identified a list of band 3 ligand candidates, of which the overrepresented  genes are the most promising for future research.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Schorn2021,

title = {A community resource for paired genomic and metabolomic data mining},

author = {Michelle A Schorn and Stefan Verhoeven and Lars Ridder and Florian Huber and Deepa D Acharya and Alexander A Aksenov and Gajender Aleti and Jamshid Amiri Moghaddam and Allegra T Aron and Saefuddin Aziz and Anelize Bauermeister and Katherine D Bauman and Martin Baunach and Christine Beemelmanns and Michael J Beman and Mar\'{i}a Victoria Berlanga-Clavero and Alex A Blacutt and Helge B Bode and Anne Boullie and Asker Brejnrod and Tim S Bugni and Alexandra Calteau and Liu Cao and V\'{i}ctor J Carri\'{o}n and Raquel Castelo-Branco and Shaurya Chanana and Alexander B Chase and Marc G Chevrette and Leticia V Costa-Lotufo and Jason M Crawford and Cameron R Currie and Bart Cuypers and Tam Dang and Tristan de Rond and Alyssa M Demko and Elke Dittmann and Chao Du and Christopher Drozd and Jean-Claude Dujardin and Rachel J Dutton and Anna Edlund and David P Fewer and Neha Garg and Julia M Gauglitz and Emily C Gentry and Lena Gerwick and Evgenia Glukhov and Harald Gross and Muriel Gugger and Dulce G Guill\'{e}n Matus and Eric J N Helfrich and Benjamin-Florian Hempel and Jae-Seoun Hur and Marianna Iorio and Paul R Jensen and Kyo Bin Kang and Leonard Kaysser and Neil L Kelleher and Chung Sub Kim and Ki Hyun Kim and Irina Koester and Gabriele M K\"{o}nig and Tiago Leao and Seoung Rak Lee and Yi-Yuan Lee and Xuanji Li and Jessica C Little and Katherine N Maloney and Daniel M\"{a}nnle and Christian Martin H. and Andrew C McAvoy and Willam W Metcalf and Hosein Mohimani and Carlos Molina-Santiago and Bradley S Moore and Michael W Mullowney and Mitchell Muskat and Louis-F\'{e}lix Nothias and Ellis C O'Neill and Elizabeth I Parkinson and Daniel Petras and J\"{o}rn Piel and Emily C Pierce and Karine Pires and Raphael Reher and Diego Romero and Caroline M Roper and Michael Rust and Hamada Saad and Carmen Saenz and Laura M Sanchez and S\oren Johannes S\orensen and Margherita Sosio and Roderich D S\"{u}ssmuth and Douglas Sweeney and Kapil Tahlan and Regan J Thomson and Nicholas J Tobias and Amaro E Trindade-Silva and Gilles P van Wezel and Mingxun Wang and Kelly C Weldon and Fan Zhang and Nadine Ziemert and Katherine R Duncan and Max Cr\"{u}semann and Simon Rogers and Pieter C Dorrestein and Marnix H Medema and Justin J J van der Hooft},

url = {https://doi.org/10.1038/s41589-020-00724-z},

doi = {10.1038/s41589-020-00724-z},

issn = {1552-4469},

year  = {2021},

date = {2021-02-15},

journal = {Nature Chemical Biology},

abstract = {Genomics and metabolomics are widely used to explore specialized metabolite diversity. The Paired Omics Data Platform is a community initiative to systematically document links between metabolome and (meta)genome data, aiding identification of natural product biosynthetic origins and metabolite structures.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{vaccines9030270,

title = {HLA-DRB1 Alleles Associated with Lower Leishmaniasis Susceptibility Share Common Amino Acid Polymorphisms and Epitope Binding Repertoires},

author = {Nicky de Vrij and Pieter Meysman and Sofie Gielis and Wim Adriaensen and Kris Laukens and Bart Cuypers},

url = {https://www.mdpi.com/2076-393X/9/3/270},

doi = {10.3390/vaccines9030270},

issn = {2076-393X},

year  = {2021},

date = {2021-01-01},

journal = {Vaccines},

volume = {9},

number = {3},

abstract = {Susceptibility for leishmaniasis is largely dependent on host genetic and immune factors. Despite the previously described association of human leukocyte antigen (HLA) gene cluster variants as genetic susceptibility factors for leishmaniasis, little is known regarding the mechanisms that underpin these associations. To better understand this underlying functionality, we first collected all known leishmaniasis-associated HLA variants in a thorough literature review. Next, we aligned and compared the protection- and risk-associated HLA-DRB1 allele sequences. This identified several amino acid polymorphisms that distinguish protection- from risk-associated HLA-DRB1 alleles. Subsequently, T cell epitope binding predictions were carried out across these alleles to map the impact of these polymorphisms on the epitope binding repertoires. For these predictions, we used epitopes derived from entire proteomes of multiple Leishmania species. Epitopes binding to protection-associated HLA-DRB1 alleles shared common binding core motifs, mapping to the identified HLA-DRB1 amino acid polymorphisms. These results strongly suggest that HLA polymorphism, resulting in differential antigen presentation, affects the association between HLA and leishmaniasis disease development. Finally, we established a valuable open-access resource of putative epitopes. A set of 14 HLA-unrestricted strong-binding epitopes, conserved across species, was prioritized for further epitope discovery in the search for novel subunit-based vaccines.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{VANHEES2021104283,

title = {Sorted B cell transcriptomes point towards actively regulated B cell responses during ongoing chronic hepatitis B infections},

author = {Stijn Van Hees and Bart Cuypers and Stefan Bourgeois and Zwier M A Groothuismink and Pieter Meysman and Pieter Van der Vlies and Rob de Knegt and Luisa Vonghia and Peter Michielsen and Sven Francque and Kris Laukens and Andre Boonstra and Thomas Vanwolleghem},

url = {https://www.sciencedirect.com/science/article/pii/S0008874921000022},

doi = {https://doi.org/10.1016/j.cellimm.2021.104283},

issn = {0008-8749},

year  = {2021},

date = {2021-01-01},

journal = {Cellular Immunology},

volume = {362},

pages = {104283},

abstract = {The natural course of chronic hepatitis B virus (HBV) infections follows distinct clinical disease phases, characterized by fluctuating levels of serum HBV DNA and ALT. The immune cells and their features that govern these clinical disease transitions remain unknown. In the current study, we performed RNA sequencing on purified B cells from blood (n = 42) and liver (n = 10) of healthy controls and chronic HBV patients. We found distinct gene expression profiles between healthy controls and chronic HBV patients, as evidenced by 190 differentially expressed genes (DEG), but also between the clinical phenotypes of a chronic HBV infection (17\textendash110 DEG between each phase). Numerous immune pathways, including the B cell receptor pathway were upregulated in liver B cells when compared to peripheral B cells. Further investigation of the detected DEG suggested an activation of B cells during HBeAg seroconversion and an active regulation of B cell signalling in the liver.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{BOULLOSA2021101949,

title = {Auranofin reveals therapeutic anticancer potential by triggering distinct molecular cell death mechanisms and innate immunity in mutant p53 non-small cell lung cancer},

author = {Laurie Freire Boullosa and Jinthe Van Loenhout and Tal Flieswasser and Jorrit De Waele and Christophe Hermans and Hilde Lambrechts and Bart Cuypers and Kris Laukens and Esther Bartholomeus and Vasiliki Siozopoulou and Winnok H De Vos and Marc Peeters and Evelien L J Smits and Christophe Deben},

