1
|
Benedict B, Kristensen SM, Duxin JP. What are the DNA lesions underlying formaldehyde toxicity? DNA Repair (Amst) 2024; 138:103667. [PMID: 38554505 DOI: 10.1016/j.dnarep.2024.103667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 04/01/2024]
Abstract
Formaldehyde is a highly reactive organic compound. Humans can be exposed to exogenous sources of formaldehyde, but formaldehyde is also produced endogenously as a byproduct of cellular metabolism. Because formaldehyde can react with DNA, it is considered a major endogenous source of DNA damage. However, the nature of the lesions underlying formaldehyde toxicity in cells remains vastly unknown. Here, we review the current knowledge of the different types of nucleic acid lesions that are induced by formaldehyde and describe the repair pathways known to counteract formaldehyde toxicity. Taking this knowledge together, we discuss and speculate on the predominant lesions generated by formaldehyde, which underly its natural toxicity.
Collapse
Affiliation(s)
- Bente Benedict
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Stella Munkholm Kristensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Julien P Duxin
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark.
| |
Collapse
|
2
|
Liu S, Zheng P, Wang CY, Jia BB, Zemke NR, Ren B, Zhuang X. Cell-type-specific 3D-genome organization and transcription regulation in the brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.04.570024. [PMID: 38105994 PMCID: PMC10723369 DOI: 10.1101/2023.12.04.570024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
3D organization of the genome plays a critical role in regulating gene expression. However, it remains unclear how chromatin organization differs among different cell types in the brain. Here we used genome-scale DNA and RNA imaging to investigate 3D-genome organization in transcriptionally distinct cell types in the primary motor cortex of the mouse brain. We uncovered a wide spectrum of differences in the nuclear architecture and 3D-genome organization among different cell types, ranging from the physical size of the cell nucleus to the active-inactive chromatin compartmentalization and radial positioning of chromatin loci within the nucleus. These cell-type-dependent variations in nuclear architecture and chromatin organization exhibited strong correlation with both total transcriptional activity of the cell and transcriptional regulation of cell-type-specific marker genes. Moreover, we found that the methylated-DNA-binding protein MeCP2 regulates transcription in a divergent manner, depending on the nuclear radial positions of chromatin loci, through modulating active-inactive chromatin compartmentalization.
Collapse
Affiliation(s)
- Shiwei Liu
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| | - Pu Zheng
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Cosmos Yuqi Wang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| | - Bojing Blair Jia
- Bioinformatics and Systems Biology Graduate Program, Medical Scientist Training Program, University of California San Diego, La Jolla, CA, USA
| | - Nathan R. Zemke
- Department of Cellular and Molecular Medicine and Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Bing Ren
- Department of Cellular and Molecular Medicine and Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| |
Collapse
|
3
|
Barman P, Kaja A, Chakraborty P, Bhaumik SR. Chromatin and non-chromatin immunoprecipitations to capture protein-protein and protein-nucleic acid interactions in living cells. Methods 2023; 218:158-166. [PMID: 37611837 PMCID: PMC10528071 DOI: 10.1016/j.ymeth.2023.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/18/2023] [Accepted: 08/19/2023] [Indexed: 08/25/2023] Open
Abstract
Proteins are expressed from genes via sequential biological processes of transcription, mRNA processing, export and translation, and play their roles in maintaining cellular functions via interactions with proteins, DNAs or RNAs. Thus, it is important to study the protein interactions during biological processes in living cells towards understanding their mechanisms-of-action in real time. Methodologies have been developed over the years to study protein interactions in vivo. One state-of-the-art approach is formaldehyde crosslinking-based immuno- or chemi-precipitation to analyze selective as well as genome/proteome-wide interactions in living cells. It is a popular and widely used methodology for cellular analysis of the protein-protein and protein-nucleic acid interactions. Here, we describe this approach to analyze protein-protein/nucleic acid interactions in vivo.
Collapse
Affiliation(s)
- Priyanka Barman
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Amala Kaja
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Pritam Chakraborty
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Sukesh R Bhaumik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA.
| |
Collapse
|
4
|
Henikoff S, Henikoff JG, Ahmad K, Paranal RM, Janssens DH, Russell ZR, Szulzewsky F, Kugel S, Holland EC. Epigenomic analysis of formalin-fixed paraffin-embedded samples by CUT&Tag. Nat Commun 2023; 14:5930. [PMID: 37739938 PMCID: PMC10516967 DOI: 10.1038/s41467-023-41666-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/14/2023] [Indexed: 09/24/2023] Open
Abstract
For more than a century, formalin-fixed paraffin-embedded (FFPE) sample preparation has been the preferred method for long-term preservation of biological material. However, the use of FFPE samples for epigenomic studies has been difficult because of chromatin damage from long exposure to high concentrations of formaldehyde. Previously, we introduced Cleavage Under Targeted Accessible Chromatin (CUTAC), an antibody-targeted chromatin accessibility mapping protocol based on CUT&Tag. Here we show that simple modifications of our CUTAC protocol either in single tubes or directly on slides produce high-resolution maps of paused RNA Polymerase II at enhancers and promoters using FFPE samples. We find that transcriptional regulatory element differences produced by FFPE-CUTAC distinguish between mouse brain tumors and identify and map regulatory element markers with high confidence and precision, including microRNAs not detectable by RNA-seq. Our simple workflows make possible affordable epigenomic profiling of archived biological samples for biomarker identification, clinical applications and retrospective studies.
Collapse
Affiliation(s)
- Steven Henikoff
- Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Jorja G Henikoff
- Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Kami Ahmad
- Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ronald M Paranal
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Derek H Janssens
- Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Zachary R Russell
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Sita Kugel
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| |
Collapse
|
5
|
Poceviciute R, Bogatyrev SR, Romano AE, Dilmore AH, Mondragón-Palomino O, Takko H, Pradhan O, Ismagilov RF. Quantitative whole-tissue 3D imaging reveals bacteria in close association with mouse jejunum mucosa. NPJ Biofilms Microbiomes 2023; 9:64. [PMID: 37679412 PMCID: PMC10485000 DOI: 10.1038/s41522-023-00423-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 07/31/2023] [Indexed: 09/09/2023] Open
Abstract
Because the small intestine (SI) epithelium lacks a thick protective mucus layer, microbes that colonize the thin SI mucosa may exert a substantial effect on the host. For example, bacterial colonization of the human SI may contribute to environmental enteropathy dysfunction (EED) in malnourished children. Thus far, potential bacterial colonization of the mucosal surface of the SI has only been documented in disease states, suggesting mucosal colonization is rare, likely requiring multiple perturbations. Furthermore, conclusive proof of bacterial colonization of the SI mucosal surface is challenging, and the three-dimensional (3D) spatial structure of mucosal colonies remains unknown. Here, we tested whether we could induce dense bacterial association with jejunum mucosa by subjecting mice to a combination of malnutrition and oral co-gavage with a bacterial cocktail (E. coli and Bacteroides spp.) known to induce EED. To visualize these events, we optimized our previously developed whole-tissue 3D imaging tools with third-generation hybridization chain reaction (HCR v3.0) probes. Only in mice that were malnourished and gavaged with the bacterial cocktail did we detect dense bacterial clusters surrounding intestinal villi suggestive of colonization. Furthermore, in these mice we detected villus loss, which may represent one possible consequence that bacterial colonization of the SI mucosa has on the host. Our results suggest that dense bacterial colonization of jejunum mucosa is possible in the presence of multiple perturbations and that whole-tissue 3D imaging tools can enable the study of these rare events.
