Molecular Biometry – Roman Zubarev group

Special research interests beyond Proteomics

Immunology

We have developed a monocyte-based proteomics assay to quantify the innate immune response to xenomolecules and used it to characterize the toxicity of various nanoparticles.

We have also pioneered “SpotLight proteomics” which is based on de novo sequencing of the repertoire of antibody motifs present in blood of a patient cohort.

Gas-phase fragmentation

Roman Zubarev is one of the pioneers of electron capture dissociation (ECD) and related ion-electron reactions. He discovered that organic radicals come in two kinds, hydrogen-abundant and hydrogen-deficient radicals, which differ significantly in their reactivity and properties.

Fasmatech (Athens, Greece) built the ultimate device for gas-phase structural analysis of polypeptides for us – the OMNI-trap. With this device, the decades-old dream of the “top-down” sequencing of large proteins may come true.

Isospartyl in Alzheimer’s disease (AD), ageing and stemness

We formulated the isoaspartate (isoAsp) hypothesis of the AD origin, that postulates that deamidation of asparagyl residue and isomerization of aspartyl residues in proteins initiate the cascade of protein aggregation, ultimately resulting in AD, but also playing an important role in ageing.

We are studying ways to:

1. measure the isoAsp content in human blood as an AD risk factor,
2. reduce the isoAsp load in the organism to prevent AD and slow down ageing,
3. study the role of isoAsp repair in stemness.

Cancer and cell death modalities

Cell morphology measured at the molecular level via abundant, structural proteins can faithfully reflect the behavior of drug targets.

Based on this finding, we are identifying all possible types of cell death by treating cancer cells with a variety of anticancer agents (work in progress).

Origin of life and Astrobiology

We have shown that abiotically produced (from simple gases and water) organic matter can support life of prokaryotes, supporting the idea that early Earth was a hospitable place for primitive life.

For the first time, a living cell was produced from dead matter.

Effect of stable isotopes on biology: Isotopic resonance hypothesis

We have discovered that the average terrestrial isotopic compositions of the elements C, H, N and O are not random but correspond to a “resonance” for molecules with Z=0, where Z = C – (N+H)/2. At an isotopic resonance, a reduction of complexity occurs, and most reactions acquire faster kinetics. Among the molecules with Z=0, 11 out of 20 amino acid residues, and many proteins.

The isotopic resonance hypothesis has been extensively tested and found truthful at p<10-15 level. Therefore, life on Earth has benefitted in early days, and continues to benefit now, by the presence of the Z=0 isotopic resonance. In contrast, neither Mars nor Venus have isotopic resonances. In general, isotopic compositions on Mars are found to be detrimental for terrestrial life.

We continue to explore the isotopic resonance phenomenon and its consequences for biology, medicine and technology.

Current research

The course of disease for clinical arthritis.

Open Diagnostics project: JointID clinical treatment research – a new unique diagnostic test for Rheumatoid Arthritis configuration options

Find out below what the research within the division of Medical Inflammation Research (MIR) is aimed at. Also listed are examples of research projects and an overview of our collaborations and recent publications.

The aims of our research are:

• To identify and functionally analyse the genes that control animal models for chronic inflammatory diseases, mainly using models for rheumatoid arthritis.
• To use the animal models not only for understanding the basic mechanism of autoimmune disease and for developing new diagnostic, preventive and therapeutic strategies.
• To understand the role of MHC class II genes in explaining the immune specificity of autoimmune disease.

We have different research projects within our division. Below, some examples of such projects.

Diagnostics project: JointID clinical treatment research – a new unique diagnostic test for Rheumatoid Arthritis

Inflammation in cartilaginous joints occurs in many common diseases such as rheumatoid arthritis (RA), osteoarthritis (OA) and psoriasis arthritis (PsA). It is known that antibodies to modified proteins (anticitrullinated protein antibodies and rheumatoid factors) are useful for predicting and classifying RA. It has however been difficult to identify specific and useful biomarkers derived from the joint inflammation itself.

