A High-Throughput PIXUL–Matrix-Based Toolbox to Profile Frozen and Formalin-Fixed Paraffin-Embedded Tissues Multiomes

Laboratory Investigation - Tập 104 - Trang 100282 - 2024
Daniel Mar1,2, Ilona M. Babenko3, Ran Zhang4, William Stafford Noble4,5, Oleg Denisenko1, Tomas Vaisar3, Karol Bomsztyk1,2,6
1UW Medicine South Lake Union, University of Washington, Seattle, Washington
2Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington
3Diabetes Institute, University of Washington, Seattle, Washington
4Department of Genome Sciences, University of Washington, Seattle, Washington
5Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington
6Matchstick Technologies, Inc, Kirkland, Washington

Tài liệu tham khảo

Krassowski, 2020, State of the field in multi-omics research: from computational needs to data mining and sharing, Front Genet, 11, 10.3389/fgene.2020.610798 Subramanian, 2020, Multi-omics data integration, interpretation, and its application, Bioinform Biol Insights, 14, 10.1177/1177932219899051 Ureta-Vidal, 2003, Comparative genomics: genome-wide analysis in metazoan eukaryotes, Nat Rev Genet, 4, 251, 10.1038/nrg1043 Bernstein, 2010, The NIH Roadmap Epigenomics Mapping Consortium, Nat Biotechnol, 28, 1045, 10.1038/nbt1010-1045 Buccitelli, 2020, mRNAs, proteins and the emerging principles of gene expression control, Nat Rev Genet, 21, 630, 10.1038/s41576-020-0258-4 Coego, 2023, Epitranscriptomics: new players in an old game, Biochem Soc Trans, 51, 783, 10.1042/BST20221417 Ranish, 2003, The study of macromolecular complexes by quantitative proteomics, Nat Genet, 33, 349, 10.1038/ng1101 Pinu, 2019, Systems biology and multi-omics integration: viewpoints from the metabolomics research community, Metabolites, 9, 76, 10.3390/metabo9040076 Hasin, 2017, Multi-omics approaches to disease, Genome Biol, 18, 83, 10.1186/s13059-017-1215-1 Eddy, 2020, Integrated multi-omics approaches to improve classification of chronic kidney disease, Nat Rev Nephrol, 16, 657, 10.1038/s41581-020-0286-5 Lim, 2011, Before you analyze a human specimen, think quality, variability, and bias, Anal Chem, 83, 8, 10.1021/ac1018974 Agrawal, 2018, Understanding preanalytical variables and their effects on clinical biomarkers of oncology and immunotherapy, Semin Cancer Biol, 52, 26, 10.1016/j.semcancer.2017.12.008 Neumeister, 2018, Tumor pre-analytics in molecular pathology: impact on protein expression and analysis, Curr Pathobiol Rep, 6, 265, 10.1007/s40139-018-0179-5 Romani, 2018, Epigenetic targeting of glioblastoma, Front Oncol, 8, 448, 10.3389/fonc.2018.00448 Kokkat, 2013, Archived formalin-fixed paraffin-embedded (FFPE) blocks: a valuable underexploited resource for extraction of DNA, RNA, and protein, Biopreserv Biobank, 11, 101, 10.1089/bio.2012.0052 Amatori, 2022, The current state of chromatin immunoprecipitation (ChIP) from FFPE tissues, Int J Mol Sci, 23, 1103, 10.3390/ijms23031103 Bomsztyk, 2019, PIXUL-ChIP: integrated high-throughput sample preparation and analytical platform for epigenetic studies, Nucleic Acids Res, 47, e69, 10.1093/nar/gkz222 Levy, 2022, dCas9 fusion to computer-designed PRC2 inhibitor reveals functional TATA box in distal promoter region, Cell Rep, 38, 10.1016/j.celrep.2022.110457 Kanter, 2019, Increased apolipoprotein C3 drives cardiovascular risk in type 1 diabetes, J Clin Invest, 129, 4165, 10.1172/JCI127308 Schactler, 2023, CryoGrid-PIXUL-RNA: high throughput RNA isolation platform for tissue transcript analysis, BMC Genomics, 24, 446, 10.1186/s12864-023-09527-7 Bomsztyk, 2013, Synchronous recruitment of epigenetic modifiers to endotoxin synergistically activated Tnf-alpha gene in acute kidney injury, PLoS One, 8, 10.1371/journal.pone.0070322 Yu, 2011, Microplate-based platform for combined chromatin and DNA methylation immunoprecipitation assays, BMC Mol Biol, 12, 49, 10.1186/1471-2199-12-49 