Collapse
Affiliation(s)
- Roberta Poceviciute
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Said R Bogatyrev
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Medically Associated Science and Technology Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Anna E Romano
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Amanda H Dilmore
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Biomedical Sciences Program, University of California San Diego, San Diego, CA, USA
| | - Octavio Mondragón-Palomino
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Heli Takko
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Ojas Pradhan
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Rustem F Ismagilov
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| |
Collapse
|
6
|
Takami S, Shibahara T, Sasai K, Matsubayashi M. Occurrence, Histopathological Findings, and Molecular Identification of Pathogenic Eimeria Infections in Rabbits (Mammalia: Lagomorpha) in Japan. Acta Parasitol 2023:10.1007/s11686-023-00678-x. [PMID: 37099073 DOI: 10.1007/s11686-023-00678-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 03/23/2023] [Indexed: 04/27/2023]
Abstract
PURPOSE Eimeria spp. are commonly found among rabbits (Mammalia: Lagomorpha) worldwide. Among the 11 Eimeria species, several are highly virulent, including E. intestinalis and E. flavescens, which cause intestinal coccidiosis, and E. stiedae, which causes hepatic coccidiosis. Unlike other countries, the occurrence of Eimeria infections in rabbits in Japan remains unknown, except for one reported case of natural infection. METHODS We surveyed Eimeria infections in clinically affected rabbits over the past approximately 10 years at Livestock Hygiene Centers in 42 prefectures. A total of 16 tissue samples (14 liver, 1 ileum, and 1 cecum) were collected from 15 rabbits in 6 prefectures. RESULTS Characteristic histopathologic findings were observed, especially around the bile ducts, depending on the developmental stages of the parasites. Eimeria stiedae and E. flavescens were successfully identified by PCR and sequencing analyses in 5 liver samples and 1 cecum sample, respectively. CONCLUSION Our results could enhance understanding of infection with Eimeria spp. in rabbits in Japan and contribute to pathological or molecular diagnoses.
Collapse
Affiliation(s)
- Shigeaki Takami
- Department of Environment, Agriculture, Forestry and Fisheries, Livestock Hygiene Service Center, Osaka Prefectural Government, Osaka, 598-0048, Japan
| | - Tomoyuki Shibahara
- Division of Pathology and Pathophysiology, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-0856, Japan
- Graduate School of Veterinary Sciences, Osaka Metropolitan University, 1-58 Rinku Orai Kita, Izumisano, Osaka, 598-8531, Japan
| | - Kazumi Sasai
- Graduate School of Veterinary Sciences, Osaka Metropolitan University, 1-58 Rinku Orai Kita, Izumisano, Osaka, 598-8531, Japan
| | - Makoto Matsubayashi
- Graduate School of Veterinary Sciences, Osaka Metropolitan University, 1-58 Rinku Orai Kita, Izumisano, Osaka, 598-8531, Japan.
- Department of Veterinary Parasitology, Faculty of Veterinary Medicine, Airlangga University, Surabaya, 60115, Indonesia.
| |
Collapse
|
7
|
Guo Q, Lakatos E, Bakir IA, Curtius K, Graham TA, Mustonen V. The mutational signatures of formalin fixation on the human genome. Nat Commun 2022; 13:4487. [PMID: 36068219 PMCID: PMC9448750 DOI: 10.1038/s41467-022-32041-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/14/2022] [Indexed: 12/02/2022] Open
Abstract
Clinical archives of patient material near-exclusively consist of formalin-fixed and paraffin-embedded (FFPE) blocks. The ability to precisely characterise mutational signatures from FFPE-derived DNA has tremendous translational potential. However, sequencing of DNA derived from FFPE material is known to be riddled with artefacts. Here we derive genome-wide mutational signatures caused by formalin fixation. We show that the FFPE-signature is highly similar to signature 30 (the signature of Base Excision Repair deficiency due to NTHL1 mutations), and chemical repair of DNA lesions leads to a signature highly similar to signature 1 (clock-like signature due to spontaneous deamination of methylcytosine). We demonstrate that using uncorrected mutational catalogues of FFPE samples leads to major mis-assignment of signature activities. To correct for this, we introduce FFPEsig, a computational algorithm to rectify the formalin-induced artefacts in the mutational catalogue. We demonstrate that FFPEsig enables accurate mutational signature analysis both in simulated and whole-genome sequenced FFPE cancer samples. FFPEsig thus provides an opportunity to unlock additional clinical potential of archival patient tissues.
Collapse
Affiliation(s)
- Qingli Guo
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, University of Helsinki, Helsinki, Finland
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Eszter Lakatos
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Genomics and Evolutionary Dynamics Laboratory, Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - Ibrahim Al Bakir
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Kit Curtius
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
- Genomics and Evolutionary Dynamics Laboratory, Centre for Evolution and Cancer, Institute of Cancer Research, London, UK.
| | - Ville Mustonen
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, University of Helsinki, Helsinki, Finland.
- Institute of Biotechnology, Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland.
| |
Collapse
|
8
|
Yadav RP, Polavarapu VK, Xing P, Chen X. FFPE-ATAC: A Highly Sensitive Method for Profiling Chromatin Accessibility in Formalin-Fixed Paraffin-Embedded Samples. Curr Protoc 2022; 2:e535. [PMID: 35994571 DOI: 10.1002/cpz1.535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In basic and translational cancer research, the majority of biopsies are stored in formalin-fixed paraffin-embedded (FFPE) samples. Chromatin accessibility reflects the degree to which nuclear macromolecules can physically interact with chromatinized DNA and plays a key role in gene regulation in different physiological conditions. As such, the profiling of chromatin accessibility in archived FFPE tissue can be critical to understanding gene regulation in health and disease. Due to the high degree of DNA damage in FFPE samples, accurate mapping of chromatin accessibility in these specimens is extremely difficult. To address this issue, we recently established FFPE-ATAC, a highly sensitive method based on T7-Tn5-mediated transposition followed by in vitro transcription (IVT), to generate high-quality chromatin accessibility profiles with 500-50,000 nuclei from a single FFPE tissue section. In FFPE-ATAC, which we describe here, the T7-Tn5 adaptors are inserted into the genome after FFPE sample preparation and are unlikely to sustain the DNA breakage that occurs during reverse cross-linking of these samples. It should, therefore, remain at the ends of broken accessible chromatin sites after reverse cross-linking. IVT is then used to convert the two ends of the broken DNA fragments to RNA molecules before making sequencing libraries from the IVT RNAs and further decoding Tn5 adaptor insertion sites in the genome. Through this strategy, users can decode the flanking sequences of the accessible chromatin even if there are breaks between adjacent pairs of T7-T5 adaptor insertion sites. This method is applicable to dissecting chromatin profiles of a small section of the tissue sample, characterizing stage and region-specific gene regulation and disease-associated chromatin regulation in FFPE tissues. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Nuclei isolation from FFPE tissue samples Basic Protocol 2: T7-Tn5 transposase tagmentation, reverse-crosslinking, and in vitro transcription Basic Protocol 3: Preparation of libraries for high-throughput sequencing.
Collapse
Affiliation(s)
- Ram Prakash Yadav
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | | | - Pengwei Xing
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Xingqi Chen
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| |
Collapse
|
9
|
Wei YB, Luo D, Xiong X, Huang YL, Xie M, Lu W, Li D. Biomimetic mimicry of formaldehyde-induced DNA-protein crosslinks in the confined space of a metal-organic framework. Chem Sci 2022; 13:4813-4820. [PMID: 35655868 PMCID: PMC9067591 DOI: 10.1039/d2sc00188h] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/18/2022] [Indexed: 02/05/2023] Open
Abstract
DNA-protein crosslinks (DPCs) are highly toxic DNA lesions induced by crosslinking agents such as formaldehyde (HCHO). Building artificial models to simulate the crosslinking process would advance our understanding of the underlying mechanisms and therefore develop coping strategies accordingly. Herein we report the design and synthesis of a Zn-based metal-organic framework with mixed ligands of 2,6-diaminopurine and amine-functionalized dicarboxylate, representing DNA and protein residues, respectively. Combined characterization techniques allow us to demonstrate the unusual efficiency of HCHO-crosslinking within the confined space of the titled MOF. Particularly, in situ single-crystal X-ray diffraction studies reveal a sequential methylene-knitting process upon HCHO addition, along with strong fluorescence that was not interfered with by other metabolites, glycine, and Tris. This work has successfully constructed a purine-based metal-organic framework with unoccupied Watson-Crick sites, serving as a crystalline model for HCHO-induced DPCs by mimicking the confinement effect of protein/DNA interactions.
