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3. Decoding chromatin states by proteomic profiling of nucleosome readers

Author

Lukauskas, Saulius, Tvardovskiy, Andrey, Nguyen, Nhuong V., Stadler, Mara, Faull, Peter, Ravnsborg, Tina, Özdemir Aygenli, Bihter, Dornauer, Scarlett, Flynn, Helen, Lindeboom, Rik G. H., Barth, Teresa K., Brockers, Kevin, Hauck, Stefanie M., Vermeulen, Michiel, Snijders, Ambrosius P., Müller, Christian L., DiMaggio, Peter A., Jensen, Ole N., Schneider, Robert, and Bartke, Till

Published
2024
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5. Dynamic de novo heterochromatin assembly and disassembly at replication forks ensures fork stability

Author

Gaggioli, Vincent, Lo, Calvin S. Y., Reverón-Gómez, Nazaret, Jasencakova, Zuzana, Domenech, Heura, Nguyen, Hong, Sidoli, Simone, Tvardovskiy, Andrey, Uruci, Sidrit, Slotman, Johan A., Chai, Yi, Gonçalves, João G. S. C. Souto, Manolika, Eleni Maria, Jensen, Ole N., Wheeler, David, Sridharan, Sriram, Chakrabarty, Sanjiban, Demmers, Jeroen, Kanaar, Roland, Groth, Anja, and Taneja, Nitika

Published
2023
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7. Publisher Correction: Decoding chromatin states by proteomic profiling of nucleosome readers

Author

Lukauskas, Saulius, Tvardovskiy, Andrey, Nguyen, Nhuong V., Stadler, Mara, Faull, Peter, Ravnsborg, Tina, Özdemir Aygenli, Bihter, Dornauer, Scarlett, Flynn, Helen, Lindeboom, Rik G. H., Barth, Teresa K., Brockers, Kevin, Hauck, Stefanie M., Vermeulen, Michiel, Snijders, Ambrosius P., Müller, Christian L., DiMaggio, Peter A., Jensen, Ole N., Schneider, Robert, and Bartke, Till

Published
2024
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8. The histone demethylase KDM5C functions as a tumor suppressor in AML by repression of bivalently marked immature genes

Author

Trempenau, Mette Louise, Schuster, Mikkel Bruhn, Pundhir, Sachin, Pereira, Mafalda Araujo, Kalvisa, Adrija, Tapia, Marta, Su, Jinyu, Ge, Ying, de Boer, Bauke, Balhuizen, Alexander, Bagger, Frederik Otzen, Shliaha, Pavel, Sroczynska, Patrycja, Walfridsson, Julian, Grønbæk, Kirsten, Theilgaard-Mönch, Kim, Jensen, Ole N., Helin, Kristian, and Porse, Bo T.

Published
2023
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12. Endothelial and neuronal engagement by AAV-BR1 gene therapy alleviates neurological symptoms and lipid deposition in a mouse model of Niemann-Pick type C2.

Author

Rasmussen, Charlotte Laurfelt Munch, Frederiksen, Signe Frost, Heegaard, Christian Würtz, Thomsen, Maj Schneider, Hede, Eva, Laczek, Bartosz, Körbelin, Jakob, Wüstner, Daniel, Thomsen, Louiza Bohn, Schwaninger, Markus, Jensen, Ole N., Moos, Torben, and Burkhart, Annette

Subjects
PURKINJE cells, MEDICAL sciences, VIRAL genes, GENE therapy, RECOMBINANT proteins
Abstract

