Clinical Phenomics

CARAMBA performs pre-clinical and clinical research, targeting endogenous and exogenous molecules, in combination with state-of-the-art bioinformatics with the global goal to improve human health care and disease prevention.

Group member Position
Kim Kultima Associate Professor
Torbjörn Åkerfeldt Physician
Eva Freyhult Researcher/Bioinformatician
Payam Khoonsari Emami Researcher/Bioinformatician
Stephanie Herman PhD student
Sandy Abujrais Laboratory technician
Niclas Rollborn Laboratory engineer

PROJECTS

Clinical Proteomics & Metabolomics
We have developed and implemented mass spectrometry-based methods for proteomics and metabolomics, including targeted and untargeted analyses of hormones, lipids and small signaling molecules in human cerebrospinal fluid and blood samples. These signals are further connected to biological pathways and demographic patient data. We are currently involved in three large efforts;

Characterization and stratification of multiple sclerosis phenotypes
Improve diagnostic markers for chronic pain states
Early detection of Alzheimer’s disease

We are also part of the EU Horizon 2020 project PhenoMeNal with focus on implementing clinical metabolomics into the clinic.

PUBLICATIONS

Abujrais, S., M. Olovsson, M. Ahnoff, A. Rasmusson, A. Larsson, T. Åkerfeldt, and K. Kultima, A sensitive method detecting trace levels of levonorgestrel using LC-HRMS.Contraception, 2019. (Accepted) (IF: 2.9).

Saul, M., A. Hegewald, A. Emmerich, E. Ossipova, M. Vogel, I. Baumann, K. Kultima, J. Lengquist, D. Steinhilber, and P. Jakobsson, Mass spectrometry-based proteomics approach characterizes the dual functionality of miR-328 in monocyte.Frontiers in Pharmacology, 2019. (Accepted for publication) (IF: 3.8).

Bergquist, F., E. Ossipova, H. Idborg, J. Raouf, A. Checa, K. Englund, P. Englund, P. Khoonsari, K. Kultima, C. Wheelock, M. Korotkova, and P. Jakobsson, Inhibition of mPGES-1 or COX-2 Results in Different Proteomic and Lipidomic Profiles in A549 Lung Cancer Cells.Frontiers in Pharmacology, 2019. (Accepted for Publication) (IF:3.8).

Idborg, H., A. Zandian, E. Ossipova, E. Wigren, C. Preger, F. Mobarezz, A. Checa, A. Sohrabian, P. Pucholt, J. Sandling, C. Fernandes-Cerqueira, J. Rönnelid, V. Oke, G. Grosso, M. Kvarnström, A. Larsson, C. Wheelock, A. Syvänen, L. Rönnblom, K. Kultima, H. Persson, S. Gräslund, I. Gunnarsson, P. Nilsson, E. Svenungsson, and P. Jakobsson, Circulating levels of Interferon Regulatory Factor-5 differentiates between subgroups of Systemic Lupus Erythematosus patients.Frontiers in Immunology, 2019. (Accepted for publication) (IF: 5.5).

Karakitsou, E., C. Foguet, P. Atauri, K. Kultima, P. Khoonsari, V. Santos, E. Saccenti, A. Rosato, and M. Cascante, Metabolomics in Systems Medicine- an overview of methods and applications.Current Opinion in Systems Biology, 2019. Accepted for publication.

Feresiadou, A., K. Nilsson, M. Ingelsson, R. Press, I. Kmezic, I. Nygren, A. Svenningsson, V. Niemela, T. Gordh, J. Cunningham, K. Kultima, A. Larsson, and J. Burman, Measurement of sCD27 in the cerebrospinal fluid identifies patients with neuroinflammatory disease.J Neuroimmunol, 2019. 332: p. 31-36. (IF: 2.7). 10.1016/j.jneuroim.2019.03.015.

Farinotti, A., G. Wigerblad, D. Nascimento, D. Bas, C. Urbina, K. Nandakumar, K. Sandor, B. Xu, S. Abdelmoaty, M. Hunt, K. Möller, A. Baharpoor, J. Sinclair, J. Jardemark, J. Lanner, I. Khmaladze, L. Borm, L. Zhang, F. Wermeling, M. Cragg, J. Lengquist, A. Chabot-Doré, L. Diachenko, I. Belfer, M. Collin, K. Kultima, B. Heyman, J. Andrade Jimenez, S. Codeluppi, R. Holmdahl, and C. Svensson, Cartilage binding antibodies induce pain through immune complex mediated stimulation of neurons.Journal of Experimental Medicine, 2019. Accepted for publication. (IF: 10.8).

