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Xu X, Hua X, Mo H, Hu S, Song J. Single-cell RNA sequencing to identify cellular heterogeneity and targets in cardiovascular diseases: from bench to bedside. Basic Res Cardiol 2023; 118:7. [PMID: 36750503 DOI: 10.1007/s00395-022-00972-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 12/09/2022] [Accepted: 12/09/2022] [Indexed: 02/09/2023]
Abstract
The mechanisms of cardiovascular diseases (CVDs) remain incompletely elucidated. Single-cell RNA sequencing (scRNA-seq) has enabled the profiling of single-cell transcriptomes at unprecedented resolution and throughput, which is critical for deciphering cardiovascular cellular heterogeneity and underlying disease mechanisms, thereby facilitating the development of therapeutic strategies. In this review, we summarize cellular heterogeneity in cardiovascular homeostasis and diseases as well as the discovery of potential disease targets based on scRNA-seq, and yield new insights into the promise of scRNA-seq technology in precision medicine and clinical application.
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Affiliation(s)
- Xinjie Xu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
| | - Xiumeng Hua
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
| | - Han Mo
- Shenzhen Key Laboratory of Cardiovascular Disease, Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen, 518057, China
| | - Shengshou Hu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China.
| | - Jiangping Song
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China.
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52
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Zhang N, Kandalai S, Zhou X, Hossain F, Zheng Q. Applying multi-omics toward tumor microbiome research. IMETA 2023; 2:e73. [PMID: 38868335 PMCID: PMC10989946 DOI: 10.1002/imt2.73] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/30/2022] [Accepted: 11/28/2022] [Indexed: 06/14/2024]
Abstract
Rather than a "short-term tenant," the tumor microbiome has been shown to play a vital role as a "permanent resident," affecting carcinogenesis, cancer development, metastasis, and cancer therapies. As the tumor microbiome has great potential to become a target for the early diagnosis and treatment of cancer, recent research on the relevance of the tumor microbiota has attracted a wide range of attention from various scientific fields, resulting in remarkable progress that benefits from the development of interdisciplinary technologies. However, there are still a great variety of challenges in this emerging area, such as the low biomass of intratumoral bacteria and unculturable character of some microbial species. Due to the complexity of tumor microbiome research (e.g., the heterogeneity of tumor microenvironment), new methods with high spatial and temporal resolution are urgently needed. Among these developing methods, multi-omics technologies (combinations of genomics, transcriptomics, proteomics, and metabolomics) are powerful approaches that can facilitate the understanding of the tumor microbiome on different levels of the central dogma. Therefore, multi-omics (especially single-cell omics) will make enormous impacts on the future studies of the interplay between microbes and tumor microenvironment. In this review, we have systematically summarized the advances in multi-omics and their existing and potential applications in tumor microbiome research, thus providing an omics toolbox for investigators to reference in the future.
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Affiliation(s)
- Nan Zhang
- Department of Radiation Oncology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
- Center for Cancer Metabolism, Ohio State University Comprehensive Cancer Center ‐ James Cancer Hospital and Solove Research InstituteThe Ohio State UniversityOhioColumbusUSA
| | - Shruthi Kandalai
- Department of Radiation Oncology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
- Center for Cancer Metabolism, Ohio State University Comprehensive Cancer Center ‐ James Cancer Hospital and Solove Research InstituteThe Ohio State UniversityOhioColumbusUSA
| | - Xiaozhuang Zhou
- Department of Radiation Oncology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
- Center for Cancer Metabolism, Ohio State University Comprehensive Cancer Center ‐ James Cancer Hospital and Solove Research InstituteThe Ohio State UniversityOhioColumbusUSA
| | - Farzana Hossain
- Department of Radiation Oncology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
- Center for Cancer Metabolism, Ohio State University Comprehensive Cancer Center ‐ James Cancer Hospital and Solove Research InstituteThe Ohio State UniversityOhioColumbusUSA
| | - Qingfei Zheng
- Department of Radiation Oncology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
- Center for Cancer Metabolism, Ohio State University Comprehensive Cancer Center ‐ James Cancer Hospital and Solove Research InstituteThe Ohio State UniversityOhioColumbusUSA
- Department of Biological Chemistry and Pharmacology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
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53
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Zhang X, Wang YC, Liu CJ. Application of single-cell transcriptome sequencing in gastric cancer. Shijie Huaren Xiaohua Zazhi 2023; 31:48-55. [DOI: 10.11569/wcjd.v31.i2.48] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Gastric cancer (GC) is the fifth most common cancer worldwide and the third leading cause of cancer death. With the development of single-cell RNA-sequencing (scRNA-seq) technology, the research on GC has gradually developed from the histopathological level to the transcriptional level. In this paper, we discuss the principle of scRNA-seq technology and its application in GC research, including the transcriptional characteristics and origin of GC precancerous lesions, intratumor heterogeneity of primary tumors, tumor microenvironment, and metastatic dissemination.
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Affiliation(s)
- Xin Zhang
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing 100071, China,Department of Pharmacy, Medical Supplies Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Yan-Chun Wang
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing 100071, China
| | - Chun-Jie Liu
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing 100071, China
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Leighton J, Hu M, Sei E, Meric-Bernstam F, Navin NE. Reconstructing mutational lineages in breast cancer by multi-patient-targeted single-cell DNA sequencing. CELL GENOMICS 2023; 3:100215. [PMID: 36777188 PMCID: PMC9903705 DOI: 10.1016/j.xgen.2022.100215] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 07/21/2022] [Accepted: 10/18/2022] [Indexed: 11/11/2022]
Abstract
Single-cell DNA sequencing (scDNA-seq) methods are powerful tools for profiling mutations in cancer cells; however, most genomic regions sequenced in single cells are non-informative. To overcome this issue, we developed a multi-patient-targeted (MPT) scDNA-seq method. MPT involves first performing bulk exome sequencing across a cohort of cancer patients to identify somatic mutations, which are then pooled together to develop a single custom targeted panel for high-throughput scDNA-seq using a microfluidics platform. We applied MPT to profile 330 mutations across 23,500 cells from 5 patients with triple negative-breast cancer (TNBC), which showed that 3 tumors were monoclonal and 2 tumors were polyclonal. From these data, we reconstructed mutational lineages and identified early mutational and copy-number events, including early TP53 mutations that occurred in all five patients. Collectively, our data suggest that MPT can overcome a major technical obstacle for studying tumor evolution using scDNA-seq by profiling information-rich mutation sites.
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Affiliation(s)
- Jake Leighton
- Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
- Graduate School of Biological Sciences, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Min Hu
- Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Emi Sei
- Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Funda Meric-Bernstam
- Graduate School of Biological Sciences, UT MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Precision Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nicholas E. Navin
- Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
- Graduate School of Biological Sciences, UT MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
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55
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Sashittal P, Zhang H, Iacobuzio-Donahue CA, Raphael BJ. ConDoR: Tumor phylogeny inference with a copy-number constrained mutation loss model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.05.522408. [PMID: 36711528 PMCID: PMC9882003 DOI: 10.1101/2023.01.05.522408] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Tumors consist of subpopulations of cells that harbor distinct collections of somatic mutations. These mutations range in scale from single nucleotide variants (SNVs) to large-scale copy-number aberrations (CNAs). While many approaches infer tumor phylogenies using SNVs as phylogenetic markers, CNAs that overlap SNVs may lead to erroneous phylogenetic inference. Specifically, an SNV may be lost in a cell due to a deletion of the genomic segment containing the SNV. Unfortunately, no current single-cell DNA sequencing (scDNA-seq) technology produces accurate measurements of both SNVs and CNAs. For instance, recent targeted scDNA-seq technologies, such as Mission Bio Tapestri, measure SNVs with high fidelity in individual cells, but yield much less reliable measurements of CNAs. We introduce a new evolutionary model, the constrained k-Dollo model, that uses SNVs as phylogenetic markers and partial information about CNAs in the form of clustering of cells with similar copy-number profiles. This copy-number clustering constrains where loss of SNVs can occur in the phylogeny. We develop ConDoR (Constrained Dollo Reconstruction), an algorithm to infer tumor phylogenies from targeted scDNA-seq data using the constrained k-Dollo model. We show that ConDoR outperforms existing methods on simulated data. We use ConDoR to analyze a new multi-region targeted scDNA-seq dataset of 2153 cells from a pancreatic ductal adenocarcinoma (PDAC) tumor and produce a more plausible phylogeny compared to existing methods that conforms to histological results for the tumor from a previous study. We also analyze a metastatic colorectal cancer dataset, deriving a more parsimonious phylogeny than previously published analyses and with a simpler monoclonal origin of metastasis compared to the original study. Code availability Software is available at https://github.com/raphael-group/constrained-Dollo.
