1
|
Krasnov GS, Ghukasyan LG, Abramov IS, Nasedkina TV. Determination of the Subclonal Tumor Structure in Childhood Acute Myeloid Leukemia and Acral Melanoma by Next-Generation Sequencing. Mol Biol 2021. [DOI: 10.1134/s0026893321040051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
2
|
An Introduction to Single-Cell RNA-Seq Analysis and its Applications. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11592-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
3
|
Matuła K, Rivello F, Huck WTS. Single-Cell Analysis Using Droplet Microfluidics. ACTA ACUST UNITED AC 2019; 4:e1900188. [PMID: 32293129 DOI: 10.1002/adbi.201900188] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/30/2019] [Indexed: 12/12/2022]
Abstract
Droplet microfluidics has revolutionized the study of single cells. The ability to compartmentalize cells within picoliter droplets in microfluidic devices has opened up a wide range of strategies to extract information at the genomic, transcriptomic, proteomic, or metabolomic level from large numbers of individual cells. Studying the different molecular landscapes at single-cell resolution has provided the authors with a detailed picture of intracellular heterogeneity and the resulting changes in cellular phenotypes. In addition, these technologies have aided in the discovery of rare cells in tumors or in the immune system, and left the authors with a deeper understanding of the fundamental biological processes that determine cell fate. This review aims to provide a detailed overview of the various droplet microfluidic strategies reported in the literature, taking into account the sometimes subtle differences in workflow or reagents that enable or improve certain protocols. Specifically, approaches to targeted- and whole-genome analysis, as well as whole-transcriptome profiling techniques, are reviewed. In addition, an up-to-date overview of new methods to characterize and quantify single-cell protein levels, and of developments to screen secreted molecules such as antibodies, cytokines, or metabolites at the single-cell level, is provided.
Collapse
Affiliation(s)
- Kinga Matuła
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - Francesca Rivello
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - Wilhelm T S Huck
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| |
Collapse
|
4
|
Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity. Nat Commun 2018; 9:2419. [PMID: 29925878 PMCID: PMC6010471 DOI: 10.1038/s41467-018-04724-5] [Citation(s) in RCA: 285] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 05/18/2018] [Indexed: 02/07/2023] Open
Abstract
Intra-tumor heterogeneity is one of the biggest challenges in cancer treatment today. Here we investigate tissue-wide gene expression heterogeneity throughout a multifocal prostate cancer using the spatial transcriptomics (ST) technology. Utilizing a novel approach for deconvolution, we analyze the transcriptomes of nearly 6750 tissue regions and extract distinct expression profiles for the different tissue components, such as stroma, normal and PIN glands, immune cells and cancer. We distinguish healthy and diseased areas and thereby provide insight into gene expression changes during the progression of prostate cancer. Compared to pathologist annotations, we delineate the extent of cancer foci more accurately, interestingly without link to histological changes. We identify gene expression gradients in stroma adjacent to tumor regions that allow for re-stratification of the tumor microenvironment. The establishment of these profiles is the first step towards an unbiased view of prostate cancer and can serve as a dictionary for future studies. Heterogeneity within tumors presents a challenge to cancer treatment. Here, the authors investigate transcriptional heterogeneity in prostate cancer, examining expression profiles of different tissue components and highlighting expression gradients in the tumor microenvironment.
Collapse
|
5
|
Yeldell SB, Ruble BK, Dmochowski IJ. Oligonucleotide modifications enhance probe stability for single cell transcriptome in vivo analysis (TIVA). Org Biomol Chem 2018; 15:10001-10009. [PMID: 29052679 DOI: 10.1039/c7ob02353g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Single cell transcriptomics provides a powerful discovery tool for identifying new cell types and functions as well as a means to probe molecular features of the etiology and treatment of human diseases, including cancer. However, such analyses are limited by the difficulty of isolating mRNA from single cells within biological samples. We recently introduced a photochemical method for isolating mRNA from single living cells, Transcriptome In Vivo Analysis (TIVA). The TIVA probe is a "caged" polyU : polyA oligonucleotide hairpin designed to enter live tissue, where site-specific activation with 405 nm laser reveals the polyU-biotin strand to bind mRNA in a target cell, enabling subsequent mRNA isolation and sequencing. The TIVA method is well suited for analysis of living cells in resected tissue, but has not yet been applied to living cells in whole organisms. Adapting TIVA to this more challenging environment requires a probe with higher thermal stability, more robust caging, and greater nuclease resistance. In this paper we present modifications to the original TIVA probe with multiple aspects of enhanced stability. These newer probes utilize an extended 22mer polyU capture strand with two 9mer polyA blocking strands ("22/9/9") for higher thermal stability pre-photolysis and improved mRNA capture affinity post-photolysis. The "22/9/9 GC" probe features a terminal GC pair to reduce pre-photolysis interactions with mRNA by more than half. The "PS-22/9/9" probe features a phosphorothioated backbone, which extends serum stability from <1 h to at least 48 h, and also mediates uptake into cultured human fibroblasts.