Collapse
Affiliation(s)
- Yu-Bai Wei
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University Guangzhou 510632 P. R. China
| | - Dong Luo
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University Guangzhou 510632 P. R. China
| | - Xiao Xiong
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University Guangzhou 510632 P. R. China
| | - Yong-Liang Huang
- Department of Chemistry, Shantou University Medical College Shantou Guangdong 515041 P. R. China
| | - Mo Xie
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University Guangzhou 510632 P. R. China
| | - Weigang Lu
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University Guangzhou 510632 P. R. China
| | - Dan Li
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University Guangzhou 510632 P. R. China
| |
Collapse
|
10
|
Cruz-Flores R, López-Carvallo JA, Cáceres-Martínez J, Dhar AK. Microbiome analysis from formalin-fixed paraffin-embedded tissues: Current challenges and future perspectives. METHODS IN MICROBIOLOGY 2022; 196:106476. [PMID: 35490989 DOI: 10.1016/j.mimet.2022.106476] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/22/2022] [Accepted: 04/22/2022] [Indexed: 12/14/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues stored in thousands of human and animal pathology laboratories around the globe represent mines of stored genetic information. In recent years, the use of FFPE tissues as a viable source of DNA for diverse genetic studies has attracted attention for interrogating microbiomes from this sample type. These studies have proven that 16S rRNA amplicon sequencing-based microbiome studies are possible from FFPE samples but present some particular challenges. In this review, we summarize all aspects of microbiome studies from FFPE tissues including the challenges associated with working highly degraded DNA, best practices for reducing environmental contamination, and we propose solutions to address these issues. Finally, we discuss how the combination of FFPE microbiome studies and Laser Capture Microdissection and/or Laser Microdissection could enable to determine the spatial heterogeneity underlying complex bacterial communities.
Collapse
Affiliation(s)
- Roberto Cruz-Flores
- Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Carretera Ensenada-Tijuana No. 3918, Zona Playitas, 22860 Ensenada, Baja California, Mexico.
| | - Jesús Antonio López-Carvallo
- Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Carretera Ensenada-Tijuana No. 3918, Zona Playitas, 22860 Ensenada, Baja California, Mexico
| | - Jorge Cáceres-Martínez
- Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Carretera Ensenada-Tijuana No. 3918, Zona Playitas, 22860 Ensenada, Baja California, Mexico
| | - Arun K Dhar
- Aquaculture Pathology Laboratory, School of Animal & Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ, United States of America
| |
Collapse
|
11
|
Henke KB, Miller RM, Knoener RA, Scalf M, Spiniello M, Smith LM. Identifying Protein Interactomes of Target RNAs Using HyPR-MS. Methods Mol Biol 2022; 2404:219-244. [PMID: 34694612 PMCID: PMC8754189 DOI: 10.1007/978-1-0716-1851-6_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
RNA-protein interactions are integral to maintaining proper cellular function and homeostasis, and the disruption of key RNA-protein interactions is central to many disease states. HyPR-MS (hybridization purification of RNA-protein complexes followed by mass spectrometry) is a highly versatile and efficient technology which enables multiplexed discovery of specific RNA-protein interactomes. This chapter provides extensive guidance for successful application of HyPR-MS to the system and target RNA(s) of interest, as well as a detailed description of the fundamental HyPR-MS procedure, including: (1) experimental design of controls, capture oligonucleotides, and qPCR assays; (2) formaldehyde cross-linking of cell culture; (3) cell lysis and RNA solubilization; (4) isolation of target RNA(s); (5) RNA purification and RT-qPCR analysis; (6) protein preparation and mass spectrometric analysis; and (7) mass spectrometric data analysis.
Collapse
Affiliation(s)
- Katherine B Henke
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Rachel M Miller
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Rachel A Knoener
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Michele Spiniello
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Immuno-Hematology and Transfusion Medicine, Cardarelli Hospital, Naples, Italy
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
| |
Collapse
|
12
|
Genome-wide spatial expression profiling in formalin-fixed tissues. CELL GENOMICS 2021; 1:100065. [PMID: 36776149 PMCID: PMC9903805 DOI: 10.1016/j.xgen.2021.100065] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 04/27/2021] [Accepted: 08/30/2021] [Indexed: 12/31/2022]
Abstract
Formalin-fixed paraffin embedding (FFPE) is the most widespread long-term tissue preservation approach. Here, we report a procedure to perform genome-wide spatial analysis of mRNA in FFPE-fixed tissue sections, using well-established, commercially available methods for imaging and spatial barcoding using slides spotted with barcoded oligo(dT) probes to capture the 3' end of mRNA molecules in tissue sections. We applied this method for expression profiling and cell type mapping in coronal sections from the mouse brain to demonstrate the method's capability to delineate anatomical regions from a molecular perspective. We also profiled the spatial composition of transcriptomic signatures in two ovarian carcinosarcoma samples, exemplifying the method's potential to elucidate molecular mechanisms in heterogeneous clinical samples. Finally, we demonstrate the applicability of the assay to characterize human lung and kidney organoids and a human lung biopsy specimen infected with SARS-CoV-2. We anticipate that genome-wide spatial gene expression profiling in FFPE biospecimens will be used for retrospective analysis of biobank samples, which will facilitate longitudinal studies of biological processes and biomarker discovery.
Collapse
|
13
|
Wang H, Qian L, Shang Z, Wang Z, Zhang Y, Cao C, Xiao H. Immobilized Titanium (IV) Ion Affinity Chromatography Contributes to Efficient Proteomics Analysis of Cellular Nucleic Acid-Binding Proteins. J Proteome Res 2021; 21:220-231. [PMID: 34780180 DOI: 10.1021/acs.jproteome.1c00788] [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: 11/30/2022]
Abstract
Cellular nucleic acid-binding proteins (NABPs), namely, DNA-binding proteins (DBPs) and RNA-binding proteins (RBPs), play important roles in many biological processes. However, extracting NABPs with high efficiency in living cells is challenging, which greatly limited their proteomics analysis and comprehensive characterization. Here, we discovered that titanium (IV) ion-immobilized metal affinity chromatography (Ti4+-IMAC) material could enrich DNA and RNA with high efficiency (96.82 ± 2.67 and 85.75 ± 2.99%, respectively). We therefore developed a Ti4+-IMAC method for the joint extraction of DBPs and RBPs. Through utilizing formaldehyde (FA) cross-linking, DBPs and RBPs were covalently linked to nucleic acids (NAs) and further denatured by organic solvents. After Ti4+-IMAC capture, 2000 proteins were identified in 293T cells, among which 417 DBPs and 999 RBPs were revealed, showing promising selectivity for NABPs. We further applied the Ti4+-IMAC capture method to lung cancer cell lines 95C and 95D, which have different tumor progression abilities. The DNA- and RNA-binding capabilities of many proteins have been dysregulated in 95D. Under our conditions, Ti4+-IMAC can be used as a selective and powerful tool for the comprehensive characterization of both DBPs and RBPs, which might be utilized to study their dynamic interactions with nucleic acids.