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Affiliation(s)
| | - Haochen Zhang
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, NY, USA
| | - Christine A. Iacobuzio-Donahue
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, NY, USA
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, NY, USA
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, NY, USA
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Kong S, Li R, Tian Y, Zhang Y, Lu Y, Ou Q, Gao P, Li K, Zhang Y. Single-cell omics: A new direction for functional genetic research in human diseases and animal models. Front Genet 2023; 13:1100016. [PMID: 36685871 PMCID: PMC9846559 DOI: 10.3389/fgene.2022.1100016] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/16/2022] [Indexed: 01/06/2023] Open
Abstract
Over the past decade, with the development of high-throughput single-cell sequencing technology, single-cell omics has been emerged as a powerful tool to understand the molecular basis of cellular mechanisms and refine our knowledge of diverse cell states. They can reveal the heterogeneity at different genetic layers and elucidate their associations by multiple omics analysis, providing a more comprehensive genetic map of biological regulatory networks. In the post-GWAS era, the molecular biological mechanisms influencing human diseases will be further elucidated by single-cell omics. This review mainly summarizes the development and trend of single-cell omics. This involves single-cell omics technologies, single-cell multi-omics technologies, multiple omics data integration methods, applications in various human organs and diseases, classic laboratory cell lines, and animal disease models. The review will reveal some perspectives for elucidating human diseases and constructing animal models.
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Affiliation(s)
- Siyuan Kong
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China,*Correspondence: Siyuan Kong, ; Yubo Zhang,
| | - Rongrong Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yunhan Tian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China,College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Yaqiu Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yuhui Lu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qiaoer Ou
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Peiwen Gao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Kui Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yubo Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China,College of Life Science and Engineering, Foshan University, Foshan, China,*Correspondence: Siyuan Kong, ; Yubo Zhang,
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57
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Jiang Z, Shi H, Tang X, Qin J. Recent advances in droplet microfluidics for single-cell analysis. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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58
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Schot M, Araújo-Gomes N, van Loo B, Kamperman T, Leijten J. Scalable fabrication, compartmentalization and applications of living microtissues. Bioact Mater 2023; 19:392-405. [PMID: 35574053 PMCID: PMC9062422 DOI: 10.1016/j.bioactmat.2022.04.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/18/2022] [Accepted: 04/06/2022] [Indexed: 10/27/2022] Open
Abstract
Living microtissues are used in a multitude of applications as they more closely resemble native tissue physiology, as compared to 2D cultures. Microtissues are typically composed of a combination of cells and materials in varying combinations, which are dictated by the applications' design requirements. Their applications range wide, from fundamental biological research such as differentiation studies to industrial applications such as cruelty-free meat production. However, their translation to industrial and clinical settings has been hindered due to the lack of scalability of microtissue production techniques. Continuous microfluidic processes provide an opportunity to overcome this limitation as they offer higher throughput production rates as compared to traditional batch techniques, while maintaining reproducible control over microtissue composition and size. In this review, we provide a comprehensive overview of the current approaches to engineer microtissues with a focus on the advantages of, and need for, the use of continuous processes to produce microtissues in large quantities. Finally, an outlook is provided that outlines the required developments to enable large-scale microtissue fabrication using continuous processes.
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Affiliation(s)
- Maik Schot
- Department of Developmental Bioengineering, Faculty of Science and Technology, Technical Medical Centre, University of Twente, Drienerlolaan 5, 7522NB, Enschede, the Netherlands
| | - Nuno Araújo-Gomes
- Department of Developmental Bioengineering, Faculty of Science and Technology, Technical Medical Centre, University of Twente, Drienerlolaan 5, 7522NB, Enschede, the Netherlands
| | - Bas van Loo
- Department of Developmental Bioengineering, Faculty of Science and Technology, Technical Medical Centre, University of Twente, Drienerlolaan 5, 7522NB, Enschede, the Netherlands
| | - Tom Kamperman
- Department of Developmental Bioengineering, Faculty of Science and Technology, Technical Medical Centre, University of Twente, Drienerlolaan 5, 7522NB, Enschede, the Netherlands
| | - Jeroen Leijten
- Department of Developmental Bioengineering, Faculty of Science and Technology, Technical Medical Centre, University of Twente, Drienerlolaan 5, 7522NB, Enschede, the Netherlands
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59
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Anderson BD, Bisanz JE. Challenges and opportunities of strain diversity in gut microbiome research. Front Microbiol 2023; 14:1117122. [PMID: 36876113 PMCID: PMC9981649 DOI: 10.3389/fmicb.2023.1117122] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/24/2023] [Indexed: 02/19/2023] Open
Abstract
Just because two things are related does not mean they are the same. In analyzing microbiome data, we are often limited to species-level analyses, and even with the ability to resolve strains, we lack comprehensive databases and understanding of the importance of strain-level variation outside of a limited number of model organisms. The bacterial genome is highly plastic with gene gain and loss occurring at rates comparable or higher than de novo mutations. As such, the conserved portion of the genome is often a fraction of the pangenome which gives rise to significant phenotypic variation, particularly in traits which are important in host microbe interactions. In this review, we discuss the mechanisms that give rise to strain variation and methods that can be used to study it. We identify that while strain diversity can act as a major barrier in interpreting and generalizing microbiome data, it can also be a powerful tool for mechanistic research. We then highlight recent examples demonstrating the importance of strain variation in colonization, virulence, and xenobiotic metabolism. Moving past taxonomy and the species concept will be crucial for future mechanistic research to understand microbiome structure and function.
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Affiliation(s)
- Benjamin D Anderson
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, United States
| | - Jordan E Bisanz
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, United States.,The Penn State Microbiome Center, Huck Institutes of the Life Sciences, University Park, PA, United States
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60
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Sieskind R, Cortajarena AL, Manteca A. Cell-Free Production Systems in Droplet Microfluidics. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 185:91-127. [PMID: 37306704 DOI: 10.1007/10_2023_224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The use of cell-free production systems in droplet microfluidic devices has gained significant interest during the last decade. Encapsulating DNA replication, RNA transcription, and protein expression systems in water-in-oil drops allows for the interrogation of unique molecules and high-throughput screening of libraries of industrial and biomedical interest. Furthermore, the use of such systems in closed compartments enables the evaluation of various properties of novel synthetic or minimal cells. In this chapter, we review the latest advances in the usage of the cell-free macromolecule production toolbox in droplets, with a special emphasis on new on-chip technologies for the amplification, transcription, expression, screening, and directed evolution of biomolecules.
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Affiliation(s)
- Rémi Sieskind
- Institut Pasteur, Université de Paris, Unité d'Architecture et de Dynamique des Macromolécules Biologiques, Paris, France
| | - Aitziber L Cortajarena
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Aitor Manteca
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain.
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61
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Ide K, Nishikawa Y, Maruyama T, Tsukada Y, Kogawa M, Takeda H, Ito H, Wagatsuma R, Miyaoka R, Nakano Y, Kinjo K, Ito M, Hosokawa M, Yura K, Suda S, Takeyama H. Targeted single-cell genomics reveals novel host adaptation strategies of the symbiotic bacteria Endozoicomonas in Acropora tenuis coral. MICROBIOME 2022; 10:220. [PMID: 36503599 PMCID: PMC9743535 DOI: 10.1186/s40168-022-01395-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Endozoicomonas bacteria symbiosis with various marine organisms is hypothesized as a potential indicator of health in corals. Although many amplicon analyses using 16S rRNA gene have suggested the diversity of Endozoicomonas species, genome analysis has been limited due to contamination of host-derived sequences and difficulties in culture and metagenomic analysis. Therefore, the evolutionary and functional potential of individual Endozoicomonas species symbiotic with the same coral species remains unresolved. RESULTS In this study, we applied a novel single-cell genomics technique using droplet microfluidics to obtain single-cell amplified genomes (SAGs) for uncultured coral-associated Endozoicomonas spp. We obtained seven novel Endozoicomonas genomes and quantitative bacterial composition from Acropora tenuis corals at four sites in Japan. Our quantitative 16S rRNA gene and comparative genomic analysis revealed that these Endozoicomonas spp. belong to different lineages (Clade A and Clade B), with widely varying abundance among individual corals. Furthermore, each Endozoicomonas species possessed various eukaryotic-like genes in clade-specific genes. It was suggested that these eukaryotic-like genes might have a potential ability of different functions in each clade, such as infection of the host coral or suppression of host immune pathways. These Endozoicomonas species may have adopted different host adaptation strategies despite living symbiotically on the same coral. CONCLUSIONS This study suggests that coral-associated Endozoicomonas spp. on the same species of coral have different evolutional strategies and functional potentials in each species and emphasizes the need to analyze the genome of each uncultured strain in future coral-Endozoicomonas relationships studies. Video Abstract.
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Affiliation(s)
- Keigo Ide
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
| | - Yohei Nishikawa
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
| | - Toru Maruyama
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Yuko Tsukada
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Masato Kogawa
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
| | - Hiroki Takeda
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Haruka Ito
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Ryota Wagatsuma
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Rimi Miyaoka
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Yoshikatsu Nakano
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
- Marine Science Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | | | - Michihiro Ito
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Masahito Hosokawa
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Tokyo, Japan
| | - Kei Yura
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Shoichiro Suda
- Faculty of Science, University of the Ryukyus, Okinawa, Japan
| | - Haruko Takeyama
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan.
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan.
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Tokyo, Japan.
