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Article: From gene to dose: Long-read sequencing and *-allele tools to refine phenotype predictions of

Graansma, Lonneke J / Zhai, Qinglian / Busscher, Loes / Menafra, Roberta / van den Berg, Redmar R / Kloet, Susan L / van der Lee, Maaike

Frontiers in pharmacology

2023 Volume 14, Page(s) 1076574

Abstract: Background: ...

Abstract	Background:
Language	English
Publishing date	2023-03-01
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587355-6
ISSN	1663-9812
ISSN	1663-9812
DOI	10.3389/fphar.2023.1076574
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Article: MBD2 and MBD3: elusive functions and mechanisms.

Menafra, Roberta / Stunnenberg, Hendrik G

Frontiers in genetics

2014 Volume 5, Page(s) 428

Abstract: Deoxyribonucleic acid methylation is a long known epigenetic mark involved in many biological processes and the 'readers' of this mark belong to several distinct protein families that 'read' and 'translate' the methylation mark into a function. Methyl- ... ...

Abstract	Deoxyribonucleic acid methylation is a long known epigenetic mark involved in many biological processes and the 'readers' of this mark belong to several distinct protein families that 'read' and 'translate' the methylation mark into a function. Methyl-CpG binding domain proteins belong to one of these families that are associated with transcriptional activation/repression, regulation of chromatin structure, pluripotency, development, and differentiation. Discovered decades ago, the systematic determination of the genomic binding sites of these readers and their epigenome make-up at a genome-wide level revealed the tip of the functional iceberg. This review focuses on two members of the methyl binding proteins, namely MBD2 and MBD3 that reside in very similar complexes, yet appear to have very different biological roles. We provide a comprehensive comparison of their genome-wide binding features and emerging roles in gene regulation.
Language	English
Publishing date	2014-12-09
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2014.00428
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Article ; Online: Acquisition of a glycosylated B-cell receptor drives follicular lymphoma toward a dark zone phenotype.

van Bergen, Cornelis A M / Kloet, Susan L / Quinten, Edwin / Sepúlveda Yáñez, Julieta H / Menafra, Roberta / Griffioen, Marieke / Jansen, Patty M / Koning, Marvyn T / Knijnenburg, Jeroen / Navarrete, Marcelo A / Kiełbasa, Szymon M / Veelken, Hendrik

Blood advances

2023 Volume 7, Issue 19, Page(s) 5812–5816

Language	English
Publishing date	2023-07-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	2915908-8
ISSN	2473-9537 ; 2473-9529
ISSN (online)	2473-9537
ISSN	2473-9529
DOI	10.1182/bloodadvances.2023010725
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Article ; Online: The establishment of variant surface glycoprotein monoallelic expression revealed by single-cell RNA-seq of Trypanosoma brucei in the tsetse fly salivary glands.

Hutchinson, Sebastian / Foulon, Sophie / Crouzols, Aline / Menafra, Roberta / Rotureau, Brice / Griffiths, Andrew D / Bastin, Philippe

PLoS pathogens

2021 Volume 17, Issue 9, Page(s) e1009904

Abstract: The long and complex Trypanosoma brucei development in the tsetse fly vector culminates when parasites gain mammalian infectivity in the salivary glands. A key step in this process is the establishment of monoallelic variant surface glycoprotein (VSG) ... ...

Abstract	The long and complex Trypanosoma brucei development in the tsetse fly vector culminates when parasites gain mammalian infectivity in the salivary glands. A key step in this process is the establishment of monoallelic variant surface glycoprotein (VSG) expression and the formation of the VSG coat. The establishment of VSG monoallelic expression is complex and poorly understood, due to the multiple parasite stages present in the salivary glands. Therefore, we sought to further our understanding of this phenomenon by performing single-cell RNA-sequencing (scRNA-seq) on these trypanosome populations. We were able to capture the developmental program of trypanosomes in the salivary glands, identifying populations of epimastigote, gamete, pre-metacyclic and metacyclic cells. Our results show that parasite metabolism is dramatically remodeled during development in the salivary glands, with a shift in transcript abundance from tricarboxylic acid metabolism to glycolytic metabolism. Analysis of VSG gene expression in pre-metacyclic and metacyclic cells revealed a dynamic VSG gene activation program. Strikingly, we found that pre-metacyclic cells contain transcripts from multiple VSG genes, which resolves to singular VSG gene expression in mature metacyclic cells. Single molecule RNA fluorescence in situ hybridisation (smRNA-FISH) of VSG gene expression following in vitro metacyclogenesis confirmed this finding. Our data demonstrate that multiple VSG genes are transcribed before a single gene is chosen. We propose a transcriptional race model governs the initiation of monoallelic expression.
MeSH term(s)	Animals ; Gene Expression Regulation/genetics ; Insect Vectors/parasitology ; RNA-Seq ; Salivary Glands/parasitology ; Trypanosoma brucei brucei/genetics ; Tsetse Flies/parasitology ; Variant Surface Glycoproteins, Trypanosoma/genetics
Chemical Substances	Variant Surface Glycoproteins, Trypanosoma
Language	English
Publishing date	2021-09-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7366
ISSN (online)	1553-7374
ISSN	1553-7366
DOI	10.1371/journal.ppat.1009904
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Article ; Online: Application of long-read sequencing to elucidate complex pharmacogenomic regions: a proof of principle.