url = {https://www.sciencedirect.com/science/article/pii/S2213231721000975},

doi = {https://doi.org/10.1016/j.redox.2021.101949},

issn = {2213-2317},

year  = {2021},

date = {2021-01-01},

journal = {Redox Biology},

pages = {101949},

abstract = {Auranofin (AF) is an FDA-approved antirheumatic drug with anticancer properties that acts as a thioredoxin reductase 1 (TrxR) inhibitor. The exact mechanisms through which AF targets cancer cells remain elusive. To shed light on the mode of action, this study provides an in-depth analysis on the molecular mechanisms and immunogenicity of AF-mediated cytotoxicity in the non-small cell lung cancer (NSCLC) cell line NCI-H1299 (p53 Null) and its two isogenic derivates with mutant p53 R175H or R273H accumulation. TrxR is highly expressed in a panel of 72 NSCLC patients, making it a valid druggable target in NSCLC for AF. The presence of mutant p53 overexpression was identified as an important sensitizer for AF in (isogenic) NSCLC cells as it was correlated with reduced thioredoxin (Trx) levels in vitro. Transcriptome analysis revealed dysregulation of genes involved in oxidative stress response, DNA damage, granzyme A (GZMA) signaling and ferroptosis. Although functionally AF appeared a potent inhibitor of GPX4 in all NCI-H1299 cell lines, the induction of lipid peroxidation and consequently ferroptosis was limited to the p53 R273H expressing cells. In the p53 R175H cells, AF mainly induced large-scale DNA damage and replication stress, leading to the induction of apoptotic cell death rather than ferroptosis. Importantly, all cell death types were immunogenic since the release of danger signals (ecto-calreticulin, ATP and HMGB1) and dendritic cell maturation occurred irrespective of (mutant) p53 expression. Finally, we show that AF sensitized cancer cells to caspase-independent natural killer cell-mediated killing by downregulation of several key targets of GZMA. Our data provides novel insights on AF as a potent, clinically available, off-patent cancer drug by targeting mutant p53 cancer cells through distinct cell death mechanisms (apoptosis and ferroptosis). In addition, AF improves the innate immune response at both cytostatic (natural killer cell-mediated killing) and cytotoxic concentrations (dendritic cell maturation).},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{VANHOUTVEN2021166966,

title = {Constrained Standardization of Count Data from Massive Parallel Sequencing},

author = {Joris Van Houtven and Bart Cuypers and Pieter Meysman and Jef Hooyberghs and Kris Laukens and Dirk Valkenborg},

url = {https://www.sciencedirect.com/science/article/pii/S0022283621001674},

doi = {https://doi.org/10.1016/j.jmb.2021.166966},

issn = {0022-2836},

year  = {2021},

date = {2021-01-01},

journal = {Journal of Molecular Biology},

pages = {166966},

abstract = {In high-throughput omics disciplines like transcriptomics, researchers face a need to assess the quality of an experiment prior to an in-depth statistical analysis. To efficiently analyze such voluminous collections of data, researchers need triage methods that are both quick and easy to use. Such a normalization method for relative quantitation, CONSTANd, was recently introduced for isobarically-labeled mass spectra in proteomics. It transforms the data matrix of abundances through an iterative, convergent process enforcing three constraints: (I) identical column sums; (II) each row sum is fixed (across matrices) and (III) identical to all other row sums. In this study, we investigate whether CONSTANd is suitable for count data from massively parallel sequencing, by qualitatively comparing its results to those of DESeq2. Further, we propose an adjustment of the method so that it may be applied to identically balanced but differently sized experiments for joint analysis. We find that CONSTANd can process large data sets at well over 1 million count records per second whilst mitigating unwanted systematic bias and thus quickly uncovering the underlying biological structure when combined with a PCA plot or hierarchical clustering. Moreover, it allows joint analysis of data sets obtained from different batches, with different protocols and from different labs but without exploiting information from the experimental setup other than the delineation of samples into identically processed sets (IPSs). CONSTANd’s simplicity and applicability to proteomics as well as transcriptomics data make it an interesting candidate for integration in multi-omics workflows.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{cancers13071618,

title = {Covalent Cysteine Targeting of Bruton’s Tyrosine Kinase (BTK) Family by Withaferin-A Reduces Survival of Glucocorticoid-Resistant Multiple Myeloma MM1 Cells},

author = {Emilie Logie and Chandra S Chirumamilla and Claudina Perez-Novo and Priyanka Shaw and Ken Declerck and Ajay Palagani and Savithri Rangarajan and Bart Cuypers and Nicolas De Neuter and Fazil Mobashar Hussain Urf Turabe and Navin Kumar Verma and Annemie Bogaerts and Kris Laukens and Fritz Offner and Pieter Van Vlierberghe and Xaveer Van Ostade and Wim Vanden Berghe},

url = {https://www.mdpi.com/2072-6694/13/7/1618},

doi = {10.3390/cancers13071618},

issn = {2072-6694},

year  = {2021},

date = {2021-01-01},

journal = {Cancers},

volume = {13},

number = {7},

abstract = {Multiple myeloma (MM) is a hematological malignancy characterized by plasma cells’ uncontrolled growth. The major barrier in treating MM is the occurrence of primary and acquired therapy resistance to anticancer drugs. Often, this therapy resistance is associated with constitutive hyperactivation of tyrosine kinase signaling. Novel covalent kinase inhibitors, such as the clinically approved BTK inhibitor ibrutinib (IBR) and the preclinical phytochemical withaferin A (WA), have, therefore, gained pharmaceutical interest. Remarkably, WA is more effective than IBR in killing BTK-overexpressing glucocorticoid (GC)-resistant MM1R cells. To further characterize the kinase inhibitor profiles of WA and IBR in GC-resistant MM cells, we applied phosphopeptidome- and transcriptome-specific tyrosine kinome profiling. In contrast to IBR, WA was found to reverse BTK overexpression in GC-resistant MM1R cells. Furthermore, WA-induced cell death involves covalent cysteine targeting of Hinge-6 domain type tyrosine kinases of the kinase cysteinome classification, including inhibition of the hyperactivated BTK. Covalent interaction between WA and BTK could further be confirmed by biotin-based affinity purification and confocal microscopy. Similarly, molecular modeling suggests WA preferably targets conserved cysteines in the Hinge-6 region of the kinase cysteinome classification, favoring inhibition of multiple B-cell receptors (BCR) family kinases. Altogether, we show that WA’s promiscuous inhibition of multiple BTK family tyrosine kinases represents a highly effective strategy to overcome GC-therapy resistance in MM.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hefnawy2021.01.05.425522,

title = {Genomic and phenotypic characterization of experimentally selected resistant Leishmania donovani reveals a role for dynamin-1 like protein in the mechanism of resistance to a novel anti-leishmanial compound},

author = {Aya Hefnawy and Gabriel Negreira and Marlene Jara and James A Cotton and Ilse Maes and Erika D{textquoteright} Haenens and Hideo Imamura and Bart Cuypers and Pieter Monsieurs and Christina Mouchtoglou and Hans De Winter and Matt Berriman and Mandy Sanders and Julio Martin and Geraldine de Muylder and Jean-Claude Dujardin and Yann G -J Sterckx and Malgorzata Anna Domagalska},

url = {https://www.biorxiv.org/content/early/2021/01/06/2021.01.05.425522},

doi = {10.1101/2021.01.05.425522},

year  = {2021},

date = {2021-01-01},

journal = {bioRxiv},

publisher = {Cold Spring Harbor Laboratory},

abstract = {The implementation of prospective drug resistance (DR) studies in the R\&D pipelines is a common practice for many infectious diseases, but not for Neglected Tropical Diseases. Here, we explored and demonstrated the importance of this approach, using as paradigms Leishmania donovani, the etiological agent of Visceral Leishmaniasis (VL), and TCMDC-143345, a promising compound of the GSK textquoteleftLeishboxtextquoteright to treat VL. We experimentally selected resistance to TCMDC-143345 in vitro and characterized resistant parasites at genomic and phenotypic levels. We found that it took more time to develop resistance to TCMDC-143345 than to other drugs in clinical use and that there was no cross resistance to these drugs, suggesting a new and unique mechanism. By whole genome sequencing, we found two mutations in the gene encoding the L. donovani dynamin-1-like protein (LdoDLP1) that were fixed at highest drug pressure. Through phylogenetic analysis, we identified LdoDLP1 as a family member of the dynamin-related proteins, a group of proteins that impacts the shapes of biological membranes by mediating fusion and fission events, with a putative role in mitochondrial fission. We found that L. donovani lines genetically engineered to harbor the two identified LdoDLP1 mutations were resistant to TCMDC-143345 and displayed altered mitochondrial properties. By homology modeling, we showed how the two LdoDLP1 mutations may influence protein structure and function. Taken together, our data reveal a clear involvement of LdoDLP1 in the adaptation/resistance of L. donovani to TCMDC-143345.Importance Humans and their pathogens are continuously locked in a molecular arms race during which the eventual emergence of pathogen drug resistance (DR) seems inevitable. For neglected tropical diseases (NTDs), DR is generally studied retrospectively, once it has already been established in clinical settings. We previously recommended to keep one step ahead in the host-pathogen arms race and implement prospective DR studies in the R\&D pipeline, a common practice for many infectious diseases, but not for NTDs. Here, using Leishmania donovani, the etiological agent of Visceral Leishmaniasis (VL), and TCMDC-143345, a promising compound of the GSK textquoteleftLeishboxtextquoteright to treat VL, as paradigms, we experimentally selected resistance to the compound and proceeded to genomic and phenotypic characterization of DR parasites. The results gathered in the present study suggest a new DR mechanism involving the L. donovani dynamin-1 like protein (LdoDLP1) and demonstrate the practical relevance of prospective DR studies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Adriaensen2020,