We have focused on the immune response to joint cartilage proteins, in particular type II collagen (CII). This is directed to exposed triple helical structures, as well as to structures modified e.g. by citrullination. The response is connected with the onset of the RA and provides very sensitive biomarkers for joint inflammation.

We have three main goals:

1. To develop a multiplex antibody diagnostic kit with post-translationally modified (citrullinated, carbamoylated, nitrosylated, oxidized and glycosylated) and conformational protein epitopes. These epitopes are selected to be of importance for development of arthritis in animal models. The purpose is to allow diagnosis of RA before disease onset and to help in determination of the type of therapy. The assay will also be used to select RA patients suitable for vaccination.
2. To develop a diagnostic kit to identify T cells specific for glycosylated CII. It will be used to predict and monitor vaccination effects of pre-RA and RA patients.
3. To extend the antibody kit with additional joint-related epitopes useful for diagnosing additional joint inflammatory diseases, including common diseases like OA and PsA

Main PI

Prof. Rikard Holmdahl.

Cooperation

Prof. Inger Gjertsson, Göteborg University; Prof. Jan Kihlberg, Uppsala University

Supported by

• Swedish Foundation for Strategic Research (SSF) 2015 – 2020 (Dnr: RB13-0156, 35,000,000 SEK)

Vaccine project: Developing vaccines to cure autoimmune diseases

The next step in the treatment of autoimmune disease will be to prevent and cure, rather than only treating the symptoms. We focus on vaccine development to both prevent and treat  rheumatoid arthritis (RA) but subsequently also other autoimmune diseases.

Vaccines have not yet been developed to any autoimmune disease, but we have several unique findings that will be tested clinically in RA. Our patent protected approach is to induce regulatory T cells by administration of a protein complex with the product of a strongly associated RA gene together with a protein fragment from collagen type II in joint cartilage that is a recognized by T cells in RA.

We have established new unique mouse strains with the human genes of interest, allowing development and validation of new vaccines not only for RA but for other autoimmune diseases as well. We have also developed new technology that allows modification of peptide structure; glycosylation and protein carrier, to develop improved personalized variants vaccines.

Open configuration options

Main PI

Prof. Rikard Holmdahl

Cooperation

Prof. Roman Zubarev, Division of Chemistry I and chemical proteomics platform, Karolinska Institutet; Prof. Jan Kihlberg, Uppsala University; Dr. Kajsa Wing, Division of Medical inflammation Research, Karolinska Institutet.

Supported by

• Swedish Science Council (VR), 2018-2022, (Dnr. 2017-06104, 19,000,000 SEK)
• Familjen Erling-Perssons Stiftelse, 2018-2020 (2017-10-09, 9,000,000 SEK)
• Novo Nordisk Foundation, 2025-2027 (0090035, 5,953,250 DKK)

Ncf1 project: Changing the view on autoimmune disease based on positional cloning of the Ncf1 gene  

We have identified several major causative polymorphisms in mouse and rat models of autoimmune disease and are now investigating their functional role. One of these projects concerns Ncf1, a component of the NOX2 complex, which induces reactive oxygen species (ROS).

We found that Ncf1 alleles causing low production of reactive oxygen species (ROS) is a major cause of autoimmune disease as well as being a pronounced risk behavior, explaining the natural selection. In addition ROS is likely to regulate the immune response to cancer cells.

The Ncf1 locus is highly polymorphic and has in fact not been sequenced in humans, due to copy number variation, and is therefore not included in genome wide association studies. However, we have found that copy number variation and amino acid polymorphism is strongly associated with both rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE).

Ncf1 is part of the NOX2 complex, which induces reactive oxygen species (ROS).

Based on our original finding and many years of combined efforts in both experimental animals and humans we have now established a unique platform and strategy to reveal a critical part of the pathogenesis of autoimmune disease. We have established CRISPR mutated and conditionally controlled Ncf1 mouse strains.

With models for RA and SLE we have also confirmed that the pathways are conserved between mice and humans. We have preliminary evidence of direct links to major pathways, such as interferon signaling and T and B cell receptor signaling. We intent to identify the immune regulatory cells expressing Ncf1 that play a critical role in the downstream pathway of autoimmune disease such as RA and SLE, but also in cancer. Also to determine the signaling oxidative and antioxidant pathways in the regulatory Ncf1 expressing cells as well as in cells exposed to secreted ROS.