Herman, S., V. Niemelä, P. Emami Khoonsari, J. Sundblom, J. Burman, A.-M. Landtblom, O. Spjuth, D. Nyholm, and K. Kultima, Alterations in the tyrosine and phenylalanine pathways revealed by biochemical profiling in cerebrospinal fluid of Huntington’s disease subjects.Scientific Reports, 2019. 9(1): p. 4129. (IF: 4.1). 10.1038/s41598-019-40186-5.

Khoonsari, P.E., G. Shevchenko, S. Herman, J. Remnestal, V. Giedraitis, R. Brundin, M. Degerman Gunnarsson, L. Kilander, H. Zetterberg, P. Nilsson, L. Lannfelt, M. Ingelsson, and K. Kultima, Improved Differential Diagnosis of Alzheimer’s Disease by Integrating ELISA and Mass Spectrometry-Based Cerebrospinal Fluid Biomarkers.J Alzheimers Dis, 2019. 67(2): p. 639-651. (IF: 3.5). 10.3233/jad-180855. Ingelsson & Kultima contributed equally as senior authors.

Khoonsari, P.E., E. Ossipova, J. Lengqvist, C.I. Svensson, E. Kosek, D. Kadetoff, P.J. Jakobsson, K. Kultima, and J. Lampa, The human CSF pain proteome.J Proteomics, 2019. 190: p. 67-76. (IF: 3.7). 10.1016/j.jprot.2018.05.012. Kultima & Lampa contributed equally as senior authors.

Khoonsari, P.E., S. Musunri, S. Herman, C.I. Svensson, L. Tanum, T. Gordh, and K. Kultima,Systematic analysis of the cerebrospinal fluid proteome of fibromyalgia patients.J Proteomics, 2019. 190: p. 35-43. (IF: 3.7). 10.1016/j.jprot.2018.04.014.

Peters, K., J. Bradbury, S. Bergmann, M. Capuccini, M. Cascante, P. de Atauri, T.M.D. Ebbels, C. Foguet, R. Glen, A. Gonzalez-Beltran, U.L. Gunther, E. Handakas, T. Hankemeier, K. Haug, S. Herman, P. Holub, M. Izzo, D. Jacob, D. Johnson, F. Jourdan, N. Kale, I. Karaman, B. Khalili, P. Emami Khonsari, K. Kultima, S. Lampa, A. Larsson, C. Ludwig, P. Moreno, S. Neumann, J.A. Novella, C. O’Donovan, J.T.M. Pearce, A. Peluso, M.E. Piras, L. Pireddu, M.A.C. Reed, P. Rocca-Serra, P. Roger, A. Rosato, R. Rueedi, C. Ruttkies, N. Sadawi, R.M. Salek, S.A. Sansone, V. Selivanov, O. Spjuth, D. Schober, E.A. Thevenot, M. Tomasoni, M. van Rijswijk, M. van Vliet, M.R. Viant, R.J.M. Weber, G. Zanetti, and C. Steinbeck, PhenoMeNal: processing and analysis of metabolomics data in the cloud.Gigascience, 2019. 8(2). (IF: 7.3). 10.1093/gigascience/giy149.

Herman, S., T. Akerfeldt, O. Spjuth, J. Burman, and K. Kultima, Biochemical Differences in Cerebrospinal Fluid between Secondary Progressive and Relapsing(-)Remitting Multiple Sclerosis.Cells, 2019. 8(2). (IF: 4.8). 10.3390/cells8020084.

Novella, J.A., P. Emami Khoonsari, S. Herman, D. Whitenack, M. Capuccini, J. Burman, K. Kultima, and O. Spjuth, Container-based bioinformatics with Pachyderm.Bioinformatics, 2019. 35(5): p. 839-846. (IF: 5.5). 10.1093/bioinformatics/bty699.

