CN113270142A - Space transcriptome sequencing decoding method based on transient coding - Google Patents
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Abstract
The invention discloses a transient coding-based spatial transcriptome sequencing decoding method, which comprises the following steps: designing a space information coding microsphere based on oligonucleotide chain coding; designing and using a transient coding primer; tissue section processing and capturing messenger RNA; and (4) library construction, sequencing, analysis and positioning. The method can obtain high-resolution space transcriptome sequencing, and can reach subcellular resolution (5 mu m) under the limit condition, thereby accurately obtaining the gene expression condition on a specific site in a tissue slice; the method is low in cost, avoids high-cost optical spatial position information decoding, and enables the method to perform spatial transcriptome sequencing at the cost similar to that of single-cell transcriptome sequencing.
Description
Technical Field
The invention relates to a two-dimensional space position information decoding method for space transcriptome sequencing, in particular to a space transcriptome sequencing method for acquiring tissue slice transcriptome information and two-dimensional space position information at one time through high-throughput sequencing.
Background
The notion that cells are the fundamental unit of life has long been a consensus among a large number of researchers. In the case of multicellular organisms, although the functions of individual cells are integrally coordinated and controlled, each cell is an independent, self-controlled, highly ordered metabolic system, and the metabolic activities of the whole organism are performed in units of cells. It has been found that for a single individual of most organisms other than unicellular organisms, different cell subsets in various tissues in the body contain a set of roughly the same genetic information, i.e., a complete set of genes. The stable differences in the morphology and function of various cell subtypes within a single individual are caused by the expression of their unique transcriptomes and proteomes by different cells at the molecular biological level. Therefore, sequencing the transcriptome in the cell is of great significance for understanding the rules of the cell in the life processes of growth, differentiation, senescence, apoptosis and the like.
However, most of the conventional sequencing samples employ population cells, which results in the final acquisition of transcriptome information as an average reading of the entire tissue sample, masking cell-to-cell heterogeneity and the discovery of new cell types. And for the same kind of cells, significant micro-heterogeneity exists among different individuals, so that the life interaction rule on the single cell level is difficult to reflect. Meanwhile, when the tissue or organ to be studied is operated, the first step is to carry out enzymolysis on the tissue or organ to form cell suspension, which can cause the loss of position information between cells, so that the finally obtained transcriptome of a single cell cannot be related to the position of the single cell in the tissue, and the research and understanding of the interaction mode among cell subtypes in the tissue by a researcher are not facilitated. The existing space transcriptome sequencing method mostly depends on multiple rounds of in situ hybridization or in situ sequencing by using a fluorescent probe, and usually needs a set of expensive optical platform and long decoding time in one time.
Disclosure of Invention
The purpose of the invention is as follows: aiming at the defects of the existing decoding method and technology of the spatial transcriptome spatial position information, the invention provides a sequencing method and technology which can simultaneously obtain the transcriptome with single cell resolution or subcellular resolution and the two-dimensional spatial position information thereof in a tissue slice through single high-throughput sequencing, and is beneficial to better researching the gene expression and histopathology molecular mechanism of cells in tissues so as to more comprehensively understand the functions of tissues and organs.
The technical scheme is as follows: the invention provides a space transcriptome sequencing decoding method based on transient coding, which comprises the following steps:
(1) designing a space information coding microsphere based on oligonucleotide chain coding;
(2) designing and using a transient coding primer;
(3) tissue section processing and capturing messenger RNA;
(4) and (4) library construction, sequencing, analysis and positioning.
Further, the design method of the step (1) is as follows: selecting monodisperse magnetic beads with carboxyl groups on the surface, and reacting the carboxyl groups (-COOH) on the surface of the microspheres with 5' -NH under the catalytic action of 1-ethyl- (3-dimethylaminopropyl) carbodiimide hydrochloride (EDC)2The modified universal joint primer is condensed to form an amido bond (-CO-NH-), and then the space information coding generation primer and the joint primer are extended complementarily, so that the mRNA capture primer with the space information coding is generated on the surface of the microsphere.
Further, each microsphere has 10 attached thereto7-9A nucleotide sequence.
