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Barker AD, Alba MM, Mallick P, Agus DB, Lee JSH. An Inflection Point in Cancer Protein Biomarkers: What Was and What's Next. Mol Cell Proteomics 2023:100569. [PMID: 37196763 PMCID: PMC10388583 DOI: 10.1016/j.mcpro.2023.100569] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 04/26/2023] [Accepted: 05/08/2023] [Indexed: 05/19/2023] Open
Abstract
Biomarkers remain the highest value proposition in cancer medicine today - especially protein biomarkers. Yet despite decades of evolving regulatory frameworks to facilitate the review of emerging technologies, biomarkers have been mostly about promise with very little to show for improvements in human health. Cancer is an emergent property of a complex system and deconvoluting the integrative and dynamic nature of the overall system through biomarkers is a daunting proposition. The last two decades have seen an explosion of multi-omics profiling and a range of advanced technologies for precision medicine, including the emergence of liquid biopsy, exciting advances in single cell analysis, artificial intelligence (machine and deep learning) for data analysis and many other advanced technologies that promise to transform biomarker discovery. Combining multiple omics modalities to acquire a more comprehensive landscape of the disease state, we are increasingly developing biomarkers to support therapy selection and patient monitoring. Furthering precision medicine, especially in oncology, necessitates moving away from the lens of reductionist thinking towards viewing and understanding that complex diseases are, in fact, complex adaptive systems. As such, we believe it is necessary to re-define biomarkers as representations of biological system states at different hierarchical levels of biological order. This definition could include traditional molecular, histologic, radiographic, or physiological characteristics, as well as emerging classes of digital markers and complex algorithms. To succeed in the future, we must move past purely observational individual studies and instead start building a mechanistic framework to enable integrative analysis of new studies within the context of prior studies. Identifying information in complex systems and applying theoretical constructs, such as information theory, to study cancer as a disease of dysregulated communication could prove to be "game changing" for the clinical outcome of cancer patients.
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Affiliation(s)
- Anna D Barker
- Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, CA; Complex Adaptive Systems Initiative and School of Life Sciences, Arizona State University, Tempe, Arizona
| | - Mario M Alba
- Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA
| | - Parag Mallick
- Canary Center at Stanford for Cancer Early Detection, Stanford University, Stanford, CA; Department of Radiology, Stanford University, Stanford, CA
| | - David B Agus
- Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, CA; Keck School of Medicine, University of Southern California, Los Angeles, CA; Viterbi School of Engineering, University of Southern California, Los Angeles, CA
| | - Jerry S H Lee
- Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, CA; Keck School of Medicine, University of Southern California, Los Angeles, CA; Viterbi School of Engineering, University of Southern California, Los Angeles, CA
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2
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Thomas CE, Dahl L, Byström S, Chen Y, Uhlén M, Mälarstig A, Czene K, Hall P, Schwenk JM, Gabrielson M. Circulating proteins reveal prior use of menopausal hormonal therapy and increased risk of breast cancer. Transl Oncol 2022; 17:101339. [PMID: 35033985 PMCID: PMC8760550 DOI: 10.1016/j.tranon.2022.101339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/18/2021] [Accepted: 12/31/2021] [Indexed: 11/15/2022] Open
Abstract
Accessible risk predictors are crucial for improving the early detection and prognosis of breast cancer. Blood samples are widely available and contain proteins that provide important information about human health and disease, however, little is still known about the contribution of circulating proteins to breast cancer risk prediction. We profiled EDTA plasma samples collected before diagnosis from the Swedish KARMA breast cancer cohort to evaluate circulating proteins as molecular predictors. A data-driven analysis strategy was applied to the molecular phenotypes built on 700 circulating proteins to identify and annotate clusters of women. The unsupervised analysis of 183 future breast cancer cases and 366 age-matched controls revealed five stable clusters with distinct proteomic plasma profiles. Among these women, those in the most stable cluster (N = 19; mean Jaccard index: 0.70 ± 0.29) were significantly more likely to have used menopausal hormonal therapy (MHT), get a breast cancer diagnosis, and were older compared to the remaining clusters. The circulating proteins associated with this cluster (FDR < 0.001) represented physiological processes related to cell junctions (F11R, CLDN15, ITGAL), DNA repair (RBBP8), cell replication (TJP3), and included proteins found in female reproductive tissue (PTCH1, ZP4). Using a data-driven approach on plasma proteomics data revealed the potential long-lasting molecular effects of menopausal hormonal therapy (MHT) on the circulating proteome, even after women had ended their treatment. This provides valuable insights concerning proteomics efforts to identify molecular markers for breast cancer risk prediction.
