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Grassmann F, Mälarstig A, Dahl L, Bendes A, Dale M, Thomas CE, Gabrielsson M, Hedman ÅK, Eriksson M, Margolin S, Huang TH, Ulfstedt M, Forsberg S, Eriksson P, Johansson M, Hall P, Schwenk JM, Czene K. The impact of circulating protein levels identified by affinity proteomics on short-term, overall breast cancer risk. Br J Cancer 2024; 130:620-627. [PMID: 38135714 PMCID: PMC10876928 DOI: 10.1038/s41416-023-02541-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 11/22/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
OBJECTIVE Current breast cancer risk prediction scores and algorithms can potentially be further improved by including molecular markers. To this end, we studied the association of circulating plasma proteins using Proximity Extension Assay (PEA) with incident breast cancer risk. SUBJECTS In this study, we included 1577 women participating in the prospective KARMA mammographic screening cohort. RESULTS In a targeted panel of 164 proteins, we found 8 candidates nominally significantly associated with short-term breast cancer risk (P < 0.05). Similarly, in an exploratory panel consisting of 2204 proteins, 115 were found nominally significantly associated (P < 0.05). However, none of the identified protein levels remained significant after adjustment for multiple testing. This lack of statistically significant findings was not due to limited power, but attributable to the small effect sizes observed even for nominally significant proteins. Similarly, adding plasma protein levels to established risk factors did not improve breast cancer risk prediction accuracy. CONCLUSIONS Our results indicate that the levels of the studied plasma proteins captured by the PEA method are unlikely to offer additional benefits for risk prediction of short-term overall breast cancer risk but could provide interesting insights into the biological basis of breast cancer in the future.
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Affiliation(s)
- Felix Grassmann
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
- Institute for Clinical Research and Systems Medicine, Health and Medical University, Potsdam, Germany.
| | - Anders Mälarstig
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Pfizer Worldwide Research, Development and Medical, Stockholm, Sweden
| | - Leo Dahl
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Solna, Sweden
| | - Annika Bendes
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Solna, Sweden
| | - Matilda Dale
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Solna, Sweden
| | - Cecilia Engel Thomas
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Solna, Sweden
| | - Marike Gabrielsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Åsa K Hedman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Pfizer Worldwide Research, Development and Medical, Stockholm, Sweden
| | - Mikael Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Sara Margolin
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
- Department of Clinical Science and Education Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Tzu-Hsuan Huang
- Cancer Immunology Discovery, Pfizer Inc., San Diego, CA, USA
| | | | | | - Per Eriksson
- Olink Proteomics, Uppsala Science Park, Uppsala, Sweden
| | - Mattias Johansson
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - Jochen M Schwenk
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Solna, Sweden
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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Mälarstig A, Grassmann F, Dahl L, Dimitriou M, McLeod D, Gabrielson M, Smith-Byrne K, Thomas CE, Huang TH, Forsberg SKG, Eriksson P, Ulfstedt M, Johansson M, Sokolov AV, Schiöth HB, Hall P, Schwenk JM, Czene K, Hedman ÅK. Evaluation of circulating plasma proteins in breast cancer using Mendelian randomisation. Nat Commun 2023; 14:7680. [PMID: 37996402 PMCID: PMC10667261 DOI: 10.1038/s41467-023-43485-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023] Open
Abstract
Biomarkers for early detection of breast cancer may complement population screening approaches to enable earlier and more precise treatment. The blood proteome is an important source for biomarker discovery but so far, few proteins have been identified with breast cancer risk. Here, we measure 2929 unique proteins in plasma from 598 women selected from the Karolinska Mammography Project to explore the association between protein levels, clinical characteristics, and gene variants, and to identify proteins with a causal role in breast cancer. We present 812 cis-acting protein quantitative trait loci for 737 proteins which are used as instruments in Mendelian randomisation analyses of breast cancer risk. Of those, we present five proteins (CD160, DNPH1, LAYN, LRRC37A2 and TLR1) that show a potential causal role in breast cancer risk with confirmatory results in independent cohorts. Our study suggests that these proteins should be further explored as biomarkers and potential drug targets in breast cancer.
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Affiliation(s)
- Anders Mälarstig
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
- Pfizer Worldwide Research Development and Medical, Stockholm, Sweden.