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Gao Y, Wang Y, Wang Y, Magaud P, Liu Y, Zeng F, Yang J, Baldas L, Song Y. Nanocatalysis meets microfluidics: A powerful platform for sensitive bioanalysis. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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63
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Munk P, Brinch C, Møller FD, Petersen TN, Hendriksen RS, Seyfarth AM, Kjeldgaard JS, Svendsen CA, van Bunnik B, Berglund F, Larsson DGJ, Koopmans M, Woolhouse M, Aarestrup FM. Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance. Nat Commun 2022; 13:7251. [PMID: 36456547 PMCID: PMC9715550 DOI: 10.1038/s41467-022-34312-7] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/20/2022] [Indexed: 12/03/2022] Open
Abstract
Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, evolution, and transmission of individual antibiotic resistance genes (ARGs) is essential to develop sustainable strategies combatting this threat. Here, we use metagenomic sequencing to analyse ARGs in 757 sewage samples from 243 cities in 101 countries, collected from 2016 to 2019. We find regional patterns in resistomes, and these differ between subsets corresponding to drug classes and are partly driven by taxonomic variation. The genetic environments of 49 common ARGs are highly diverse, with most common ARGs carried by multiple distinct genomic contexts globally and sometimes on plasmids. Analysis of flanking sequence revealed ARG-specific patterns of dispersal limitation and global transmission. Our data furthermore suggest certain geographies are more prone to transmission events and should receive additional attention.
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Affiliation(s)
- Patrick Munk
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark.
| | - Christian Brinch
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Frederik Duus Møller
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Thomas N Petersen
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Rene S Hendriksen
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Anne Mette Seyfarth
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Jette S Kjeldgaard
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Christina Aaby Svendsen
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Bram van Bunnik
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK
| | - Fanny Berglund
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - D G Joakim Larsson
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Marion Koopmans
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Mark Woolhouse
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK
| | - Frank M Aarestrup
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
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64
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Jeyhani M, Navi M, Chan KWY, Kieda J, Tsai SSH. Water-in-water droplet microfluidics: A design manual. BIOMICROFLUIDICS 2022; 16:061503. [PMID: 36406338 PMCID: PMC9674389 DOI: 10.1063/5.0119316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
Droplet microfluidics is utilized in a wide range of applications in biomedicine and biology. Applications include rapid biochemical analysis, materials generation, biochemical assays, and point-of-care medicine. The integration of aqueous two-phase systems (ATPSs) into droplet microfluidic platforms has potential utility in oil-free biological and biomedical applications, namely, reducing cytotoxicity and preserving the native form and function of costly biomolecular reagents. In this review, we present a design manual for the chemist, biologist, and engineer to design experiments in the context of their biological applications using all-in-water droplet microfluidic systems. We describe the studies achievable using these systems and the corresponding fabrication and stabilization methods. With this information, readers may apply the fundamental principles and recent advancements in ATPS droplet microfluidics to their research. Finally, we propose a development roadmap of opportunities to utilize ATPS droplet microfluidics in applications that remain underexplored.
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65
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Recent advances in microfluidic single-cell analysis and its applications in drug development. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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66
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Aoki H, Masahiro Y, Shimizu M, Hongoh Y, Ohkuma M, Yamagata Y. Agarose gel microcapsules enable easy-to-prepare, picolitre-scale, single-cell genomics, yielding high-coverage genome sequences. Sci Rep 2022; 12:17014. [PMID: 36257967 PMCID: PMC9579161 DOI: 10.1038/s41598-022-20923-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 09/21/2022] [Indexed: 12/29/2022] Open
Abstract
A novel type of agarose gel microcapsule (AGM), consisting of an alginate picolitre sol core and an agarose gel shell, was developed to obtain high-quality, single-cell, amplified genomic DNA of bacteria. The AGM is easy to prepare in a stable emulsion with oil of water-equivalent density, which prevents AGM aggregation, with only standard laboratory equipment. Single cells from a pure culture of Escherichia coli, a mock community comprising 15 strains of human gut bacteria, and a termite gut bacterial community were encapsulated within AGMs, and their genomic DNA samples were prepared with massively parallel amplifications in a tube. The genome sequencing did not need second-round amplification and showed an average genome completeness that was much higher than that obtained using a conventional amplification method on the microlitre scale, regardless of the genomic guanine-cytosine content. Our novel method using AGM will allow many researchers to perform single-cell genomics easily and effectively, and can accelerate genomic analysis of yet-uncultured microorganisms.
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Affiliation(s)
- Hiroyoshi Aoki
- grid.509457.aUltrahigh Precision Optics Technology Team, Advanced Photonics Technology Group, RIKEN Center for Advanced Photonics, 3-1, Hirosawa, Wako, Saitama 351-0198 Japan
| | - Yuki Masahiro
- grid.509462.cJapan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, 3-1-1, Koyadai, Tsukuba, Ibaraki 305-0074 Japan
| | - Michiru Shimizu
- grid.509462.cJapan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, 3-1-1, Koyadai, Tsukuba, Ibaraki 305-0074 Japan
| | - Yuichi Hongoh
- grid.509462.cJapan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, 3-1-1, Koyadai, Tsukuba, Ibaraki 305-0074 Japan ,grid.32197.3e0000 0001 2179 2105School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Moriya Ohkuma
- grid.509462.cJapan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, 3-1-1, Koyadai, Tsukuba, Ibaraki 305-0074 Japan
| | - Yutaka Yamagata
- grid.509457.aUltrahigh Precision Optics Technology Team, Advanced Photonics Technology Group, RIKEN Center for Advanced Photonics, 3-1, Hirosawa, Wako, Saitama 351-0198 Japan
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67
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Nishikawa Y, Kogawa M, Hosokawa M, Wagatsuma R, Mineta K, Takahashi K, Ide K, Yura K, Behzad H, Gojobori T, Takeyama H. Validation of the application of gel beads-based single-cell genome sequencing platform to soil and seawater. ISME COMMUNICATIONS 2022; 2:92. [PMID: 37938694 PMCID: PMC9723564 DOI: 10.1038/s43705-022-00179-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 09/07/2022] [Accepted: 09/13/2022] [Indexed: 04/26/2023]
Abstract
Single-cell genomics is applied to environmental samples as a method to solve the problems of current metagenomics. However, in the fluorescence-activated cell sorting-based cell isolation and subsequent whole genome amplification, the sorting efficiency and the sequence quality are greatly affected by the type of target environment, limiting its adaptability. Here, we developed an improved single-cell genomics platform, named SAG-gel, which utilizes gel beads for single-cell isolation, lysis, and whole genome amplification. To validate the versatility of SAG-gel, single-cell genome sequencing was performed with model bacteria and microbial samples collected from eight environmental sites, including soil and seawater. Gel beads enabled multiple lysis treatments. The genome coverage with model bacteria was improved by 9.1-25%. A total of 734 single amplified genomes were collected from the diverse environmental samples, and almost full-length 16S rRNA genes were recovered from 57.8% of them. We also revealed two marine Rhodobacter strains harboring nearly identical 16S rRNA genes but having different genome contents. In addition, searching for viral sequences elucidated the virus-host linkage over the sampling sites, revealing the geographic distribution and diverse host range of viruses.
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Affiliation(s)
- Yohei Nishikawa
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda tsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
- Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Masato Kogawa
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda tsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
| | - Masahito Hosokawa
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda tsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan.
- Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan.
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.
| | - Ryota Wagatsuma
- Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Katsuhiko Mineta
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda tsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
- Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Kai Takahashi
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Keigo Ide
- Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Kei Yura
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda tsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
- Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo, 112-8610, Japan
| | - Hayedeh Behzad
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Takashi Gojobori
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Haruko Takeyama
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda tsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan.
- Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan.
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.
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68
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Postek W, Pacocha N, Garstecki P. Microfluidics for antibiotic susceptibility testing. LAB ON A CHIP 2022; 22:3637-3662. [PMID: 36069631 DOI: 10.1039/d2lc00394e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The rise of antibiotic resistance is a threat to global health. Rapid and comprehensive analysis of infectious strains is critical to reducing the global use of antibiotics, as informed antibiotic use could slow down the emergence of resistant strains worldwide. Multiple platforms for antibiotic susceptibility testing (AST) have been developed with the use of microfluidic solutions. Here we describe microfluidic systems that have been proposed to aid AST. We identify the key contributions in overcoming outstanding challenges associated with the required degree of multiplexing, reduction of detection time, scalability, ease of use, and capacity for commercialization. We introduce the reader to microfluidics in general, and we analyze the challenges and opportunities related to the field of microfluidic AST.
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Affiliation(s)
- Witold Postek
- Institute of Physical Chemistry of the Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland.
- Broad Institute of MIT and Harvard, Merkin Building, 415 Main St, Cambridge, MA 02142, USA.
| | - Natalia Pacocha
- Institute of Physical Chemistry of the Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland.
| | - Piotr Garstecki
- Institute of Physical Chemistry of the Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland.