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Affiliation(s)
- Cecilia E Thomas
- Science for Life Laboratory, Department of Protein Science School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Tomtebodavägen 23, Solna, Stockholm 171 65, Sweden
| | - Leo Dahl
- Science for Life Laboratory, Department of Protein Science School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Tomtebodavägen 23, Solna, Stockholm 171 65, Sweden
| | - Sanna Byström
- Science for Life Laboratory, Department of Protein Science School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Tomtebodavägen 23, Solna, Stockholm 171 65, Sweden
| | - Yan Chen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet Nobels väg 12A, Stockholm SE-171 77, Sweden; Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, Department of Protein Science School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Tomtebodavägen 23, Solna, Stockholm 171 65, Sweden
| | - Anders Mälarstig
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet Nobels väg 12A, Stockholm SE-171 77, Sweden; Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet Nobels väg 12A, Stockholm SE-171 77, Sweden
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet Nobels väg 12A, Stockholm SE-171 77, Sweden; Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - Jochen M Schwenk
- Science for Life Laboratory, Department of Protein Science School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Tomtebodavägen 23, Solna, Stockholm 171 65, Sweden.
| | - Marike Gabrielson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet Nobels väg 12A, Stockholm SE-171 77, Sweden.
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Yeh CY, Adusumilli R, Kullolli M, Mallick P, John EM, Pitteri SJ. Assessing biological and technological variability in protein levels measured in pre-diagnostic plasma samples of women with breast cancer. Biomark Res 2017; 5:30. [PMID: 29075496 PMCID: PMC5645980 DOI: 10.1186/s40364-017-0110-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 10/03/2017] [Indexed: 12/30/2022] Open
Abstract
Background Quantitative proteomics allows for the discovery and functional investigation of blood-based pre-diagnostic biomarkers for early cancer detection. However, a major limitation of proteomic investigations in biomarker studies remains the biological and technical variability in the analysis of complex clinical samples. Moreover, unlike ‘omics analogues such as genomics and transcriptomics, proteomics has yet to achieve reproducibility and long-term stability on a unified technological platform. Few studies have thoroughly investigated protein variability in pre-diagnostic samples of cancer patients across multiple platforms. Methods We obtained ten blood plasma “case” samples collected up to 2 years prior to breast cancer diagnosis. Each case sample was paired with a matched control plasma from a full biological sister without breast cancer. We measured protein levels using both mass-spectrometry and antibody-based technologies to: (1) assess the technical considerations in different protein assays when analyzing limited clinical samples, and (2) evaluate the statistical power of potential diagnostic analytes. Results Although we found inherent technical variation in the three assays used, we detected protein dependent biological signal from the limited samples. The three assay types yielded 32 proteins with statistically significantly (p < 1E-01) altered expression levels between cases and controls, with no proteins retaining statistical significance after false discovery correction. Conclusions Technical, practical, and study design considerations are essential to maximize information obtained in limited pre-diagnostic samples of cancer patients. This study provides a framework that estimates biological effect sizes critical for consideration in designing studies for pre-diagnostic blood-based biomarker detection. Electronic supplementary material The online version of this article (10.1186/s40364-017-0110-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christine Y Yeh
- Department of Biomedical Informatics, Stanford University School of Medicine, Stanford, CA 93405 USA.,Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA 94304 USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA 93405 USA
| | - Ravali Adusumilli
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA 94304 USA
| | - Majlinda Kullolli
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA 94304 USA
| | - Parag Mallick
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA 94304 USA.,Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Esther M John
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305 USA.,Cancer Prevention Institute of California, Fremont, CA 94538 USA
| | - Sharon J Pitteri
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA 94304 USA.,Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305 USA
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Pedersen JW, Gentry-Maharaj A, Nøstdal A, Fourkala EO, Dawnay A, Burnell M, Zaikin A, Burchell J, Papadimitriou JT, Clausen H, Jacobs I, Menon U, Wandall HH. Cancer-associated autoantibodies to MUC1 and MUC4--a blinded case–control study of colorectal cancer in UK collaborative trial of ovarian cancer screening. Int J Cancer 2014; 134:2180-88. [PMID: 24122770 PMCID: PMC4234004 DOI: 10.1002/ijc.28538] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 07/25/2013] [Accepted: 09/03/2013] [Indexed: 12/14/2022]