Collapse
Affiliation(s)
- S B Yeldell
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104-6323, USA.
| | | | | |
Collapse
|
6
|
Varma VB, Wu RG, Wang ZP, Ramanujan RV. Magnetic Janus particles synthesized using droplet micro-magnetofluidic techniques for protein detection. LAB ON A CHIP 2017; 17:3514-3525. [PMID: 28936512 DOI: 10.1039/c7lc00830a] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Magnetic droplets on a microfluidic platform can act as micro-robots, providing wireless, remote, and programmable control. This field of droplet micro-magnetofluidics (DMMF) is useful for droplet merging, mixing and synthesis of Janus structures. Specifically, magnetic Janus particles (MJP) are useful for protein and DNA detection as well as magnetically controlled bioprinting. However, synthesis of MJP with control of the functional phases is a challenge. Hence, we developed a high flow rate, surfactant-free, wash-less method to synthesize MJP by integration of DMMF with hybrid magnetic fields. The effects of the flow rate, flow rate ratio, and hybrid magnetic field on the magnetic component of the Janus droplets and the MJP were investigated. It was found that the magnetization, particle size, and phase distribution inside MJP could be readily tuned by the flow rates and the magnetic field. The magnetic component in the MJP could be concentrated after mixing at flow rate ratio values less than 7.5 and flow rates less than 3 ml h-1. The experimental results and our simulations are in good agreement. The synthesized magnetic-fluorescent Janus particles were used for protein detection, with BSA as a model protein.
Collapse
Affiliation(s)
- V B Varma
- School of Materials Science and Engineering, Nanyang Technological University, 639798, Singapore.
| | | | | | | |
Collapse
|
7
|
Guo F, Li L, Li J, Wu X, Hu B, Zhu P, Wen L, Tang F. Single-cell multi-omics sequencing of mouse early embryos and embryonic stem cells. Cell Res 2017. [PMID: 28621329 PMCID: PMC5539349 DOI: 10.1038/cr.2017.82] [Citation(s) in RCA: 219] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Single-cell epigenome sequencing techniques have recently been developed. However, the combination of different layers of epigenome sequencing in an individual cell has not yet been achieved. Here, we developed a single-cell multi-omics sequencing technology (single-cell COOL-seq) that can analyze the chromatin state/nucleosome positioning, DNA methylation, copy number variation and ploidy simultaneously from the same individual mammalian cell. We used this method to analyze the reprogramming of the chromatin state and DNA methylation in mouse preimplantation embryos. We found that within < 12 h of fertilization, each individual cell undergoes global genome demethylation together with the rapid and global reprogramming of both maternal and paternal genomes to a highly opened chromatin state. This was followed by decreased openness after the late zygote stage. Furthermore, from the late zygote to the 4-cell stage, the residual DNA methylation is preferentially preserved on intergenic regions of the paternal alleles and intragenic regions of maternal alleles in each individual blastomere. However, chromatin accessibility is similar between paternal and maternal alleles in each individual cell from the late zygote to the blastocyst stage. The binding motifs of several pluripotency regulators are enriched at distal nucleosome depleted regions from as early as the 2-cell stage. This indicates that the cis-regulatory elements of such target genes have been primed to an open state from the 2-cell stage onward, long before pluripotency is eventually established in the ICM of the blastocyst. Genes may be classified into homogeneously open, homogeneously closed and divergent states based on the chromatin accessibility of their promoter regions among individual cells. This can be traced to step-wise transitions during preimplantation development. Our study offers the first single-cell and parental allele-specific analysis of the genome-scale chromatin state and DNA methylation dynamics at single-base resolution in early mouse embryos and provides new insights into the heterogeneous yet highly ordered features of epigenomic reprogramming during this process.