Collapse
Affiliation(s)
- Huiyu Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liqiang Qian
- Department of Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Zhi Shang
- Institute of Clinical Immunology, Department of Liver Diseases, Central Laboratory, ShuGuang Hospital Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai 200021, China
| | - Zeyuan Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Zhang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chengxi Cao
- Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hua Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
14
|
Housh K, Jha JS, Haldar T, Amin SBM, Islam T, Wallace A, Gomina A, Guo X, Nel C, Wyatt JW, Gates KS. Formation and repair of unavoidable, endogenous interstrand cross-links in cellular DNA. DNA Repair (Amst) 2020; 98:103029. [PMID: 33385969 DOI: 10.1016/j.dnarep.2020.103029] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 02/08/2023]
Abstract
Genome integrity is essential for life and, as a result, DNA repair systems evolved to remove unavoidable DNA lesions from cellular DNA. Many forms of life possess the capacity to remove interstrand DNA cross-links (ICLs) from their genome but the identity of the naturally-occurring, endogenous substrates that drove the evolution and retention of these DNA repair systems across a wide range of life forms remains uncertain. In this review, we describe more than a dozen chemical processes by which endogenous ICLs plausibly can be introduced into cellular DNA. The majority involve DNA degradation processes that introduce aldehyde residues into the double helix or reactions of DNA with endogenous low molecular weight aldehyde metabolites. A smaller number of the cross-linking processes involve reactions of DNA radicals generated by oxidation.
Collapse
Affiliation(s)
- Kurt Housh
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Jay S Jha
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Tuhin Haldar
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Saosan Binth Md Amin
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Tanhaul Islam
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Amanda Wallace
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Anuoluwapo Gomina
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Xu Guo
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Christopher Nel
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Jesse W Wyatt
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Kent S Gates
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States; University of Missouri, Department of Biochemistry, Columbia, MO 65211, United States.
| |
Collapse
|
15
|
Flores Bueso Y, Walker SP, Tangney M. Characterization of FFPE-induced bacterial DNA damage and development of a repair method. Biol Methods Protoc 2020; 5:bpaa015. [PMID: 33072872 PMCID: PMC7548031 DOI: 10.1093/biomethods/bpaa015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/15/2020] [Accepted: 07/18/2020] [Indexed: 01/13/2023] Open
Abstract
Formalin-fixed, paraffin-embedded (FFPE) specimens have huge potential as source material in the field of human microbiome research. However, the effects of FFPE processing on bacterial DNA remain uncharacterized. Any effects are relevant for microbiome studies, where DNA template is often minimal and sequences studied are not limited to one genome. As such, we aimed to both characterize this FFPE-induced bacterial DNA damage and develop strategies to reduce and repair this damage. Our analyses indicate that bacterial FFPE DNA is highly fragmented, a poor template for PCR, crosslinked and bears sequence artefacts derived predominantly from oxidative DNA damage. Two strategies to reduce this damage were devised – an optimized decrosslinking procedure reducing sequence artefacts generated by high-temperature incubation, and secondly, an in vitro reconstitution of the base excision repair pathway. As evidenced by whole genome sequencing, treatment with these strategies significantly increased fragment length, reduced the appearance of sequence artefacts and improved the sequencing readability of bacterial and mammalian FFPE DNA. This study provides a new understanding of the condition of bacterial DNA in FFPE specimens and how this impacts downstream analyses, in addition to a strategy to improve the sequencing quality of bacterial and possibly mammalian FFPE DNA.
Collapse
Affiliation(s)
- Yensi Flores Bueso
- CancerResearch@UCC, University College Cork, Cork, T12 XF62, Ireland.,SynBioCentre, University College Cork, Cork, T12 XF62, Ireland.,APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland
| | - Sidney P Walker
- CancerResearch@UCC, University College Cork, Cork, T12 XF62, Ireland.,SynBioCentre, University College Cork, Cork, T12 XF62, Ireland.,APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland
| | - Mark Tangney
- CancerResearch@UCC, University College Cork, Cork, T12 XF62, Ireland.,SynBioCentre, University College Cork, Cork, T12 XF62, Ireland.,APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland
| |
Collapse
|
16
|
Yun BH, Guo J, Bellamri M, Turesky RJ. DNA adducts: Formation, biological effects, and new biospecimens for mass spectrometric measurements in humans. MASS SPECTROMETRY REVIEWS 2020; 39:55-82. [PMID: 29889312 PMCID: PMC6289887 DOI: 10.1002/mas.21570] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/25/2018] [Indexed: 05/18/2023]
Abstract
Hazardous chemicals in the environment and diet or their electrophilic metabolites can form adducts with genomic DNA, which can lead to mutations and the initiation of cancer. In addition, reactive intermediates can be generated in the body through oxidative stress and damage the genome. The identification and measurement of DNA adducts are required for understanding exposure and the causal role of a genotoxic chemical in cancer risk. Over the past three decades, 32 P-postlabeling, immunoassays, gas chromatography/mass spectrometry, and liquid chromatography/mass spectrometry (LC/MS) methods have been established to assess exposures to chemicals through measurements of DNA adducts. It is now possible to measure some DNA adducts in human biopsy samples, by LC/MS, with as little as several milligrams of tissue. In this review article, we highlight the formation and biological effects of DNA adducts, and highlight our advances in human biomonitoring by mass spectrometric analysis of formalin-fixed paraffin-embedded tissues, untapped biospecimens for carcinogen DNA adduct biomarker research.
Collapse
Affiliation(s)
- Byeong Hwa Yun
- Masonic Cancer Center and Department of Medicinal Chemistry, University of Minnesota, 2231 6 St. SE, Minneapolis, Minnesota, 55455, United States
| | - Jingshu Guo
- Masonic Cancer Center and Department of Medicinal Chemistry, University of Minnesota, 2231 6 St. SE, Minneapolis, Minnesota, 55455, United States
| | - Medjda Bellamri
- Masonic Cancer Center and Department of Medicinal Chemistry, University of Minnesota, 2231 6 St. SE, Minneapolis, Minnesota, 55455, United States
| | - Robert J. Turesky
- Masonic Cancer Center and Department of Medicinal Chemistry, University of Minnesota, 2231 6 St. SE, Minneapolis, Minnesota, 55455, United States
| |
Collapse
|
17
|
Totoiu CA, Phillips JM, Reese AT, Majumdar S, Girguis PR, Raston CL, Weiss GA. Vortex fluidics-mediated DNA rescue from formalin-fixed museum specimens. PLoS One 2020; 15:e0225807. [PMID: 31999723 PMCID: PMC6992170 DOI: 10.1371/journal.pone.0225807] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 01/06/2020] [Indexed: 12/25/2022] Open
Abstract
DNA from formalin-preserved tissue could unlock a vast repository of genetic information stored in museums worldwide. However, formaldehyde crosslinks proteins and DNA, and prevents ready amplification and DNA sequencing. Formaldehyde acylation also fragments the DNA. Treatment with proteinase K proteolyzes crosslinked proteins to rescue the DNA, though the process is quite slow. To reduce processing time and improve rescue efficiency, we applied the mechanical energy of a vortex fluidic device (VFD) to drive the catalytic activity of proteinase K and recover DNA from American lobster tissue (Homarus americanus) fixed in 3.7% formalin for >1-year. A scan of VFD rotational speeds identified the optimal rotational speed for recovery of PCR-amplifiable DNA and while 500+ base pairs were sequenced, shorter read lengths were more consistently obtained. This VFD-based method also effectively recovered DNA from formalin-preserved samples. The results provide a roadmap for exploring DNA from millions of historical and even extinct species.