title = {Host transcriptomic signature as alternative test-of-cure in visceral leishmaniasis patients co-infected with HIV},

author = {Wim Adriaensen and Bart Cuypers and Carlota F Cordero and Bewketu Mengasha and S\'{e}verine Blesson and Lieselotte Cnops and Paul M Kaye and Fabiana Alves and Ermias Diro and Johan van Griensven},

url = {https://doi.org/10.1016/j.ebiom.2020.102748},

doi = {10.1016/j.ebiom.2020.102748},

issn = {2352-3964},

year  = {2020},

date = {2020-05-01},

journal = {EBioMedicine},

volume = {55},

publisher = {Elsevier},

abstract = {BackgroundVisceral leishmaniasis (VL) treatment in HIV patients very often fails and is followed by high relapse and case-fatality rates. Hence, treatment efficacy assessment is imperative but based on invasive organ aspiration for parasite detection. In the search of a less-invasive alternative and because the host immune response is pivotal for treatment outcome in immunocompromised VL patients, we studied changes in the whole blood transcriptional profile of VL-HIV patients during treatment.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{UZUREAU20203821,

title = {APOL1 C-Terminal Variants May Trigger Kidney Disease through Interference with APOL3 Control of Actomyosin},

author = {Sophie Uzureau and Laurence Lecordier and Pierrick Uzureau and Dorle Hennig and Jonas H Graversen and Fabrice Hombl\'{e} and Pepe Ekulu Mfutu and Fanny [Oliveira Arcolino] and Ana Raquel Ramos and Rita [La M Rovere] and Tomas Luyten and Marjorie Vermeersch and Patricia Tebabi and Marc Dieu and Bart Cuypers and Stijn Deborggraeve and Marion Rabant and Christophe Legendre and S\oren K Moestrup and Elena Levtchenko and Geert Bultynck and Christophe Erneux and David P\'{e}rez-Morga and Etienne Pays},

url = {http://www.sciencedirect.com/science/article/pii/S2211124720302321},

doi = {https://doi.org/10.1016/j.celrep.2020.02.064},

issn = {2211-1247},

year  = {2020},

date = {2020-01-01},

journal = {Cell Reports},

volume = {30},

number = {11},

pages = {3821 - 3836.e13},

abstract = {Summary 

The C-terminal variants G1 and G2 of apolipoprotein L1 (APOL1) confer human resistance to the sleeping sickness parasite Trypanosoma rhodesiense, but they also increase the risk of kidney disease. APOL1 and APOL3 are death-promoting proteins that are partially associated with the endoplasmic reticulum and Golgi membranes. We report that in podocytes, either APOL1 C-terminal helix truncation (APOL1Δ) or APOL3 deletion (APOL3KO) induces similar actomyosin reorganization linked to the inhibition of phosphatidylinositol-4-phosphate [PI(4)P] synthesis by the Golgi PI(4)-kinase IIIB (PI4KB). Both APOL1 and APOL3 can form K+ channels, but only APOL3 exhibits Ca2+-dependent binding of high affinity to neuronal calcium sensor-1 (NCS-1), promoting NCS-1-PI4KB interaction and stimulating PI4KB activity. Alteration of the APOL1 C-terminal helix triggers APOL1 unfolding and increased binding to APOL3, affecting APOL3-NCS-1 interaction. Since the podocytes of G1 and G2 patients exhibit an APOL1Δ or APOL3KO-like phenotype, APOL1 C-terminal variants may induce kidney disease by preventing APOL3 from activating PI4KB, with consecutive actomyosin reorganization of podocytes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{microorganisms8081252,

title = {The Absence of C-5 DNA Methylation in Leishmania donovani Allows DNA Enrichment from Complex Samples},

author = {Bart Cuypers and Franck Dumetz and Pieter Meysman and Kris Laukens and G\'{e}raldine De Muylder and Jean-Claude Dujardin and Malgorzata Anna Domagalska},

url = {https://www.mdpi.com/2076-2607/8/8/1252},

doi = {10.3390/microorganisms8081252},

issn = {2076-2607},

year  = {2020},

date = {2020-01-01},

journal = {Microorganisms},

volume = {8},

number = {8},

abstract = {Cytosine C5 methylation is an important epigenetic control mechanism in a wide array of eukaryotic organisms and generally carried out by proteins of the C-5 DNA methyltransferase family (DNMTs). In several protozoans, the status of this mechanism remains elusive, such as in Leishmania, the causative agent of the disease leishmaniasis in humans and a wide array of vertebrate animals. In this work, we showed that the Leishmania donovani genome contains a C-5 DNA methyltransferase (DNMT) from the DNMT6 subfamily, whose function is still unclear, and verified its expression at the RNA level. We created viable overexpressor and knock-out lines of this enzyme and characterized their genome-wide methylation patterns using whole-genome bisulfite sequencing, together with promastigote and amastigote control lines. Interestingly, despite the DNMT6 presence, we found that methylation levels were equal to or lower than 0.0003% at CpG sites, 0.0005% at CHG sites, and 0.0126% at CHH sites at the genomic scale. As none of the methylated sites were retained after manual verification, we conclude that there is no evidence for DNA methylation in this species. We demonstrated that this difference in DNA methylation between the parasite (no detectable DNA methylation) and the vertebrate host (DNA methylation) allowed enrichment of parasite vs. host DNA using methyl-CpG-binding domain columns, readily available in commercial kits. As such, we depleted methylated DNA from mixes of Leishmania promastigote and amastigote DNA with human DNA, resulting in average Leishmania:human enrichments from 62\× up to 263\×. These results open a promising avenue for unmethylated DNA enrichment as a pre-enrichment step before sequencing Leishmania clinical samples.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Deben2020,

title = {Characterization of acquired nutlin-3 resistant non-small cell lung cancer cells},

author = {Christophe Deben and Laurie Freire Boullosa and Andreas Domen and An Wouters and Bart Cuypers and Kris Laukens and Filip Lardon and Patrick Pauwels},

url = {https://doi.org/10.20517/cdr.2020.91},

doi = {10.20517/cdr.2020.91},

issn = {2578-532X},

year  = {2020},

date = {2020-01-01},

journal = {Cancer Drug Resistance},

volume = {3},

pages = {[Online First]},

abstract = {Aim: The purpose of this manuscript is to study the potential characteristics of acquired nutlin-3 resistant non-small cell lung cancer cells (NSCLC). Nutlin-3 is an inhibitor of the murine-double minute 2 protein, the main negative regulator of wild type p53, of which several derivatives are currently in clinical development.Methods: A549 NSCLC cells were exposed to increasing concentrations of nutlin-3 for a period of 18 weeks. Monoclonal derivates were cultured, and the most resistance subclone was selected for whole transcriptome analysis. Gene set enrichment analysis was performed on differentially expressed genes between A549 nutlin-3 resistant cancer cells and the parental A549 p53 wild type cancer cells. Relevant findings were validated at the gene, protein and/or functional level.Results: All nutlin-3 resistant subclones acquired mutations in the TP53 gene, resulting in overexpression of the mutant p53 protein. The most resistant subclone was enriched for genes related to epithelial to mesenchymal transition (EMT), resulting in increased migratory and invasive potential. Furthermore, these cells were enriched in genes related to inflammation, tissue remodelling, and angiogenesis. Importantly, expression of several immune checkpoints, including PD-L1 and PD-L2, was significantly upregulated, and cisplatin-induced cell death was reduced.Conclusion: Transcriptome analysis of a highly nutlin-3 resistant A549 subclone shows the relevance of studying (1) resistance to standard of care chemotherapy; (2) secretion of immunomodulating chemo- and cytokines; (3) immune checkpoint expression; and (4) EMT and invasion in nutlin-3 resistant cancer cells in addition to acquired mutations in the TP53 gene.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10.12688/f1000research.20408.1,