Collapse
Affiliation(s)
- Fan Guo
- Beijing Advanced Innovation Center for Genomics, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing 100871, China.,Biomedical Institute for Pioneering Investigation via Convergence, Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.,Group of Translational Medicine, Department of Obstetrics and Gynecology, Ministry of Education Key Laboratory of Obstetric, Gynecologic &Pediatric Diseases and Birth Defects, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Lin Li
- Beijing Advanced Innovation Center for Genomics, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing 100871, China.,Biomedical Institute for Pioneering Investigation via Convergence, Peking University, Beijing 100871, China
| | - Jingyun Li
- Beijing Advanced Innovation Center for Genomics, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing 100871, China.,Biomedical Institute for Pioneering Investigation via Convergence, Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Xinglong Wu
- Beijing Advanced Innovation Center for Genomics, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing 100871, China.,Biomedical Institute for Pioneering Investigation via Convergence, Peking University, Beijing 100871, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Boqiang Hu
- Beijing Advanced Innovation Center for Genomics, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing 100871, China.,Biomedical Institute for Pioneering Investigation via Convergence, Peking University, Beijing 100871, China
| | - Ping Zhu
- Beijing Advanced Innovation Center for Genomics, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing 100871, China.,Biomedical Institute for Pioneering Investigation via Convergence, Peking University, Beijing 100871, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Lu Wen
- Beijing Advanced Innovation Center for Genomics, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing 100871, China.,Biomedical Institute for Pioneering Investigation via Convergence, Peking University, Beijing 100871, China
| | - Fuchou Tang
- Beijing Advanced Innovation Center for Genomics, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing 100871, China.,Biomedical Institute for Pioneering Investigation via Convergence, Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| |
Collapse
|
8
|
Platform for combined analysis of functional and biomolecular phenotypes of the same cell. Sci Rep 2017; 7:44636. [PMID: 28300162 PMCID: PMC5353596 DOI: 10.1038/srep44636] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 02/13/2017] [Indexed: 02/06/2023] Open
Abstract
Functional and molecular cell-to-cell variability is pivotal at the cellular, tissue and whole-organism levels. Yet, the ultimate goal of directly correlating the function of the individual cell with its biomolecular profile remains elusive. We present a platform for integrated analysis of functional and transcriptional phenotypes in the same single cells. We investigated changes in the cellular respiration and gene expression diversity resulting from adaptation to repeated episodes of acute hypoxia in a premalignant progression model. We find differential, progression stage-specific alterations in phenotypic heterogeneity and identify cells with aberrant phenotypes. To our knowledge, this study is the first demonstration of an integrated approach to elucidate how heterogeneity at the transcriptional level manifests in the physiologic profile of individual cells in the context of disease progression.
Collapse
|
9
|
YIZHAR-BARNEA OFER, AVRAHAM KARENB. Single cell analysis of the inner ear sensory organs. THE INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY 2017; 61:205-213. [PMID: 28621418 PMCID: PMC5709810 DOI: 10.1387/ijdb.160453ka] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The inner ear is composed of a complex mixture of cells, which together allow organisms to hear and maintain balance. The cells in the inner ear, which undergo an extraordinary process of development, have only recently begun to be studied on an individual level. As it has recently become clear that individual cells, previously considered to be of uniform character, may differ dramatically from each other, the need to study cell-to-cell variation, along with distinct transcriptional and regulatory signatures, has taken hold in the scientific community. In conjunction with high-throughput technologies, attempts are underway to dissect the inter- and intra-cellular variability of different cell types and developmental states of the inner ear from a novel perspective. Single cell analysis of the inner ear sensory organs holds the promise of providing a significant boost in building an omics network that translates into a comprehensive understanding of the mechanisms of hearing and balance. These networks may uncover critical elements for trans-differentiation, regeneration and/or reprogramming, providing entry points for therapeutics of deafness and vestibular pathologies.