Background: Patients with the genetic disorder Niemann-Pick type C2 disease (NP-C2) suffer from lysosomal accumulation of cholesterol causing both systemic and severe neurological symptoms. In a murine NP-C2 model, otherwise successful intravenous Niemann-Pick C2 protein (NPC2) replacement therapy fails to alleviate progressive neurodegeneration as infused NPC2 cannot cross the blood–brain barrier (BBB). Genetic modification of brain endothelial cells (BECs) is thought to enable secretion of recombinant proteins thereby overcoming the restrictions of the BBB. We hypothesized that an adeno-associated virus (AAV-BR1) encoding the Npc2 gene could cure neurological symptoms in Npc2−/− mice through transduction of BECs, and possibly neurons via viral passage across the BBB. Methods: Six weeks old Npc2−/− mice were intravenously injected with the AAV-BR1-NPC2 vector. Composite phenotype scores and behavioral tests were assessed for the following 6 weeks and visually documented. Post-mortem analyses included gene expression analyses, verification of neurodegeneration in Purkinje cells, determination of NPC2 transduction in the CNS, assessment of gliosis, quantification of gangliosides, and co-detection of cholesterol with NPC2 in degenerating neurons. Results: Treatment with the AAV-BR1-NPC2 vector improved motor functions, reduced neocortical inflammation, and preserved Purkinje cells in most of the mice, referred to as high responders. The vector exerted tropism for BECs and neurons resulting in a widespread NPC2 distribution in the brain with a concomitant reduction of cholesterol in adjacent neurons, presumably not transduced by the vector. Mass spectrometry imaging revealed distinct lipid alterations in the brains of Npc2−/− mice, with increased GM2 and GM3 ganglioside accumulation in the cerebellum and hippocampus. AAV-BR1-NPC2 treatment partially normalized these ganglioside distributions in high responders, including restoration of lipid profiles towards those of Npc2+/+ controls. Conclusion: The data suggests cross-correcting gene therapy to the brain via delivery of NPC2 from BECs and neurons. [ABSTRACT FROM AUTHOR]

Published
2025
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15. Distinct Roles of Two Histone Methyltransferases in Transmitting H3K36me3-Based Epigenetic Memory Across Generations in Caenorhabditis elegans

Author

Kreher, Jeremy, Takasaki, Teruaki, Cockrum, Chad, Sidoli, Simone, Garcia, Benjamin A, Jensen, Ole N, and Strome, Susan

Subjects
Biochemistry and Cell Biology, Biological Sciences, Genetics, Human Genome, Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, Animals, Biocatalysis, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Embryonic Development, Epigenesis, Genetic, Female, Histones, Lysine, Male, Methylation, Oocytes, Spermatozoa, Temperature, X Chromosome, epigenetics, chromatin, H3K36 methylation, development, germ cells, WormBase, Developmental Biology, Biochemistry and cell biology
Abstract

Epigenetic information contributes to proper gene expression and development, and can be transmitted not only through mitotic divisions but also from parents to progeny. We investigated the roles in epigenetic inheritance of MES-4 and MET-1, the two Caenorhabditis elegans enzymes that methylate H3K36 (histone H3 Lys 36). Mass spectrometry analysis confirmed immunostaining results showing that both MES-4 and MET-1 catalyze H3K36me3. In the adult germline, MES-4 is enriched in the distal mitotic zone and MET-1 is enriched in the meiotic pachytene zone. Embryos inherit H3K36me3-marked chromosomes from both the oocyte and sperm, and a maternal load of MES-4 and MET-1 Maternal MES-4 quickly associates with sperm chromosomes; that association requires that the sperm chromosomes bear H3K36me3, suggesting that MES-4 is recruited to chromosomes by preexisting H3K36me3. In embryos that inherit H3K36me3-positive oocyte chromosomes and H3K36me3-negative sperm chromosomes, MES-4 and H3K36me3 are maintained on only a subset of chromosomes until at least the 32-cell stage, likely because MES-4 propagates H3K36me3 on regions of the genome with preexisting H3K36me3. In embryos lacking MES-4, H3K36me3 levels on chromosomes drop precipitously postfertilization. In contrast to the relatively high levels of MES-4 in early-stage embryos, MET-1 levels are low at early stages and start increasing by the ∼26-cell stage, consistent with expression from the zygotic genome. Our findings support the model that MET-1 mediates transcription-coupled H3K36me3 in the parental germline and transcriptionally active embryos, and that MES-4 transmits an epigenetic memory of H3K36me3 across generations and through early embryo cell divisions by maintaining inherited patterns of H3K36me3.