Collapse
Affiliation(s)
- Christian A. Totoiu
- Department of Chemistry, University of California, Irvine, California, United States of America
| | - Jessica M. Phillips
- Flinders Institute for Nanoscale Science and Technology, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Aspen T. Reese
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Sudipta Majumdar
- Department of Chemistry, University of California, Irvine, California, United States of America
| | - Peter R. Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Colin L. Raston
- Flinders Institute for Nanoscale Science and Technology, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Gregory A. Weiss
- Department of Chemistry, University of California, Irvine, California, United States of America
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, United States of America
- Department of Pharmaceutical Sciences, University of California, Irvine, California, United States of America
| |
Collapse
|
18
|
Controlled cross‐linking of porcine cholecyst extracellular matrix for preparing tissue engineering scaffold. J Biomed Mater Res B Appl Biomater 2019; 108:1057-1067. [DOI: 10.1002/jbm.b.34457] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 06/27/2019] [Accepted: 07/17/2019] [Indexed: 12/31/2022]
|
19
|
Ruf-Zamojski F, Ge Y, Nair V, Zamojski M, Pincas H, Toufaily C, Tome-Garcia J, Stoeckius M, Stephenson W, Smith GR, Bernard DJ, Tsankova NM, Hartmann BM, Fribourg M, Smibert P, Swerdlow H, Turgeon JL, Sealfon SC. Single-cell stabilization method identifies gonadotrope transcriptional dynamics and pituitary cell type heterogeneity. Nucleic Acids Res 2019; 46:11370-11380. [PMID: 30357357 PMCID: PMC6265460 DOI: 10.1093/nar/gky991] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 10/19/2018] [Indexed: 12/23/2022] Open
Abstract
Immediate-early response genes (IEGs) are rapidly and transiently induced following an extracellular signal. Elucidating the IEG response patterns in single cells (SCs) requires assaying large numbers of timed samples at high accuracy while minimizing handling effects. To achieve this, we developed and validated RNA stabilization Buffer for Examination of Single-cell Transcriptomes (RNA-Best), a versatile single-step cell and tissue preservation protocol that stabilizes RNA in intact SCs without perturbing transcription patterns. We characterize for the first time SC heterogeneity in IEG responses to pulsatile gonadotropin-releasing hormone (GnRH) stimuli in pituitary gonadotrope cells. Our study identifies a gene-specific hierarchical pattern of all-or-none transcript induction elicited by increasing concentrations of GnRH. This quantal pattern of gene activation raises the possibility that IEG activation, when accurately resolved at the SC level, may be mediated by gene bits that behave as pure binary switches.
Collapse
Affiliation(s)
- Frederique Ruf-Zamojski
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yongchao Ge
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Venugopalan Nair
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michel Zamojski
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hanna Pincas
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chirine Toufaily
- Dept. of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Jessica Tome-Garcia
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | | | - Gregory R Smith
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daniel J Bernard
- Dept. of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Nadejda M Tsankova
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Boris M Hartmann
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Miguel Fribourg
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | | | - Judith L Turgeon
- Department of Internal Medicine, University of California, Davis, CA 95616, USA
| | - Stuart C Sealfon
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| |
Collapse
|
20
|
Mathieson W, Thomas G. Using FFPE Tissue in Genomic Analyses: Advantages, Disadvantages and the Role of Biospecimen Science. CURRENT PATHOBIOLOGY REPORTS 2019. [DOI: 10.1007/s40139-019-00194-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
21
|
Venters BJ. Insights from resolving protein-DNA interactions at near base-pair resolution. Brief Funct Genomics 2019; 17:80-88. [PMID: 29211822 DOI: 10.1093/bfgp/elx043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
One of the central goals in molecular biology is to understand how cell-type-specific expression patterns arise through selective recruitment of RNA polymerase II (Pol II) to a subset of gene promoters. Pol II needs to be recruited to a precise genomic position at the proper time to produce messenger RNA from a DNA template. Ostensibly, transcription is a relatively simple cellular process; yet, experimentally measuring and then understanding the combinatorial possibilities of transcriptional regulators remain a daunting task. Since its introduction in 1985, chromatin immunoprecipitation (ChIP) has remained a key tool for investigating protein-DNA contacts in vivo. Over 30 years of intensive research using ChIP have provided numerous insights into mechanisms of gene regulation. As functional genomic technologies improve, they present new opportunities to address key biological questions. ChIP-exo is a refined version of ChIP-seq that significantly reduces background signal, while providing near base-pair mapping resolution for protein-DNA interactions. This review discusses the evolution of the ChIP assay over the years; the methodological differences between ChIP-seq, ChIP-exo and ChIP-nexus; and highlight new insights into epigenetic and transcriptional mechanisms that were uniquely enabled with the near base-pair resolution of ChIP-exo.
Collapse
|
22
|
Santhakumar K, Viswanath V. Novel Methods for Efficacy Testing of Disinfectants – Part I. TENSIDE SURFACT DET 2019. [DOI: 10.3139/113.110597] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Abstract
The pathogens which are the effective transmitters of various infections pose a serious problem in restraining their interference in maintaining a sterile environment. The practical applicability of traditional methods of disinfection is restricted due to their cumbersomeness, toxic product generation, and cost-effectiveness. Therefore, the objective of the current review is to elaborate the efficacies and limitations of various novel disinfectants that can show their activity in a few minutes of treatment. The expected outcome would be feasibility for selection of a favorable disinfectant through various technologies that can generate uniform results and form a basis for the true estimation required parameters. Hence, the current paper ends with the consideration of unique new techniques that distinguishes their simplicity, safety, and efficacy in generating a sterile environment.
Collapse
Affiliation(s)
| | - Valikala Viswanath
- Carbon dioxide Research and Green Technologies Center , VIT University, Tamil Nadu , India
| |
Collapse
|
23
|
RELACS nuclei barcoding enables high-throughput ChIP-seq. Commun Biol 2018; 1:214. [PMID: 30534606 PMCID: PMC6281648 DOI: 10.1038/s42003-018-0219-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 10/31/2018] [Indexed: 02/07/2023] Open
Abstract
Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) is an invaluable tool for mapping chromatin-associated proteins. Current barcoding strategies aim to improve assay throughput and scalability but intense sample handling and lack of standardization over cell types, cell numbers and epitopes hinder wide-spread use in the field. Here, we present a barcoding method to enable high-throughput ChIP-seq using common molecular biology techniques. The method, called RELACS (restriction enzyme-based labeling of chromatin in situ) relies on standardized nuclei extraction from any source and employs chromatin cutting and barcoding within intact nuclei. Barcoded nuclei are pooled and processed within the same ChIP reaction, for maximal comparability and workload reduction. The innovative barcoding concept is particularly user-friendly and suitable for implementation to standardized large-scale clinical studies and scarce samples. Aiming to maximize universality and scalability, RELACS can generate ChIP-seq libraries for transcription factors and histone modifications from hundreds of samples within three days. Laura Arrigoni et al. present RELACS, a method enabling high-throughput ChIP-seq which involves barcoding and processing intact nuclei in the same ChIP reaction. The method is useful for broad cell types and epitopes, robust to experimental conditions, and drastically decreases workload.
Collapse
|
24
|
Yun BH, Guo J, Turesky RJ. Formalin-Fixed Paraffin-Embedded Tissues-An Untapped Biospecimen for Biomonitoring DNA Adducts by Mass Spectrometry. TOXICS 2018; 6:E30. [PMID: 29865161 PMCID: PMC6027047 DOI: 10.3390/toxics6020030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 05/21/2018] [Accepted: 05/25/2018] [Indexed: 01/03/2023]
Abstract
The measurement of DNA adducts provides important information about human exposure to genotoxic chemicals and can be employed to elucidate mechanisms of DNA damage and repair. DNA adducts can serve as biomarkers for interspecies comparisons of the biologically effective dose of procarcinogens and permit extrapolation of genotoxicity data from animal studies for human risk assessment. One major challenge in DNA adduct biomarker research is the paucity of fresh frozen biopsy samples available for study. However, archived formalin-fixed paraffin-embedded (FFPE) tissues with clinical diagnosis of disease are often available. We have established robust methods to recover DNA free of crosslinks from FFPE tissues under mild conditions which permit quantitative measurements of DNA adducts by liquid chromatography-mass spectrometry. The technology is versatile and can be employed to screen for DNA adducts formed with a wide range of environmental and dietary carcinogens, some of which were retrieved from section-cuts of FFPE blocks stored at ambient temperature for up to nine years. The ability to retrospectively analyze FFPE tissues for DNA adducts for which there is clinical diagnosis of disease opens a previously untapped source of biospecimens for molecular epidemiology studies that seek to assess the causal role of environmental chemicals in cancer etiology.