Collapse
Affiliation(s)
- OFER YIZHAR-BARNEA
- Department of Human Molecular Genetics and Biochemistry, Sackler
Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel
Aviv, Israel
| | - KAREN B. AVRAHAM
- Department of Human Molecular Genetics and Biochemistry, Sackler
Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel
Aviv, Israel
| |
Collapse
|
10
|
Lombard-Banek C, Moody SA, Nemes P. High-Sensitivity Mass Spectrometry for Probing Gene Translation in Single Embryonic Cells in the Early Frog ( Xenopus) Embryo. Front Cell Dev Biol 2016; 4:100. [PMID: 27761436 PMCID: PMC5050209 DOI: 10.3389/fcell.2016.00100] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/29/2016] [Indexed: 01/01/2023] Open
Abstract
Direct measurement of protein expression with single-cell resolution promises to deepen the understanding of the basic molecular processes during normal and impaired development. High-resolution mass spectrometry provides detailed coverage of the proteomic composition of large numbers of cells. Here we discuss recent mass spectrometry developments based on single-cell capillary electrophoresis that extend discovery proteomics to sufficient sensitivity to enable the measurement of proteins in single cells. The single-cell mass spectrometry system is used to detect a large number of proteins in single embryonic cells in the 16-cell embryo of the South African clawed frog (Xenopus laevis) that give rise to distinct tissue types. Single-cell measurements of protein expression provide complementary information on gene transcription during early development of the vertebrate embryo, raising a potential to understand how differential gene expression coordinates normal cell heterogeneity during development.
Collapse
Affiliation(s)
| | - Sally A Moody
- Department of Anatomy and Regenerative Biology, The George Washington University Washington, DC, USA
| | - Peter Nemes
- Department of Chemistry, The George Washington University Washington, DC, USA
| |
Collapse
|
11
|
Petropoulos S, Panula SP, Schell JP, Lanner F. Single-cell RNA sequencing: revealing human pre-implantation development, pluripotency and germline development. J Intern Med 2016; 280:252-64. [PMID: 27046137 DOI: 10.1111/joim.12493] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Early human development is a dynamic, heterogeneous, complex and multidimensional process. During the first week, the single-cell zygote undergoes eight to nine rounds of cell division generating the multicellular blastocyst, which consists of hundreds of cells forming spatially organized embryonic and extra-embryonic tissues. At the level of transcription, degradation of maternal RNA commences at around the two-cell stage, coinciding with embryonic genome activation. Although numerous efforts have recently focused on delineating this process in humans, many questions still remain as thorough investigation has been limited by ethical issues, scarce availability of human embryos and the presence of minute amounts of DNA and RNA. In vitro cultures of embryonic stem cells provide some insight into early human development, but such studies have been confounded by analysis on a population level failing to appreciate cellular heterogeneity. Recent technical developments in single-cell RNA sequencing have provided a novel and powerful tool to explore the early human embryo in a systematic manner. In this review, we will discuss the advantages and disadvantages of the techniques utilized to specifically investigate human development and consider how the technology has yielded new insights into pre-implantation development, embryonic stem cells and the establishment of the germ line.