title = {Global network of computational biology communities: ISCB's Regional Student Groups breaking barriers},

author = {S Shome and RG Parra and N Fatima and AM Monzon and B Cuypers and Y Moosa and NDR Coimbra and J Assis and C Giner-Delgado and HM D\"{o}nerta? and Y Cuesta-Astroz and G Saarunya and I Allali and S Gupta and A Srivastava and M Kalsan and C Valdivia and G J. Olguin-Orellana and S Papadimitriou and D Parisi and NP Kristensen and L Rib and MB Guebila and E Bauer and G Zaffaroni and A Bekkar and E Ashano and L Paladin and M Necci and NN Moreyra and M Ryd\'{e}n and J Villalobos-Sol\'{i}s and N Papadopoulos and C Rafael and T Karakulak and Y Kaya and Y Gladbach and SK Dhanda and N ?o?tari? and A Alex and D DeBlasio and F Rahman},

doi = {10.12688/f1000research.20408.1},

year  = {2019},

date = {2019-01-01},

journal = {F1000Research},

volume = {8},

number = {1574},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hassan2018,

title = {Reflections on a journey: a retrospective of the ISCB Student Council symposium series},

author = {Mehedi Hassan and Aishwarya Alex Namasivayam and Dan DeBlasio and Nazeefa Fatima and Benjamin Siranosian and Gonzalo R Parra and Bart Cuypers and Sayane Shome and Alexander Miguel Monzon and Julien Fumey and Farzana Rahman},

url = {https://doi.org/10.1186/s12859-018-2369-x},

doi = {10.1186/s12859-018-2369-x},

issn = {1471-2105},

year  = {2018},

date = {2018-10-09},

journal = {BMC Bioinformatics},

volume = {19},

number = {12},

pages = {347},

abstract = {This article describes the motivation, origin and evolution of the student symposia series organised by the ISCB Student Council. The meeting series started thirteen years ago in Madrid and has spread to four continents. The article concludes with the highlights of the most recent edition of annual Student Council Symposium held in conjunction with the 25th Conference on Intelligent Systems for Molecular Biology and the 16th European Conference on Computational Biology, in Prague, in July 2017.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Krivoshiev2018b,

title = {Transcriptome profiling of HepG2 cells exposed to the flame retardant 9,10-dihydro-9-oxa-10-phosphaphenanthrene 10-oxide (DOPO)},

author = {Boris V Krivoshiev and Gerrit T S Beemster and Katrien Sprangers and Bart Cuypers and Kris Laukens and Ronny Blust and Steven J Husson},

url = {https://doi.org/10.1039/c8tx00006a},

doi = {10.1039/c8tx00006a},

issn = {2045-452X},

year  = {2018},

date = {2018-03-12},

journal = {Toxicology research},

volume = {7},

number = {3},

pages = {492-502},

publisher = {Royal Society of Chemistry},

abstract = {The flame retardant, 9,10-dihydro-9-oxa-10-phosphaphenanthrene 10-oxide (DOPO), has been receiving great interest given its superior fire protection properties, and its predicted low level of persistence, bioaccumulation, and toxicity. However, empirical toxicological data that are essential for a complete hazard assessment are severely lacking. In this study, we attempted to identify the potential toxicological modes of action by transcriptome (RNA-seq) profiling of the human liver hepatocellular carcinoma cell line, HepG2. Such insight may help in identifying compounds of concern and potential toxicological phenotypes. DOPO was found to have little cytotoxic potential, with lower effective concentrations compared to other flame retardants studied in the same cell line. Differentially expressed genes revealed a wide range of molecular effects including changes in protein, energy, DNA, and lipid metabolism, along with changes in cellular stress response pathways. In response to 250 $mu$M DOPO, the most perturbed biological processes were fatty acid metabolism, androgen metabolism, glucose transport, and renal function and development, which is in agreement with other studies that observed similar effects of other flame retardants in other species. However, treatment with 2.5 $mu$M DOPO resulted in very few differentially expressed genes and failed to indicate any potential effects on biology, despite such concentrations likely being orders of magnitude greater than would be encountered in the environment. This, together with the low levels of cytotoxicity, supports the potential replacement of the current flame retardants by DOPO, although further studies are needed to establish the nephrotoxicity and endocrine disruption of DOPO.},

note = {c8tx00006a[PII]},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DeNeuter2018,

title = {On the feasibility of mining CD8+ T cell receptor patterns underlying immunogenic peptide recognition},

author = {Nicolas De Neuter and Wout Bittremieux and Charlie Beirnaert and Bart Cuypers and Aida Mrzic and Pieter Moris and Arvid Suls and Viggo Van Tendeloo and Benson Ogunjimi and Kris Laukens and Pieter Meysman},

url = {https://doi.org/10.1007/s00251-017-1023-5},

doi = {10.1007/s00251-017-1023-5},

issn = {1432-1211},

year  = {2018},

date = {2018-03-01},

journal = {Immunogenetics},

volume = {70},

number = {3},

pages = {159-168},

abstract = {Current T cell epitope prediction tools are a valuable resource in designing targeted immunogenicity experiments. They typically focus on, and are able to, accurately predict peptide binding and presentation by major histocompatibility complex (MHC) molecules on the surface of antigen-presenting cells. However, recognition of the peptide-MHC complex by a T cell receptor (TCR) is often not included in these tools. We developed a classification approach based on random forest classifiers to predict recognition of a peptide by a T cell receptor and discover patterns that contribute to recognition. We considered two approaches to solve this problem: (1) distinguishing between two sets of TCRs that each bind to a known peptide and (2) retrieving TCRs that bind to a given peptide from a large pool of TCRs. Evaluation of the models on two HIV-1, B*08-restricted epitopes reveals good performance and hints towards structural CDR3 features that can determine peptide immunogenicity. These results are of particular importance as they show that prediction of T cell epitope and T cell epitope recognition based on sequence data is a feasible approach. In addition, the validity of our models not only serves as a proof of concept for the prediction of immunogenic T cell epitopes but also paves the way for more general and high-performing models.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Dumetze00548-17,

title = {Molecular Preadaptation to Antimony Resistance in Leishmania donovani on the Indian Subcontinent},

author = {F Dumetz and B Cuypers and H Imamura and D Zander and E D{textquoteright}Haenens and I Maes and M A Domagalska and J Clos and J -C Dujardin and G De Muylder},

editor = {Margaret Phillips},

url = {https://msphere.asm.org/content/3/2/e00548-17},

doi = {10.1128/mSphere.00548-17},

year  = {2018},

date = {2018-01-01},

journal = {mSphere},

volume = {3},

number = {2},

publisher = {American Society for Microbiology Journals},

abstract = {Antimonials (Sb) were used for decades for chemotherapy of visceral leishmaniasis (VL). Now abandoned in the Indian subcontinent (ISC) because of Leishmania donovani resistance, this drug offers a unique model for understanding drug resistance dynamics. In a previous phylogenomic study, we found two distinct populations of L. donovani: the core group (CG) in the Gangetic plains and ISC1 in the Nepalese highlands. Sb resistance was only encountered within the CG, and a series of potential markers were identified. Here, we analyzed the development of resistance to trivalent antimonials (SbIII) upon experimental selection in ISC1 and CG strains. We observed that (i) baseline SbIII susceptibility of parasites was higher in ISC1 than in the CG, (ii) time to SbIII resistance was higher for ISC1 parasites than for CG strains, and (iii) untargeted genomic and metabolomic analyses revealed molecular changes along the selection process: these were more numerous in ISC1 than in the CG. Altogether these observations led to the hypothesis that CG parasites are preadapted to SbIII resistance. This hypothesis was experimentally confirmed by showing that only wild-type CG strains could survive a direct exposure to the maximal concentration of SbIII. The main driver of this preadaptation was shown to be MRPA, a gene involved in SbIII sequestration and amplified in an intrachromosomal amplicon in all CG strains characterized so far. This amplicon emerged around 1850 in the CG, well before the implementation of antimonials for VL chemotherapy, and we discuss here several hypotheses of selective pressure that could have accompanied its emergence.IMPORTANCE The textquotedblleftantibiotic resistance crisistextquotedblright is a major challenge for scientists and medical professionals. This steady rise in drug-resistant pathogens also extends to parasitic diseases, with antimony being the first anti-Leishmania drug that fell in the Indian subcontinent (ISC). Leishmaniasis is a major but neglected infectious disease with limited therapeutic options. Therefore, understanding how parasites became resistant to antimonials is of commanding importance. In this study, we experimentally characterized the dynamics of this resistance acquisition and show for the first time that some Leishmania populations of the ISC were preadapted to antimony resistance, likely driven by environmental factors or by drugs used in the 19th century.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{KRIVOSHIEV2018178,