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69
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Dai J, Huang C, Zhang H, Samuel R, Li Y, Jayaraman A, de Figueiredo P, Han A. Microfluidic Dielectrophoretic Method Enables On-Demand Spatial Arrangement of Bacteria-Encapsulated Agarose Gel Microparticles. Anal Chem 2022; 94:13197-13204. [DOI: 10.1021/acs.analchem.2c02724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jing Dai
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Can Huang
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Han Zhang
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Ryan Samuel
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Yuwen Li
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Arul Jayaraman
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Paul de Figueiredo
- Department of Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, Texas 77807, United States
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas 77843, United States
| | - Arum Han
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas 77843, United States
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
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70
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Liu Y, Chen L, Yu J, Ye L, Hu H, Wang J, Wu B. Advances in Single-Cell Toxicogenomics in Environmental Toxicology. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:11132-11145. [PMID: 35881918 DOI: 10.1021/acs.est.2c01098] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The toxicity evaluation system of environmental pollutants has undergone numerous changes due to the application of new technologies. Single-cell toxicogenomics is rapidly changing our view on environmental toxicology by increasing the resolution of our analysis to the level of a single cell. Applications of this technology in environmental toxicology have begun to emerge and are rapidly expanding the portfolio of existing technologies and applications. Here, we first summarized different methods involved in single-cell isolation and amplification in single-cell sequencing process, compared the advantages and disadvantages of different methods, and analyzed their development trends. Then, we reviewed the main advances of single-cell toxicogenomics in environmental toxicology, emphatically analyzed the application prospects of this technology in identifying the target cells of pollutants in early embryos, clarifying the heterogeneous response of cell subtypes to pollutants, and finding pathogenic bacteria in unknown microbes, and highlighted the unique characteristics of this approach with high resolution, high throughput, and high specificity by examples. We also offered a prediction of the further application of this technology and the revolution it brings in environmental toxicology. Overall, these advances will provide practical solutions for controlling or mitigating exogenous toxicological effects that threaten human and ecosystem health, contribute to improving our understanding of the physiological processes affected by pollutants, and lead to the emergence of new methods of pollution control.
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Affiliation(s)
- Yuxuan Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Ling Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Jing Yu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Haidong Hu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Jinfeng Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Bing Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
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71
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Eitzmann DR, Anderson JL. Evaluating commercial thermoplastic materials in fused deposition modeling 3D printing for their compatibility with DNA storage and analysis by quantitative polymerase chain reaction. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:2682-2688. [PMID: 35766132 DOI: 10.1039/d2ay00772j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Nucleic acids are ubiquitous in biological samples and can be sensitively detected using nucleic acid amplification assays. To achieve highly accurate and reliable results, nucleic acid isolation and purification is often required and can limit the accessibility of these assays. Encapsulation of these workflows onto a single device may be achieved through fabrication methodologies featuring commercial three-dimensional (3D) printers. This study aims to characterize fused deposition modeling (FDM) filaments based on their compatibility with nucleic acid storage using quantitative polymerase chain reaction (qPCR). To study the adsorption of nucleic acids, storage vessels were fabricated using six common thermoplastics including: polylactic acid (PLA), nylon, acrylonitrile butadiene styrene (ABS), co-polyester (CPE), polycarbonate (PC), and polypropylene (PP). DNA adsorption of a short 98 base pair and a longer 830 base pair fragment to the walls of the vessel was shown to vary significantly among the polymer materials as well as the color varieties of the same polymer. PLA storage vessels were found to adsorb the least amount of the 98 base pair DNA after 12 hours of storage in 2.5 M NaCl TE buffer whereas the ABS and PC vessels adsorbed up to 97.2 ± 0.2% and 97.5 ± 0.2%. DNA adsorption could be reduced by decreasing the layer height of the 3D printed object, thereby increasing the functionality of the ABS storage vessel. Nylon was found to desorb qPCR inhibiting components into the stored solution which led to erroneous DNA quantification data from qPCR analysis.
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Affiliation(s)
- Derek R Eitzmann
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA.
| | - Jared L Anderson
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA.
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72
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Zhang H, Huang C, Li Y, Gupte R, Samuel R, Dai J, Guzman A, Sabnis R, de Figueiredo P, Han A. FIDELITY: A quality control system for droplet microfluidics. SCIENCE ADVANCES 2022; 8:eabc9108. [PMID: 35857442 PMCID: PMC9269891 DOI: 10.1126/sciadv.abc9108] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/25/2022] [Indexed: 05/21/2023]
Abstract
Droplet microfluidic systems have been widely deployed to interrogate biological and chemical systems. The major limitations of these systems are the relatively high error rates from critical droplet manipulation functions. To address these limitations, we describe the development of FIDELITY (Flotation and Interdigitated electrode forces on Droplets to Enable Lasting system IntegriTY), a highly sensitive and accurate size-based droplet bandpass filter that leverages the natural buoyancy of aqueous droplets and highly localized dielectrophoretic force generated by interdigitated electrode arrays. Droplet manipulation accuracies greater than 99% were achieved at a throughput of up to 100 droplets/s and separation of droplets that differed in diameter by only 6 μm was demonstrated. Last, the utility of FIDELITY was demonstrated in a droplet size quality control application and also in a droplet-based in vitro transcription/translation workflow. We anticipate FIDELITY to be integrated into a broad range of droplet microfluidic configurations to achieve exceptional operational accuracy.
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Affiliation(s)
- Han Zhang
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Can Huang
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Yuwen Li
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Rohit Gupte
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Ryan Samuel
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Jing Dai
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Adrian Guzman
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Rushant Sabnis
- Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Paul de Figueiredo
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX 77807, USA
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843, USA
| | - Arum Han
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843, USA
- Corresponding author.
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73
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Lloréns-Rico V, Simcock JA, Huys GR, Raes J. Single-cell approaches in human microbiome research. Cell 2022; 185:2725-2738. [DOI: 10.1016/j.cell.2022.06.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/20/2022] [Accepted: 06/20/2022] [Indexed: 10/17/2022]
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74
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Zheng W, Zhao S, Yin Y, Zhang H, Needham DM, Evans ED, Dai CL, Lu PJ, Alm EJ, Weitz DA. High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome. Science 2022; 376:eabm1483. [PMID: 35653470 DOI: 10.1126/science.abm1483] [Citation(s) in RCA: 88] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Characterizing complex microbial communities with single-cell resolution has been a long-standing goal of microbiology. We present Microbe-seq, a high-throughput method that yields the genomes of individual microbes from complex microbial communities. We encapsulate individual microbes in droplets with microfluidics and liberate their DNA, which we then amplify, tag with droplet-specific barcodes, and sequence. We explore the human gut microbiome, sequencing more than 20,000 microbial single-amplified genomes (SAGs) from a single human donor and coassembling genomes of almost 100 bacterial species, including several with multiple subspecies strains. We use these genomes to probe microbial interactions, reconstructing the horizontal gene transfer (HGT) network and observing HGT between 92 species pairs; we also identify a significant in vivo host-phage association between crAssphage and one strain of Bacteroides vulgatus. Microbe-seq contributes high-throughput culture-free capabilities to investigate genomic blueprints of complex microbial communities with single-microbe resolution.
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Affiliation(s)
- Wenshan Zheng
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Shijie Zhao
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yehang Yin
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,College of Computer Science and Technology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Huidan Zhang
- School of Engineering and Applied Sciences (SEAS), Harvard University, Cambridge, MA, USA
| | - David M Needham
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Ocean Ecosystems Biology, GEOMAR, Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Ethan D Evans
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Chengzhen L Dai
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peter J Lu
- School of Engineering and Applied Sciences (SEAS), Harvard University, Cambridge, MA, USA.,Department of Physics, Harvard University, Cambridge, MA, USA
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David A Weitz
- School of Engineering and Applied Sciences (SEAS), Harvard University, Cambridge, MA, USA.,Department of Physics, Harvard University, Cambridge, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
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75
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Sun D, Cao F, Yi X, Zhu H, Qi G, Xu W, Xu S. MicroRNA-21 expression in single living cells revealed by fluorescence and SERS dual-response microfluidic droplet platform. LAB ON A CHIP 2022; 22:2165-2172. [PMID: 35522901 DOI: 10.1039/d2lc00096b] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Analysis of single-cell microRNA is essential to reveal cell heterogeneity at the genetic level. It raises a high demand for single-cell analytical methods because single-cell microRNA sequences are highly similar and small in size and feature low-level expression. Herein, SERS and fluorescence imaging technology were introduced into a microfluidic droplet platform to realize direct in situ, nondestructive, and highly sensitive detection of a small number of microRNA-21 (miR-21) in a single intact living cell. A multifunctional plasmonic nanoprobe was designed by decorating a gold nanoparticle with fluorescent dye (ROX)-labeled probe DNA and capture DNA strands. The dual-signal switching of fluorescence turn-off and SERS turn-on of ROX in response to miR-21 achieves highly sensitive and reliable detection of miR-21 in a single cell. The turn-on of SERS signal with a zero background guarantees the sensitivity of the detection. The fluorescence-SERS simultaneous response strategy was able to mutually corroborate the test results, improving the reliability of determining low-level expression of miR-21. SERS combined with encapsulation of microdroplets provides a feasible way to conduct in situ, nondestructive determination of miR-21 secreted by single cells, avoiding cell lysis and tedious time-consuming steps of miR-21 isolation. As a result, the miR-21 expressed by various types of single cells was investigated by fluorescence imaging and the cellular heterogeneity in miR-21 expression was evaluated accurately and quantitatively by SERS. This research would provide important reference information for understanding the effects of miRNAs on cancer diseases at the single-cell level.