Collapse
Affiliation(s)
- S Petropoulos
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet and, Division of Obstetrics and Gynecology, Karolinska University Hospital, Stockholm, Sweden.,Ludwig Institute for Cancer Research, Stockholm, Sweden
| | - S P Panula
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet and, Division of Obstetrics and Gynecology, Karolinska University Hospital, Stockholm, Sweden
| | - J P Schell
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet and, Division of Obstetrics and Gynecology, Karolinska University Hospital, Stockholm, Sweden
| | - F Lanner
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet and, Division of Obstetrics and Gynecology, Karolinska University Hospital, Stockholm, Sweden
| |
Collapse
|
12
|
Caiado F, Silva-Santos B, Norell H. Intra-tumour heterogeneity - going beyond genetics. FEBS J 2016; 283:2245-58. [PMID: 26945550 DOI: 10.1111/febs.13705] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 02/01/2016] [Accepted: 03/02/2016] [Indexed: 12/15/2022]
Abstract
Cancer patients die primarily due to disease recurrence after transient treatment responses. The emergence of therapy-resistant escape variants is fuelled by intra-tumour heterogeneity, underpinned by interference and Darwinian evolution among continuously developing sub-clones in the mutating tumour. Novel cancer cell variants build upon the pre-existing genetic landscape and tumour heterogeneity is often ascribed largely to genetic variability. While mutations are required for cancer development and studies of genetic evolution of tumours have improved our understanding of cancer biology, genetics only represents one dimension of the fitness of each cancer cell. Beyond the mutations, several non-genetic factors also add significant variability, resulting in a complex and highly dynamic tumour cell population that can drive disease under almost any condition. This viewpoint article summarizes the genetic basis of intra-tumour heterogeneity, before dissecting four major interdependent non-genetic factors we think critically contribute to the overall variability of tumour cells in all types of cancer: epigenetic regulation, cellular differentiation hierarchies, gene expression stochasticity and tumour microenvironment. We finally present the relevant technological approaches to address the combined contribution of both genetic and non-genetic factors to intra-tumour heterogeneity, focusing on genomic profiling, cellular lineage tracing and single-cell RNA sequencing technologies. This strategy will ultimately allow dissection of the full range and depth of intra-tumour heterogeneity. We thus believe that understanding how cancer genetics synergize with the emerging non-genetic factors will be key for development of therapies able to tackle tumour escape and thereby improve cancer patient survival.
Collapse
Affiliation(s)
- Francisco Caiado
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Portugal
| | - Bruno Silva-Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Portugal
| | - Håkan Norell
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Portugal
| |
Collapse
|
13
|
Groen N, Guvendiren M, Rabitz H, Welsh WJ, Kohn J, de Boer J. Stepping into the omics era: Opportunities and challenges for biomaterials science and engineering. Acta Biomater 2016; 34:133-142. [PMID: 26876875 DOI: 10.1016/j.actbio.2016.02.015] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 01/22/2016] [Accepted: 02/10/2016] [Indexed: 12/11/2022]
Abstract
The research paradigm in biomaterials science and engineering is evolving from using low-throughput and iterative experimental designs towards high-throughput experimental designs for materials optimization and the evaluation of materials properties. Computational science plays an important role in this transition. With the emergence of the omics approach in the biomaterials field, referred to as materiomics, high-throughput approaches hold the promise of tackling the complexity of materials and understanding correlations between material properties and their effects on complex biological systems. The intrinsic complexity of biological systems is an important factor that is often oversimplified when characterizing biological responses to materials and establishing property-activity relationships. Indeed, in vitro tests designed to predict in vivo performance of a given biomaterial are largely lacking as we are not able to capture the biological complexity of whole tissues in an in vitro model. In this opinion paper, we explain how we reached our opinion that converging genomics and materiomics into a new field would enable a significant acceleration of the development of new and improved medical devices. The use of computational modeling to correlate high-throughput gene expression profiling with high throughput combinatorial material design strategies would add power to the analysis of biological effects induced by material properties. We believe that this extra layer of complexity on top of high-throughput material experimentation is necessary to tackle the biological complexity and further advance the biomaterials field. STATEMENT OF SIGNIFICANCE In this opinion paper, we postulate that converging genomics and materiomics into a new field would enable a significant acceleration of the development of new and improved medical devices. The use of computational modeling to correlate high-throughput gene expression profiling with high throughput combinatorial material design strategies would add power to the analysis of biological effects induced by material properties. We believe that this extra layer of complexity on top of high-throughput material experimentation is necessary to tackle the biological complexity and further advance the biomaterials field.
Collapse
Affiliation(s)
- Nathalie Groen
- Department of Tissue Regeneration, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands
| | - Murat Guvendiren
- New Jersey Center for Biomaterials, Rutgers University, Piscataway, NJ, USA
| | - Herschel Rabitz
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - William J Welsh
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA
| | - Joachim Kohn
- New Jersey Center for Biomaterials, Rutgers University, Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, New Jersey Center for Biomaterials, Rutgers University, Piscataway, NJ, USA
| | - Jan de Boer
- Department of Tissue Regeneration, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands
- cBITE Lab, Merln Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Maastricht, The Netherlands
| |
Collapse
|