van der Lee, Maaike / Rowell, William J / Menafra, Roberta / Guchelaar, Henk-Jan / Swen, Jesse J / Anvar, Seyed Yahya

The pharmacogenomics journal

2021 Volume 22, Issue 1, Page(s) 75–81

Abstract: The use of pharmacogenomics in clinical practice is becoming standard of care. However, due to the complex genetic makeup of pharmacogenes, not all genetic variation is currently accounted for. Here, we show the utility of long-read sequencing to resolve ...

Abstract	The use of pharmacogenomics in clinical practice is becoming standard of care. However, due to the complex genetic makeup of pharmacogenes, not all genetic variation is currently accounted for. Here, we show the utility of long-read sequencing to resolve complex pharmacogenes by analyzing a well-characterised sample. This data consists of long reads that were processed to resolve phased haploblocks. 73% of pharmacogenes were fully covered in one phased haploblock, including 9/15 genes that are 100% complex. Variant calling accuracy in the pharmacogenes was high, with 99.8% recall and 100% precision for SNVs and 98.7% precision and 98.0% recall for Indels. For the majority of gene-drug interactions in the DPWG and CPIC guidelines, the associated genes could be fully resolved (62% and 63% respectively). Together, these findings suggest that long-read sequencing data offers promising opportunities in elucidating complex pharmacogenes and haplotype phasing while maintaining accurate variant calling.
MeSH term(s)	Genetic Variation ; Genome, Human ; Haplotypes ; High-Throughput Nucleotide Sequencing ; Humans ; Pharmacogenetics/methods ; Reproducibility of Results ; Sequence Analysis, DNA/methods
Language	English
Publishing date	2021-11-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2106831-8
ISSN	1473-1150 ; 1470-269X
ISSN (online)	1473-1150
ISSN	1470-269X
DOI	10.1038/s41397-021-00259-z
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Article ; Online: IL-7 receptor signaling drives human B-cell progenitor differentiation and expansion.

Kaiser, Fabian M P / Janowska, Iga / Menafra, Roberta / de Gier, Melanie / Korzhenevich, Jakov / Pico-Knijnenburg, Ingrid / Khatri, Indu / Schulz, Ansgar / Kuijpers, Taco W / Lankester, Arjan C / Konstantinidis, Lukas / Erlacher, Miriam / Kloet, Susan / van Schouwenburg, Pauline A / Rizzi, Marta / van der Burg, Mirjam

Blood

2023 Volume 142, Issue 13, Page(s) 1113–1130

Abstract: Although absence of interleukin-7 (IL-7) signaling completely abrogates T and B lymphopoiesis in mice, patients with severe combined immunodeficiency caused by mutations in the IL-7 receptor α chain (IL-7Rα) still generate peripheral blood B cells. ... ...