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Affiliation(s)
- Dan Sun
- School of Pharmacy, Nantong University, Nantong, Jiangsu 226001, China.
| | - Fanghao Cao
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xuan Yi
- School of Pharmacy, Nantong University, Nantong, Jiangsu 226001, China.
| | - Hongyan Zhu
- School of Pharmacy, Nantong University, Nantong, Jiangsu 226001, China.
| | - Guohua Qi
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China
| | - Weiqing Xu
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Shuping Xu
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130012, P. R. China
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76
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Abstract
Microfluidics has enabled a new era of cellular and molecular assays due to the small length scales, parallelization, and the modularity of various analysis and actuation functions. Droplet microfluidics, in particular, has been instrumental in providing new tools for biology with its ability to quickly and reproducibly generate drops that act as individual reactors. A notable beneficiary of this technology has been single-cell RNA sequencing, which has revealed new heterogeneities and interactions for the fundamental unit of life. However, viruses far surpass the diversity of cellular life, affect the dynamics of all ecosystems, and are a chronic source of global health crises. Despite their impact on the world, high-throughput and high-resolution viral profiling has been difficult, with conventional methods being limited to population-level averaging, large sample volumes, and few cultivable hosts. Consequently, most viruses have not been identified and studied. Droplet microfluidics holds the potential to address many of these limitations and offers new levels of sensitivity and throughput for virology. This Feature highlights recent efforts that have applied droplet microfluidics to the detection and study of viruses, including for diagnostics, virus-host interactions, and cell-independent virus assays. In combination with traditional virology methods, droplet microfluidics should prove a potent tool toward achieving a better understanding of the most abundant biological species on Earth.
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Affiliation(s)
- Wenyang Jing
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Hee-Sun Han
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
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77
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Caligola S, De Sanctis F, Canè S, Ugel S. Breaking the Immune Complexity of the Tumor Microenvironment Using Single-Cell Technologies. Front Genet 2022; 13:867880. [PMID: 35651929 PMCID: PMC9149246 DOI: 10.3389/fgene.2022.867880] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/27/2022] [Indexed: 12/31/2022] Open
Abstract
Tumors are not a simple aggregate of transformed cells but rather a complicated ecosystem containing various components, including infiltrating immune cells, tumor-related stromal cells, endothelial cells, soluble factors, and extracellular matrix proteins. Profiling the immune contexture of this intricate framework is now mandatory to develop more effective cancer therapies and precise immunotherapeutic approaches by identifying exact targets or predictive biomarkers, respectively. Conventional technologies are limited in reaching this goal because they lack high resolution. Recent developments in single-cell technologies, such as single-cell RNA transcriptomics, mass cytometry, and multiparameter immunofluorescence, have revolutionized the cancer immunology field, capturing the heterogeneity of tumor-infiltrating immune cells and the dynamic complexity of tenets that regulate cell networks in the tumor microenvironment. In this review, we describe some of the current single-cell technologies and computational techniques applied for immune-profiling the cancer landscape and discuss future directions of how integrating multi-omics data can guide a new "precision oncology" advancement.
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Affiliation(s)
| | | | | | - Stefano Ugel
- Immunology Section, Department of Medicine, University of Verona, Verona, Italy
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78
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79
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Anggraini D, Ota N, Shen Y, Tang T, Tanaka Y, Hosokawa Y, Li M, Yalikun Y. Recent advances in microfluidic devices for single-cell cultivation: methods and applications. LAB ON A CHIP 2022; 22:1438-1468. [PMID: 35274649 DOI: 10.1039/d1lc01030a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Single-cell analysis is essential to improve our understanding of cell functionality from cellular and subcellular aspects for diagnosis and therapy. Single-cell cultivation is one of the most important processes in single-cell analysis, which allows the monitoring of actual information of individual cells and provides sufficient single-cell clones and cell-derived products for further analysis. The microfluidic device is a fast-rising system that offers efficient, effective, and sensitive single-cell cultivation and real-time single-cell analysis conducted either on-chip or off-chip. Here, we introduce the importance of single-cell cultivation from the aspects of cellular and subcellular studies. We highlight the materials and structures utilized in microfluidic devices for single-cell cultivation. We further discuss biological applications utilizing single-cell cultivation-based microfluidics, such as cellular phenotyping, cell-cell interactions, and omics profiling. Finally, present limitations and future prospects of microfluidics for single-cell cultivation are also discussed.
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Affiliation(s)
- Dian Anggraini
- Division of Materials Science, Nara Institute of Science and Technology, Nara 630-0192, Japan.
| | - Nobutoshi Ota
- Center for Biosystems Dynamics Research (BDR), RIKEN, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yigang Shen
- Center for Biosystems Dynamics Research (BDR), RIKEN, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Tao Tang
- Division of Materials Science, Nara Institute of Science and Technology, Nara 630-0192, Japan.
| | - Yo Tanaka
- Center for Biosystems Dynamics Research (BDR), RIKEN, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoichiroh Hosokawa
- Division of Materials Science, Nara Institute of Science and Technology, Nara 630-0192, Japan.
| | - Ming Li
- School of Engineering, Macquarie University, Sydney 2122, Australia.
| | - Yaxiaer Yalikun
- Division of Materials Science, Nara Institute of Science and Technology, Nara 630-0192, Japan.
- Center for Biosystems Dynamics Research (BDR), RIKEN, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
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80
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81
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Droplet-microfluidics-assisted sequencing of HIV proviruses and their integration sites in cells from people on antiretroviral therapy. Nat Biomed Eng 2022; 6:1004-1012. [PMID: 35347274 PMCID: PMC9398922 DOI: 10.1038/s41551-022-00864-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 01/28/2022] [Indexed: 01/03/2023]
Abstract
The human immunodeficiency virus (HIV) integrates its genome in that of infected cells and may enter an inactive state of reversible latency that cannot be targeted using antiretroviral therapy. The resulting HIV DNA is termed a provirus. Sequencing individual proviruses with the adjacent human cellular junctions may elucidate mechanisms of infected cell persistence in humans. Here, we introduce a high throughput microfluidic assay where droplet-based whole genome amplification of the HIV DNA in its native context is followed by a polymerase chain reaction to tag droplets containing proviruses for sequencing, resulting in the assembly of full-length viral genomes connected to their contiguous HIV-human DNA junctions, regardless of the 150 million-fold higher amount of human DNA present in the background. We analyzed infected cells from patients with HIV receiving suppressive antiretroviral therapy, resulting in the detection and sequencing of paired proviral genomes and integration sites, 90% of which weren’t recovered by commonly used nested PCR methods. The sequencing of individual proviral genomes with their integration sites could improve the genetic analysis of persistent HIV-infected cell reservoirs.
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82
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Liu YF, Yang L, Liu ZL, Chen J, Fang B, Zhou L, Liu JF, Yang SZ, Gu JD, Mu BZ. Discovery of the non-cosmopolitan lineages in Candidatus Thermoprofundales. Environ Microbiol 2022; 24:3063-3080. [PMID: 35254697 DOI: 10.1111/1462-2920.15965] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 11/27/2022]
Abstract
The recently proposed order Candidatus Thermoprofundales, currently containing only one family-level lineage Marine Benthic Group-D (MBG-D), is distributed in global subsurface ecosystems and ecologically important, but its diversity, evolution and metabolism remain largely unknown. Here we described two novel family-level specialized lineages in Ca. Thermoprofundales, JdFR-43 and HyVt, which are restricted to specific biotopes (primarily in marine hydrothermal vents and occasionally in oil reservoirs and hot springs) in contrast to the cosmopolitan lineage MBG-D. The comparative genomics revealed that the specialized lineages have streamlined genomes, higher GC contents, enriched genes associated with nucleotide biosynthesis, ribosome biogenesis and DNA repair and additional thermostable aminopeptidases, enabling them to adapt to high-temperature habitats such as marine hydrothermal vents, deep subsurface oil reservoirs and hot springs. On the contrary, the unique metabolic traits of the cosmopolitan MBG-D, motility, glycolysis, butanoate metabolism, secondary metabolites production and additional genes for specific peptides and carbohydrates degradation potentially enhance its response to environmental change. Substrate preference is found for most MAGs across all lineages with the ability to utilize both polysaccharides (chitin and starch) and proteinaceous substances, whereas JdFR-43 members from oil reservoirs can only utilize proteins. These results expand the diversity of Ca. Thermoprofundales significantly and further improve our understandings of the adaptations of Ca. Thermoprofundales to various environments. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yi-Fan Liu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China.,Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China.,Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, P.R. China
| | - Liu Yang
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China.,Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China
| | - Zhong-Lin Liu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China.,Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China
| | - Jing Chen
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China.,Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China
| | - Bo Fang
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China.,Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China
| | - Lei Zhou
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China.,Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China
| | - Jin-Feng Liu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China.,Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China
| | - Shi-Zhong Yang
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China.,Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China
| | - Ji-Dong Gu
- Environmental Science and Engineering Group, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong, 515063, P.R. China
| | - Bo-Zhong Mu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China.,Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China
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83
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Melnekoff DT, Laganà A. Single-Cell Sequencing Technologies in Precision Oncology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1361:269-282. [PMID: 35230694 DOI: 10.1007/978-3-030-91836-1_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Single-cell sequencing technologies are revolutionizing cancer research and are poised to become the standard for translational cancer studies. Rapidly decreasing costs and increasing throughput and resolution are paving the way for the adoption of single-cell technologies in clinical settings for personalized medicine applications. In this chapter, we review the state of the art of single-cell DNA and RNA sequencing technologies, the computational tools to analyze the data, and their potential application to precision oncology. We also discuss the advantages of single-cell over bulk sequencing for the dissection of intra-tumor heterogeneity and the characterization of subclonal cell populations, the implementation of targeted drug repurposing approaches, and describe advanced methodologies for multi-omics data integration and to assess cell signaling at single-cell resolution.