Abstract
Recent reports suggest that autoantibodies directed to aberrantly glycosylated mucins, in particular MUC1 and MUC4, are found in patients with colorectal cancer. There is, however, limited information on the autoantibody levels before clinical diagnosis, and their utility in cancer screening in the general population. In our study, we have generated O-glycosylated synthetic MUC1 and MUC4 peptides in vitro, to mimic cancer-associated glycoforms, and displayed these on microarrays. The assay’s performance was tested through an initial screening of serum samples taken from patients at the time of colorectal cancer diagnosis and healthy controls. Subsequently, the selected biomarkers were evaluated in a blinded nested case–control study using stored serum samples from among the 50,640 women randomized to the multimodal arm of the UK Collaborative Trial of Ovarian Cancer Screening (UKCTOCS), where women gave annual blood samples for several years. Cases were 97 postmenopausal women who developed colorectal cancer after recruitment and were age-matched to 97 women without any history of cancer. MUC1-STn and MUC1-Core3 IgG autoantibodies identified cases with 8.2 and 13.4% sensitivity, respectively, at 95% specificity. IgA to MUC4 glycoforms were unable to discriminate between cases and controls in the UKCTOCS sera. Additional analysis was undertaken by combining the data of MUC1-STn and MUC1-Core3 with previously generated data on autoantibodies to p53 peptides, which increased the sensitivity to 32.0% at 95% specificity. These findings suggest that a combination of antibody signatures may have a role as part of a biomarker panel for the early detection of colorectal cancer.
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Affiliation(s)
- Johannes W Pedersen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of CopenhagenCopenhagen, Denmark
| | | | - Alexander Nøstdal
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of CopenhagenCopenhagen, Denmark
| | | | - Anne Dawnay
- Department of Clinical Biochemistry, University College London HospitalsLondon, United Kingdom
| | - Matthew Burnell
- Women’s Cancer, Institute for Women’s Health, University College LondonLondon, United Kingdom
| | - Alexey Zaikin
- Women’s Cancer, Institute for Women’s Health, University College LondonLondon, United Kingdom
- Department of Mathematics, University College LondonLondon, United Kingdom
| | - Joy Burchell
- Breast Cancer Biology, King’s College London, Guy’s HospitalLondon, United Kingdom
| | | | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of CopenhagenCopenhagen, Denmark
| | - Ian Jacobs
- Women’s Cancer, Institute for Women’s Health, University College LondonLondon, United Kingdom
| | - Usha Menon
- Women’s Cancer, Institute for Women’s Health, University College LondonLondon, United Kingdom
- Usha Menon, Gynaecological Cancer Research Centre, Women’s Cancer, Institute for Women’s Health, University College London, 149 Tottenham Court Road, London W1T 7DN, United Kingdom, Tel.: +020-3447-2108, Fax: +020-3447-2129, E-mail:
| | - Hans H Wandall
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of CopenhagenCopenhagen, Denmark
- Correspondence to: Hans H. Wandall, Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark, E-mail:
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Chao T, Ladd JJ, Qiu J, Johnson MM, Israel R, Chin A, Wang H, Prentice RL, Feng Z, Disis ML, Hanash S. Proteomic profiling of the autoimmune response to breast cancer antigens uncovers a suppressive effect of hormone therapy. Proteomics Clin Appl 2013; 7:327-36. [PMID: 23401414 DOI: 10.1002/prca.201200058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 10/11/2012] [Accepted: 12/03/2012] [Indexed: 11/11/2022]
Abstract
PURPOSE Proteomics technologies are well suited for harnessing the immune response to tumor antigens for diagnostic applications as in the case of breast cancer. We previously reported a substantial impact of hormone therapy (HT) on the proteome. Here, we investigated the effect of HT on the immune response toward breast tumor antigens. EXPERIMENTAL DESIGN Plasmas collected 0-10 months prior to diagnosis of ER+ breast cancer from 190 postmenopausal women and 190 controls that participated in the Women's Health Initiative Observational Study were analyzed for the effect of HT on IgG reactivity against arrayed proteins from MCF-7 or SKBR3 breast cancer cell line lysates following extensive fractionation. RESULTS HT user cases exhibited significantly reduced autoantibody reactivity against arrayed proteins compared to cases who were Not Current users. An associated reduced level of IL-6 and other immune-related cytokines was observed among HT users relative to nonusers. CONCLUSION AND CLINICAL RELEVANCE Our findings suggest occurrence of a global altered immune response to breast cancer-derived proteins associated with HT. Thus a full understanding of factors that modulate the immune response is necessary to translate autoantibody panels into clinical applications.