This project will provide new insights into key pathogenic mechanisms based on redox regulation, leading to autoimmune and malignant diseases.

Main PI

Prof. Rikard Holmdahl

Cooperation

Prof. Elias Arnér, Division of Biochemistry, Karolinska Institute; Prof. Roman Zubarev, Division of Chemistry I and chemical proteomics platform, Karolinska Institute

Supported by

• Knut och Alice Wallenbergs Stiftelse, 2020 – 2024 (Dnr KAW 2019.0059, 36,500,000 SEK)
  Details about the project funding: "Genfynd kan bana väg för vaccin mot autoimmuna sjukdomar"
• Swedish Science Research Council (VR), 2020-2024 (Dnr. 2019-01209, 9,000,000 SEK)

Open configuration options

COSMIC webpage

Psoriasis vulgaris project: New therapy and diagnostics of psoriasis vulgaris and psoriatic arthritis based on new animal models

Psoriasis vulgaris (PsV) is an immune mediated disease of the skin, which is associated in one third of the patients with the development of psoriatic arthritis (PsA). PsV is a complex chronic disease driven by adaptive and innate lymphocytes involving the IL-17/22/23 signaling pathway. It is associated with the PSORS1 locus within the major histocompatibility complex (MHC) region, containing non-classical MHC genes regulating IL-17 producing innate lymphocytes. Besides the strong influence of the MHC region, a locus with the inducible nitric oxide synthase (NOS2) gene is associated with PsV/PsA susceptibility and the NOS2 locus regulate the exposure of various reactive oxygen species (ROS). Thus, genetic evidence argues for that non-classical MHC genes involved in the innate immune responses are regulated by RNS/ROS mediated functions.

The environmental causes of the PsV/ PsA in humans is not known but some sort of environmental challenges triggering the immune system in pathogenic way is likely. And  it is likely that an immune adjuvant type of exposure, mediated by infections, pollution or smoking, will trigger or promote disease. Our project is based on the unique discovery that mannan exposure could induce the development of a disease in mice mimicking PsV and PsA. In this project, we will use the MIP model to investigate PsV and PsA with the aim to develop new type of diagnostics and treatments.

The mechanisms by which mannan triggers disease is not known but is likely involving activation of inflammatory cells through CLRs. These receptors could be both inflammatory and anti-inflammatory, partially dependent on their ability to activate the NOX2 complex that could induce reactive oxygen species (ROS), protecting disease development in the MIP model. Based on this, we will use mouse strains with and without the Ncf1 mutation to determine whether the observed therapeutic effect is dependent of the proposed mechanisms of action through the NOX2 complex. We will also use the model to facilitate the development of better diagnostics for PsV and PsA, with developed a multiplex peptide-based antibody test to investigate the ongoing autoantibody responses in in autoimmune diseases.

Main PI

Prof. Rikard Holmdahl

Supported by

1. Leo Foundation 2023- 2025 (LF-OC-22-001023, DKK 3,622,500)
2. Psoriasisförbundet 2021-2022 (2021-2022, 200,000 SEK)

Publications

See all our publications on PubMed and Google Scholar

Collaborations

• Partner in network for Cancer Redox - targeting redox pathways for improved cancer therapy, Coord. Prof. Elias Arnér, Biochemistry, Karolinska Institute, Supported by Knut och Alice Wallenbergs Stiftelse, 2016 – 2021 (Dnr. 2015.0063)
• Partner in network for A new unique diagnostics test for Rheumatoid Arthritis, Coord Prof. Inger Gjertsson, Göteborg university,  supported by Swedish Research council, 2017 – 2019 (Dnr 2016-00288)
• Longstanding collaboration with Xian Jiaotong university and the 2nd affiliated hospital in Xian, China.
• Cooperation with Fraunhofer research institute in Frankfurt Am Main.
• Guangdong province team project with Southern Medical university in Guangzhou, China
• Cooperation project with Prof. Gregg Fields, Florida Atlantic University, funded by NIH 2021-2023 (KR-K210)
• Cooperation with BioInvent international AB, Lund
• Cooperation with Sichuan University, West China Hospital in Chendu, China