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Affiliation(s)
- David T Melnekoff
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alessandro Laganà
- Department of Genetics and Genomic Sciences, Department of Oncological Sciences, Mount Sinai Icahn School of Medicine, New York, NY, USA.
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84
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Wang X, Liu Y, Liu H, Pan W, Ren J, Zheng X, Tan Y, Chen Z, Deng Y, He N, Chen H, Li S. Recent advances and application of whole genome amplification in molecular diagnosis and medicine. MedComm (Beijing) 2022; 3:e116. [PMID: 35281794 PMCID: PMC8906466 DOI: 10.1002/mco2.116] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 11/30/2022] Open
Abstract
Whole genome amplification (WGA) is a technology for non-selective amplification of the whole genome sequence, first appearing in 1992. Its primary purpose is to amplify and reflect the whole genome of trace tissues and single cells without sequence bias and to provide sufficient DNA template for subsequent multigene and multilocus analysis, along with comprehensive genome research. WGA provides a method to obtain a large amount of genetic information from a small amount of DNA and provides a valuable tool for preserving limited samples in molecular biology. WGA technology is especially suitable for forensic identification and genetic disease research, along with new technologies such as next-generation sequencing (NGS). In addition, WGA is also widely used in single-cell sequencing. Due to the small amount of DNA in a single cell, it is often unable to meet the amount of samples needed for sequencing, so WGA is generally used to achieve the amplification of trace samples. This paper reviews WGA methods based on different principles, summarizes both amplification principle and amplification quality, and discusses the application prospects and challenges of WGA technology in molecular diagnosis and medicine.
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Affiliation(s)
- Xiaoyu Wang
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Yapeng Liu
- School of Early‐Childhood Education, Nanjing Xiaozhuang UniversityNanjingChina
| | - Hongna Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Wenjing Pan
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Jie Ren
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Xiangming Zheng
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Yimin Tan
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Nongyue He
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
- State Key Laboratory of BioelectronicsSoutheast UniversityNanjingChina
| | - Hui Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
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85
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Postek W, Garstecki P. Droplet Microfluidics for High-Throughput Analysis of Antibiotic Susceptibility in Bacterial Cells and Populations. Acc Chem Res 2022; 55:605-615. [PMID: 35119826 PMCID: PMC8892833 DOI: 10.1021/acs.accounts.1c00729] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Antibiotic-resistant bacteria are an increasing concern both in everyday life and specialized environments such as healthcare. As the rate of antibiotic-resistant infections rises, so do complications to health and the risk of disability and death. Urgent action is required regarding the discovery of new antibiotics and rapid diagnosis of the resistance profile of an infectious pathogen as well as a better understanding of population and single-cell distribution of the resistance level. High-throughput screening is the major affordance of droplet microfluidics. Droplet screens can be exploited both to look for combinations of drugs that could stop an infection of multidrug-resistant bacteria and to search for the source of resistance via directed-evolution experiments or the analysis of various responses to a drug by genetically identical bacteria. In droplet techniques that have been used in this way for over a decade, aqueous droplets containing antibiotics and bacteria are manipulated both within and outside of the microfluidic devices. The diagnostics problem was approached by producing a series of microfluidic systems with integrated dilution modules for automated preparation of antibiotic concentration gradients, achieving the speed that allowed for high-throughput combinatorial assays. We developed a method for automated emulsification of a series of samples that facilitated measuring the resistance levels of thousands of individual cells encapsulated in droplets and quantifying the inoculum effect, the dependence of resistance level on bacterial cell count. Screening of single cells encapsulated in droplets with varying antibiotic contents has revealed a distribution of resistance levels within populations of clonally identical cells. To be able to screen bacteria from clinical samples, a study of fluorescent dyes in droplets determined that a derivative of a popular viability marker is more suitable for droplet assays. We have developed a detection system that analyzes the growth or death state of bacteria with antibiotics for thousands of droplets per second by measuring the scattering of light hitting the droplets without labeling the cells or droplets. The droplet-based microchemostats enabled long-term evolution of resistance experiments, which will be integrated with high-throughput single-cell assays to better understand the mechanism of resistance acquisition and loss. These techniques underlie automated combinatorial screens of antibiotic resistance in single cells from clinical samples. We hope that this Account will inspire new droplet-based research on the antibiotic susceptibility of bacteria.
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Affiliation(s)
- Witold Postek
- Institute of Physical Chemistry, Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland
| | - Piotr Garstecki
- Institute of Physical Chemistry, Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland
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86
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Rodriguez-Romaguera J, Namboodiri VMK, Basiri ML, Stamatakis AM, Stuber GD. Developments from Bulk Optogenetics to Single-Cell Strategies to Dissect the Neural Circuits that Underlie Aberrant Motivational States. Cold Spring Harb Perspect Med 2022; 12:a039792. [PMID: 32513671 PMCID: PMC7799172 DOI: 10.1101/cshperspect.a039792] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Motivational states are regulated by complex networks across brain regions that are composed of genetically and functionally distinct neuronal populations. Disruption within these neural circuits leads to aberrant motivational states and are thought to be the root cause of psychiatric disorders related to reward processing and addiction. Critical technological advances in the field have revolutionized the study of neural systems by allowing the use of optical strategies to precisely control and visualize neural activity within genetically identified neural populations in the brain. This review will provide a brief introduction into the history of how technological advances in single-cell strategies have been applied to elucidate the neural circuits that underlie aberrant motivational states that often lead to dysfunction in reward processing and addiction.
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Affiliation(s)
- Jose Rodriguez-Romaguera
- Department of Psychiatry, University of North Carolina, Chapel Hill, North Carolina 27514, USA
- Neuroscience Center, University of North Carolina, Chapel Hill, North Carolina 27514, USA
| | - Vijay M K Namboodiri
- Center for the Neurobiology of Addiction, Pain, and Emotion, Department of Anesthesiology and Pain Medicine & Department of Pharmacology, University of Washington, Seattle, Washington 98195-6410, USA
| | - Marcus L Basiri
- Neuroscience Curriculum, University of North Carolina, Chapel Hill, North Carolina 27514, USA
| | - Alice M Stamatakis
- Neuroscience Curriculum, University of North Carolina, Chapel Hill, North Carolina 27514, USA
| | - Garret D Stuber
- Center for the Neurobiology of Addiction, Pain, and Emotion, Department of Anesthesiology and Pain Medicine & Department of Pharmacology, University of Washington, Seattle, Washington 98195-6410, USA
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87
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Battat S, Weitz DA, Whitesides GM. An outlook on microfluidics: the promise and the challenge. LAB ON A CHIP 2022; 22:530-536. [PMID: 35048918 DOI: 10.1039/d1lc00731a] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
This perspective considers ways in which the field of microfluidics can increase its impact by improving existing technologies and enabling new functionalities. We highlight applications where microfluidics has made or can make important contributions, including diagnostics, food safety, and the production of materials. The success of microfluidics assumes several forms, including fundamental innovations in fluid mechanics that enable the precise manipulation of fluids at small scales and the development of portable microfluidic chips for commercial purposes. We identify outstanding technical challenges whose resolution could increase the accessibility of microfluidics to users with both scientific and non-technical backgrounds. They include the simplification of procedures for sample preparation, the identification of materials for the production of microfluidic devices in both laboratory and commercial settings, and the replacement of auxiliary equipment with automated components for the operation of microfluidic devices.
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Affiliation(s)
- Sarah Battat
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA.
| | - David A Weitz
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA.
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
| | - George M Whitesides
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
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88
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Mathekga BSP, Nxumalo Z, Thimiri Govinda Raj DB. Micro and nanofluidics for high throughput drug screening. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 187:93-120. [PMID: 35094783 DOI: 10.1016/bs.pmbts.2021.07.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In this book chapter, we elaborate on the state-of-the-art technology developments in high throughput screening, microfluidics and nanofluidics. This book chapter further elaborated on the application of microfluidics and nanofluidics for high throughput drug screening with respect to communicable diseases and non-communicable diseases such as cancer. As a future perspective, there is tremendous potential for microfluidics and nanofluidics to be applied in high throughput drug screening which could be applied for various biotechnology applications such as in cancer precision medicine, point-of-care diagnostics and imaging. With the integration of Fourth industrial revolution (4IR) technologies with micro and nanofluidics technologies, it envisioned that such integration along with digital health would enable next generation technology development in medical field.