title = {Toxicogenomics of the flame retardant tris (2-butoxyethyl) phosphate in HepG2 cells using RNA-seq},

author = {Boris V Krivoshiev and Gerrit T S Beemster and Katrien Sprangers and Bart Cuypers and Kris Laukens and Ronny Blust and Steven J Husson},

url = {http://www.sciencedirect.com/science/article/pii/S0887233317303089},

doi = {https://doi.org/10.1016/j.tiv.2017.10.011},

issn = {0887-2333},

year  = {2018},

date = {2018-01-01},

journal = {Toxicology in Vitro},

volume = {46},

pages = {178 - 188},

abstract = {Tris (2-butoxyethyl) phosphate (TBOEP) is a compound produced at high volume that is used as both a flame retardant and a plasticizer. It is persistent and bioaccumulative, yet little is known of its toxicological modes of action. Such insight may aid risk assessment in a weight-of-evidence approach supplementing current testing strategies. We used an RNA sequencing approach as an unbiased and sensitive tool to explore potential negative health effects of sub-cytotoxic concentrations of TBOEP on the transcriptome of the human liver hepatocellular carcinoma cell line, HepG2, with the lowest concentration used potentially holding relevance to human physiological levels. Over-representation and gene set enrichment analysis corresponded well and revealed that TBOEP treatments resulted in an upregulation of genes involved in protein and energy metabolism, along with DNA replication. Such increases in cell and macromolecule metabolism could explain the increase in mitochondrial activity at lower TBOEP concentrations. In addition, TBOEP affected a wide variety of biological processes, the most notable one being the general stress response, wound healing. Finally, TBOEP showed effects on steroid hormone biosynthesis and activation, regulation, and potentiation of immune responses, in agreement with other studies. As such, this study is the first study investigating genome-wide changes in gene transcription in response to TBOEP in human cells.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{CUYPERS2018170,

title = {Integrated genomic and metabolomic profiling of ISC1, an emerging Leishmania donovani population in the Indian subcontinent},

author = {Bart Cuypers and Maya Berg and Hideo Imamura and Franck Dumetz and G\'{e}raldine [De Muylder] and Malgorzata A Domagalska and Suman Rijal and Narayan Raj Bhattarai and Ilse Maes and Mandy Sanders and James A Cotton and Pieter Meysman and Kris Laukens and Jean-Claude Dujardin},

url = {http://www.sciencedirect.com/science/article/pii/S1567134818302004},

doi = {https://doi.org/10.1016/j.meegid.2018.04.021},

issn = {1567-1348},

year  = {2018},

date = {2018-01-01},

journal = {Infection, Genetics and Evolution},

volume = {62},

pages = {170 - 178},

abstract = {Leishmania donovani is the responsible agent for visceral leishmaniasis (VL) in the Indian subcontinent (ISC). The disease is lethal without treatment and causes 0.2 to 0.4 million cases each year. Recently, reports of VL in Nepalese hilly districts have increased as well as VL cases caused by L. donovani from the ISC1 genetic group, a new and emerging genotype. In this study, we perform for the first time an integrated, untargeted genomics and metabolomics approach to characterize ISC1, in comparison with the Core Group (CG), main population that drove the most recent outbreak of VL in the ISC. We show that the ISC1 population is very different from the CG, both at genome and metabolome levels. The genomic differences include SNPs, CNV and small indels in genes coding for known virulence factors, immunogens and surface proteins. Both genomic and metabolic approaches highlighted dissimilarities related to membrane lipids, the nucleotide salvage pathway and the urea cycle in ISC1 versus CG. Many of these pathways and molecules are important for the interaction with the host/extracellular environment. Altogether, our data predict major functional differences in ISC1 versus CG parasites, including virulence. Therefore, particular attention is required to monitor the fate of this emerging ISC1 population in the ISC, especially in a post-VL elimination context.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Cuypers2017,

title = {Multiplexed Spliced-Leader Sequencing: A high-throughput, selective method for RNA-seq in Trypanosomatids},

author = {Bart Cuypers and Malgorzata A Domagalska and Pieter Meysman and G\'{e}raldine de Muylder and Manu Vanaerschot and Hideo Imamura and Franck Dumetz and Thomas Wolf Verdonckt and Peter J Myler and Gowthaman Ramasamy and Kris Laukens and Jean-Claude Dujardin},

url = {https://doi.org/10.1038/s41598-017-03987-0},

doi = {10.1038/s41598-017-03987-0},

issn = {2045-2322},

year  = {2017},

date = {2017-06-16},

journal = {Scientific Reports},

volume = {7},

number = {1},

pages = {3725},

abstract = {High throughput sequencing techniques are poorly adapted for in vivo studies of parasites, which require prior in vitro culturing and purification. Trypanosomatids, a group of kinetoplastid protozoans, possess a distinctive feature in their transcriptional mechanism whereby a specific Spliced Leader (SL) sequence is added to the 5textasciiacutexend of each mRNA by trans-splicing. This allows to discriminate Trypansomatid RNA from mammalian RNA and forms the basis of our new multiplexed protocol for high-throughput, selective RNA-sequencing called SL-seq. We provided a proof-of-concept of SL-seq in Leishmania donovani, the main causative agent of visceral leishmaniasis in humans, and successfully applied the method to sequence Leishmania mRNA directly from infected macrophages and from highly diluted mixes with human RNA. mRNA profiles obtained with SL-seq corresponded largely to those obtained from conventional poly-A tail purification methods, indicating both enumerate the same mRNA pool. However, SL-seq offers additional advantages, including lower sequencing depth requirements, fast and simple library prep and high resolution splice site detection. SL-seq is therefore ideal for fast and massive parallel sequencing of parasite transcriptomes directly from host tissues. Since SLs are also present in Nematodes, Cnidaria and primitive chordates, this method could also have high potential for transcriptomics studies in other organisms.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Cuypers2017b,

title = {Genome-Wide SNP Analysis Reveals Distinct Origins of Trypanosoma evansi and Trypanosoma equiperdum},

author = {Bart Cuypers and Frederik Van den Broeck and Nick Van Reet and Conor J Meehan and Julien Cauchard and Jonathan M Wilkes and Filip Claes and Bruno Goddeeris and Hadush Birhanu and Jean-Claude Dujardin and Kris Laukens and Philippe B\"{u}scher and Stijn Deborggraeve},

url = {https://doi.org/10.1093/gbe/evx102},

doi = {10.1093/gbe/evx102},

issn = {1759-6653},

year  = {2017},

date = {2017-05-25},

journal = {Genome Biology and Evolution},

volume = {9},

number = {8},

pages = {1990-1997},

abstract = {Trypanosomes cause a variety of diseases in man and domestic animals in Africa, Latin America, and Asia. In the Trypanozoon subgenus, Trypanosoma brucei gambiense and Trypanosoma brucei rhodesiense cause human African trypanosomiasis, whereas Trypanosoma brucei brucei, Trypanosoma evansi, and Trypanosoma equiperdum are responsible for nagana, surra, and dourine in domestic animals, respectively. The genetic relationships between T. evansi and T. equiperdum and other Trypanozoon species remain unclear because the majority of phylogenetic analyses has been based on only a few genes. In this study, we have conducted a phylogenetic analysis based on genome-wide SNP analysis comprising 56 genomes from the Trypanozoon subgenus. Our data reveal that T. equiperdum has emerged at least once in Eastern Africa and T. evansi at two independent occasions in Western Africa. The genomes within the T. equiperdum and T. evansi monophyletic clusters show extremely little variation, probably due to the clonal spread linked to the independence from tsetse flies for their transmission.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10.1371/journal.pone.0180532,

title = {Macromolecular biosynthetic parameters and metabolic profile in different life stages of Leishmania braziliensis: Amastigotes as a functionally less active stage},

author = {Marlene Jara and Maya Berg and Guy Caljon and Geraldine de Muylder and Bart Cuypers and Denis Castillo and Ilse Maes and Mar\'{i}a Carmen del Orozco and Manu Vanaerschot and Jean-Claude Dujardin and Jorge Arevalo},