Former and current PhD students

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Awarded PhDs

Main supervision

1. Mikael Andersson: 901214, "Self reactivity and tolerance in the immune system. Studies on T cells in murine type II collagen-induced arthritis", Medical Faculty, Uppsala University, opponent Antonio Coutinho, Paris.
2. Tom J Goldschmidt: 910927, “T lymphocytes in autoimmune arthritis. Monoclonal antibody treatments in mouse and rat”, Medical Faculty, Uppsala University, opponent Anne Cooke, Cambridge.
3. Liselotte Jansson, 940330; “Sex mediated influence in experimental models for rheumatoid arthritis and multiple sclerosis” Medical Faculty, Uppsala University, opponent Paul Wooley, Detroit.
4. John A Mo, 941007; “B cell recognition of type II collagen in mouse cartilage” Medical Faculty, Uppsala University opponent Dan Holmberg, Umeå.
5. Erik Michaëlsson, 960404, “T cell recognition of type II collagen - A cartilage glycoprotein of importance for autoimmune arthritis”, Medical Faculty, Lund University, opponent Polly Matzinger, New York.
6. Vivianne Malmström, 970920, “Arthritis susceptibility and tolerance in collagen transgenic mice”, Medical Faculty, Lund University, opponent Erna Möller, Stockholm.
7. Carina Vingsbo-Lundberg, 971108, “Chronic autoimmune arthritis in rats; pathogenesis and genetic factors”, Medical Faculty, Lund University, opponent Frank Emmrich, Leipzig.
8. Ulrica Brunsberg, 980516, "The importance of major histocompatibility complex class II genes for the development of autoimmune inflammation", Medical Faculty, Lund University, opponent Ulf Gyllensten, Uppsala.
9. Peter Kjellén, 991201, "The structural basis of MHC control in experimental autoimmunity", Medical Faculty, Lund University, opponent Sören Buus, Copenhagen.
10. Alexandre Corthay, 000310, “T cells in autoimmunity, studies on murine type II collagen induced arthritis”, Medical faculty, Lund University, opponent George Kollias, Athens.
11. Johan Jirholt, 001215, “A search for genes influencing autoimmunity. Focus on rheumatoid arthritis and multiple sclerosis”, Medical faculty, Lund University, opponent Holger Luthman, Stockholm.
12. Mikael Vestberg, 010126, “MHC and transgenic mice. A study into function and polymorphism of class I and class II molecules”, Medical faculty, Lund University, opponent Jan Böhme, Stockholm.
13. Ann-Sofie Hansson, 011019, “New models for relapsing polychondritis and rheumatoid arthritis, focus on the tissue specific response”, Medical faculty, Lund University, opponent Norman Staines, London.
14. Åsa Johansson, 011019, “T cells, cytokines, and genetic factors in autoimmunity. Studies of experimental models of arthritis and sialadenitis”, Medical faculty, Lund University, opponent Linda Wicker, Cambridge.
15. Shemin Lu, 020212, “Genetic analyses and vaccination of rat models of arthritis”, Medical faculty, Lund University, opponent Raimund Kinne, Jena.
16. Lars Svensson, 020213, “Role of B cells and cytokines in arthritis”, Medical faculty, Lund University, opponent Hans Carlsten, Göteborg.
17. Johan Bäcklund, 020924, “Studies on T cells reactive with posttranslational modification in arthritis”, Medical faculty, Lund University, opponent Ludvig Sollid, Oslo.
18. Patrik Wernhoff, 020924, “Genetic control of autoantibodies in experimental autoimmune disease”, Medical faculty, Lund University, opponent Claudia Berek, Berlin.
19. Peter Olofsson, 030527, “Identification of arthritis regulating genes in rats”Medical faculty, Lund University, opponent Tim Aitman, London.
20. Jens Holmberg, 041210, “Reduced ROS production triggers arthritis”Medical faculty, Lund University, opponent Cor Verweij, Amsterdam.
21. Martina Johannesson, 050128, “Novel strategies to explore the complex genetics of autoimmune diseases”Medical faculty, Lund University, opponent Karl Broman, Baltimore, USA.
22. Robert Bockermann, 050523 “The role of T cells and T cell receptor polymorphism in controlling pathways leading to arthritis”Medical faculty, Lund University, opponent Juan Lafaille, New York, USA.
23. Estelle Bajtner, 050917, “Role of collagen type II specific antibodies in arthritis”. Medical faculty, Lund University, opponent Marie Wahren, KI, Stockholm.
24. Stefan Carlsen, 051015, “Cartilage proteins and their antigenic properties in arthritis”, Medical faculty, Lund University, opponent Richard Williams, London, UK.
25. Kutty Selva Nandakumar, 060127, “Analysis of effector pathways in arthritis”, Medical faculty, Lund University, opponent Birgitta Heyman, Uppsala, Sweden
26. Lina Olsson, 071130, “Genetic and genomic analysis of arthritis regulating regions in human and mouse.” Medical faculty, Lund University, opponent Janna Saarela, National Public Health Institute, Helsinki, Finland.
