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Liu S, Punthambaker S, Iyer EPR, Ferrante T, Goodwin D, Fürth D, Pawlowski AC, Jindal K, Tam JM, Mifflin L, Alon S, Sinha A, Wassie AT, Chen F, Cheng A, Willocq V, Meyer K, Ling KH, Camplisson CK, Kohman RE, Aach J, Lee JH, Yankner BA, Boyden ES, Church GM. Barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel in situ analyses. Nucleic Acids Res 2021; 49:e58. [PMID: 33693773 PMCID: PMC8191787 DOI: 10.1093/nar/gkab120] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 01/29/2021] [Accepted: 03/02/2021] [Indexed: 12/13/2022] Open
Abstract
We present barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel insitu analyses (BOLORAMIS), a reverse transcription-free method for spatially-resolved, targeted, in situ RNA identification of single or multiple targets. BOLORAMIS was demonstrated on a range of cell types and human cerebral organoids. Singleplex experiments to detect coding and non-coding RNAs in human iPSCs showed a stem-cell signature pattern. Specificity of BOLORAMIS was found to be 92% as illustrated by a clear distinction between human and mouse housekeeping genes in a co-culture system, as well as by recapitulation of subcellular localization of lncRNA MALAT1. Sensitivity of BOLORAMIS was quantified by comparing with single molecule FISH experiments and found to be 11%, 12% and 35% for GAPDH, TFRC and POLR2A, respectively. To demonstrate BOLORAMIS for multiplexed gene analysis, we targeted 96 mRNAs within a co-culture of iNGN neurons and HMC3 human microglial cells. We used fluorescence in situ sequencing to detect error-robust 8-base barcodes associated with each of these genes. We then used this data to uncover the spatial relationship among cells and transcripts by performing single-cell clustering and gene–gene proximity analyses. We anticipate the BOLORAMIS technology for in situ RNA detection to find applications in basic and translational research.
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Affiliation(s)
- Songlei Liu
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sukanya Punthambaker
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Eswar P R Iyer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Thomas Ferrante
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Daniel Goodwin
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Media Arts and Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Daniel Fürth
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Andrew C Pawlowski
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Kunal Jindal
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Jenny M Tam
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Lauren Mifflin
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Shahar Alon
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Media Arts and Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anubhav Sinha
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Media Arts and Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Asmamaw T Wassie
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Media Arts and Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Fei Chen
- Media Arts and Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Broad Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Anne Cheng
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Valerie Willocq
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Katharina Meyer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - King-Hwa Ling
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Conor K Camplisson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Richie E Kohman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - John Aach
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Je Hyuk Lee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Bruce A Yankner
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Edward S Boyden
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Media Arts and Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USAHoward Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
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