Patent Description:
Spatial sequencing is a collective term for methods that allow direct sequencing of the mRNA content of a cell in tissue context. These methods can on the one hand serve to analyze mRNA expression profiles of cells in a kind of highly multiplexed fluorescence in situ hybridization (FISH) assay.

On the other hand, in situ sequencing can also enable the read-out of mRNA sequence information, using specific mRNA-binding probes, which can take up a copy of predefined portion of specific mRNA or cDNA sequence ("<NPL>). Recently also in situ genome sequencing (IGS) approaches were published (<NPL>)). All in situ sequencing methods require a signal amplification step, which is in most cases performed by circularization of mRNA- or cDNA-binding probes or gDNA insert circularization by hairpin ligation and subsequent rolling circle amplification (RCA), creating a DNA molecule containing multiple copies of the probe and/or target sequence, the so called Nanoballs, Rolonies or Rolling circle amplification products (RCPs). As these are large molecules with size in nm or µm scale, the number of rolonies that can be formed within one cell is strictly limited by the size of this cell.

Furthermore, if the density of rolonies within cells is too high, discrimination of single mRNA signals during the optical detection step of the sequencing procedure is strongly impaired. As this is a major drawback of the technology, various techniques have been developed to circumvent this, e.g. design of smaller rolonies or generation and clearing of tissue-hydrogel complexes (<NPL>) or to expand the cellular target termed expansion sequencing (<NPL>)).

A general process for light-directed in situ barcoding is known from <CIT> and <CIT> and a general in situ enzymatic polynucleotide synthesis is described in <CIT> and <CIT>.

However, these methods do still not fully evade the inherent spatial limitations of in situ sequencing. Another approach avoids in situ signal amplification: In situ capturing relies on the transfer of mRNA molecules from tissue onto a surface coated with spots of barcoded primers, allowing backtracking of the ex situ gained sequence information to the specific tissue region the sequenced mRNA was extracted from. Nevertheless, this method is also limited, as RNA capture efficiency is restricted and resolution is poor (no single-cell analysis) due to the relatively large size of the barcoded capturing spots (<NPL>).

The present invention is directed to a method which uses optical methods to insert a barcode into a polynucleotide, preferable a DNA sequence. This code can be used to retrieve the position at which the coding was carried out. The aim here is that the limitations of existing in situ sequencing methods with regard to the number of measurable mRNA sequences in situ and also the expression dynamics are largely overcome. Optical coding can have a resolution in the range of one µm and a variability of the code that is sufficient for each cell to receive its own code in tissue sections of typical size. The proposed coding and decoding workflow is depicted in <FIG>.

The basic principle as disclosed herein is based on spatial barcoding of nucleic acids by universal template directed DNA synthesis. The method will subsequently be referred to as UNIT-DNA (UNIversal Template DNA).

Object of the invention is therefore a method for in situ spatial barcoding of a polynucleotide comprising a first and a second strand with a barcode nucleotide sequence characterized in that the first strand is provided at its <NUM>' end with an overhang of at least one universal base and the corresponding recessed <NUM>' end of the second strand of the polynucleotide with at least one nucleotide provided with a blocking group, wherein the blocking groups are removed from the incorporated nucleotides by irradiation with light.

Removal of the blocking group may be accomplished by either providing the blocking groups with appropriate photocleavable units or by adding cleaving reagents which are activated or provided in their active form by irradiation with light.

In a first variant of the method, the blocking groups are removed from the incorporated nucleotides by irradiation with light by providing a cleaving reagent, wherein the cleaving reagent is provided by irradiation of a progenitor of the cleaving reagent with light.

In a second variant of the method, wherein the nucleotides are provided with a photocleavable blocking group which is removed from the incorporated nucleotides by irradiation with light. Such reagents are known, for example "Cy5-TECP" which is cleaved by irradiation with light into the active cleaving reagent "Cy5".

In the following, the term "polynucleotide" refers to double stranded nucleic acids, like DNA, RNA, DNA-RNA, c-DNA, ssDNA and similars such as PNA or LNA.

The proposed UNIT-DNA workflow is depicted in <FIG> for the coding workflow according to embodiment A. Sample Preparation, tissue staining and imaging (Transmission, Fluorescence) is followed by segmentation or cluster analysis and calculation of masks for the structured illumination. For the decoding workflow depicted in <FIG> with UNIT-DNA, a tissue section is provided with spatial barcoding of cells, guided by structured illumination and cyclic incorporation of nucleotides (fixation of coded UNIT-DNA to tissue before cell release is not shown). Release of cells from tissue section and encapsulation of cells for single cell sequencing.

For the decoding workflow depicted in <FIG> according to embodiment H with UNIT-DNA, a tissue section is provided with spatial barcoding of target molecules guided by structured illumination and cyclic incorporation of nucleotides. The sequence obtained for the target mRNA, as well as the spatial barcode are annotated to images. Bioinformatics analysis and relation of the results to initial sample source complete the workflow.