Further, the sequence information of the nucleotide sequence includes (5 '-3'): a disruption group (UUUUU), an amplification and sequencing linker sequence (PCR-handle), a spatial position coding sequence (barcodes), a molecular tag sequence (UMI), and an mRNA capture probe sequence (Poly-T).
Furthermore, the microspheres are monodisperse magnetic microspheres, and the inner cores of the microspheres are SiO2Or polystyrene, with a layer of Fe coated over the inner core3O4The surface is wrapped with a chemical modification layer modified into carboxyl.
Furthermore, the particle size of the microspheres is 0.1-100 microns, and four particles of 4 microns, 10 microns, 20 microns and 40 microns are adopted in specific operation.
Further, the transient coding primer in step (2) is designed as follows: (5 '-3') batch schematic sequence (sign), transient coding sequence (barcodeA, barcodeB), captured sequence (Poly-a).
Further, the method for using the transient coding primer in the step (2) is as follows:
loading the spatial information coding magnetic beads into a PDMS or PMMA micropore plate, wherein the diameter and the depth of each micropore hole can ensure that only a single microsphere is filled into a single micropore; covering a micro-fluidic chip with a plurality of micro-fluidic channels (1-1000) on a micro-porous plate, adding each transient coding primer into each sample adding hole of the micro-fluidic chip according to a specific sequence, wherein the transient coding sequence in the transient coding primer is known, and capturing the transient coding primer corresponding to the two-dimensional space position information of the micro-fluidic chip by microspheres in each micro-hole through base complementary pairing.
Further, the microplate is manufactured as follows: the microporous plate is square, and the side length of the microporous plate is consistent with the width and length of the microfluidic chip; the diameter and depth of the micro-pores on the micro-pore plate can ensure that only a single micro-pore is filled with a single microsphere in one loading.
Further, the microfluidic chip is manufactured as follows: the microfluidic chip is rectangular, two ends of the microfluidic chip are respectively provided with a sample inlet and a sample outlet which penetrate through the chip and correspond to the number of microfluidic channels, and a pair of corresponding sample inlets and sample outlets are connected through the microfluidic channels on the lower surface of the microfluidic chip; the height of the micro-channel of the micro-flow channel connecting a pair of corresponding sample inlets and sample outlets is equal to the width of the micro-channel (1-1000 μm), and the interval between the micro-channels is half of the width of the micro-channel.
The preferred scheme is as follows:
the microsphere is monodisperse magnetic microsphere with carboxyl group on surface, the size of the microsphere can be 0.1 μm to 100 μm, the specific operation adopts four types of 4 μm, 10 μm, 20 μm and 40 μm, and the core of the magnetic bead is Fe3O4The surface is wrapped with SiO2Or a polystyrene layer. Having an amino group (NH) at the 5' end2-) the universal linker primer and the carboxyl group (-COOH) on the surface of the magnetic bead are condensed to form amido bond (-CO-NH-) under the catalysis of 1-ethyl- (3-dimethylaminopropyl) carbodiimide hydrochloride (EDC), and then the generated primer is extended complementarily with the linker primer through spatial information coding, thereby forming 10 on the surface of the magnetic bead7-9With spaces for stripsThe information-encoding mRNA capture primer whose nucleotide sequence information includes (5 '-3'): a fragmentation group (UUUUUU), an amplification and sequencing linker sequence (PCR-handle), a space coding sequence (barcodes), a molecular tag sequence (UMI) and an mRNA capture probe sequence (Poly-T), wherein the barcodes among the space information coding microspheres are different from each other, and the UMI on the mRNA capture primer with the space information coding on a single microsphere is different from each other.
The PDMS microporous plate is manufactured by inverse mould manufacturing of an SU-8 silicon chip with an inverse structure, and one side face of the manufactured microporous plate is randomly selected to be marked as the X direction, and the face perpendicular to the side face is marked as the Y direction. The magnetic microspheres are loaded in a microporous plate with a corresponding size after incomplete capture primers are removed through enzymolysis, the hole diameter and the hole depth of a single micropore on the microporous plate are equal to 120-150% of the particle size of a magnetic bead, so that the single micropore is provided with only one spatial information coding microsphere, and the hole distance is half of the hole diameter. The microfluidic chip is designed to be rectangular, two ends of the microfluidic chip are respectively provided with small holes which penetrate through the chip and correspond to the number of microfluidic channels, the diameter of each small hole is 1-2 mm, the small holes are used for sampling and discharging transient coding primers, and the corresponding sampling ports are connected with the microfluidic channels of the lower surface of the microfluidic chip through the sampling ports.