Collapse
Affiliation(s)
- Byeong Hwa Yun
- Masonic Cancer Center and Department of Medicinal Chemistry, University of Minnesota, 2231 6th St. SE, Minneapolis, MN 55455, USA.
| | - Jingshu Guo
- Masonic Cancer Center and Department of Medicinal Chemistry, University of Minnesota, 2231 6th St. SE, Minneapolis, MN 55455, USA.
| | - Robert J Turesky
- Masonic Cancer Center and Department of Medicinal Chemistry, University of Minnesota, 2231 6th St. SE, Minneapolis, MN 55455, USA.
| |
Collapse
|
25
|
Bifunctional cross-linking approaches for mass spectrometry-based investigation of nucleic acids and protein-nucleic acid assemblies. Methods 2018; 144:64-78. [PMID: 29753003 DOI: 10.1016/j.ymeth.2018.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/30/2018] [Accepted: 05/04/2018] [Indexed: 12/13/2022] Open
Abstract
With the goal of expanding the very limited toolkit of cross-linking agents available for nucleic acids and their protein complexes, we evaluated the merits of a wide range of bifunctional agents that may be capable of reacting with the functional groups characteristic of these types of biopolymers. The survey specifically focused on the ability of test reagents to produce desirable inter-molecular conjugates, which could reveal the identity of interacting components and the position of mutual contacts, while also considering a series of practical criteria for their utilization as viable nucleic acid probes. The survey employed models consisting of DNA, RNA, and corresponding protein complexes to mimic as close as possible typical applications. Denaturing polyacrylamide gel electrophoresis (PAGE) and mass spectrometric (MS) analyses were implemented in concert to monitor the formation of the desired conjugates. In particular, the former was used as a rapid and inexpensive tool for the efficient evaluation of cross-linker activity under a broad range of experimental conditions. The latter was applied after preliminary rounds of reaction optimization to enable full-fledged product characterization and, more significantly, differentiation between mono-functional and intra- versus inter-molecular conjugates. This information provided the feedback necessary to further optimize reaction conditions and explain possible outcomes. Among the reagents tested in the study, platinum complexes and nitrogen mustards manifested the most favorable characteristics for practical cross-linking applications, whereas other compounds provided inferior yields, or produced rather unstable conjugates that did not survive the selected analytical conditions. The observed outcomes will help guide the selection of the most appropriate cross-linking reagent for a specific task, whereas the experimental conditions described here will provide an excellent starting point for approaching these types of applications. As a whole, the results of the survey clearly emphasize that finding a universal reagent, which may afford excellent performance with all types of nucleic acid substrates, will require extending the exploration beyond the traditional chemistries employed to modify the constitutive functional groups of these vital biopolymers.
Collapse
|
26
|
Yi Z, Sun Z, Chen G, Zhang H, Ma X, Su W, Cui X, Li X. Size-controlled, colloidally stable and functional nanoparticles based on the molecular assembly of green tea polyphenols and keratins for cancer therapy. J Mater Chem B 2018; 6:1373-1386. [DOI: 10.1039/c7tb03293e] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Molecular assembly of green tea polyphenols and keratins into size-controlled, colloidally stable and functional nanoparticles for enhanced cancer therapy was achieved.
Collapse
Affiliation(s)
- Zeng Yi
- National Engineering Research Center for Biomaterials, Sichuan University
- Chengdu 610064
- P. R. China
| | - Zhe Sun
- National Engineering Research Center for Biomaterials, Sichuan University
- Chengdu 610064
- P. R. China
| | - Guangcan Chen
- National Engineering Research Center for Biomaterials, Sichuan University
- Chengdu 610064
- P. R. China
| | - Huaiying Zhang
- National Engineering Research Center for Biomaterials, Sichuan University
- Chengdu 610064
- P. R. China
| | - Xiaomin Ma
- National Engineering Research Center for Biomaterials, Sichuan University
- Chengdu 610064
- P. R. China
| | - Wen Su
- National Engineering Research Center for Biomaterials, Sichuan University
- Chengdu 610064
- P. R. China
| | - Xinxing Cui
- National Engineering Research Center for Biomaterials, Sichuan University
- Chengdu 610064
- P. R. China
| | - Xudong Li
- National Engineering Research Center for Biomaterials, Sichuan University
- Chengdu 610064
- P. R. China
| |
Collapse
|
27
|
Jordán-Pla A, Visa N. Considerations on Experimental Design and Data Analysis of Chromatin Immunoprecipitation Experiments. Methods Mol Biol 2018; 1689:9-28. [PMID: 29027161 DOI: 10.1007/978-1-4939-7380-4_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Arguably one of the most valuable techniques to study chromatin organization, ChIP is the method of choice to map the contacts established between proteins and genomic DNA. Ever since its inception, more than 30 years ago, ChIP has been constantly evolving, improving, and expanding its capabilities and reach. Despite its widespread use by many laboratories across a wide variety of disciplines, ChIP assays can be sometimes challenging to design, and are often sensitive to variations in practical implementation.In this chapter, we provide a general overview of the ChIP method and its most common variations, with a special focus on ChIP-seq. We try to address some of the most important aspects that need to be taken into account in order to design and perform experiments that generate the most reproducible, high-quality data. Some of the main topics covered include the use of properly characterized antibodies, alternatives to chromatin preparation, the need for proper controls, and some recommendations about ChIP-seq data analysis.
Collapse
Affiliation(s)
- Antonio Jordán-Pla
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20c, 10691, Stockholm, Sweden.
| | - Neus Visa
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20c, 10691, Stockholm, Sweden
| |
Collapse
|
28
|
Wei Y, Wahome N, VanSlyke G, Whitaker N, Kumar P, Barta ML, Picking WL, Volkin DB, Mantis NJ, Middaugh CR. Evaluation of lumazine synthase from Bacillus anthracis as a presentation platform for polyvalent antigen display. Protein Sci 2017; 26:2059-2072. [PMID: 28736824 DOI: 10.1002/pro.3243] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 07/08/2017] [Accepted: 07/19/2017] [Indexed: 12/31/2022]
Abstract
Polyvalent antigen display is an effective strategy to enhance the immunogenicity of subunit vaccines by clustering them in an array-like manner on a scaffold system. This strategy results in a higher local density of antigens, increased high avidity interactions with B cells and other antigen presenting cells, and therefore a more effective presentation of vaccine antigens. In this study, we used lumazine synthase (LS), an icosahedral symmetry capsid derived from Bacillus anthracis, as a scaffold to present 60 copies of a linear B cell epitope (PB10) from the ricin toxin fused to the C terminus of LS via four different linkers. We then investigated the effects of linker length, linker rigidity and formaldehyde crosslinking on the protein assembly, conformational integrity, thermal stability, in vitro antibody binding, and immunogenicity in mice. Fusion of the PB10 peptide onto LS, with varying linker lengths, did not affect protein assembly, thermal stability or exposure of the epitope, but had a minor impact on protein conformation. Formaldehyde crosslinking considerably improved protein thermal stability with only minor impact on protein conformation. All LS_PB10 constructs, when administered to mice by injection without adjuvant, elicited measurable anti-ricin serum IgG titers, although the titers were not sufficient to confer protection against a 10× lethal dose ricin challenge. This work sheds light on the biophysical properties, immunogenicity and potential feasibility of LS from B. anthracis as a scaffold system for polyvalent antigen display.