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Affiliation(s)
- Timothy Chao
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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Pedersen JW, Gentry-Maharaj A, Fourkala EO, Dawnay A, Burnell M, Zaikin A, Pedersen AE, Jacobs I, Menon U, Wandall HH. Early detection of cancer in the general population: a blinded case-control study of p53 autoantibodies in colorectal cancer. Br J Cancer 2012; 108:107-14. [PMID: 23169294 PMCID: PMC3553520 DOI: 10.1038/bjc.2012.517] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background: Recent reports from cancer screening trials in high-risk populations suggest that autoantibodies can be detected before clinical diagnosis. However, there is minimal data on the role of autoantibody signatures in cancer screening in the general population. Methods: Informative p53 peptides were identified in sera from patients with colorectal cancer using an autoantibody microarray with 15-mer overlapping peptides covering the complete p53 sequence. The selected peptides were evaluated in a blinded case–control study using stored serum from the multimodal arm of the United Kingdom Collaborative Trial of Ovarian Cancer Screening where women gave annual blood samples. Cases were postmenopausal women who developed colorectal cancer following recruitment, with 2 or more serum samples preceding diagnosis. Controls were age-matched women with no history of cancer. Results: The 50 640 women randomised to the multimodal group were followed up for a median of 6.8 (inter-quartile range 5.9–8.4) years. Colorectal cancer notification was received in 101 women with serial samples of whom 97 (297 samples) had given consent for secondary studies. They were matched 1 : 1 with 97 controls (296 serial samples). The four most informative peptides identified 25.8% of colorectal cancer patients with a specificity of 95%. The median lead time was 1.4 (range 0.12–3.8) years before clinical diagnosis. Conclusion: Our findings suggest that in the general population, autoantibody signatures are detectable during preclinical disease and may be of value in cancer screening. In colorectal cancer screening in particular, where the current need is to improve compliance, it suggests that p53 autoantibodies may contribute towards risk stratification.
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Affiliation(s)
- J W Pedersen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen N, DK-2200, Denmark
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Opstal-van Winden AWJ, Krop EJM, Kåredal MH, Gast MCW, Lindh CH, Jeppsson MC, Jönsson BAG, Grobbee DE, Peeters PHM, Beijnen JH, van Gils CH, Vermeulen RCH. Searching for early breast cancer biomarkers by serum protein profiling of pre-diagnostic serum; a nested case-control study. BMC Cancer 2011; 11:381. [PMID: 21871081 PMCID: PMC3189190 DOI: 10.1186/1471-2407-11-381] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 08/26/2011] [Indexed: 11/22/2022] Open
Abstract
Background Serum protein profiles have been investigated frequently to discover early biomarkers for breast cancer. So far, these studies used biological samples collected at or after diagnosis. This may limit these studies' value in the search for cancer biomarkers because of the often advanced tumor stage, and consequently risk of reverse causality. We present for the first time pre-diagnostic serum protein profiles in relation to breast cancer, using the Prospect-EPIC (European Prospective Investigation into Cancer and nutrition) cohort. Methods In a nested case-control design we compared 68 women diagnosed with breast cancer within three years after enrollment, with 68 matched controls for differences in serum protein profiles. All samples were analyzed with SELDI-TOF MS (surface enhanced laser desorption/ionization time-of-flight mass spectrometry). In a subset of 20 case-control pairs, the serum proteome was identified and relatively quantified using isobaric Tags for Relative and Absolute Quantification (iTRAQ) and online two-dimensional nano-liquid chromatography coupled with tandem MS (2D-nanoLC-MS/MS). Results Two SELDI-TOF MS peaks with m/z 3323 and 8939, which probably represent doubly charged apolipoprotein C-I and C3a des-arginine anaphylatoxin (C3adesArg), were higher in pre-diagnostic breast cancer serum (p = 0.02 and p = 0.06, respectively). With 2D-nanoLC-MS/MS, afamin, apolipoprotein E and isoform 1 of inter-alpha trypsin inhibitor heavy chain H4 (ITIH4) were found to be higher in pre-diagnostic breast cancer (p < 0.05), while alpha-2-macroglobulin and ceruloplasmin were lower (p < 0.05). C3adesArg and ITIH4 have previously been related to the presence of symptomatic and/or mammographically detectable breast cancer. Conclusions We show that serum protein profiles are already altered up to three years before breast cancer detection.
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