Flanagin, 2008, Microplate-based chromatin immunoprecipitation method, Matrix ChIP: a platform to study signaling of complex genomic events, Nucleic Acids Res, 36, e17, 10.1093/nar/gkn001 Guo, 2007, Proteome analysis of microdissected formalin-fixed and paraffin-embedded tissue specimens, J Histochem Cytochem, 55, 763, 10.1369/jhc.7A7177.2007 Zhong, 2019, Enhanced and controlled chromatin extraction from FFPE tissues and the application to ChIP-seq, BMC Genomics, 20, 249, 10.1186/s12864-019-5639-8 Langmead, 2012, Fast gapped-read alignment with Bowtie 2, Nat Methods, 9, 357, 10.1038/nmeth.1923 Hughes, 2019, A standardized and reproducible proteomics protocol for bottom-up quantitative analysis of protein samples using SP3 and mass spectrometry, Methods Mol Biol, 1959, 65, 10.1007/978-1-4939-9164-8_5 Stejskal, 2021, Ultrasensitive NanoLC-MS of subnanogram protein samples using second generation micropillar array LC technology with Orbitrap Exploris 480 and FAIMS PRO, Anal Chem, 93, 8704, 10.1021/acs.analchem.1c00990 Libbrecht, 2019, A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types, Genome Biol, 20, 180, 10.1186/s13059-019-1784-2 Hoffman, 2012, Unsupervised pattern discovery in human chromatin structure through genomic segmentation, Nat Methods, 9, 473, 10.1038/nmeth.1937 Dietrich, 2013, Improved PCR performance using template DNA from formalin-fixed and paraffin-embedded tissues by overcoming PCR inhibition, PLoS One, 8, 10.1371/journal.pone.0077771 Hennig, 2010, Automated extraction of DNA and RNA from a single formalin-fixed paraffin-embedded tissue section for analysis of both single-nucleotide polymorphisms and mRNA expression, Clin Chem, 56, 1845, 10.1373/clinchem.2010.151233 Pikor, 2011, DNA extraction from paraffin embedded material for genetic and epigenetic analyses, J Vis Exp, 49, 2763 Font-Tello, 2020, FiTAc-seq: fixed-tissue ChIP-seq for H3K27ac profiling and super-enhancer analysis of FFPE tissues, Nat Protoc, 15, 2503, 10.1038/s41596-020-0340-6 Shi, 2019, New dimensions of antigen retrieval technique: 28 years of development, practice, and expansion, Appl Immunohistochem Mol Morphol, 27, 715, 10.1097/PAI.0000000000000778 Amatori, 2018, Epigenomic profiling of archived FFPE tissues by enhanced PAT-ChIP (EPAT-ChIP) technology, Clin Epigenetics, 10, 143, 10.1186/s13148-018-0576-y Fanelli, 2010, Pathology tissue-chromatin immunoprecipitation, coupled with high-throughput sequencing, allows the epigenetic profiling of patient samples, Proc Natl Acad Sci U S A, 107, 21535, 10.1073/pnas.1007647107 Cejas, 2016, Chromatin immunoprecipitation from fixed clinical tissues reveals tumor-specific enhancer profiles, Nat Med, 22, 685, 10.1038/nm.4085 Brown, 2018, Total RNA extraction from tissues for microRNA and target gene expression analysis: not all kits are created equal, BMC Biotechnol, 18, 16, 10.1186/s12896-018-0421-6 Desrosiers, 1974, Identification of methylated nucleosides in messenger RNA from Novikoff hepatoma cells, Proc Natl Acad Sci U S A, 71, 3971, 10.1073/pnas.71.10.3971 Canaani, 1979, Identification and mapping of N6-methyladenosine containing sequences in simian virus 40 RNA, Nucleic Acids Res, 6, 2879, 10.1093/nar/6.8.2879 Moshitch-Moshkovitz, 2022, The epitranscriptome toolbox, Cell, 185, 764, 10.1016/j.cell.2022.02.007 Ke, 2017, m6A mRNA modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover, Genes Dev, 31, 990, 10.1101/gad.301036.117 Shi, 2017, New insights into 5hmC DNA modification: generation, distribution and function, Front Genet, 8, 100, 10.3389/fgene.2017.00100 Rose, 2014, Understanding the relationship between DNA methylation and histone lysine methylation, Biochim Biophys Acta, 1839, 1362, 10.1016/j.bbagrm.2014.02.007 Cuklina, 2020, Review of batch effects prevention, diagnostics, and correction approaches, Methods Mol Biol, 2051, 373, 