Maria Pernemalm

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About me

The analysis of human blood plasma with modern -omics technologies holds an
enormous potential to reveal biomarkers for diagnosis and treatment
selection, as well as studying complex systemic signalling events that are
involved in immune modulation, metastatic spread and disease progression.
My primary research interest is exploring how events on tissue and cellular
level are reflected on the molecular level in human blood plasma and how
these can be monitored using -omics methods. I have a long-standing interest
and expertise in method development for mass spectrometry (MS) based plasma
proteomics and in combining different analytical approaches and data sources
with the aim to improve the understanding of the dynamics in the plasma
proteome, in particularly related to biomarker discovery in lung cancer and
malignant melanoma.
The plasma team works both on method development and applied projects
involving expanded applications of plasma proteome analysis such as plasma
protein interaction with viruses and nanoparticles, proteogenomics biomarker
discovery, and approaches to combine biochemical plasma markers with symptoms
clusters for improved accuracy and sensitivity in precision medicine.
*2022* Associate professor in Medical Proteomics, KI, Dept. Oncology
Pathology
*2009* PhD KI, Dept. Oncology Pathology
*2010-2011* KI, Dept. Oncology Pathology, Post Doc
*2011-2012* Scilifelab/KI/Dept. Oncology Pathology, Post Doc
*2012-2013* The University of Manchester, Stem cell &
leukemia proteomics
lab, Post Doc
*2013-2014* Scilifelab/KI/Dept. Oncology Pathology, Post Doc
*2014-* Scilifelab/KI/Dept. Oncology Pathology, Assistant professor