27. Emma Ahlqvist, 071201, “Identification of arthritis susceptibility genes in mice and humans” Medical faculty, Lund University, opponent Jonathan Flint, Oxford University, Oxford, UK.
28. Malin Hultqvist, 071214, “The role of reactive oxygen species in animal models of autoimmunity” Medical faculty, Lund University, opponent Philip Hawkins, The Babraham Institute, Cambridge, UK.
29. Carola Rintisch, 090213, "From Disease to the Gene-identification of arthritis-regulating loci in rats" Medical faculty, Lund University, opponent Abdelhadi Saoudi, National Institute of Health and Medical Research, University Paul Sabatier, Hospital Purpan, Toulouse, France
30. Therese Lindvall, 091127, "From Disease to Genes in Animal Models of Rheumatoid Arthritis and Multiple Sclerosis" Medical faculty, Lund University, opponent Krisitna Lejon, Immunology, Umeå University
31. Angela Pizzolla, 111209, "The role of Macrophages in Regulating Inflammation by Oxidative Burst". Karolinska Institutet, opponent Kristoffer Hellstrand, Gothenburg University
32. Michael Förster, 121027, "The Genetics of Experimental Arthritis in Rodents", Karolinska Institutet, opponent Göran Andersson, Swedish University of Agricultural Sciences, Uppsala
33. Bruno Raposo, 121130, "Genetic Regulation of Autoantibodies in Arthritis: Lessons From Mouse Models". Karolinska Institutet, opponent Dan Holmberg, Copenhagen University, Denmark
34. Ingrid Lindh, 130412, "Autoantibody Recognition of Collagen Type II in Arthritis". Karolinska Institutet, opponent Leendert Trouw, Leiden University, Netherlands
35. Tiina Kelkka, 130426, "Reactive oxygen species in inflammation", University of Turku, opponent Lars Rönnblom, Uppsala University, Sweden
36. Jonatan Tuncel, 130601, "Functional and Genetic Analyses of the MHC and its impact on Autoimmunity in the Rat", Karolinska Institute, opponent Jacques Neefjes, Netherlands Cancer Institute, Netherlands
37. Sabrina Haag, 140412, "The MHC and the Recognition of Self and Altered Self in Experimental and Rheumatoid Arthritis" Karolinska Institute, Lars Fugger, University of Oxford, UK
38. Anthony Yau 161209 “Positional identification and functional analysis of genes regulating autoimmune arthritis” Karolinska Institutet, opponent Prof Edward Wakeland, Dallas.
39. Ulrika Norin 170324 "Identification of genetic variants and their implications in autoimmunity", opponent Marie Malissen, från Centre d’Immunologic de Marseille-Luminy France.
40. Cecilia Hagert 171202 “The innate immune system as a driver of Rheumatoid Arthritis”, opponent Prof. Robert Harris, Karolinska Institutet
41. Daniëlle Vaartjes 180616 “From genes to function in autoimmunity - a salty story” Karolinska Institutet, opponent Bryce Binstadt, Univ. of Minnesota
42. Erik Lönnblom 210610 “Antibodies as pathogenic factors and biomarkers in rheumatoid arthritis”, opponent  Prof. Carl Turesson, Lund University
43. Gonzalo Fernandez Lahore 210820 “Identifying genetic determinants of T cell-dependent autoimmunity using forward genetics", Opponent: Prof. Vijay Kuchroo, Harvard Medical School, USA
44. Jaime James 210924 “Redox Regulation of T cells in autoimmunity”, Opponent: Prof. Tomas Mustelin, University of Washington, USA
45. Weiwei Cai 211105 ”Analysis of Antibodies to Cartilage Oligomeric matrix Protein in Rheumatoid Arthritis and in mouse Models”, Opponent: Prof. Silke Appel, University of Bergen, Norway
46. Yanpeng Li 220524 “Human NCF1-339 polymorphism regulates JAK-STAT pathway through reactive oxygen species in autoimmune diseases”, Southern Medical University, China
47. Alexander Krämer 230526 “Characterisation of epitope-specfic B cells and the role of IgG Fc sialylation in murine arthritis models”, Opponent Prof. Lars Nitschke, University of Erlangen, Germany
48. Huqiao Luo 230605 “Unveiling the protective mechanisms of NOX2-derived ROS against autoimmune diseases”, Opponent Prof. Ann-Sophie Korganow, Strasbourg University Hospital, France
49. Ana do Carmo Oliveira Coelho 230606 “Oxidative regulation of NCF1 in B cells and mouse models of arthritis”, Opponent Prof. Hans Martin Jäck, University of Erlangen, Germany
50. Yibo He 230615 “Identification and functional analysis of anti-citrullinated protein antibodies in rheumatoid arthritis”, Opponent Associate Prof. Felipe Andrade, Johns Hopkins University, USA
51. Taotao Li 230616 “Functional studies of anti-gpi monoclonal antibodies and anti-citrullinated protein antibodies (ACPAs)”, Opponent Prof. Thomas Pap, University of Münster, Germany
52. Zhongwei Xu 231121 “Beyond conventional care: developing novel therapeutic approaches to combat arthritis”, opponent: Caroline Ospelt, University Hospital Zurich, Switzerland
53. Alex Moreno Giro 240913 “Functional characterization of protective antibodies in murine models of rheumatoid arthritis”, opponent: Gestur Vidarsson, Utrecht University, the Netherlands