url = {https://doi.org/10.1371/journal.pone.0180532},

doi = {10.1371/journal.pone.0180532},

year  = {2017},

date = {2017-01-01},

journal = {PLOS ONE},

volume = {12},

number = {7},

pages = {1-22},

publisher = {Public Library of Science},

abstract = {It was recently hypothesized that Leishmania amastigotes could constitute a semi-quiescent stage characterized by low replication and reduced metabolic activity. This concept developed with Leishmania (Leishmania) mexicana and Leishmania (Leishmania) major models might explain numerous clinical and sub-clinical features of Leishmania (Viannia) braziliensis infections, like reactivation of the disease, non-response to chemotherapy or asymptomatic infections. We compared here in vitro the proliferative capability of L. (V.) braziliensis amastigotes and promastigotes, assessed the expression of key molecular parameters and performed metabolomic analysis. We found that contrary to the highly proliferative promastigotes, amastigotes (axenic and intracellular) do not show evidence of extensive proliferation. In parallel, amastigotes showed a significant decrease of (i) the kDNA mini-circle abundance, (ii) the intracellular ATP level, (iii) the ribosomal components: rRNA subunits 18S and 28S α and ribosomal proteins RPS15 and RPL19, (iv) total RNA and protein levels. An untargeted metabolomic study identified clear differences between the different life stages: in comparison to logarithmic promastigotes, axenic amastigotes showed (a) a strong decrease of 14 essential and non-essential amino acids and eight metabolites involved in polyamine synthesis, (b) extensive changes in the phospholipids composition and (c) increased levels of several endogenous and exogenous sterols. Altogether, our results show that L. (V.) braziliensis amastigotes can show a phenotype with negligible rate of proliferation, a lower capacity of biosynthesis, a reduced bio-energetic level and a strongly altered metabolism. Our results pave the way for further exploration of quiescence among amastigotes of this species.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Dumetze00599-17,

title = {Modulation of Aneuploidy in Leishmania donovani during Adaptation to Different In Vitro and In Vivo Environments and Its Impact on Gene Expression},

author = {F Dumetz and H Imamura and M Sanders and V Seblova and J Myskova and P Pescher and M Vanaerschot and C J Meehan and B Cuypers and G De Muylder and G F Sp\"{a}th and G Bussotti and J R Vermeesch and M Berriman and J A Cotton and P Volf and J C Dujardin and M A Domagalska},

editor = {Keith Gull},

url = {https://mbio.asm.org/content/8/3/e00599-17},

doi = {10.1128/mBio.00599-17},

year  = {2017},

date = {2017-01-01},

journal = {mBio},

volume = {8},

number = {3},

publisher = {American Society for Microbiology},

abstract = {Aneuploidy is usually deleterious in multicellular organisms but appears to be tolerated and potentially beneficial in unicellular organisms, including pathogens. Leishmania, a major protozoan parasite, is emerging as a new model for aneuploidy, since in vitro-cultivated strains are highly aneuploid, with interstrain diversity and intrastrain mosaicism. The alternation of two life stages in different environments (extracellular promastigotes and intracellular amastigotes) offers a unique opportunity to study the impact of environment on aneuploidy and gene expression. We sequenced the whole genomes and transcriptomes of Leishmania donovani strains throughout their adaptation to in vivo conditions mimicking natural vertebrate and invertebrate host environments. The nucleotide sequences were almost unchanged within a strain, in contrast to highly variable aneuploidy. Although high in promastigotes in vitro, aneuploidy dropped significantly in hamster amastigotes, in a progressive and strain-specific manner, accompanied by the emergence of new polysomies. After a passage through a sand fly, smaller yet consistent karyotype changes were detected. Changes in chromosome copy numbers were correlated with the corresponding transcript levels, but additional aneuploidy-independent regulation of gene expression was observed. This affected stage-specific gene expression, downregulation of the entire chromosome 31, and upregulation of gene arrays on chromosomes 5 and 8. Aneuploidy changes in Leishmania are probably adaptive and exploited to modulate the dosage and expression of specific genes; they are well tolerated, but additional mechanisms may exist to regulate the transcript levels of other genes located on aneuploid chromosomes. Our model should allow studies of the impact of aneuploidy on molecular adaptations and cellular fitness.IMPORTANCE Aneuploidy is usually detrimental in multicellular organisms, but in several microorganisms, it can be tolerated and even beneficial. Leishmania\textemdasha protozoan parasite that kills more than 30,000 people each year\textemdashis emerging as a new model for aneuploidy studies, as unexpectedly high levels of aneuploidy are found in clinical isolates. Leishmania lacks classical regulation of transcription at initiation through promoters, so aneuploidy could represent a major adaptive strategy of this parasite to modulate gene dosage in response to stressful environments. For the first time, we document the dynamics of aneuploidy throughout the life cycle of the parasite, in vitro and in vivo. We show its adaptive impact on transcription and its interaction with regulation. Besides offering a new model for aneuploidy studies, we show that further genomic studies should be done directly in clinical samples without parasite isolation and that adequate methods should be developed for this.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10.7554/eLife.12613,

title = {Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent},

author = {Hideo Imamura and Tim Downing and Frederik Van den Broeck and Mandy J Sanders and Suman Rijal and Shyam Sundar and An Mannaert and Manu Vanaerschot and Maya Berg and G\'{e}raldine De Muylder and Franck Dumetz and Bart Cuypers and Ilse Maes and Malgorzata Domagalska and Saskia Decuypere and Keshav Rai and Surendra Uranw and Narayan Raj Bhattarai and Basudha Khanal and Vijay Kumar Prajapati and Smriti Sharma and Olivia Stark and Gabriele Sch\"{o}nian and Harry P De Koning and Luca Settimo and Benoit Vanhollebeke and Syamal Roy and Bart Ostyn and Marleen Boelaert and Louis Maes and Matthew Berriman and Jean-Claude Dujardin and James A Cotton},

editor = {Dominique Soldati-Favre},

url = {https://doi.org/10.7554/eLife.12613},

doi = {10.7554/eLife.12613},

issn = {2050-084X},

year  = {2016},

date = {2016-03-01},

journal = {eLife},

volume = {5},

pages = {e12613},

publisher = {eLife Sciences Publications, Ltd},

abstract = {textitLeishmania donovani causes visceral leishmaniasis (VL), the second most deadly vector-borne parasitic disease. A recent epidemic in the Indian subcontinent (ISC) caused up to 80% of global VL and over 30,000 deaths per year. Resistance against antimonial drugs has probably been a contributing factor in the persistence of this epidemic. Here we use whole genome sequences from 204 clinical isolates to track the evolution and epidemiology of textitL. donovani from the ISC. We identify independent radiations that have emerged since a bottleneck coincident with 1960s DDT spraying campaigns. A genetically distinct population frequently resistant to antimonials has a two base-pair insertion in the aquaglyceroporin gene LdAQP1 that prevents the transport of trivalent antimonials. We find evidence of genetic exchange between ISC populations, and show that the mutation in LdAQP1 has spread by recombination. Our results reveal the complexity of textitL. donovani evolution in the ISC in response to drug treatment.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Wilkins2016,

title = {Highlights from the 11th ISCB Student Council Symposium 2015},

author = {Katie Wilkins and Mehedi Hassan and Margherita Francescatto and Jakob Jespersen and Gonzalo R Parra and Bart Cuypers and Dan DeBlasio and Alexander Junge and Anupama Jigisha and Farzana Rahman and Griet Laenen and Sander Willems and Lieven Thorrez and Yves Moreau and Nagarajan Raju and Sonia Pankaj Chothani and C Ramakrishnan and Masakazu Sekijima and Michael M Gromiha and Paddy J Slator and Nigel J Burroughs and Przemys{\l}aw Sza{\l}aj and Zhonghui Tang and Paul Michalski and Oskar Luo and Xingwang Li and Yijun Ruan and Dariusz Plewczynski and Giulia Fiscon and Emanuel Weitschek and Massimo Ciccozzi and Paola Bertolazzi and Giovanni Felici and Pieter Meysman and Manu Vanaerschot and Maya Berg and Hideo Imamura and Jean-Claude Dujardin and Kris Laukens and Westa Domanova and James R Krycer and Rima Chaudhuri and Pengyi Yang and Fatemeh Vafaee and Daniel J Fazakerley and Sean J Humphrey and David E James and Zdenka Kuncic},