Collapse
Affiliation(s)
- Yangjie Wei
- Macromolecule and Vaccine Stabilization Center, Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas, 66047.,Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas, 66047
| | - Newton Wahome
- Macromolecule and Vaccine Stabilization Center, Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas, 66047.,Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas, 66047
| | - Greta VanSlyke
- Division of Infectious Disease, Wadsworth Center, New York State Department of Health, Albany, New York, 12208
| | - Neal Whitaker
- Macromolecule and Vaccine Stabilization Center, Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas, 66047.,Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas, 66047
| | - Prashant Kumar
- Macromolecule and Vaccine Stabilization Center, Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas, 66047.,Division of Infectious Disease, Wadsworth Center, New York State Department of Health, Albany, New York, 12208
| | - Michael L Barta
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas, 66047
| | - Wendy L Picking
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas, 66047
| | - David B Volkin
- Macromolecule and Vaccine Stabilization Center, Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas, 66047.,Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas, 66047
| | - Nicholas J Mantis
- Division of Infectious Disease, Wadsworth Center, New York State Department of Health, Albany, New York, 12208
| | - C Russell Middaugh
- Macromolecule and Vaccine Stabilization Center, Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas, 66047.,Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas, 66047
| |
Collapse
|
29
|
Buxton KE, Kennedy-Darling J, Shortreed MR, Zaidan NZ, Olivier M, Scalf M, Sridharan R, Smith LM. Elucidating Protein-DNA Interactions in Human Alphoid Chromatin via Hybridization Capture and Mass Spectrometry. J Proteome Res 2017; 16:3433-3442. [PMID: 28704058 DOI: 10.1021/acs.jproteome.7b00448] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The centromere is the chromosomal locus where the kinetochore forms and is critical for ensuring proper segregation of sister chromatids during cell division. A substantial amount of effort has been devoted to understanding the characteristic features and roles of the centromere, yet some fundamental aspects of the centromere, such as the complete list of elements that define it, remain obscure. It is well-known that human centromeres include a highly repetitive class of DNA known as alpha satellite, or alphoid, DNA. We present here the first DNA-centric examination of human protein-alpha satellite interactions, employing an approach known as HyCCAPP (hybridization capture of chromatin-associated proteins for proteomics) to identify the protein components of alphoid chromatin in a human cell line. Using HyCCAPP, cross-linked alpha satellite chromatin was isolated from cell lysate, and captured proteins were analyzed via mass spectrometry. After being compared to proteins identified in control pulldown experiments, 90 proteins were identified as enriched at alphoid DNA. This list included many known centromere-binding proteins in addition to multiple novel alpha satellite-binding proteins, such as LRIF1, a heterochromatin-associated protein. The ability of HyCCAPP to reveal both known as well as novel alphoid DNA-interacting proteins highlights the validity and utility of this approach.
Collapse
Affiliation(s)
| | | | | | | | - Michael Olivier
- Department of Genetics, Texas Biomedical Research Institute , San Antonio, Texas 78227, United States
| | | | | | | |
Collapse
|
30
|
Einaga N, Yoshida A, Noda H, Suemitsu M, Nakayama Y, Sakurada A, Kawaji Y, Yamaguchi H, Sasaki Y, Tokino T, Esumi M. Assessment of the quality of DNA from various formalin-fixed paraffin-embedded (FFPE) tissues and the use of this DNA for next-generation sequencing (NGS) with no artifactual mutation. PLoS One 2017; 12:e0176280. [PMID: 28498833 PMCID: PMC5428915 DOI: 10.1371/journal.pone.0176280] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 04/07/2017] [Indexed: 01/09/2023] Open
Abstract
Formalin-fixed, paraffin-embedded (FFPE) tissues used for pathological diagnosis are valuable for studying cancer genomics. In particular, laser-capture microdissection of target cells determined by histopathology combined with FFPE tissue section immunohistochemistry (IHC) enables precise analysis by next-generation sequencing (NGS) of the genetic events occurring in cancer. The result is a new strategy for a pathological tool for cancer diagnosis: 'microgenomics'. To more conveniently and precisely perform microgenomics, we revealed by systematic analysis the following three details regarding FFPE DNA compared with paired frozen tissue DNA. 1) The best quality of FFPE DNA is obtained by tissue fixation with 10% neutral buffered formalin for 1 day and heat treatment of tissue lysates at 95°C for 30 minutes. 2) IHC staining of FFPE tissues decreases the quantity and quality of FFPE DNA to one-fourth, and antigen retrieval (at 120°C for 15 minutes, pH 6.0) is the major reason for this decrease. 3) FFPE DNA prepared as described herein is sufficient for NGS. For non-mutated tissue specimens, no artifactual mutation occurs during FFPE preparation, as shown by precise comparison of NGS of FFPE DNA and paired frozen tissue DNA followed by validation. These results demonstrate that even FFPE tissues used for routine clinical diagnosis can be utilized to obtain reliable NGS data if appropriate conditions of fixation and validation are applied.
Collapse
Affiliation(s)
- Naoki Einaga
- Department of Pathology, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan
| | - Akio Yoshida
- Department of Pathology, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan
- Department of Orthopaedic Surgery, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan
| | - Hiroko Noda
- Department of Pathology, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan
| | - Masaaki Suemitsu
- Department of Pathology, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan
- Department of Oral Pathology, Nihon University School of Dentistry at Matsudo, Matsudo, Chiba, Japan
| | - Yuki Nakayama
- Department of Pathology, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan
| | - Akihisa Sakurada
- Department of Pathology, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan
| | - Yoshiko Kawaji
- Department of Pathology, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan
| | - Hiromi Yamaguchi
- Department of Pathology, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan
| | - Yasushi Sasaki
- Department of Medical Genome Sciences, Sapporo Medical University, Sapporo, Hokkaido, Japan
| | - Takashi Tokino
- Department of Medical Genome Sciences, Sapporo Medical University, Sapporo, Hokkaido, Japan
| | - Mariko Esumi
- Department of Pathology, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan
- * E-mail:
| |
Collapse
|
31
|
Ni Y, Cao B, Ma T, Niu G, Huo Y, Huang J, Chen D, Liu Y, Yu B, Zhang MQ, Niu H. Super-resolution imaging of a 2.5 kb non-repetitive DNA in situ in the nuclear genome using molecular beacon probes. eLife 2017; 6. [PMID: 28485713 PMCID: PMC5433842 DOI: 10.7554/elife.21660] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 04/24/2017] [Indexed: 12/17/2022] Open
Abstract
High-resolution visualization of short non-repetitive DNA in situ in the nuclear genome is essential for studying looping interactions and chromatin organization in single cells. Recent advances in fluorescence in situ hybridization (FISH) using Oligopaint probes have enabled super-resolution imaging of genomic domains with a resolution limit of 4.9 kb. To target shorter elements, we developed a simple FISH method that uses molecular beacon (MB) probes to facilitate the probe-target binding, while minimizing non-specific fluorescence. We used three-dimensional stochastic optical reconstruction microscopy (3D-STORM) with optimized imaging conditions to efficiently distinguish sparsely distributed Alexa-647 from background cellular autofluorescence. Utilizing 3D-STORM and only 29–34 individual MB probes, we observed 3D fine-scale nanostructures of 2.5 kb integrated or endogenous unique DNA in situ in human or mouse genome, respectively. We demonstrated our MB-based FISH method was capable of visualizing the so far shortest non-repetitive genomic sequence in 3D at super-resolution. DOI:http://dx.doi.org/10.7554/eLife.21660.001
Collapse
Affiliation(s)
- Yanxiang Ni
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China.,MOE Key laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST; School of Medicine, Tsinghua University, Beijing, China.,School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Bo Cao
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Tszshan Ma
- MOE Key laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST; School of Medicine, Tsinghua University, Beijing, China
| | - Gang Niu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China.,LemonData Biotech, Shenzhen, China.,Phil Rivers Technology, Beijing, China
| | - Yingdong Huo
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Jiandong Huang
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Danni Chen
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Yi Liu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Bin Yu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Michael Q Zhang
- MOE Key laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST; School of Medicine, Tsinghua University, Beijing, China.,Department of Biological Sciences, Center for Systems Biology, The University of Texas at Dallas, Dallas, United States