Articles

Article: STEM CELL RESEARCH & THERAPY. 2024;15(1):77
Transcriptomic and proteomic profiles of fetal versus adult mesenchymal stromal cells and mesenchymal stromal cell-derived extracellular vesicles
Gencer EB; Lor YK; Abomaray F; El Andaloussi S; Pernemalm M; Sharma N; Hagey DW; Gorgens A; Gustafsson MO; Le Blanc K; Toonsi MA; Walther-Jallow L; Goetherstrom C
Article: NATURE COMMUNICATIONS. 2023;14(1):5921
Comprehensive proteomics and meta-analysis of COVID-19 host response
Babacic H; Christ W; Araujo JE; Mermelekas G; Sharma N; Tynell J; Garcia M; Varnaite R; Asgeirsson H; Glans H; Lehtioe J; Gredmark-Russ S; Klingstroem J; Pernemalm M
Article: RESPIRATORY RESEARCH. 2023;24(1):62
Targeted plasma proteomics reveals signatures discriminating COVID-19 from sepsis with pneumonia
Palma Medina LM; Babacic H; Dzidic M; Parke A; Garcia M; Maleki KT; Unge C; Lourda M; Kvedaraite E; Chen P; Muvva JR; Cornillet M; Emgard J; Moll K; Michaelsson J; Flodstrom-Tullberg M; Brighenti S; Buggert M; Mjosberg J; Malmberg K-JK; Sandberg J; Gredmark-Russ S; Rooyackers O; Svensson MJ; Chambers BI; Eriksson L; Pernemalm MK; Bjorkstrom N; Aleman S; Ljunggren H-G; Klingstrom J; Stralin K; Norrby-Teglund A
Article: MOLECULAR ONCOLOGY. 2023;17(2):238-260
Glioblastoma stem cells express non-canonical proteins and exclusive mesenchymal-like or non-mesenchymal-like protein signatures
Babacic H; Galardi S; Umer HM; Hellstrom M; Uhrbom L; Maturi N; Cardinali D; Pellegatta S; Michienzi A; Trevisi G; Mangiola A; Lehtio J; Ciafre SA; Pernemalm M
Article: FRONTIERS IN ENDOCRINOLOGY. 2022;13:971313
Proteome profiling of whole plasma and plasma-derived extracellular vesicles facilitates the detection of tissue biomarkers in the non-obese diabetic mouse
Lozano IMD; Sork H; Stone VM; Eldh M; Cao X; Pernemalm M; Gabrielsson S; Flodstrom-Tullberg M
Article: JOURNAL OF PROTEOME RESEARCH. 2021;20(9):4610-4620
Evaluation of Spin Columns for Human Plasma Depletion to Facilitate MS-Based Proteomics Analysis of Plasma
Cao X; Sandberg A; Araujo JE; Cvetkovski F; Berglund E; Eriksson LE; Pernemalm M
Article: NEOPLASIA. 2021;23(8):783-791
Plasma proteome alterations by MAPK inhibitors in BRAF^V600-mutated metastatic cutaneous melanoma
Babacic H; Eriksson H; Pernemalm M
Article: JOURNAL OF EXTRACELLULAR VESICLES. 2021;10(9):e12128
Molecular evaluation of five different isolation methods for extracellular vesicles reveals different clinical applicability and subcellular origin
Veerman RE; Teeuwen L; Czarnewski P; Gucluler Akpinar G; Sandberg A; Cao X; Pernemalm M; Orre LM; Gabrielsson S; Eldh M
Article: MOLECULAR ONCOLOGY. 2021;15(2):429-461
High-throughput proteomics of breast cancer interstitial fluid: identification of tumor subtype-specific serologically relevant biomarkers
Terkelsen T; Pernemalm M; Gromov P; Borresen-Dale A-L; Krogh A; Haakensen VD; Lethio J; Papaleo E; Gromova I
Article: JOURNAL FOR IMMUNOTHERAPY OF CANCER. 2020;8(1):e000204
In-depth plasma proteomics reveals increase in circulating PD-1 during anti-PD-1 immunotherapy in patients with metastatic cutaneous melanoma
Babacic H; Lehtio J; de Coana YP; Pernemalm M; Eriksson H
Article: FRONTIERS IN ONCOLOGY. 2020;10:51
Immunometabolic Network Interactions of the Kynurenine Pathway in Cutaneous Malignant Melanoma
Rad Pour S; Morikawa H; Kiani NA; Gomez-Cabrero D; Hayes A; Zheng X; Pernemalm M; Lehtio J; Mole DJ; Hansson J; Eriksson H; Tegner J
Article: SCIENTIFIC REPORTS. 2019;9(1):16504
Early symptoms and sensations as predictors of lung cancer: a machine learning multivariate model
Levitsky A; Pernemalm M; Bernhardson B-M; Forshed J; Kolbeck K; Olin M; Henriksson R; Lehtio J; Tishelman C; Eriksson LE
Article: JOURNAL OF PROTEOME RESEARCH. 2019;18(9):3369-3382
Identification of a Biomarker Panel for Early Detection of Lung Cancer Patients
Geary B; Walker MJ; Snow JT; Lee DCH; Pernemalm M; Maleki-Dizaji S; Azadbakht N; Apostolidou S; Barnes J; Krysiak P; Shah R; Booton R; Dive C; Crosbie PA; Whetton AD
Article: NATURE COMMUNICATIONS. 2019;10(1):2331
The viral protein corona directs viral pathogenesis and amyloid aggregation
Ezzat K; Pernemalm M; Palsson S; Roberts TC; Jarver P; Dondalska A; Bestas B; Sobkowiak MJ; Levanen B; Skold M; Thompson EA; Saher O; Kari OK; Lajunen T; Ekstrom ES; Nilsson C; Ishchenko Y; Malm T; Wood MJA; Power UF; Masich S; Linden A; Sandberg JK; Lehtio J; Spetz A-L; EL Andaloussi S
Article: CLINICAL CANCER RESEARCH. 2019;25(10):3115-3127
Ultrasensitive Immunoprofiling of Plasma Extracellular Vesicles Identifies Syndecan-1 as a Potential Tool for Minimally Invasive Diagnosis of Glioma
Chandran VI; Welinder C; Mansson A-S; Offer S; Freyhult E; Pernemalm M; Lund SM; Pedersen S; Lehtio J; Marko-Varga G; Johansson MC; Englund E; Sundgren PC; Belting M
Article: ELIFE. 2019;8:e41608
In-depth human plasma proteome analysis captures tissue proteins and transfer of protein variants across the placenta
Pernemalm M; Sandberg A; Zhu Y; Boekel J; Tamburro D; Schwenk JM; Bjork A; Wahren-Herlenius M; Amark H; Ostenson C-G; Westgren M; Lehtio J
Article: CELL DEATH & DISEASE. 2017;8(8):e3029
Silencing FLI or targeting CD13/ANPEP lead to dephosphorylation of EPHA2, a mediator of BRAF inhibitor resistance, and induce growth arrest or apoptosis in melanoma cells