url = {https://doi.org/10.1186/s12859-016-0901-4},

doi = {10.1186/s12859-016-0901-4},

issn = {1471-2105},

year  = {2016},

date = {2016-02-25},

journal = {BMC Bioinformatics},

volume = {17},

number = {3},

pages = {95},

abstract = {A1 Highlights from the eleventh ISCB Student Council Symposium 2015},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10.1371/journal.pone.0154101,

title = {Genomic and Molecular Characterization of Miltefosine Resistance in Leishmania infantum Strains with Either Natural or Acquired Resistance through Experimental Selection of Intracellular Amastigotes},

author = {Annelies Mondelaers and Maria P Sanchez-Ca\~{n}ete and Sarah Hendrickx and Eline Eberhardt and Raquel Garcia-Hernandez and Laurence Lachaud and James Cotton and Mandy Sanders and Bart Cuypers and Hideo Imamura and Jean-Claude Dujardin and Peter Delputte and Paul Cos and Guy Caljon and Francisco Gamarro and Santiago Castanys and Louis Maes},

url = {https://doi.org/10.1371/journal.pone.0154101},

doi = {10.1371/journal.pone.0154101},

year  = {2016},

date = {2016-01-01},

journal = {PLOS ONE},

volume = {11},

number = {4},

pages = {1-15},

publisher = {Public Library of Science},

abstract = {During the last decade miltefosine (MIL) has been used as first-line treatment for visceral leishmaniasis in endemic areas with antimonial resistance, but a decline in clinical effectiveness is now being reported. While only two MIL-resistant Leishmania infantum strains from HIV co-infected patients have been documented, phenotypic MIL-resistance for L. donovani has not yet been identified in the laboratory. Hence, a better understanding of the factors contributing to increased MIL-treatment failure is necessary. Given the paucity of defined MIL-resistant L. donovani clinical isolates, this study used an experimental amastigote-selected MIL-resistant L. infantum isolate (LEM3323). In-depth exploration of the MIL-resistant phenotype was performed by coupling genomic with phenotypic data to gain insight into gene function and the mutant phenotype. A naturally MIL-resistant L. infantum clinical isolate (LEM5159) was included to compare both datasets. Phenotypically, resistance was evaluated by determining intracellular amastigote susceptibility in vitro and actual MIL-uptake. Genomic analysis provided supportive evidence that the resistance selection model on intracellular amastigotes can be a good proxy for the in vivo field situation since both resistant strains showed mutations in the same inward transporter system responsible for the acquired MIL-resistant phenotype. In line with previous literature findings in promastigotes, our data confirm a defective import machinery through inactivation of the LiMT/LiRos3 protein complex as the main mechanism for MIL-resistance also in intracellular amastigotes. Whole genome sequencing analysis of LEM3323 revealed a 2 base pair deletion in the LiMT gene that led to the formation an early stop codon and a truncation of the LiMT protein. Interestingly, LEM5159 revealed mutations in both the LiMT and LiRos3 genes, resulting in an aberrant expression of the LiMT protein. To verify that these mutations were indeed accountable for the acquired resistance, transfection experiments were performed to re-establish MIL-susceptibility. In LEM3323, susceptibility was restored upon expression of a LiMT wild-type gene, whereas the MIL-susceptibility of LEM5159 could be reversed after expression of the LiRos3 wild-type gene. The aberrant expression profile of the LiMT protein could be restored upon rescue of the LiRos3 gene both in the LEM5159 clinical isolate and a ΔLiRos3 strain, showing that expression of LdMT is dependent on LdRos3 expression. The present findings clearly corroborate the pivotal role of the LiMT/LiRos3 complex in resistance towards MIL.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Cuyperse02198-15,

title = {Apolipoprotein L1 Variant Associated with Increased Susceptibility to Trypanosome Infection},

author = {Bart Cuypers and Laurence Lecordier and Conor J Meehan and Frederik Van den Broeck and Hideo Imamura and Philippe B\"{u}scher and Jean-Claude Dujardin and Kris Laukens and Achim Schnaufer and Caroline Dewar and Michael Lewis and Oliver Balmer and Thomas Azurago and Sardick Kyei-Faried and Sally-Ann Ohene and Boateng Duah and Prince Homiah and Ebenezer Kofi Mensah and Francis Anleah and Jose Ramon Franco and Etienne Pays and Stijn Deborggraeve},

editor = {Michael P Barrett and John C Boothroyd},

url = {https://mbio.asm.org/content/7/2/e02198-15},

doi = {10.1128/mBio.02198-15},

year  = {2016},

date = {2016-01-01},

journal = {mBio},

volume = {7},

number = {2},

publisher = {American Society for Microbiology},

abstract = {African trypanosomes, except Trypanosoma brucei gambiense and Trypanosoma~brucei~rhodesiense, which cause human African trypanosomiasis, are lysed by the human serum protein apolipoprotein L1 (ApoL1). These two subspecies can resist human ApoL1 because they express the serum resistance proteins T. b. gambiense glycoprotein (TgsGP) and serum resistance-associated protein (SRA), respectively. Whereas in T.~b.~rhodesiense, SRA is necessary and sufficient to inhibit ApoL1, in T.~b.~gambiense, TgsGP cannot protect against high ApoL1 uptake, so different additional mechanisms contribute to limit this uptake. Here we report a complex interplay between trypanosomes and an ApoL1 variant, revealing important insights into innate human immunity against these parasites. Using whole-genome sequencing, we characterized an atypical T.~b.~gambiense infection in a patient in Ghana. We show that the infecting trypanosome has diverged from the classical T.~b.~gambiense strains and lacks the TgsGP defense mechanism against human serum. By sequencing the ApoL1 gene of the patient and subsequent in vitro mutagenesis experiments, we demonstrate that a homozygous missense substitution (N264K) in the membrane-addressing domain of this ApoL1 variant knocks down the trypanolytic activity, allowing the trypanosome to avoid ApoL1-mediated immunity.IMPORTANCE Most African trypanosomes are lysed by the ApoL1 protein in human serum. Only the subspecies Trypanosoma b. gambiense and T.~b.~rhodesiense can resist lysis by ApoL1 because they express specific serum resistance proteins. We here report a complex interplay between trypanosomes and an ApoL1 variant characterized by a homozygous missense substitution (N264K) in the domain that we hypothesize interacts with the endolysosomal membranes of trypanosomes. The N264K substitution knocks down the lytic activity of ApoL1 against T.~b.~gambiense strains lacking the TgsGP defense mechanism and against T.~b.~rhodesiense if N264K is accompanied by additional substitutions in the SRA-interacting domain. Our data suggest that populations with high frequencies of the homozygous N264K ApoL1 variant may be at increased risk of contracting human African trypanosomiasis.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10.12688/f1000research.10389.1,

title = {Highlights from the ISCB Student Council Symposia in 2016},

author = {B Cuypers and A Jacobsen and B Siranosian and K Schwahn and AM Conard and N Aben and M Hassan and N Fatima and SMA Hermans and M Woghiren and P Meysman and F Rahman and A Jigisha},

doi = {10.12688/f1000research.10389.1},

year  = {2016},

date = {2016-01-01},

journal = {F1000Research},

volume = {5},

number = {2852},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Berg2242,

title = {Experimental Resistance to Drug Combinations in Leishmania donovani: Metabolic and Phenotypic Adaptations},

author = {Maya Berg and Raquel Garc{'i}a-Hern\'{a}ndez and Bart Cuypers and Manu Vanaerschot and Jos\'{e} I Manzano and Jos\'{e} A Poveda and Jos\'{e} A Ferragut and Santiago Castanys and Jean-Claude Dujardin and Francisco Gamarro},