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Affiliation(s)
| | - Zandile Nxumalo
- Synthetic Nanobiotechnology and Biomachines Group, Synthetic Biology and Precision Medicine Centre, CSIR, Pretoria, South Africa
| | - Deepak B Thimiri Govinda Raj
- Synthetic Nanobiotechnology and Biomachines Group, Synthetic Biology and Precision Medicine Centre, CSIR, Pretoria, South Africa.
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89
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Skoufos G, Almodaresi F, Zakeri M, Paulson JN, Patro R, Hatzigeorgiou AG, Vlachos IS. AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite. Genome Biol 2022; 23:39. [PMID: 35101114 PMCID: PMC8802518 DOI: 10.1186/s13059-022-02610-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 01/03/2022] [Indexed: 12/03/2022] Open
Abstract
We introduce AGAMEMNON ( https://github.com/ivlachos/agamemnon ) for the acquisition of microbial abundances from shotgun metagenomics and metatranscriptomic samples, single-microbe sequencing experiments, or sequenced host samples. AGAMEMNON delivers accurate abundances at genus, species, and strain resolution. It incorporates a time and space-efficient indexing scheme for fast pattern matching, enabling indexing and analysis of vast datasets with widely available computational resources. Host-specific modules provide exceptional accuracy for microbial abundance quantification from tissue RNA/DNA sequencing, enabling the expansion of experiments lacking metagenomic/metatranscriptomic analyses. AGAMEMNON provides an R-Shiny application, permitting performance of investigations and visualizations from a graphics interface.
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Affiliation(s)
- Giorgos Skoufos
- Department of Electrical & Computer Engineering, University of Thessaly, 38221, Volos, Greece.
- Hellenic Pasteur Institute, 11521, Athens, Greece.
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, Univ. of Thessaly, 351 31, Lamia, Greece.
| | - Fatemeh Almodaresi
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Mohsen Zakeri
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Joseph N Paulson
- Department of Data Sciences, Genentech Inc., South San Francisco, CA, USA
| | - Rob Patro
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Artemis G Hatzigeorgiou
- Department of Electrical & Computer Engineering, University of Thessaly, 38221, Volos, Greece.
- Hellenic Pasteur Institute, 11521, Athens, Greece.
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, Univ. of Thessaly, 351 31, Lamia, Greece.
| | - Ioannis S Vlachos
- Cancer Research Institute | HMS Initiative for RNA Medicine | Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02115, USA.
- Spatial Technologies Unit, Beth Israel Deaconess Medical Center, MA, Boston, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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90
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Hatori MN, Modavi C, Xu P, Weisgerber D, Abate AR. Dual-layered hydrogels allow complete genome recovery with nucleic acid cytometry. Biotechnol J 2022; 17:e2100483. [PMID: 35088927 PMCID: PMC9208836 DOI: 10.1002/biot.202100483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 12/09/2021] [Accepted: 12/09/2021] [Indexed: 11/09/2022]
Abstract
Targeting specific cells for sequencing is important for applications in cancer, microbiology, and infectious disease. Nucleic acid cytometry is a powerful approach for accomplishing this because it allows specific cells to be isolated based on sequence biomarkers that are otherwise impossible to detect. However, existing methods require specialized microfluidic devices, limiting adoption. Here, we describe a modified workflow that uses particle-templated emulsification and flow cytometry to conduct the essential steps of cell detection and sorting normally accomplished by microfluidics. Our microfluidic-free workflow allows facile isolation and sequencing of cells, viruses, and nucleic acids and thus provides a powerful enrichment approach for targeted sequencing applications. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Makiko N Hatori
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, 94158, USA
| | - Cyrus Modavi
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, 94158, USA
| | - Peng Xu
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, 94158, USA
| | - Daniel Weisgerber
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, 94158, USA
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, 94158, USA.,Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
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91
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Pryszlak A, Wenzel T, Seitz KW, Hildebrand F, Kartal E, Cosenza MR, Benes V, Bork P, Merten CA. Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics. CELL REPORTS METHODS 2022; 2:None. [PMID: 35118437 PMCID: PMC8787643 DOI: 10.1016/j.crmeth.2021.100137] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 10/05/2021] [Accepted: 12/07/2021] [Indexed: 11/25/2022]
Abstract
We report a droplet microfluidic method to target and sort individual cells directly from complex microbiome samples and to prepare these cells for bulk whole-genome sequencing without cultivation. We characterize this approach by recovering bacteria spiked into human stool samples at a ratio as low as 1:250 and by successfully enriching endogenous Bacteroides vulgatus to the level required for de novo assembly of high-quality genomes. Although microbiome strains are increasingly demanded for biomedical applications, a vast majority of species and strains are uncultivated and without reference genomes. We address this shortcoming by encapsulating complex microbiome samples directly into microfluidic droplets and amplifying a target-specific genomic fragment using a custom molecular TaqMan probe. We separate those positive droplets by droplet sorting, selectively enriching single target strain cells. Finally, we present a protocol to purify the genomic DNA while specifically removing amplicons and cell debris for high-quality genome sequencing.
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Affiliation(s)
- Anna Pryszlak
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Tobias Wenzel
- European Molecular Biology Laboratory, Heidelberg, Germany
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Falk Hildebrand
- European Molecular Biology Laboratory, Heidelberg, Germany
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
- Digital Biology, Earlham Institute, Norwich, UK
| | - Ece Kartal
- European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Vladimir Benes
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Peer Bork
- European Molecular Biology Laboratory, Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, Berlin, Germany
- University of Würzburg, Würzburg, Germany
| | - Christoph A. Merten
- European Molecular Biology Laboratory, Heidelberg, Germany
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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92
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Luo X, Chen JY, Ataei M, Lee A. Microfluidic Compartmentalization Platforms for Single Cell Analysis. BIOSENSORS 2022; 12:58. [PMID: 35200319 PMCID: PMC8869497 DOI: 10.3390/bios12020058] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 12/25/2022]
Abstract
Many cellular analytical technologies measure only the average response from a cell population with an assumption that a clonal population is homogenous. The ensemble measurement often masks the difference among individual cells that can lead to misinterpretation. The advent of microfluidic technology has revolutionized single-cell analysis through precise manipulation of liquid and compartmentalizing single cells in small volumes (pico- to nano-liter). Due to its advantages from miniaturization, microfluidic systems offer an array of capabilities to study genomics, transcriptomics, and proteomics of a large number of individual cells. In this regard, microfluidic systems have emerged as a powerful technology to uncover cellular heterogeneity and expand the depth and breadth of single-cell analysis. This review will focus on recent developments of three microfluidic compartmentalization platforms (microvalve, microwell, and microdroplets) that target single-cell analysis spanning from proteomics to genomics. We also compare and contrast these three microfluidic platforms and discuss their respective advantages and disadvantages in single-cell analysis.
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Affiliation(s)
- Xuhao Luo
- Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA; (X.L.); (J.-Y.C.)
| | - Jui-Yi Chen
- Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA; (X.L.); (J.-Y.C.)
| | - Marzieh Ataei
- Department of Mechanical and Aerospace Engineering, University of California, Irvine, CA 92697, USA;
| | - Abraham Lee
- Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA; (X.L.); (J.-Y.C.)
- Department of Mechanical and Aerospace Engineering, University of California, Irvine, CA 92697, USA;
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93
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dCITI-Seq: droplet combinational indexed transposon insertion sequencing. Anal Bioanal Chem 2022; 414:2661-2670. [DOI: 10.1007/s00216-022-03902-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/08/2022] [Accepted: 01/13/2022] [Indexed: 11/25/2022]
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94
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Zhang Z, Li X, Liu H, Zamyadi A, Guo W, Wen H, Gao L, Nghiem LD, Wang Q. Advancements in detection and removal of antibiotic resistance genes in sludge digestion: A state-of-art review. BIORESOURCE TECHNOLOGY 2022; 344:126197. [PMID: 34710608 DOI: 10.1016/j.biortech.2021.126197] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 10/16/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
Sludge from wastewater treatment plants can act as a repository and crucial environmental provider of antibiotic resistance genes (ARGs). Over the past few years, people's knowledge regarding the occurrence and removal of ARGs in sludge has broadened remarkably with advancements in molecular biological techniques. Anaerobic and aerobic digestion were found to effectively achieve sludge reduction and ARGs removal. This review summarized advanced detection and removal techniques of ARGs, in the last decade, in the sludge digestion field. The fate of ARGs due to different sludge digestion strategies (i.e., anaerobic and aerobic digestion under mesophilic or thermophilic conditions, and in combination with relevant pretreatment technologies (e.g., thermal hydrolysis pretreatment, microwave pretreatment and alkaline pretreatment) and additives (e.g., ferric chloride and zero-valent iron) were systematically summarized and compared in this review. To date, this is the first review that provides a comprehensive assessment of the state-of-the-art technologies and future recommendations.