The method of UNIT-DNA consists of providing a double stranded DNA molecule comprising a first and a second strand with a barcode nucleotide sequence with at least one <NUM> overhang, where the <NUM>' overhang includes at least one universal base and the recessed <NUM>' end has a free <NUM>'-OH.

<FIG> shows an example of a composition obtained by the method of the invention for a <NUM> bp double stranded nucleic acid (N) and for a <NUM> universal base (B) <NUM>'overhang. The number of bp for the double stranded nucleic acid or the number of universal bases for single stranded <NUM>' overhang may vary in length.

The term "universal base" refers to nucleotides which are able to bind to all natural nucleotides. Such universal base designs have been described in the literature mainly as part of degenerate primers or probes due to their property to pair with all natural bases (e. g by <NPL>).

The UNIT-DNA composition obtained by the method of the invention is shown in <FIG> and consists of a double stranded nucleic acid with at least one <NUM> overhang, where the <NUM>' overhang includes at least one universal base and the recessed <NUM>' end has a free <NUM>'-OH. Here as an example the UNIT-DNA composition for a <NUM> bp double stranded nucleic acid and for a <NUM> universal base <NUM> overhang is shown. N stands for natural base (G or C or T or A) and B stands for universal base.

<FIG> shows the basic principle of coding by the UNIT-DNA method. With the support of a polymerase (not shown) the recessed free <NUM>'-OH of the second strand is incorporating the nucleotide provided (G). Thereby the recessed <NUM>'-OH second strand is extended and coded by the first nucleotide. Any nucleotide provided will pair with the composition as long as the <NUM>' overhang of the first strand is including universal bases which support the universal template directed DNA synthesis. The recessed <NUM>'-OH is only extended by one nucleotide as the <NUM>' end of the nucleotide is blocked. As a next step, the blocked <NUM>'-OH is unblocked by a cleave reagent which allows the next coding cycle to occur.

The incorporation of an optionally fluorescently labeled <NUM>'-OH blocked nucleotides which are later unblocked by a cleave reagent is also known from Sequencing by Synthesis (<NPL>). Opposite to Sequencing by Synthesis, the UNIT-DNA process is used to write a DNA code and not to read a DNA code.

In order to write the spatial polynucleotide barcode, structured illumination may be used as part of the coding workflow which was already conceptually introduced by <FIG>. How the structured illumination of individual cells by light (e. UV light) is chemically releasing the cleave reagent (e. TCEP) spatially is detailed in <FIG>. The chemical reaction to release TCEP after illumination of Cy5-TCEP conjugate by UV light has been described before (<NPL>).

In summary, the sequence of the spatial code written by the UNIT-DNA method depends on the order of the nucleotides provided and the spatial activation of the cleave reagent by light. The total number of spatial codes which can be written by UNIT-DNA depends on the number universal bases within the <NUM>'overhang which allow nucleotide incorporation (e. <NUM> universal bases would translate to ~<NUM> million codes (<NUM><NUM>)). The spatial resolution of the coding principle is dependent on the resolution of light used for illumination (~<NUM> for UVB) and the local reaction kinetics of the released cleave reagent and is therefore easily achieving a cellular (~<NUM>) or subcellular (~<NUM>) resolution level.

After the coding has been completed, all cells (or nuclei and organells) may be isolated from the tissue sample and are subjected to single cell sequencing. In principle, the method is not limited in terms of the number of cells examined simultaneously. The number of cells examined individually at the same time is dependent on the number of universal bases within the <NUM> overhang to provide a unique spatial barcode. The real limitation is eventually only in the capacity and throughput of the sequencer.

The embodiments of the method of the invention for spatial barcoding are summarized in <FIG> and referred to as embodiments A to H. As visualized by the dotted box, the core functional elements of the UNIT-DNA method is maintained. Additional functionality is introduced by modifications of the <NUM>' and <NUM> ends and combines the core UNIT-DNA composition for spatial barcoding with further nucleic acid manipulation workflows.

The embodiments are described in more detail as follows.

<FIG> shows an example for UNIT-DNA embodiment H (<FIG>) which is used as part of the template switch oligonucleotide process within the single cell sequencing workflow (<NPL>)). After generation of the spatial DNA barcode by the UNIT-DNA, the resulting nucleic acid can be further analyzed by sequencing using the unique molecular identifier (UMI) for error correction.

It is worth to mention that the TSO shown in <FIG> does not include a Cell Identifier. The UNIT-DNA composition provides the spatial barcode which can serve as a cell identifier in case resolution of structured illumination was chosen to be aligned with the cellular resolution level.

<FIG> is updating the coding and decoding workflow for use of the UNIT-DNA derivate in embodiment H. After coding a sequencing library is prepared and the spatial barcode as well as the target nucleic acid is sequenced. As the spatial barcode is physically linked to the target nucleic acid, the spatial information of the target sequence can be derived by in vitro sequencing and the relation of the results to the initial sample source is provided.