Azimi A; Tuominen R; Svedman FC; Caramuta S; Pernemalm M; Stolt MF; Kanter L; Kharaziha P; Lehtio J; Johansson CH; Holom V; Hansson J; Brage SE
Article: INTERNATIONAL JOURNAL OF CANCER. 2016;138(12):2984-2992
Protein Z: A putative novel biomarker for early detection of ovarian cancer
Russell MR; Walker MJ; Williamson AJK; Gentry-Maharaj A; Ryan A; Kalsi J; Skates S; D'Amato A; Dive C; Pernemalm M; Humphryes PC; Fourkala E-O; Whetton AD; Menon U; Jacobs I; Graham RLJ
Article: BMJ OPEN RESPIRATORY RESEARCH. 2016;3(1):e000114
ERK and AKT phosphorylation status in lung cancer and emphysema using nanocapillary isoelectric focusing.
Crosbie PAJ; Crosbie EJ; Aspinall-O'Dea M; Walker M; Harrison R; Pernemalm M; Shah R; Joseph L; Booton R; Pierce A; Whetton AD
Article: EBIOMEDICINE. 2015;2(8):841-850
Discovery and Validation of Predictive Biomarkers of Survival for Non-small Cell Lung Cancer Patients Undergoing Radical Radiotherapy: Two Proteins With Predictive Value
Walker MJ; Zhou C; Backen A; Pernemalma M; Williamson AJK; Priest LJC; Koh P; Faivre-Finn C; Blackhall FH; Dive C; Whetton AD
Article: PLOS ONE. 2015;10(5):e0126472
Differential Protein Expression Profiles of Cyst Fluid from Papillary Thyroid Carcinoma and Benign Thyroid Lesions
Dinets A; Pernemalm M; Kjellin H; Sviatoha V; Sofiadis A; Juhlin CC; Zedenius J; Larsson C; Lehtio J; Hoog A
Article: PLOS ONE. 2015;10(10):e0129008
Proteomics Analysis Reveals Distinct Corona Composition on Magnetic Nanoparticles with Different Surface Coatings: Implications for Interactions with Primary Human Macrophages
Vogt C; Pernemalm M; Kohonen P; Laurent S; Hultenby K; Vahter M; Lehtio J; Toprak MS; Fadeel B
Article: BIOMED RESEARCH INTERNATIONAL. 2015;2015:462549-13
Identifying and Assessing Interesting Subgroups in a Heterogeneous Population
Lee W; Alexeyenko A; Pernemalm M; Guegan J; Dessen P; Lazar V; Lehtio J; Pawitan Y
Article: BRITISH JOURNAL OF CANCER. 2014;110(10):2489-2495
Proteomics analysis of melanoma metastases: association between S100A13 expression and chemotherapy resistance
Azimi A; Pernemalm M; Stolt MF; Hansson J; Lehtio J; Brage SE; Johansson CH
Article: JOURNAL OF PROTEOME RESEARCH. 2013;12(9):3934-3943
Quantitative Proteomics Profiling of Primary Lung Adenocarcinoma Tumors Reveals Functional Perturbations in Tumor Metabolism
Pernemalm M; De Petris L; Branca RM; Forshed J; Kanter L; Soria J-C; Girard P; Validire P; Pawitan Y; van den Oord J; Lazar V; Pahlman S; Lewensohn R; Lehtio J
Article: JOURNAL OF PROTEOME RESEARCH. 2013;12(2):1014-1019
A Novel Prefractionation Method Combining Protein and Peptide Isoelectric Focusing in Immobilized pH Gradient Strips
Pernemalm M; Lehtio J
Article: METHODS IN MOLECULAR BIOLOGY. 2013;1023:3-11
Narrow-range peptide isoelectric focusing as peptide prefractionation method prior to tandem mass spectrometry analysis.
Pernemalm M
Article: BMC BIOINFORMATICS. 2012;13:226
Network enrichment analysis: extension of gene-set enrichment analysis to gene networks
Alexeyenko A; Lee W; Pernemalm M; Guegan J; Dessen P; Lazar V; Lehtio J; Pawitan Y
Article: MOLECULAR & CELLULAR PROTEOMICS. 2011;10(10):m111.010264
Enhanced Information Output From Shotgun Proteomics Data by Protein Quantification and Peptide Quality Control (PQPQ)
Forshed J; Johansson HJ; Pernemalm M; Branca RMM; Sandberg A; Lehtio J
Article: PROTEOME SCIENCE. 2010;8:9
A novel method for sample preparation of fresh lung cancer tissue for proteomics analysis by tumor cell enrichment and removal of blood contaminants
De Petris L; Pernemalm M; Elmberger G; Bergman P; Orre L; Lewensohn R; Lehtio J
Article: PROTEOMICS. 2009;9(13):3414-3424
Use of narrow-range peptide IEF to improve detection of lung adenocarcinoma markers in plasma and pleural effusion
Pernemalm M; De Petris L; Eriksson H; Branden E; Koyi H; Kanter L; Lewensohn R; Lehtio J
Article: LUNG CANCER. 2009;63(3):410-417
Tumor expression of S100A6 correlates with survival of patients with stage I non-small-cell lung cancer
De Petris L; Orre LM; Kanter L; Pernemalm M; Koyi H; Lewensohn R; Lehtio J
Article: JOURNAL OF PROTEOME RESEARCH. 2008;7(7):2712-2722
Evaluation of three principally different intact protein prefractionation methods for plasma biomarker discovery
Pernemalm M; Orre LM; Lengqvist J; Wikstrom P; Lewensohn R; Lehtio J
Article: JOURNAL OF PROTEOME RESEARCH. 2008;7(6):2332-2341
Proteomic data analysis workflow for discovery of candidate biomarker peaks predictive of clinical outcome for patients with acute myeloid leukemia
Forshed J; Pernemalm M; Tan CS; Lindberg M; Kanter L; Pawitan Y; Lewensohn R; Stenke L; Lehtio J
Article: MOLECULAR & CELLULAR PROTEOMICS. 2007;6(12):2122-2131
Up-regulation, modification, and translocation of S100A6 induced by exposure to ionizing radiation revealed by proteomics profiling
Orre LM; Pernemalm M; Lengqvist J; Lewensohn R; Lehtio J
Article: PROTEOMICS. 2006;6(23):6124-6133
Annotated regions of significance of SELDI-TOF-MS spectra for detecting protein biornarkers
Tan CS; Ploner A; Quandt A; Lehtio J; Pernemalm M; Lewensohn R; Pawitan Y
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All other publications