Published
2018

17. How many human proteoforms are there?

Author

Aebersold, Ruedi, Agar, Jeffrey N, Amster, I Jonathan, Baker, Mark S, Bertozzi, Carolyn R, Boja, Emily S, Costello, Catherine E, Cravatt, Benjamin F, Fenselau, Catherine, Garcia, Benjamin A, Ge, Ying, Gunawardena, Jeremy, Hendrickson, Ronald C, Hergenrother, Paul J, Huber, Christian G, Ivanov, Alexander R, Jensen, Ole N, Jewett, Michael C, Kelleher, Neil L, Kiessling, Laura L, Krogan, Nevan J, Larsen, Martin R, Loo, Joseph A, Ogorzalek Loo, Rachel R, Lundberg, Emma, MacCoss, Michael J, Mallick, Parag, Mootha, Vamsi K, Mrksich, Milan, Muir, Tom W, Patrie, Steven M, Pesavento, James J, Pitteri, Sharon J, Rodriguez, Henry, Saghatelian, Alan, Sandoval, Wendy, Schlüter, Hartmut, Sechi, Salvatore, Slavoff, Sarah A, Smith, Lloyd M, Snyder, Michael P, Thomas, Paul M, Uhlén, Mathias, Van Eyk, Jennifer E, Vidal, Marc, Walt, David R, White, Forest M, Williams, Evan R, Wohlschlager, Therese, Wysocki, Vicki H, Yates, Nathan A, Young, Nicolas L, and Zhang, Bing

Subjects
Humans, Proteins, Protein Isoforms, Proteome, Ubiquitin, Proteomics, Protein Biosynthesis, Protein Processing, Post-Translational, Phenotype, Genome, Human, Databases, Protein, Mass Spectrometry, Genetics, Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, Medicinal and Biomolecular Chemistry, Biochemistry and Cell Biology, Biochemistry & Molecular Biology
Abstract

Despite decades of accumulated knowledge about proteins and their post-translational modifications (PTMs), numerous questions remain regarding their molecular composition and biological function. One of the most fundamental queries is the extent to which the combinations of DNA-, RNA- and PTM-level variations explode the complexity of the human proteome. Here, we outline what we know from current databases and measurement strategies including mass spectrometry-based proteomics. In doing so, we examine prevailing notions about the number of modifications displayed on human proteins and how they combine to generate the protein diversity underlying health and disease. We frame central issues regarding determination of protein-level variation and PTMs, including some paradoxes present in the field today. We use this framework to assess existing data and to ask the question, "How many distinct primary structures of proteins (proteoforms) are created from the 20,300 human genes?" We also explore prospects for improving measurements to better regularize protein-level biology and efficiently associate PTMs to function and phenotype.

Published
2018

26. Supplementary information for the article: Đurašinović, T.; Lopandić, Z.; Protić-Rosić, I.; Ravnsborg, T.; Blagojević, G.; Burazer, L.; Jensen, O. N.; Gavrović-Jankulović, M. Utilizing the Banana S-Adenosyl-L-Homocysteine Hydrolase Allergen to Identify Cross-Reactive IgE in Ryegrass-, Latex-, and Kiwifruit-Allergic Individuals. International Journal of Molecular Sciences 2024, 25 (11), 5800. https://doi.org/10.3390/ijms25115800.

Author

Đurašinović, Tatjana, Lopandić, Zorana, Protić-Rosić, Isidora, Ravnsborg, Tina, Blagojević, Gordan, Burazer, Lidija, Jensen, Ole N., Gavrović-Jankulović, Marija, Đurašinović, Tatjana, Lopandić, Zorana, Protić-Rosić, Isidora, Ravnsborg, Tina, Blagojević, Gordan, Burazer, Lidija, Jensen, Ole N., and Gavrović-Jankulović, Marija

Abstract

Supplementary Table S2: A)List of T-cell epitopes in kiwifruit SAHH. B)List of T cell epitopes in latex SAHH.C)List of T-cell epitopes in ryegrass SAHH

Published
2024

27. Utilizing the Banana S-Adenosyl-L-Homocysteine Hydrolase Allergen to Identify Cross-Reactive IgE in Ryegrass-, Latex-, and Kiwifruit-Allergic Individuals

Author

Đurašinović, Tatjana, Lopandić, Zorana, Protić-Rosić, Isidora, Ravnsborg, Tina, Blagojević, Gordan, Burazer, Lidija, Jensen, Ole N., Gavrović-Jankulović, Marija, Đurašinović, Tatjana, Lopandić, Zorana, Protić-Rosić, Isidora, Ravnsborg, Tina, Blagojević, Gordan, Burazer, Lidija, Jensen, Ole N., and Gavrović-Jankulović, Marija