The UNIT-DNA composition H for spatial barcoding of the target nucleic acid can also be used within a padlock workflow leading to a circularized ssDNA (see <FIG>) or within a targeted DNA workflow (see <FIG>). After coding, the resulting nucleic acid would be subjected to sequencing in order to determine the spatial barcode and the linked target nucleic acid.

Depending on the molecular workflow different UNIT-DNA embodiments may be used to combine the spatial coding with the sequencing and decoding workflow. The UNIT-DNA embodiments as shown in <FIG> may also be used for multimodal targeted RNA and DNA workflows or solid support workflows (not shown).

The UNIT-DNA process may be performed within a cyclic process, which is triggered by a structured illumination of the tissue sample by treating it with another spatially structured pattern of light in each cycle. "Structured illumination" and "spatially structured pattern of light" refer to illuminating only a part or selected areas of the sample.

<FIG> shows structured illumination of three cells by light (as indicated by the thunder symbol) is releasing the cleave reagent TCEP (tris(<NUM>-carboxyethyl)phosphine) in the illuminated cells. Cy5-TECP conjugate is used as a substrate for the light induced cleave reagent release.

Further, in <FIG> it is shown how a tissue section <NUM> (optionally stained) is obtained from tissue donor <NUM> which is then subjected to imaging <NUM>, allowing segmentation or cluster analysis, i.e. the selection of the parts of the sample to be further investigated by the method of the invention. Such segmentation/clustering/selection enables calculation of masks for the structured illumination and/or for spatially structured pattern of light.

Further downstream in the method of the invention, the information obtained for structured illumination and/or for spatially structured pattern of light is utilized during photo-treatment for UNIT-DNA code generation (<NUM>) which leads to the encoded UNIT-DNA which is encapsulated together with the cellular mRNA and the single cell indexing reagents (<NUM>) for later sequencing (<NUM>). With the aid of the structured illumination, only the selected areas/cells of the sample <NUM> which are provided with the spatial barcode are spatially decoded by Next generation sequencing (<NUM>) and Sequence analysis (<NUM>).

One step in the method of the invention is directed to determine the sequence of nucleotides encoded on the UNIT-DNA probes which is read out by sequencing (<NUM>). One method for sequencing can be sequencing be synthesis (SBS). For increasing readout signals, amplification of the UNIT-DNA probe sequences can be performed. One method for clonal amplification can be rolling circle amplification (RCA) of the encoded UNIT-DNA probes, which is performed before starting the sequencing process on the rolonies.

In a variant of the invention, the sequence of the UNIT-DNA code may be read separately from the sequence of the target gene. This can be realized by splitting up the sequencing procedure into two runs with two different sequencing primers.

Eight embodiments (A - H) of the UNIT-DNA method are shown in <FIG>. The core elements of the UNIT-DNA composition are maintained for all embodiments (as indicated by the dotted box). The additional elements added to the <NUM>' and <NUM> end of the UNIT-DNA are as follows.

Embodiment H may be conducted in a first variant as shown in <FIG>. Here, the UNIT-DNA method of the invention is combined with a Template Switch Oligonucleotide (TSO) process.

The variant as shown in <FIG> comprises that (A) mRNA is reverse transcribed (in situ) by oligo dT primer generating cDNA with triple C at the <NUM>' end. (B) TSO with <NUM>' PCR handle (shown as N), Unique Molecular Identifier (UMI) and triple G at <NUM> end. (C) Result of in situ template switching of cDNA (from A) with TSO (from B) generates captured cDNA with PCR handle at both ends (optional in situ PCR amplification for increased sensitivity not shown). (D) Hybridization of oligonucleotide which includes universal bases with PCR handle is leading to formation of UNIT-DNA derivate H (as indicated by the dotted box).

A further variant of embodiment H is shown in <FIG>. Here, the UNIT-DNA method of the invention is combined with a circular ssDNA.

The variant as shown in <FIG> comprises (A) Circular ssDNA (including captured target sequence, unique molecular identifier (UMI) and PCR handle (shown as N)). UMIs are added before amplification and are often used within NGS workflows to reduce errors and quantitative bias introduced by the amplification. The Circular ssDNA may have been generated in situ by Padlock (no gap), Padlock (gap) or Direct (FISSEQ) method as described by <NPL>). (B) Oligo hybridization will generate a double strand and allows restriction endonuclease digestion as shown under (B) to generate a linear ssDNA (C) (optional in situ PCR amplification for increased sensitivity not shown). (D) Hybridization of oligonucleotide which includes universal bases with PCR handle is leading to formation of UNIT-DNA derivate H (as indicated by the dotted box).

Claim 1:
Method for in situ spatial barcoding of a polynucleotide comprising a first and a second strand with a barcode nucleotide sequence characterized in that the first strand is provided at its <NUM>' end with an overhang of at least one universal base and the corresponding recessed <NUM>' end of the second strand of the polynucleotide with at least one nucleotide provided with a blocking group, wherein the blocking groups are removed from the incorporated nucleotides by irradiation with light.