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Affiliation(s)
- Zehao Zhang
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Xuan Li
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia.
| | - Huan Liu
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Arash Zamyadi
- Water Research Australia Limited, Melbourne & Adelaide SA 5001, Australia
| | - Wenshan Guo
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Haiting Wen
- School of Environment and Nature Resources, Renmin University of China, Beijing 100872, PR China
| | - Li Gao
- South East Water, 101 Wells Street, Frankston, VIC 3199, Australia
| | - Long D Nghiem
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Qilin Wang
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
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95
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Liu D, Sun M, Zhang J, Hu R, Fu W, Xuanyuan T, Liu W. Single-cell droplet microfluidics for biomedical applications. Analyst 2022; 147:2294-2316. [DOI: 10.1039/d1an02321g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review focuses on the recent advances in the fundamentals of single-cell droplet microfluidics and its applications in biomedicine, providing insights into design and establishment of single-cell microsystems and their further performance.
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Affiliation(s)
- Dan Liu
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Meilin Sun
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Jinwei Zhang
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Rui Hu
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Wenzhu Fu
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Tingting Xuanyuan
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Wenming Liu
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
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96
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Siedlik MJ, Issadore D. Pico-washing: simultaneous liquid addition and removal for continuous-flow washing of microdroplets. MICROSYSTEMS & NANOENGINEERING 2022; 8:46. [PMID: 35498338 PMCID: PMC9050730 DOI: 10.1038/s41378-022-00381-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/02/2022] [Accepted: 03/07/2022] [Indexed: 05/19/2023]
Abstract
Droplet microfluidics is based on a toolbox of several established unit operations, including droplet generation, incubation, mixing, pico-injection, and sorting. In the last two decades, the development of droplet microfluidic systems, which incorporate these multiple unit operations into a workflow, has demonstrated unique capabilities in fields ranging from single-cell transcriptomic analyses to materials optimization. One unit operation that is sorely underdeveloped in droplet microfluidics is washing, exchange of the fluid in a droplet with a different fluid. Here, we demonstrate what we name the "pico-washer," a unit operation capable of simultaneously adding fluid to and removing fluid from droplets in flow while requiring only a small footprint on a microfluidic chip. We describe the fabrication strategy, device architecture, and process parameters required for stable operation of this technology, which is capable of operating with kHz droplet throughput. Furthermore, we provide an image processing workflow to characterize the washing process with microsecond and micrometer resolution. Finally, we demonstrate the potential for integrated droplet workflows by arranging two of these unit operations in series with a droplet generator, describe a design rule for stable operation of the pico-washer when integrated into a system, and validate this design rule experimentally. We anticipate that this technology will contribute to continued development of the droplet microfluidics toolbox and the realization of novel droplet-based, multistep biological and chemical assays.
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Affiliation(s)
- Michael J. Siedlik
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104 United States
| | - David Issadore
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104 United States
- Department of Electrical and Systems Engineering, University of Pennsylvania, Philadelphia, PA 19104 United States
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97
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Tran TM, Kim SC, Modavi C, Abate AR. Robotic automation of droplet microfluidics. BIOMICROFLUIDICS 2022; 16:014102. [PMID: 35145570 PMCID: PMC8816516 DOI: 10.1063/5.0064265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/23/2021] [Indexed: 06/14/2023]
Abstract
Droplet microfluidics enables powerful analytic capabilities but often requires workflows involving macro- and microfluidic processing steps that are cumbersome to perform manually. Here, we demonstrate the automation of droplet microfluidics with commercial fluid-handling robotics. The workflows incorporate common microfluidic devices including droplet generators, mergers, and sorters and utilize the robot's native capabilities for thermal control, incubation, and plate scanning. The ability to automate microfluidic devices using commercial fluid handling will speed up the integration of these methods into biological workflows.
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Affiliation(s)
- Tuan M. Tran
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, USA
| | - Samuel C. Kim
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, USA
| | - Cyrus Modavi
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, USA
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98
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Kim SC, Haliburton JR, Gartner ZJ, Abate AR. Single-Cell Protein Profiling by Microdroplet Barcoding and Next-Generation Sequencing. Methods Mol Biol 2022; 2386:101-111. [PMID: 34766267 PMCID: PMC9122841 DOI: 10.1007/978-1-0716-1771-7_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
DNA barcoding of individual cells combined with next-generation sequencing enables high-throughput parallel analysis of biomolecules at the single-cell level. Encoding protein identity with DNA barcoding of specific antibody binders achieves sequencing-based protein quantitation by converting protein signals into DNA signals. Here, we describe how to prepare DNA-barcoded antibodies and connect protein identities to cellular identities using droplet microfluidics. This approach allows for multiplex single-cell protein analysis compatible with single-cell transcriptomic and mutational profiling methods.
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Affiliation(s)
- Samuel C. Kim
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA,Current address: Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, USA
| | - John R. Haliburton
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Zev J. Gartner
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Adam R. Abate
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
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99
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Dong Z, Wang Y, Yin D, Hang X, Pu L, Zhang J, Geng J, Chang L. Advanced techniques for gene heterogeneity research: Single‐cell sequencing and on‐chip gene analysis systems. VIEW 2022. [DOI: 10.1002/viw.20210011] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Zaizai Dong
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering Beihang University Beijing China
| | - Yu Wang
- Department of Laboratory Medicine State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University/Collaborative Innovation Center Chengdu China
| | - Dedong Yin
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering Beihang University Beijing China
| | - Xinxin Hang
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering Beihang University Beijing China
| | - Lei Pu
- Department of Laboratory Medicine State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University/Collaborative Innovation Center Chengdu China
| | - Jianfu Zhang
- Department of Laboratory Medicine State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University/Collaborative Innovation Center Chengdu China
| | - Jia Geng
- Department of Laboratory Medicine State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University/Collaborative Innovation Center Chengdu China
| | - Lingqian Chang
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering Beihang University Beijing China
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100
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Nazari H, Heirani-Tabasi A, Ghorbani S, Eyni H, Razavi Bazaz S, Khayati M, Gheidari F, Moradpour K, Kehtari M, Ahmadi Tafti SM, Ahmadi Tafti SH, Ebrahimi Warkiani M. Microfluidic-Based Droplets for Advanced Regenerative Medicine: Current Challenges and Future Trends. BIOSENSORS 2021; 12:20. [PMID: 35049648 PMCID: PMC8773546 DOI: 10.3390/bios12010020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 12/29/2021] [Accepted: 12/29/2021] [Indexed: 11/30/2022]
Abstract
Microfluidics is a promising approach for the facile and large-scale fabrication of monodispersed droplets for various applications in biomedicine. This technology has demonstrated great potential to address the limitations of regenerative medicine. Microfluidics provides safe, accurate, reliable, and cost-effective methods for encapsulating different stem cells, gametes, biomaterials, biomolecules, reagents, genes, and nanoparticles inside picoliter-sized droplets or droplet-derived microgels for different applications. Moreover, microenvironments made using such droplets can mimic niches of stem cells for cell therapy purposes, simulate native extracellular matrix (ECM) for tissue engineering applications, and remove challenges in cell encapsulation and three-dimensional (3D) culture methods. The fabrication of droplets using microfluidics also provides controllable microenvironments for manipulating gametes, fertilization, and embryo cultures for reproductive medicine. This review focuses on the relevant studies, and the latest progress in applying droplets in stem cell therapy, tissue engineering, reproductive biology, and gene therapy are separately evaluated. In the end, we discuss the challenges ahead in the field of microfluidics-based droplets for advanced regenerative medicine.
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Affiliation(s)
- Hojjatollah Nazari
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (H.N.); (S.R.B.)
| | - Asieh Heirani-Tabasi
- Research Center for Advanced Technologies in Cardiovascular Medicine, Tehran Heart Center Hospital, Tehran University of Medical Sciences, Tehran 14535, Iran; (A.H.-T.); (S.H.A.T.)
- Department of Cell Therapy and Hematology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran 14535, Iran
| | - Sadegh Ghorbani
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus, Denmark;
| | - Hossein Eyni
- Cellular and Molecular Research Center, School of Medicine, Iran University of Medical Sciences, Tehran 14535, Iran;
- Department of Anatomical Sciences, School of Medicine, Iran University of Medical Sciences, Tehran 14535, Iran
| | - Sajad Razavi Bazaz
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (H.N.); (S.R.B.)
| | - Maryam Khayati
- Department of Pharmaceutical Nanotechnology, School of Pharmacy, Zanjan University of Medical Sciences, Zanjan 45371, Iran;
| | - Fatemeh Gheidari
- Department of Biotechnology, University of Tehran, Tehran 14535, Iran;
| | - Keyvan Moradpour
- Department of Chemical Engineering, Sharif University of Technology, Tehran 14535, Iran;
| | - Mousa Kehtari
- Department of Biology, Faculty of Science, University of Tehran, Tehran 14535, Iran;
| | - Seyed Mohsen Ahmadi Tafti
- Colorectal Surgery Research Center, Imam Hospital Complex, Tehran University of Medical Sciences, Tehran 14535, Iran;
| | - Seyed Hossein Ahmadi Tafti
- Research Center for Advanced Technologies in Cardiovascular Medicine, Tehran Heart Center Hospital, Tehran University of Medical Sciences, Tehran 14535, Iran; (A.H.-T.); (S.H.A.T.)
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (H.N.); (S.R.B.)
- Institute of Molecular Medicine, Sechenov University, 119991 Moscow, Russia
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