Introduction to bioimaging-based spatial multi-omic novel methods

Abstract

Background: Spatial multi-omics are demonstrated to be a powerful method to assist researchers on genetic studies. In this review, bioimaging-based spatial multi-omics techniques such as seqFISH+, merFISH, integrated DNA seqFISH+, DNA merFISH, and MINA are introduced along with each technique’s probe design, development, and imaging processes.

Results: seqFISH employed 4–5 fluorophores to barcode and conducted multiple rounds of hybridization, in order that mRNA can be identified through color-coding. seqFISH+ added 60 pseudo-color and distributed them equally into three channels to enhance imaging power, in order that i.e., 24,000 genes can be imaged in total. merFISH utilized 4 out 16 Hamming distance to innovatively provide a robust error-detecting method. MINA, a methodology combining merFISH (multiplexed error-robust fluorescence in situ hybridization) and chromosomal tracing, enabled multiplexed genomic architecture imaged in mammalian single cells. Optical reconstruction of chromatin architecture (ORCA) a method that could conduct DNA path tracing in nanoscale manner with kilobase resolution, an FISH variation that improved genetic resolution, enable high-precision fiducial registration and sequential imaging, and utilized Oligopaint probe to hybridize the short genomic region ranging from 2 to 10 kilobase. ORCA then prescribes these short section primary probes with individual barcodes to attach fluorophore and to be imaged.

Conclusion: This review concentrated on providing a comprehensive overview for these spatial-multi-omics techniques with the intention on helping researchers on selecting appropriate technique for their research.

Author summary

In this review, we introduced five different multiplex FISH methods used for image-based spatial multi-omics: seqFISH+, merFISH, DNA seqFISH+, DNA merFISH, and MINA. We provided a systematic collective perspective to review these FISH methods that could significantly benefit researchers on conducting their studies in the field. Our study provided an informative survey on these multiplex FISH methods. Therefore, this review would provide better understanding for researchers in the community to help them select the proper method, in order to understand the molecular mechanism in life sciences.

Graphical abstract

Keywords

FISH / multiplex FISH / super-resolution imaging / gene regulation

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Conflicts of interest The authors Yan Yan, Liheng Yang, Leyuan Meng, Haochen Su, Cheng Zhou, Le Yu, Zhengtu Li, Xu Zhang, Huihua Cai and Juntao Gao declare that they have no competing interests.

The article is a review and does not contain any human or animal subjects performed by any of the authors.

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