Abstract

Food allergies mediated by specific IgE (sIgE) have a significant socioeconomic impact on society. Evaluating the IgE cross-reactivity between allergens from different allergen sources can enable the better management of these potentially life-threatening adverse reactions to food proteins and enhance food safety. A novel banana fruit allergen, S-adenosyl-L-homocysteine hydrolase (SAHH), has been recently identified and its recombinant homolog was heterologously overproduced in E. coli. In this study, we performed a search in the NCBI (National Center for Biotechnology Information) for SAHH homologs in ryegrass, latex, and kiwifruit, all of which are commonly associated with pollen-latex-fruit syndrome. In addition, Western immunoblot analysis was utilized to identify the cross-reactive IgE to banana SAHH in the sera of patients with a latex allergy, kiwifruit allergy, and ryegrass allergy. ClustalOmega analysis showed more than 92% amino acid sequence identity among the banana SAHH homologs in ryegrass, latex, and kiwifruit. In addition to five B-cell epitopes, in silico analysis predicted eleven T-cell epitopes in banana SAHH, seventeen in kiwifruit SAHH, twelve in ryegrass SAHH, and eight in latex SAHH, which were related to the seven-allele HLA reference set (HLA-DRB1*03:01, HLA-DRB1*07:01, HLA-DRB1*15:01, HLA-DRB3*01:01, HLA-DRB3*02:02, HLA-DRB4*01:01, HLA-DRB5*01:01). Four T-cell epitopes were identical in banana and kiwifruit SAHH (positions 328, 278, 142, 341), as well as banana and ryegrass SAHH (positions 278, 142, 96, and 341). All four SAHHs shared two T-cell epitopes (positions 278 and 341). In line with the high amino acid sequence identity and B-cell epitope homology among the analyzed proteins, the cross-reactive IgE to banana SAHH was detected in three of three latex-allergic patients, five of six ryegrass-allergic patients, and two of three kiwifruit-allergic patients. Although banana SAHH has only been studied in a small group of allergic individu

Published
2024

28. A simple and fast method to determine the parameters for fuzzy c-means cluster validation

Author

Schwämmle, Veit and Jensen, Ole N.

Subjects
Quantitative Biology - Quantitative Methods, Quantitative Biology - Genomics
Abstract

Fuzzy c-means clustering is widely used to identify cluster structures in high-dimensional data sets, such as those obtained in DNA microarray and quantitative proteomics experiments. One of its main limitations is the lack of a computationally fast method to determine the two parameters fuzzifier and cluster number. Wrong parameter values may either lead to the inclusion of purely random fluctuations in the results or ignore potentially important data. The optimal solution has parameter values for which the clustering does not yield any results for a purely random data set but which detects cluster formation with maximum resolution on the edge of randomness. Estimation of the optimal parameter values is achieved by evaluation of the results of the clustering procedure applied to randomized data sets. In this case, the optimal value of the fuzzifier follows common rules that depend only on the main properties of the data set. Taking the dimension of the set and the number of objects as input values instead of evaluating the entire data set allows us to propose a functional relationship determining its value directly. This result speaks strongly against setting the fuzzifier equal to 2 as typically done in many previous studies. Validation indices are generally used for the estimation of the optimal number of clusters. A comparison shows that the minimum distance between the centroids provides results that are at least equivalent or better than those obtained by other computationally more expensive indices., Comment: 9 pages, 9 figures

Published
2010

46. Terminally phosphorylated triblock polyethers acting both as templates and pore-forming agents for surface molecular imprinting of monoliths targeting phosphopeptides

Author

Huynh, Chau Minh, Arribas Díez, Ignacio, Thi, Hien Kim Le, Jensen, Ole N., Sellergren, Börje, Irgum, Knut, Huynh, Chau Minh, Arribas Díez, Ignacio, Thi, Hien Kim Le, Jensen, Ole N., Sellergren, Börje, and Irgum, Knut

Abstract

The novel process reported here described the manufacture of monolithic molecularly imprinted polymers (MIPs) using a terminally functionalized block copolymer as the imprinting template and pore-forming agent. The MIPs were prepared through a step-growth polymerization process using a melamine-formaldehyde precondensate in a biphasic solvent system. Despite having a relatively low imprinting factor, the use of MIP monolith in liquid chromatography demonstrated the ability to selectively target desired analytes. An MIP capillary column was able to separate monophosphorylated peptides from a tryptic digest of bovine serum albumin. Multivariate data analysis and modeling of the phosphorylated and nonphosphorylated peptide retention times revealed that the number of phosphorylations was the strongest retention contributor for peptide retention on the monolithic MIP capillary column.

Published
2023
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