Review: JOURNAL OF PROTEOME RESEARCH. 2021;20(12):5241-5263
Advances and Utility of the Human Plasma Proteome
Deutsch EW; Omenn GS; Sun Z; Maes M; Pernemalm M; Palaniappan KK; Letunica N; Vandenbrouck Y; Brun V; Tao S-C; Yu X; Geyer PE; Ignjatovic V; Moritz RL; Schwenk JM
Review: CANCER TREATMENT REVIEWS. 2015;41(4):361-375
Molecular histology of lung cancer: From targets to treatments
Wood SL; Pernemalm M; Crosbie PA; Whetton AD
Review: EXPERT REVIEW OF PROTEOMICS. 2014;11(4):431-448
Mass spectrometry-based plasma proteomics: state of the art and future outlook
Pernemalm M; Lehtio J
Review: CANCER TREATMENT REVIEWS. 2014;40(4):558-566
The role of the tumor-microenvironment in lung cancer-metastasis and its relationship to potential therapeutic targets
Wood SL; Pernemalm M; Crosbie PA; Whetton AD
Thesis / dissertation: 2009
Cancer proteomics : method development for mass spectrometry based analysis of clinical materials
Pernemalm, Maria
Review: PROTEOMICS. 2009;9(6):1420-1427
Affinity prefractionation for MS-based plasma proteomics
Pernemalm M; Lewensohn R; Lehtio J
Meeting abstract: JOURNAL OF THORACIC ONCOLOGY. 2007;2(8):S356-S357
Mass spectrometry profiling of low molecular weight platelet Proteome for the detection of lung cancer specific biomarkers
De Petris L; Pernemalm M; Branden E; Koyi H; Forshed J; Sundelin B; Lewensohn R; Lehtio J

Employments

Principal Researcher, Department of Oncology-Pathology, Karolinska Institutet, 2022-

Degrees and Education

Docent, Karolinska Institutet, 2022
Degree Of Doctor Of Philosophy, Department of Oncology-Pathology, Karolinska Institutet, 2009
Master Of Medical Science, Karolinska Institutet, 2005

About me

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