Transient coding primer sequences were designed as (5 '-3'): (1) a batch signaling sequence (sign), which is fixed in sequence, known in sequence and corresponds to a batch of transient encoding primers and is used for explaining whether the transient encoding primer is a primer for carrying out X-axis encoding or a primer for carrying out Y-axis encoding; (2) transient coding sequences (barcodeA 1-n, barcodeB 1-n), the sequences being known and added in a particular order when used, X is added1-Xn、Y1-YnThe two-dimensional spatial position information of (a) is associated with the sequence thereof; captured sequence (Poly-A) was used for capture by primers with Poly-T on the surface of the spatial information encoding microspheres. Through 90 rotatory micropore boards for micro flow channel on the micro flow chip covers the micropore board with X earlier to being parallel later with X to the vertically form, and the micro flow chip has many micro flow channel (1-1000) and micro flow channel is parallel to each other when the micropore board flows through, and after the micro flow chip laminating was to the micropore board at every turn, according to specific order (X)1-Xn，Y1-Yn) And adding each transient coding primer into each sample adding hole of the microfluidic chip. After the micro-fluidic chip is used for respectively adding transient coding primers in the X direction and the Y direction to the microporous plate to encode the space position information of microspheres in the microporous plate, corresponding relations are generated between each magnetic bead in the microporous plate and two-dimensional space position information of the magnetic bead, and the magnetic beads are respectively marked as (X)a，Yb). This correspondence will be detected by high throughput sequencing after the sequencing by pooling. Thus, the preparation of the sequencing decoding micro-porous plate for tissue slice space transcriptome sequencing is completed.
The tissue to be analyzed is sliced and then attached to a microporous plate loaded with space information coding microspheres, and then the tissue slices are subjected to permeabilization treatment, so that mRNA in the tissue can permeate out to flow into micropores. In a proper buffer solution, mRNA capture primers with spatial information on the surfaces of the magnetic beads capture Poly-A tail ends on mRNA through Poly-T at the 3' end, so that the mRNA in a tissue section is bound to the magnetic beads. And then, adding reverse transcriptase and related reagents into the micropores for reverse transcription to synthesize a corresponding cDNA sequence, and after removing tissues on the surface of the microplate, cutting a breaking group (UUUUUUU) by using USER enzyme to release a spatial information coding primer carrying mRNA sequence information in the tissues.
Collecting the released space information coding primer carrying mRNA sequence information in the tissue into a centrifuge tube, and performing computer sequencing to obtain the sequence information of cDNA after library construction. And finally, performing bioinformatics analysis, classifying the transcriptome captured on the single microsphere and the transient coding primer together, and filling the transcriptome information back to the two-dimensional space position read out by the transient coding primer so as to achieve the purpose of spatial transcriptome sequencing.
The invention aims to provide a sequencing method and a sequencing technology which can realize sequencing of a single-cell resolution transcriptome in a tissue slice and acquire two-dimensional spatial position information of a single pixel point. The invention is used for carrying out transient coding on a micropore plate filled with space information coding microspheres, the sequence of transient coding primers is known and is added according to a specific sequence, so that a space information coding sequence filled with the microspheres in the micropore is linked with two-dimensional space position information of the micropore plate, the micropore plate is used for tissue section, transcriptome capture of single cell resolution is carried out on the tissue section, and then the microspheres which capture the transient coding primers and the transcriptome in the tissue are subjected to subsequent library building sequencing, so that the transcriptome information in the tissue section and the two-dimensional space position information thereof can be obtained simultaneously, namely the transcriptome sequencing of single cell resolution on a two-dimensional space is realized.
Has the advantages that:
1. the method can obtain high-resolution space transcriptome sequencing, and can reach subcellular resolution (5 mu m) under the limit condition, thereby accurately obtaining the gene expression condition on a specific site in a tissue slice;
2. the method is low in cost, avoids high-cost optical spatial position information decoding, and enables the method to perform spatial transcriptome sequencing at the cost similar to that of single-cell transcriptome sequencing.