| | - Felix Grassmann
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Institute of Clinical Research and Systems Medicine, Health and Medical University, Potsdam, Germany
| | - Leo Dahl
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Solna, Sweden
| | - Marios Dimitriou
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Pfizer Worldwide Research Development and Medical, Stockholm, Sweden
| | - Dianna McLeod
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Marike Gabrielson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Karl Smith-Byrne
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Cecilia E Thomas
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Solna, Sweden
| | - Tzu-Hsuan Huang
- Cancer Immunology Discovery, Pfizer Inc., San Diego, California, USA
| | | | | | | | - Mattias Johansson
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Aleksandr V Sokolov
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Uppsala, Sweden
| | - Helgi B Schiöth
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Uppsala, Sweden
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - Jochen M Schwenk
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Solna, Sweden
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Åsa K Hedman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Pfizer Worldwide Research Development and Medical, Stockholm, Sweden
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Ulfstedt M, Hu GZ, Eklund DM, Ronne H. The Ability of a Charophyte Alga Hexokinase to Restore Glucose Signaling and Glucose Repression of Gene Expression in a Glucose-Insensitive Arabidopsis Hexokinase Mutant Depends on Its Catalytic Activity. Front Plant Sci 2018; 9:1887. [PMID: 30619433 PMCID: PMC6306471 DOI: 10.3389/fpls.2018.01887] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 12/06/2018] [Indexed: 05/14/2023]
Abstract
Hexokinases is a family of proteins that is found in all eukaryotes. Hexokinases play key roles in the primary carbon metabolism, where they catalyze the phosphorylation of glucose and fructose, but they have also been shown to be involved in glucose signaling in both yeast and plants. We have characterized the Klebsormidium nitens KnHXK1 gene, the only hexokinase-encoding gene in this charophyte alga. The encoded protein, KnHXK1, is a type B plant hexokinase with an N-terminal membrane anchor localizing the protein to the mitochondrial membranes. We found that KnHXK1 expressed in Arabidopsis thaliana can restore the glucose sensing and glucose repression defects of the glucose-insensitive hexokinase mutant gin2-1. Interestingly, both functions require a catalytically active enzyme, since an inactive double mutant was unable to complement gin2-1. These findings differ from previous results on Arabidopsis AtHXK1 and its orthologs in rice, where catalytic and glucose sensing functions could be separated, but are consistent with recent results on the rice cytoplasmic hexokinase OsHXK7. A model with both catalytic and non-catalytic roles for hexokinases in glucose sensing and glucose repression is discussed.
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Affiliation(s)
- Mikael Ulfstedt
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Guo-Zhen Hu
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - D. Magnus Eklund
- Department of Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Hans Ronne
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- *Correspondence: Hans Ronne,
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Ulfstedt M, Hu GZ, Johansson M, Ronne H. Testing of Auxotrophic Selection Markers for Use in the Moss Physcomitrella Provides New Insights into the Mechanisms of Targeted Recombination. Front Plant Sci 2017; 8:1850. [PMID: 29163580 PMCID: PMC5675891 DOI: 10.3389/fpls.2017.01850] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 10/11/2017] [Indexed: 05/30/2023]
Abstract
The moss Physcomitrella patens is unique among plants in that homologous recombination can be used to knock out genes, just like in yeast. Furthermore, transformed plasmids can be rescued from Physcomitrella back into Escherichia coli, similar to yeast. In the present study, we have tested if a third important tool from yeast molecular genetics, auxotrophic selection markers, can be used in Physcomitrella. Two auxotrophic moss strains were made by knocking out the PpHIS3 gene encoding imidazoleglycerol-phosphate dehydratase, and the PpTRP1 gene encoding phosphoribosylanthranilate isomerase, disrupting the biosynthesis of histidine and tryptophan, respectively. The resulting PpHIS3Δ and PpTRP1Δ knockout strains were unable to grow on medium lacking histidine or tryptophan. The PpHIS3Δ strain was used to test selection of transformants by complementation of an auxotrophic marker. We found that the PpHIS3Δ strain could be complemented by transformation with a plasmid expressing the PpHIS3 gene from the CaMV 35S promoter, allowing the strain to grow on medium lacking histidine. Both linearized plasmids and circular supercoiled plasmids could complement the auxotrophic marker, and plasmids from both types of transformants could be rescued back into E. coli. Plasmids rescued from circular transformants were identical to the original plasmid, whereas plasmids rescued from linearized transformants had deletions generated by recombination between micro-homologies in the plasmids. Our results show that cloning by complementation of an auxotrophic marker works in Physcomitrella, which opens the door for using auxotrophic selection markers in moss molecular genetics. This will facilitate the adaptation of shuttle plasmid dependent methods from yeast molecular genetics for use in Physcomitrella.