url = {https://aac.asm.org/content/59/4/2242},

doi = {10.1128/AAC.04231-14},

issn = {0066-4804},

year  = {2015},

date = {2015-01-01},

journal = {Antimicrobial Agents and Chemotherapy},

volume = {59},

number = {4},

pages = {2242--2255},

publisher = {American Society for Microbiology Journals},

abstract = {Together with vector control, chemotherapy is an essential tool for the control of visceral leishmaniasis (VL), but its efficacy is jeopardized by growing resistance and treatment failure against first-line drugs. To delay the emergence of resistance, the use of drug combinations of existing antileishmanial agents has been tested systematically in clinical trials for the treatment of visceral leishmaniasis (VL). In vitro, Leishmania donovani promastigotes are able to develop experimental resistance to several combinations of different antileishmanial drugs after 10 weeks of drug pressure. Using an untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomics approach, we identified metabolic changes in lines that were experimentally resistant to drug combinations and their respective single-resistant lines. This highlighted both collective metabolic changes (found in all combination therapy-resistant [CTR] lines) and specific ones (found in certain CTR lines). We demonstrated that single-resistant and CTR parasite cell lines show distinct metabolic adaptations, which all converge on the same defensive mechanisms that were experimentally validated: protection against drug-induced and external oxidative stress and changes in membrane fluidity. The membrane fluidity changes were accompanied by changes in drug uptake only in the lines that were resistant against drug combinations with antimonials, and surprisingly, drug accumulation was higher in these lines. Together, these results highlight the importance and the central role of protection against oxidative stress in the different resistant lines. Ultimately, these phenotypic changes might interfere with the mode of action of all drugs that are currently used for the treatment of VL and should be taken into account in drug development.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{GRYSEELS2015249,

title = {Gairo virus, a novel arenavirus of the widespread Mastomys natalensis: Genetically divergent, but ecologically similar to Lassa and Morogoro viruses},

author = {Sophie Gryseels and Toni Rieger and Lisa Oestereich and Bart Cuypers and Benny Borremans and Rhodes Makundi and Herwig Leirs and Stephan G\"{u}nther and Jo\"{e}lle [Go\"{u}y de Bellocq]},

url = {http://www.sciencedirect.com/science/article/pii/S0042682214005480},

doi = {https://doi.org/10.1016/j.virol.2014.12.011},

issn = {0042-6822},

year  = {2015},

date = {2015-01-01},

journal = {Virology},

volume = {476},

pages = {249 - 256},

abstract = {Despite its near pan-African range, the Natal multimammate mouse, Mastomys natalensis, carries the human pathogen Lassa virus only in West Africa, while the seemingly non-pathogenic arenaviruses Mopeia, Morogoro, and Luna have been detected in this semi-commensal rodent in Mozambique/Zimbabwe, Tanzania and Zambia, respectively. Here, we describe a novel arenavirus in M. natalensis from Gairo district of central Tanzania, for which we propose the name “Gairo virus”. Surprisingly, the virus is not closely related with Morogoro virus that infects M. natalensis only 90km south of Gairo, but clusters phylogenetically with Mobala-like viruses that infect non-M. natalensis host species in Central African Republic and Ethiopia. Despite the evolutionary distance, Gairo virus shares basic ecological features with the other M. natalensis-borne viruses Lassa and Morogoro. Our data show that M. natalensis, carrying distantly related viruses even in the same geographical area, is a potent reservoir host for a variety of arenaviruses.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{doi:10.1111/mmi.12374,

title = {Metabolic adaptations of Leishmania donovani in relation to differentiation, drug resistance, and drug pressure},

author = {Maya Berg and Manu Vanaerschot and Andris Jankevics and Bart Cuypers and Ilse Maes and Sandip Mukherjee and Basudha Khanal and Suman Rijal and Syamal Roy and Fred Opperdoes and Rainer Breitling and Jean-Claude Dujardin},

url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/mmi.12374},

doi = {10.1111/mmi.12374},

year  = {2013},

date = {2013-01-01},

journal = {Molecular Microbiology},

volume = {90},

number = {2},

pages = {428-442},

abstract = {Summary Antimonial (sodium stibogluconate, SSG) resistance and differentiation have been shown to be closely linked in Leishmania donovani, with SSG-resistant strains showing an increased capacity to generate infectious (metacyclic) forms. This is the first untargeted LC-MS metabolomics study which integrated both phenomena in one experimental design and provided insights into metabolic differences between three clinical L. donovani strains with a similar genetic background but different SSG-susceptibilities. We performed this analysis at different stages during promastigote growth and in the absence or presence of drug pressure. When comparing SSG-resistant and SSG-sensitive strains, a number of metabolic changes appeared to be constitutively present in all growth stages, pointing towards a clear link with SSG-resistance, whereas most metabolic changes were only detected in the stationary stage. These changes reflect the close intertwinement between SSG-resistance and an increased metacyclogenesis in resistant parasites. The metabolic changes suggest that SSG-resistant parasites have (i) an increased capacity for protection against oxidative stress; (ii) a higher fluidity of the plasma membrane; and (iii) a metabolic survival kit to better endure infection. These changes were even more pronounced in a resistant strain kept under SbIII drug pressure.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Raie00611-13b,

title = {Relapse after Treatment with Miltefosine for Visceral Leishmaniasis Is Associated with Increased Infectivity of the Infecting Leishmania donovani Strain},

author = {Keshav Rai and Bart Cuypers and Narayan Raj Bhattarai and Surendra Uranw and Maya Berg and Bart Ostyn and Jean-Claude Dujardin and Suman Rijal and Manu Vanaerschot},

editor = {Louis M Weiss},

url = {https://mbio.asm.org/content/4/5/e00611-13},

doi = {10.1128/mBio.00611-13},

year  = {2013},

date = {2013-01-01},

journal = {mBio},

volume = {4},

number = {5},

publisher = {American Society for Microbiology},

abstract = {Leishmania donovani is an intracellular protozoan parasite that causes leishmaniasis, which can range from a self-healing cutaneous disease to a fatal visceral disease depending on the infecting species. Miltefosine is currently the latest and only oral antileishmanial that came out of drug discovery pipelines in the past few decades, but recent reports indicate a significant decline in its efficacy against visceral leishmaniasis (also known as kala-azar) in the Indian subcontinent. This relapse rate of up to 20% within 12~months after treatment was shown not to be related to reinfection, drug quality, drug exposure, or drug-resistant parasites. We therefore aimed to assess other phenotypes of the parasite that may affect treatment outcome and found a significant association between the number of metacyclic parasites, parasite infectivity, and patient treatment outcome in the Indian subcontinent. Together with previous studies on resistance of L. donovani against pentavalent antimonials, these data suggest that the infectivity of the parasite, or related phenotypes, might be a more determinant factor for treatment failure in visceral leishmaniasis than drug susceptibility, warranting a reassessment of our current view on treatment failure and drug resistance in leishmaniasis and beyond.IMPORTANCE The high miltefosine relapse rate poses a major challenge for the current Kala-Azar Elimination Program in the Indian subcontinent and other leishmaniasis control programs worldwide. This relapse rate could not be related to reinfection, drug-resistant parasites, or reduced treatment quality. Here we report that an increased infectivity of the parasite is associated with miltefosine relapse of visceral leishmaniasis (VL) patients. These results supplement those obtained with antimonial-resistant L. donovani where an increased infectivity was also observed. This challenges the current view of Leishmania drug susceptibility being the biggest parasitic factor that contributes to treatment failure in leishmaniasis. These selected more infectious parasites may pose an additional burden to leishmaniasis control programs, highlighting the importance of multifaceted control measures to achieve leishmaniasis elimination in the Indian subcontinent and other regions where leishmaniasis is endemic.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{BERG2013e201301002,

title = {LC-MS Metabolomics from study design to data-analysis \textendash using a versatile pathogen as a test case},

author = {Maya Berg and Manu Vanaerschot and Andris Jankevics and Bart Cuypers and Rainer Breitling and Jean-Claude Dujardin},

url = {http://www.sciencedirect.com/science/article/pii/S2001037014600453},

doi = {https://doi.org/10.5936/csbj.201301002},

issn = {2001-0370},

year  = {2013},

date = {2013-01-01},

journal = {Computational and Structural Biotechnology Journal},

volume = {4},

number = {5},

pages = {e201301002},

abstract = {Thanks to significant improvements in LC-MS technology, metabolomics is increasingly used as a tool to discriminate the responses of organisms to various stimuli or drugs. In this minireview we discuss all aspects of the LC-MS metabolomics pipeline, using a complex and versatile model organism, Leishmania donovani, as an illustrative example. The benefits of a hyphenated mass spectrometry platform and a detailed overview of the entire experimental pipeline from sampling, sample storage and sample list set-up to LC-MS measurements and the generation of meaningful results with state-of-the-art data-analysis software will be thoroughly discussed. Finally, we also highlight important pitfalls in the processing of LC-MS data and comment on the benefits of implementing metabolomics in a systems biology approach.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}