Drawings
FIG. 1 is a schematic diagram of sequences on spatial information-encoded microspheres and sequences of transient encoding primers;
FIG. 2 is a schematic view of a microfluidic chip;
FIG. 3 is a flow chart of two-dimensional spatial position encoding and decoding of a microplate loaded with microspheres using microfluidic chips.
Detailed Description
Washing spatial information encoding microspheres with particle size of 10 μm with 1ml TE buffer (10mM Tris-HCl, 1mM EDTA) for three times, and dispersing in 1ml TE buffer to obtain final concentration of 106And (3) dripping 100 mu L of microsphere solution into a microporous plate with the hole diameter of 12 mu m and the hole depth of 12 mu m from the microsphere suspension per ml, then placing the microporous plate on a magnet and standing for 1min to improve the microsphere filling efficiency of the microporous plate, and marking the X direction and the Y direction on the microporous plate. Then covering the micro-flow channels on a microporous plate, adding transient coding primer solution with known sequence into the sample adding holes according to a certain sequence, connecting a negative pressure pump at the sample outlet, providing power to make the transient coding primer solution flow through the microporous plate through each micro-flow channel, and forming n on the microporous plate2([x1，y1]，[x1，y2]...[xn，yn]) And the spatial information coding sequence of the microsphere in the micropore is associated with the transient coding sequence of the two-dimensional space site.
Taking out the mouse brain tissue embedded and frozen in advance from a refrigerator at minus 80 ℃, transferring the mouse brain tissue to a frozen section machine after being placed in the refrigerator at minus 20 ℃ for 2 hours, setting the section thickness to be 10 mu m, then starting to section, attaching the obtained tissue section with the thickness of 10 mu m to a micropore plate loaded with space information coding microspheres and establishing position association in advance, and transferring the chip to a clean bench for the next experiment after finishing tissue attachment.
The microporous plate with the tissue slices is placed in an ultra-clean workbench, firstly, tissue permeabilization is carried out, I-type exonuclease is dripped on the tissue slices, incubation is carried out for 25min at 37 ℃, and then pepsin is added to keep the temperature at 37 ℃ for treatment for 10 min. After the permeabilization is complete, in situ reverse transcription of the mRNA is performed, and the cDNA strand is synthesized using the captured mRNA as a template. Subsequently, the tissue sections were subjected to digestion treatment with proteinase K at 56 ℃ for 1h, and the whole section tissues were completely cleaned. Finally, the cleavage groups (UUUUUU) on the space capture primers are cut by using USER enzyme, and the cDNA with the space information coding sequence is released from the surface of the microspheres and collected into a centrifuge tube. The collected cDNA sequence is subjected to library construction and on-machine sequencing, transcriptome information of single cell resolution or subcellular resolution in the tissue slice can be obtained at one time by analyzing the obtained sequence information, two-dimensional spatial position information of the transcriptome information is obtained by decoding the association of the spatial information coding sequence and the transient coding sequence, and finally the transcriptome information is visualized on the morphology contour of the tissue.
FIG. 1 is a structural diagram of a coding sequence on a spatial information coding microsphere, which comprises: a cleavage site sequence (UUUUU), an amplification and sequencing linker sequence (PCR-handle), a space coding sequence (barcodes), a molecular tag sequence (UMI), and a messenger RNA capture sequence (Poly-T); the structure diagram of the transient coding primer sequence comprises: batch schematic sequence (sign), transient coding sequence (barcodeA, barcodeB), captured sequence (Poly-a).
FIG. 2 is a schematic diagram of two microfluidic chips for transporting transient state coding primers, the two microfluidic chips have the same number of sample outlets and sample inlets, the number of the sample outlets and the number of the sample inlets are equal, the diameter of the sample outlet and the sample inlet is 2mm, the sample outlet and the sample inlet are connected through a microfluidic channel, and the width range of the microfluidic channel is 4-250 μm.
FIG. 3 is a diagram of the overall process of two rounds of transient encoding of a microplate using a microfluidic chip and spatial transcriptome sequencing of histological sections using a microplate, and finally obtaining single-cell resolution transcriptome and its two-dimensional spatial position in histological sections by biochemical analysis.