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Affiliation(s)
- Mikael Ulfstedt
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Guo-Zhen Hu
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Monika Johansson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Hans Ronne
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Hörnblad E, Ulfstedt M, Ronne H, Marchant A. Partial functional conservation of IRX10 homologs in physcomitrella patens and Arabidopsis thaliana indicates an evolutionary step contributing to vascular formation in land plants. BMC Plant Biol 2013; 13:3. [PMID: 23286876 PMCID: PMC3543728 DOI: 10.1186/1471-2229-13-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 12/21/2012] [Indexed: 05/07/2023]
Abstract
BACKGROUND Plant cell walls are complex multicomponent structures that have evolved to fulfil an essential function in providing strength and protection to cells. Hemicelluloses constitute a key component of the cell wall and recently a number of the genes thought to encode the enzymes required for its synthesis have been identified in Arabidopsis. The acquisition of hemicellulose synthesis capability is hypothesised to have been an important step in the evolution of higher plants. RESULTS Analysis of the Physcomitrella patens genome has revealed the presence of homologs for all of the Arabidopsis glycosyltransferases including IRX9, IRX10 and IRX14 required for the synthesis of the glucuronoxylan backbone. The Physcomitrella IRX10 homolog is expressed in a variety of moss tissues which were newly formed or undergoing expansion. There is a high degree of sequence conservation between the Physcomitrella IRX10 and Arabidopsis IRX10 and IRX10-L. Despite this sequence similarity, the Physcomitrella IRX10 gene is only able to partially rescue the Arabidopsis irx10 irx10-L double mutant indicating that there has been a neo- or sub-functionalisation during the evolution of higher plants. Analysis of the monosaccharide composition of stems from the partially rescued Arabidopsis plants does not show any significant change in xylose content compared to the irx10 irx10-L double mutant. Likewise, knockout mutants of the Physcomitrella IRX10 gene do not result in any visible phenotype and there is no significant change in monosaccharide composition of the cell walls. CONCLUSIONS The fact that the Physcomitrella IRX10 (PpGT47A) protein can partially complement an Arabidopsis irx10 irx10-L double mutant suggests that it shares some function with the Arabidopsis proteins, but the lack of a phenotype in knockout lines shows that the function is not required for growth or development under normal conditions in Physcomitrella. In contrast, the Arabidopsis irx10 and irx10 irx10-L mutants have strong phenotypes indicating an important function in growth and development. We conclude that the evolution of vascular plants has been associated with a significant change or adaptation in the function of the IRX10 gene family.
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Affiliation(s)
- Emma Hörnblad
- UPSC, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, SE-90183, Sweden
| | - Mikael Ulfstedt
- Department of Microbiology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Box 7025, Uppsala, SE-750 07, Sweden
| | - Hans Ronne
- Department of Microbiology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Box 7025, Uppsala, SE-750 07, Sweden
| | - Alan Marchant
- UPSC, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, SE-90183, Sweden
- Centre for Biological Sciences, Life Sciences Building 85, University of Southampton, Southampton, SO17 1BJ, UK
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Nilsson A, Olsson T, Ulfstedt M, Thelander M, Ronne H. Two novel types of hexokinases in the moss Physcomitrella patens. BMC Plant Biol 2011; 11:32. [PMID: 21320325 PMCID: PMC3045890 DOI: 10.1186/1471-2229-11-32] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Accepted: 02/14/2011] [Indexed: 05/22/2023]
Abstract
BACKGROUND Hexokinase catalyzes the phosphorylation of glucose and fructose, but it is also involved in sugar sensing in both fungi and plants. We have previously described two types of hexokinases in the moss Physcomitrella. Type A, exemplified by PpHxk1, the major hexokinase in Physcomitrella, is a soluble protein that localizes to the chloroplast stroma. Type B, exemplified by PpHxk2, has an N-terminal membrane anchor. Both types are found also in vascular plants, and localize to the chloroplast stroma and mitochondrial membranes, respectively. RESULTS We have now characterized all 11 hexokinase encoding genes in Physcomitrella. Based on their N-terminal sequences and intracellular localizations, three of the encoded proteins are type A hexokinases and four are type B hexokinases. One of the type B hexokinases has a splice variant without a membrane anchor, that localizes to the cytosol and the nucleus. However, we also found two new types of hexokinases with no obvious orthologs in vascular plants. Type C, encoded by a single gene, has neither transit peptide nor membrane anchor, and is found in the cytosol and in the nucleus. Type D hexokinases, encoded by three genes, have membrane anchors and localize to mitochondrial membranes, but their sequences differ from those of the type B hexokinases. Interestingly, all moss hexokinases are more similar to each other in overall sequence than to hexokinases from other plants, even though characteristic sequence motifs such as the membrane anchor of the type B hexokinases are highly conserved between moss and vascular plants, indicating a common origin for hexokinases of the same type. CONCLUSIONS We conclude that the hexokinase gene family is more diverse in Physcomitrella, encoding two additional types of hexokinases that are absent in vascular plants. In particular, the presence of a cytosolic and nuclear hexokinase (type C) sets Physcomitrella apart from vascular plants, and instead resembles yeast, where all hexokinases localize to the cytosol. The fact that all moss hexokinases are more similar to each other than to hexokinases from vascular plants, even though both type A and type B hexokinases are present in all plants, further suggests that the hexokinase gene family in Physcomitrella has undergone concerted evolution.
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Affiliation(s)
- Anders Nilsson
- Department of Microbiology, Swedish University of Agricultural Sciences, Box 7025, SE-750 07 Uppsala, Sweden
| | - Tina Olsson
- Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences, Box 7080, SE-750 07 Uppsala, Sweden
| | - Mikael Ulfstedt
- Department of Microbiology, Swedish University of Agricultural Sciences, Box 7025, SE-750 07 Uppsala, Sweden
| | - Mattias Thelander
- Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences, Box 7080, SE-750 07 Uppsala, Sweden
| | - Hans Ronne
- Department of Microbiology, Swedish University of Agricultural Sciences, Box 7025, SE-750 07 Uppsala, Sweden
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