Abstract	Although absence of interleukin-7 (IL-7) signaling completely abrogates T and B lymphopoiesis in mice, patients with severe combined immunodeficiency caused by mutations in the IL-7 receptor α chain (IL-7Rα) still generate peripheral blood B cells. Consequently, human B lymphopoiesis has been thought to be independent of IL-7 signaling. Using flow cytometric analysis and single-cell RNA sequencing of bone marrow samples from healthy controls and patients who are IL-7Rα deficient, in combination with in vitro modeling of human B-cell differentiation, we demonstrate that IL-7R signaling plays a crucial role in human B lymphopoiesis. IL-7 drives proliferation and expansion of early B-cell progenitors but not of pre-BII large cells and has a limited role in the prevention of cell death. Furthermore, IL-7 guides cell fate decisions by enhancing the expression of BACH2, EBF1, and PAX5, which jointly orchestrate the specification and commitment of early B-cell progenitors. In line with this observation, early B-cell progenitors of patients with IL-7Rα deficiency still expressed myeloid-specific genes. Collectively, our results unveil a previously unknown role for IL-7 signaling in promoting the B-lymphoid fate and expanding early human B-cell progenitors while defining important differences between mice and humans. Our results have implications for hematopoietic stem cell transplantation strategies in patients with T- B+ severe combined immunodeficiency and provide insights into the role of IL-7R signaling in leukemogenesis.
MeSH term(s)	Humans ; Animals ; Mice ; Interleukin-7/metabolism ; Severe Combined Immunodeficiency ; Receptors, Interleukin-7/genetics ; Cell Differentiation ; Hematopoiesis
Chemical Substances	Interleukin-7 ; Receptors, Interleukin-7
Language	English
Publishing date	2023-06-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80069-7
ISSN	1528-0020 ; 0006-4971
ISSN (online)	1528-0020
ISSN	0006-4971
DOI	10.1182/blood.2023019721
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Article ; Online: CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells.

Shafighi, Shadi Darvish / Kiełbasa, Szymon M / Sepúlveda-Yáñez, Julieta / Monajemi, Ramin / Cats, Davy / Mei, Hailiang / Menafra, Roberta / Kloet, Susan / Veelken, Hendrik / van Bergen, Cornelis A M / Szczurek, Ewa

Genome medicine

2021 Volume 13, Issue 1, Page(s) 45

Abstract: Background: Drawing genotype-to-phenotype maps in tumors is of paramount importance for understanding tumor heterogeneity. Assignment of single cells to their tumor clones of origin can be approached by matching the genotypes of the clones to the ... ...

Abstract	Background: Drawing genotype-to-phenotype maps in tumors is of paramount importance for understanding tumor heterogeneity. Assignment of single cells to their tumor clones of origin can be approached by matching the genotypes of the clones to the mutations found in RNA sequencing of the cells. The confidence of the cell-to-clone mapping can be increased by accounting for additional measurements. Follicular lymphoma, a malignancy of mature B cells that continuously acquire mutations in parallel in the exome and in B cell receptor loci, presents a unique opportunity to join exome-derived mutations with B cell receptor sequences as independent sources of evidence for clonal evolution. Methods: Here, we propose CACTUS, a probabilistic model that leverages the information from an independent genomic clustering of cells and exploits the scarce single cell RNA sequencing data to map single cells to given imperfect genotypes of tumor clones. Results: We apply CACTUS to two follicular lymphoma patient samples, integrating three measurements: whole exome, single-cell RNA, and B cell receptor sequencing. CACTUS outperforms a predecessor model by confidently assigning cells and B cell receptor-based clusters to the tumor clones. Conclusions: The integration of independent measurements increases model certainty and is the key to improving model performance in the challenging task of charting the genotype-to-phenotype maps in tumors. CACTUS opens the avenue to study the functional implications of tumor heterogeneity, and origins of resistance to targeted therapies. CACTUS is written in R and source code, along with all supporting files, are available on GitHub ( https://github.com/LUMC/CACTUS ).
MeSH term(s)	Clone Cells ; Cluster Analysis ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Genomics ; Humans ; Lymphoma, Follicular/genetics ; Models, Statistical ; Neoplasms/genetics ; Reproducibility of Results ; Single-Cell Analysis ; Software ; Whole Exome Sequencing
Language	English
Publishing date	2021-03-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2484394-5
ISSN	1756-994X ; 1756-994X
ISSN (online)	1756-994X
ISSN	1756-994X
DOI	10.1186/s13073-021-00842-w
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Article ; Online: Correction: Inflammatory and tolerogenic myeloid cells determine outcome following human allergen challenge.

Voskamp, Astrid L / Tak, Tamar / Gerdes, Maarten L / Menafra, Roberta / Duijster, Ellen / Jochems, Simon P / Kielbasa, Szymon M / Kormelink, Tom Groot / Stam, Koen A / van Hengel, Oscar R J / de Jong, Nicolette W / Hendriks, Rudi W / Kloet, Susan L / Yazdanbakhsh, Maria / de Jong, Esther C / Gerth van Wijk, Roy / Smits, Hermelijn H

The Journal of experimental medicine

2023 Volume 220, Issue 9

Language	English
Publishing date	2023-08-18
Publishing country	United States
Document type	Published Erratum
ZDB-ID	218343-2
ISSN	1540-9538 ; 0022-1007
ISSN (online)	1540-9538
ISSN	0022-1007
DOI	10.1084/jem.2022111108162023c
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Article ; Online: Inflammatory and tolerogenic myeloid cells determine outcome following human allergen challenge.