Emami Khoonsari, P., P. Moreno, S. Bergmann, J. Burman, M. Capuccini, M. Carone, M. Cascante, P. de Atauri, C. Foguet, A. Gonzalez-Beltran, T. Hankemeier, K. Haug, S. He, S. Herman, D. Johnson, N. Kale, A. Larsson, S. Neumann, K. Peters, L. Pireddu, P. Rocca-Serra, P. Roger, R. Rueedi, C. Ruttkies, N. Sadawi, R.M. Salek, S.A. Sansone, D. Schober, V. Selivanov, E.A. Thevenot, M. van Vliet, G. Zanetti, C. Steinbeck, K. Kultima, and O. Spjuth, Interoperable and scalable data analysis with microservices: Applications in Metabolomics.Bioinformatics, 2019. (IF: 5.5). 10.1093/bioinformatics/btz160.

2018

Herman, S., P.E. Khoonsari, A. Tolf, J. Steinmetz, H. Zetterberg, T. Akerfeldt, P.J. Jakobsson, A. Larsson, O. Spjuth, J. Burman, and K. Kultima, Integration of magnetic resonance imaging and protein and metabolite CSF measurements to enable early diagnosis of secondary progressive multiple sclerosis.Theranostics, 2018. 8(16): p. 4477-4490. (IF: 8.5). 10.7150/thno.26249.

Sandor, K., S. Krishnan, N.M. Agalave, E. Krock, J.V. Salcido, T. Fernandez-Zafra, P.E. Khoonsari, C.I. Svensson, and K. Kultima, Spinal injection of newly identified cerebellin-1 and cerebellin-2 peptides induce mechanical hypersensitivity in mice.Neuropeptides, 2018. 69: p. 53-59. (IF: 2.9). 10.1016/j.npep.2018.04.004.

2017

Herman, S., P. Emami Khoonsari, O. Aftab, S. Krishnan, E. Strombom, R. Larsson, U. Hammerling, O. Spjuth, K. Kultima, and M. Gustafsson, Mass spectrometry based metabolomics for in vitro systems pharmacology: pitfalls, challenges, and computational solutions.Metabolomics, 2017. 13(7): p. 79. (IF: 3.5). 10.1007/s11306-017-1213-z. Kultima & Gustafsson contributed equally as senior authors.

Almandoz-Gil, L., H. Welander, E. Ihse, P.E. Khoonsari, S. Musunuri, C. Lendel, J. Sigvardson, M. Karlsson, M. Ingelsson, K. Kultima, and J. Bergstrom, Low molar excess of 4-oxo-2-nonenal and 4-hydroxy-2-nonenal promote oligomerization of alpha-synuclein through different pathways.Free Radic Biol Med, 2017. 110: p. 421-431. (IF: 6.0). 10.1016/j.freeradbiomed.2017.07.004. Kultima & Bergström contributed equally as senior authors.

van Rijswijk, M., C. Beirnaert, C. Caron, M. Cascante, V. Dominguez, W.B. Dunn, T.M.D. Ebbels, F. Giacomoni, A. Gonzalez-Beltran, T. Hankemeier, K. Haug, J.L. Izquierdo-Garcia, R.C. Jimenez, F. Jourdan, N. Kale, M.I. Klapa, O. Kohlbacher, K. Koort, K. Kultima, G. Le Corguille, P. Moreno, N.K. Moschonas, S. Neumann, C. O’Donovan, M. Reczko, P. Rocca-Serra, A. Rosato, R.M. Salek, S.A. Sansone, V. Satagopam, D. Schober, R. Shimmo, R.A. Spicer, O. Spjuth, E.A. Thevenot, M.R. Viant, R.J.M. Weber, E.L. Willighagen, G. Zanetti, and C. Steinbeck, The future of metabolomics in ELIXIR.F1000Res, 2017. 6. (IF: NA). 10.12688/f1000research.12342.2.

 Nikitidou, E., P.E. Khoonsari, G. Shevchenko, M. Ingelsson, K. Kultima, and A. Erlandsson,Increased Release of Apolipoprotein E in Extracellular Vesicles Following Amyloid-beta Protofibril Exposure of Neuroglial Co-Cultures.J Alzheimers Dis, 2017. 60(1): p. 305-321. (IF: 3.5). 10.3233/jad-170278.