10.1007/978-1-4939-9744-2_16 Wang, 2019, A deep proteome and transcriptome abundance atlas of 29 healthy human tissues, Mol Syst Biol, 15, 10.15252/msb.20188503 Khan, 2016, dbSUPER: a database of super-enhancers in mouse and human genome, Nucleic Acids Res, 44, D164, 10.1093/nar/gkv1002 Franks, 2017, Post-transcriptional regulation across human tissues, PLoS Comput Biol, 13, 10.1371/journal.pcbi.1005535 Edfors, 2016, Gene-specific correlation of RNA and protein levels in human cells and tissues, Mol Syst Biol, 12, 883, 10.15252/msb.20167144 Takemon, 2021, Proteomic and transcriptomic profiling reveal different aspects of aging in the kidney, elife, 10, 10.7554/eLife.62585 Goelz, 1985, Purification of DNA from formaldehyde fixed and paraffin embedded human tissue, Biochem Biophys Res Commun, 130, 118, 10.1016/0006-291X(85)90390-0 Jackson, 1989, Detection of measles virus RNA in paraffin-embedded tissue, Lancet, 1, 1391, 10.1016/S0140-6736(89)92837-7 Coates, 1991, Simplified procedures for applying the polymerase chain reaction to routinely fixed paraffin wax sections, J Clin Pathol, 44, 115, 10.1136/jcp.44.2.115 Sepp, 1994, Rapid techniques for DNA extraction from routinely processed archival tissue for use in PCR, J Clin Pathol, 47, 318, 10.1136/jcp.47.4.318 Kocjan, 2015, Commercially available kits for manual and automatic extraction of nucleic acids from formalin-fixed, paraffin-embedded (FFPE) tissues, Acta Dermatovenerol Alp Pannonica Adriat, 24, 47 McDonough, 2019, Use of FFPE-derived DNA in next generation sequencing: DNA extraction methods, PLoS One, 14, 10.1371/journal.pone.0211400 Patel, 2017, Reliability and performance of commercial RNA and DNA extraction kits for FFPE tissue cores, PLoS One, 12, 10.1371/journal.pone.0179732 Kresse, 2018, Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples, PLoS One, 13, 10.1371/journal.pone.0197456 Marczyk, 2019, The impact of RNA extraction method on accurate RNA sequencing from formalin-fixed paraffin-embedded tissues, BMC Cancer, 19, 1189, 10.1186/s12885-019-6363-0 Gao, 2020, Comparison of fresh frozen tissue with formalin-fixed paraffin-embedded tissue for mutation analysis using a multi-gene panel in patients with colorectal cancer, Front Oncol, 10, 310, 10.3389/fonc.2020.00310 Turnbull, 2020, Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: comparison of gene expression profiling approaches, BMC Bioinformatics, 21, 30, 10.1186/s12859-020-3365-5 Hood, 2005, Proteomic analysis of formalin-fixed prostate cancer tissue, Mol Cell Proteomics, 4, 1741, 10.1074/mcp.M500102-MCP200 Marchione, 2020, HYPERsol: High-quality data from archival FFPE tissue for clinical proteomics, J Proteome Res, 19, 973, 10.1021/acs.jproteome.9b00686 Coscia, 2020, A streamlined mass spectrometry-based proteomics workflow for large-scale FFPE tissue analysis, J Pathol, 251, 100, 10.1002/path.5420 Zhu, 2019, High-throughput proteomic analysis of FFPE tissue samples facilitates tumor stratification, Mol Oncol, 13, 2305, 10.1002/1878-0261.12570 Slobodin, 2017, Transcription impacts the efficiency of mRNA translation via co-transcriptional N6-adenosine methylation, Cell, 169, 326, 10.1016/j.cell.2017.03.031 Wiener, 2021, The epitranscriptome beyond m6A, Nat Rev Genet, 22, 119, 10.1038/s41576-020-00295-8 Yu, 2022, An evaluation of the National Institutes of Health grants portfolio: identifying opportunities and challenges for multi-omics research that leverage metabolomics data, Metabolomics, 18, 29, 10.1007/s11306-022-01878-8 Misra BB, Langefeld CD, Olivier M, Cox LA. Integrated omics: tools, advances, and future approaches. J Mol Endocrinol. Published online July 13, 2018. https://doi.org/10.1530/JME-18-0055 Piehowski, 2013, Sources of technical variability in quantitative LC-MS proteomics: human brain tissue sample analysis, J Proteome Res, 12, 2128, 10.1021/pr301146m