Voskamp, Astrid L / Tak, Tamar / Gerdes, Maarten L / Menafra, Roberta / Duijster, Ellen / Jochems, Simon P. / Kielbasa, Szymon M / Kormelink, Tom Groot / Stam, Koen A / van Hengel, Oscar R J / de Jong, Nicolette W / Hendriks, Rudi W / Kloet, Susan L / Yazdanbakhsh, Maria / de Jong, Esther C / Gerth van Wijk, Roy / Smits, Hermelijn H

The Journal of experimental medicine

2023 Volume 220, Issue 9

Abstract: Innate mononuclear phagocytic system (MPS) cells preserve mucosal immune homeostasis. We investigated their role at nasal mucosa following allergen challenge with house dust mite. We combined single-cell proteome and transcriptome profiling on nasal ... ...

Abstract	Innate mononuclear phagocytic system (MPS) cells preserve mucosal immune homeostasis. We investigated their role at nasal mucosa following allergen challenge with house dust mite. We combined single-cell proteome and transcriptome profiling on nasal immune cells from nasal biopsies cells from 30 allergic rhinitis and 27 non-allergic subjects before and after repeated nasal allergen challenge. Biopsies of patients showed infiltrating inflammatory HLA-DRhi/CD14+ and CD16+ monocytes and proallergic transcriptional changes in resident CD1C+/CD1A+ conventional dendritic cells (cDC)2 following challenge. In contrast, non-allergic individuals displayed distinct innate MPS responses to allergen challenge: predominant infiltration of myeloid-derived suppressor cells (MDSC: HLA-DRlow/CD14+ monocytes) and cDC2 expressing inhibitory/tolerogenic transcripts. These divergent patterns were confirmed in ex vivo stimulated MPS nasal biopsy cells. Thus, we identified not only MPS cell clusters involved in airway allergic inflammation but also highlight novel roles for non-inflammatory innate MPS responses by MDSC to allergens in non-allergic individuals. Future therapies should address MDSC activity as treatment for inflammatory airway diseases.
MeSH term(s)	Humans ; Allergens ; Rhinitis, Allergic, Perennial/pathology ; Nasal Mucosa ; Myeloid Cells/pathology ; Inflammation/pathology
Chemical Substances	Allergens
Language	English
Publishing date	2023-07-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218343-2
ISSN	1540-9538 ; 0022-1007
ISSN (online)	1540-9538
ISSN	0022-1007
DOI	10.1084/jem.20221111
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Article ; Online: Toward predicting CYP2D6-mediated variable drug response from

van der Lee, Maaike / Allard, William G / Vossen, Rolf H A M / Baak-Pablo, Renée F / Menafra, Roberta / Deiman, Birgit A L M / Deenen, Maarten J / Neven, Patrick / Johansson, Inger / Gastaldello, Stefano / Ingelman-Sundberg, Magnus / Guchelaar, Henk-Jan / Swen, Jesse J / Anvar, Seyed Yahya

Science translational medicine

2021 Volume 13, Issue 603

Abstract: Pharmacogenomics is a key component of personalized medicine that promises safer and more effective drug treatment by individualizing drug choice and dose based on genetic profiles. In clinical practice, genetic biomarkers are used to categorize patients ...

Abstract	Pharmacogenomics is a key component of personalized medicine that promises safer and more effective drug treatment by individualizing drug choice and dose based on genetic profiles. In clinical practice, genetic biomarkers are used to categorize patients into *-alleles to predict CYP450 enzyme activity and adjust drug dosages accordingly. However, this approach leaves a large part of variability in drug response unexplained. Here, we present a proof-of-concept approach that uses continuous-scale (instead of categorical) assignments to predict enzyme activity. We used full
MeSH term(s)	Alleles ; Cytochrome P-450 CYP2D6/genetics ; Genotype ; Humans ; Pharmaceutical Preparations ; Prospective Studies ; Tamoxifen
Chemical Substances	Pharmaceutical Preparations ; Tamoxifen (094ZI81Y45) ; Cytochrome P-450 CYP2D6 (EC 1.14.14.1)
Language	English
Publishing date	2021-09-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2518854-9
ISSN	1946-6242 ; 1946-6234
ISSN (online)	1946-6242
ISSN	1946-6234
DOI	10.1126/scitranslmed.abf3637
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