2016

Khoonsari, P.E., A. Haggmark, M. Lonnberg, M. Mikus, L. Kilander, L. Lannfelt, J. Bergquist, M. Ingelsson, P. Nilsson, K. Kultima, and G. Shevchenko, Analysis of the Cerebrospinal Fluid Proteome in Alzheimer’s Disease.PLoS One, 2016. 11(3): p. e0150672. (IF: 2.8). 10.1371/journal.pone.0150672. Kultima & Shevchenko contributed equally as senior authors.

Remnestal, J., D. Just, N. Mitsios, C. Fredolini, J. Mulder, J.M. Schwenk, M. Uhlen, K. Kultima, M. Ingelsson, L. Kilander, L. Lannfelt, P. Svenningsson, B. Nellgard, H. Zetterberg, K. Blennow, P. Nilsson, and A. Haggmark-Manberg, CSF profiling of the human brain enriched proteome reveals associations of neuromodulin and neurogranin to Alzheimer’s disease.Proteomics Clin Appl, 2016. 10(12): p. 1242-1253. (IF: 3.6). 10.1002/prca.201500150.

 Lind, A.L., P. Emami Khoonsari, M. Sjodin, L. Katila, M. Wetterhall, T. Gordh, and K. Kultima, Spinal Cord Stimulation Alters Protein Levels in the Cerebrospinal Fluid of Neuropathic Pain Patients: A Proteomic Mass Spectrometric Analysis.Neuromodulation, 2016. 19(6): p. 549-62. (IF: 2.8). 10.1111/ner.12473.

Musunuri, S., P.E. Khoonsari, M. Mikus, M. Wetterhall, A. Haggmark-Manberg, L. Lannfelt, A. Erlandsson, J. Bergquist, M. Ingelsson, G. Shevchenko, P. Nilsson, and K. Kultima, Increased Levels of Extracellular Microvesicle Markers and Decreased Levels of Endocytic/Exocytic Proteins in the Alzheimer’s Disease Brain.J Alzheimers Dis, 2016. 54(4): p. 1671-1686. (IF: 3.5). 10.3233/jad-160271.

 Senkowski, W., M. Jarvius, J. Rubin, J. Lengqvist, M.G. Gustafsson, P. Nygren, K. Kultima, R. Larsson, and M. Fryknas, Large-Scale Gene Expression Profiling Platform for Identification of Context-Dependent Drug Responses in Multicellular Tumor Spheroids.Cell Chem Biol, 2016. 23(11): p. 1428-1438. (IF: 4.5). 10.1016/j.chembiol.2016.09.013.

Adori, C., S. Barde, S. Vas, K. Ebner, J. Su, C. Svensson, A.A. Mathe, N. Singewald, R.R. Reinscheid, M. Uhlen, K. Kultima, G. Bagdy, and T. Hokfelt, Exploring the role of neuropeptide S in the regulation of arousal: a functional anatomical study.Brain Struct Funct, 2016. 221(7): p. 3521-46. (IF: 4.2). 10.1007/s00429-015-1117-5.

2015

Musunuri, S., K. Kultima, B.C. Richard, M. Ingelsson, L. Lannfelt, J. Bergquist, and G. Shevchenko, Micellar extraction possesses a new advantage for the analysis of Alzheimer’s disease brain proteome.Anal Bioanal Chem, 2015. 407(4): p. 1041-57. (IF: 3.3). 10.1007/s00216-014-8320-8.

Musunuri, S., M. Wetterhall, M. Ingelsson, L. Lannfelt, K. Artemenko, J. Bergquist, K. Kultima, and G. Shevchenko, Quantification of the brain proteome in Alzheimer’s disease using multiplexed mass spectrometry.J Proteome Res, 2014. 13(4): p. 2056-68. (IF: 4.0). 10.1021/pr401202d.

Su, J., K. Sandor, K. Skold, T. Hokfelt, C.I. Svensson, and K. Kultima, Identification and quantification of neuropeptides in naive mouse spinal cord using mass spectrometry reveals [des-Ser1]-cerebellin as a novel modulator of nociception.J Neurochem, 2014. 130(2): p. 199-214. (IF: 4.6). 10.1111/jnc.12730.

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