Claims (10)
1. A spatial transcriptome sequencing decoding method based on transient coding is characterized in that: the method comprises the following steps:
(1) designing a space information coding microsphere based on oligonucleotide chain coding;
(2) designing and using a transient coding primer;
(3) tissue section processing and capturing messenger RNA;
(4) and (4) library construction, sequencing, analysis and positioning.
2. The transient coding-based spatial transcriptome sequencing decoding method of claim 1, wherein: the design method of the step (1) is as follows: selecting monodisperse magnetic beads with carboxyl groups on the surface, and reacting the carboxyl groups (-COOH) on the surface of the microspheres with 5' -NH under the catalytic action of 1-ethyl- (3-dimethylaminopropyl) carbodiimide hydrochloride (EDC)2The modified universal joint primer is condensed to form an amido bond (-CO-NH-), and then the space information coding generation primer and the joint primer are extended complementarily, so that the mRNA capture primer with the space information coding is generated on the surface of the microsphere.
3. The transient coding-based spatial transcriptome sequencing decoding method of claim 2, wherein: each microsphere has 10 attached thereto7-9A nucleotide sequence.
4. The transient coding-based spatial transcriptome sequencing decoding method of claim 3, wherein: the sequence information of the nucleotide sequence includes (5 '-3'): a disruption group (UUUUU), an amplification and sequencing linker sequence (PCR-handle), a spatial position coding sequence (barcodes), a molecular tag sequence (UMI), and an mRNA capture probe sequence (Poly-T).
5. The transient coding-based spatial transcriptome sequencing decoding method of claim 2, wherein: the microsphere is a monodisperse magnetic microsphere, and the microsphere core is SiO2Or polystyrene, with a layer of Fe coated over the inner core3O4The surface is wrapped with a chemical modification layer modified into carboxyl.
6. The transient coding-based spatial transcriptome sequencing decoding method of claim 5, wherein: the particle size of the microspheres is 0.1-100 microns, and four microspheres with particle sizes of 4 microns, 10 microns, 20 microns and 40 microns are adopted in specific operation.
7. The transient coding-based spatial transcriptome sequencing decoding method of claim 1, wherein: the transient coding primer in the step (2) is designed as follows: (5 '-3') batch schematic sequence (sign), transient coding sequence (barcodeA, barcodeB), captured sequence (Poly-a).
8. The transient coding-based spatial transcriptome sequencing decoding method of claim 1, wherein: the application method of the transient coding primer in the step (2) is as follows:
(1) loading the spatial information coding magnetic beads into a PDMS or PMMA micropore plate, wherein the diameter and the depth of each micropore hole can ensure that only a single microsphere is filled into a single micropore; covering a micro-fluidic chip with a plurality of micro-fluidic channels (1-1000) on a micro-porous plate, adding each transient coding primer into each sample adding hole of the micro-fluidic chip according to a specific sequence, wherein the transient coding sequence in the transient coding primer is known, and capturing the transient coding primer corresponding to the two-dimensional space position information of the micro-fluidic chip by microspheres in each micro-hole through base complementary pairing.
9. The transient coding-based spatial transcriptome sequencing decoding method of claim 8, wherein: the micro-porous plate is manufactured as follows: the microporous plate is square, and the side length of the microporous plate is consistent with the width and length of the microfluidic chip; the diameter and depth of the micro-pores on the micro-pore plate can ensure that only a single micro-pore is filled with a single microsphere in one loading.
10. The transient coding-based spatial transcriptome sequencing decoding method of claim 8, wherein: the microfluidic chip is manufactured as follows: the microfluidic chip is rectangular, two ends of the microfluidic chip are respectively provided with a sample inlet and a sample outlet which penetrate through the chip and correspond to the number of microfluidic channels, and a pair of corresponding sample inlets and sample outlets are connected through the microfluidic channels on the lower surface of the microfluidic chip; the height of the micro-channel of the micro-flow channel connecting a pair of corresponding sample inlets and sample outlets is equal to the width of the micro-channel (1-1000 μm), and the interval between the micro-channels is half of the width of the micro-channel.
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