| | - Hanben Niu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| |
Collapse
|
32
|
Wen X, Jeong S, Kim Y, Bae JM, Cho NY, Kim JH, Kang GH. Improved results of LINE-1 methylation analysis in formalin-fixed, paraffin-embedded tissues with the application of a heating step during the DNA extraction process. Clin Epigenetics 2017; 9:1. [PMID: 28149329 PMCID: PMC5270344 DOI: 10.1186/s13148-016-0308-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 12/26/2016] [Indexed: 12/20/2022] Open
Abstract
Background Formalin-fixed, paraffin-embedded (FFPE) tissues are important resources for profiling DNA methylation changes and for studying a variety of diseases. However, formalin fixation introduces inter-strand crosslinking, which might cause incomplete bisulfite conversion of unmethylated cytosines, which might lead to falsely elevated measurements of methylation levels in pyrosequencing assays. Long interspersed nucleotide element-1 (LINE-1) is a major constituent of repetitive transposable DNA elements, and its methylation is referred to correlates with global DNA methylation. To identify whether formalin fixation might impact the measured values of methylation in LINE-1 repetitive elements and whether prolonged heat-induced denaturation of DNA might reduce the artificial increases in measured values caused by formalin fixation, we analyzed paired fresh-frozen (FF) and FFPE xenograft tissue samples for their methylation levels in LINE-1 using a pyrosequencing assay. To further confirm the effect of a heating step in the measurement of LINE-1 or single gene methylation levels, we analyzed FFPE tissue samples of gastric cancer and colorectal cancer for their methylation status in LINE-1 and eight single genes, respectively. Results Formalin fixation led to an increase in the measured values of LINE-1 methylation regardless of the duration of fixation. Prolonged heating of the DNA at 95 °C for 30 min before bisulfite conversion was found (1) to decrease the discrepancy in the measured values between the paired FF and FFPE tissue samples, (2) to decrease the standard deviation of the measured value of LINE-1 methylation levels in FFPE tissue samples of gastric cancer, and (3) to improve the performance in the measurement of single gene methylation levels in FFPE tissue samples of colorectal cancer. Conclusions Formalin fixation leads to artificial increases in the measured values of LINE-1 methylation, and the application of prolonged heating of DNA samples decreases the discrepancy in the measured values of LINE-1 methylation between paired FF and FFPE tissue samples. The application of prolonged heating of DNA samples improves bisulfite conversion-based measurement of LINE-1 or single gene methylation levels in FFPE tissue samples. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0308-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Xianyu Wen
- Department of Pathology, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-744, South Korea.,Laboratory of Epigenetics, Seoul National University College of Medicine, Seoul, South Korea
| | - Seorin Jeong
- Laboratory of Epigenetics, Seoul National University College of Medicine, Seoul, South Korea
| | - Younghoon Kim
- Department of Pathology, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-744, South Korea.,Laboratory of Epigenetics, Seoul National University College of Medicine, Seoul, South Korea
| | - Jeong Mo Bae
- Laboratory of Epigenetics, Seoul National University College of Medicine, Seoul, South Korea.,Department of Pathology, SMG-SNU Boramae Medical Centre, Seoul, South Korea
| | - Nam Yun Cho
- Laboratory of Epigenetics, Seoul National University College of Medicine, Seoul, South Korea
| | - Jung Ho Kim
- Laboratory of Epigenetics, Seoul National University College of Medicine, Seoul, South Korea.,Department of Pathology, SMG-SNU Boramae Medical Centre, Seoul, South Korea
| | - Gyeong Hoon Kang
- Department of Pathology, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-744, South Korea.,Laboratory of Epigenetics, Seoul National University College of Medicine, Seoul, South Korea
| |
Collapse
|
33
|
Bajpai SK, Bajpai M, Shah FF. Alginate dialdehyde (AD)-crosslinked casein films: synthesis, characterization and water absorption behavior. Des Monomers Polym 2016. [DOI: 10.1080/15685551.2016.1169374] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
|
34
|
Hoffman EA, Frey BL, Smith LM, Auble DT. Formaldehyde crosslinking: a tool for the study of chromatin complexes. J Biol Chem 2015; 290:26404-11. [PMID: 26354429 DOI: 10.1074/jbc.r115.651679] [Citation(s) in RCA: 229] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Formaldehyde has been used for decades to probe macromolecular structure and function and to trap complexes, cells, and tissues for further analysis. Formaldehyde crosslinking is routinely employed for detection and quantification of protein-DNA interactions, interactions between chromatin proteins, and interactions between distal segments of the chromatin fiber. Despite widespread use and a rich biochemical literature, important aspects of formaldehyde behavior in cells have not been well described. Here, we highlight features of formaldehyde chemistry relevant to its use in analyses of chromatin complexes, focusing on how its properties may influence studies of chromatin structure and function.
Collapse
Affiliation(s)
- Elizabeth A Hoffman
- From the Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908 and
| | - Brian L Frey
- the Department of Chemistry and Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706
| | - Lloyd M Smith
- the Department of Chemistry and Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706
| | - David T Auble
- From the Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908 and
| |
Collapse
|
35
|
Do H, Dobrovic A. Sequence Artifacts in DNA from Formalin-Fixed Tissues: Causes and Strategies for Minimization. Clin Chem 2015; 61:64-71. [DOI: 10.1373/clinchem.2014.223040] [Citation(s) in RCA: 331] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Abstract
BACKGROUND
Precision medicine is dependent on identifying actionable mutations in tumors. Accurate detection of mutations is often problematic in formalin-fixed paraffin-embedded (FFPE) tissues. DNA extracted from formalin-fixed tissues is fragmented and also contains DNA lesions that are the sources of sequence artifacts. Sequence artifacts can be difficult to distinguish from true mutations, especially in the context of tumor heterogeneity, and are an increasing interpretive problem in this era of massively parallel sequencing. Understanding of the sources of sequence artifacts in FFPE tissues and implementation of preventative strategies are critical to improve the accurate detection of actionable mutations.
CONTENT
This mini-review focuses on DNA template lesions in FFPE tissues as the source of sequence artifacts in molecular analysis. In particular, fragmentation, base modification (including uracil and thymine deriving from cytosine deamination), and abasic sites are discussed as indirect or direct sources of sequence artifacts. We discuss strategies that can be implemented to minimize sequence artifacts and to distinguish true mutations from sequence artifacts. These strategies are applicable for the detection of actionable mutations in both single amplicon and massively parallel amplicon sequencing approaches.
SUMMARY
Because FFPE tissues are usually the only available material for DNA analysis, it is important to maximize the accurate informational content from FFPE DNA. Careful consideration of each step in the work flow is needed to minimize sequence artifacts. In addition, validation of actionable mutations either by appropriate experimental design or by orthogonal methods should be considered.
Collapse
Affiliation(s)
- Hongdo Do
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- Department of Pathology, University of Melbourne, Parkville, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
| | - Alexander Dobrovic
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- Department of Pathology, University of Melbourne, Parkville, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
| |
Collapse
|
36
|
Viswanathan R, Hoffman EA, Shetty SJ, Bekiranov S, Auble DT. Analysis of chromatin binding dynamics using the crosslinking kinetics (CLK) method. Methods 2014; 70:97-107. [PMID: 25448301 PMCID: PMC4267959 DOI: 10.1016/j.ymeth.2014.10.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 10/17/2014] [Accepted: 10/27/2014] [Indexed: 02/03/2023] Open
Abstract
Transcription factor binding sites in chromatin are routinely inventoried by the chromatin immunoprecipitation assay, and these binding patterns can provide precise and detailed information about cell state. However, some fundamental molecular questions regarding transcription factor function require an understanding of in vivo binding dynamics as well as location information. Here we describe the crosslinking kinetics (CLK) assay, in which the time-dependence of formaldehyde crosslinking is used to extract on- and off-rates for chromatin binding in vivo.
Collapse
Affiliation(s)
- Ramya Viswanathan
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, United States
| | - Elizabeth A Hoffman
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, United States
| | - Savera J Shetty
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, United States
| | - Stefan Bekiranov
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, United States
| | - David T Auble
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, United States.
| |
Collapse
|