Current PhD students (as a main supervisor)

54. Michael Bonner (KI), 

55. Carolin Svensson (KI)

Assistant supervisor for the following PhD

1) Per Larsson, UU 1989, main supervisor Lars Klareskog, 2) Inga Hansson, UU 1993, main supervisor Ragnar Mattsson, 5) Jinan Li, UmeåU 2004, main supervisor Tor Ny 3) Hai Tao Yang, UU 2000, main supervisor Prof. Ulf Pettersson; 4) Ingrid Teige, LU 2004, main supervisor Prof. Shoreh Issasadeh; 6) Meirav Holmdahl, LU 2005, main supervisor Prof. Anders Grubb  7) Jenny Karlsson, LU 2005, main supervisor Prof. Shoreh Issasadeh, 8) Alexandra Treschow, LU 2005, main supervisor Prof. Shoreh Issasadeh 9) Patrick Merky, KI 2011, main supervisor Docent Johan Bäcklund; 11) Ia Khalmadze, KI 2014, main supervisor Prof. Kutty Selva Nandakumar; 12) Simon Guerad, KI 2016 main supervisor Dr Kajsa Wing:; 13) Katrin Klocke, KI 2017, main supervisor Dr Kajsa Wing; 14) Bibo Liang, SMU 2017, main supervisor Prof. Zhao Ming; 15) Dongmei Tong, SMU 2018, main supervisor Prof. Zhao Ming, 16) Mike Aoun, Main supervisor Dr Liselotte Bäckdahl,  210903 “Positional cloning of polymorphic loci that control autoreactive T cells”, Opponent: Prof. Marc K. Jenkins, University of Minnesota, USA