Methods of detecting spatial heterogeneity of a biological sample
Provided herein are methods of characterizing tumors or a region of interest in a biological sample.
1. A method of determining a location of a mRNA expressed in an ovarian sample tissue section, the method comprising:
(a) contacting the tissue section obtained from a subject with an array comprising a plurality of capture probes, wherein a capture probe of the plurality of capture probes comprises a spatial barcode and a capture domain, wherein the plurality of capture probes hybridizes to a plurality of mRNAs expressed by an infiltrating M0 macrophage in the tissue section, wherein the plurality of mRNAs expressed by the infiltrating M0 macrophage surround an ovarian tumor in the tissue section, and wherein an mRNA of the mRNAs expressed by the infiltrating M0 macrophage is selected from the group consisting of CA1, SCARA5, and ARAF, or any combination thereof,
wherein CA1 mRNA expression is increased in the infiltrating M0 macrophage, SCARA5 mRNA expression is decreased in the infiltrating M0 macrophage, and ARAF mRNA expression is decreased in the infiltrating M0 macrophage compared to CA1 mRNA SCARA5 mRNA, and ARAF mRNA respectively, in non-M0 macrophage cells of the tissue section;
(b) hybridizing the plurality of mRNAs to the plurality of capture probes, wherein the mRNA hybridizes to the capture probe;
(c) extending the plurality of capture probes, thereby generating a plurality of extended capture probes, wherein a 3′ end of the capture probe uses the mRNA as a template to generate an extended capture probe; and
(d) sequencing (i) all or part of the plurality of extended capture probes, (ii) the spatial barcode or a complement thereof, and (iii) all or a part of a sequence corresponding to the mRNA expressed by the infiltrating M0 macrophage, or a complement thereof, and using the determined sequences of (ii) and (iii) to identify the location of the mRNA expressed by the infiltrating M0 macrophage in the ovarian sample tissue section.
2. The method of claim 1 , further comprising comparing expression of the mRNA in the tissue section to expression of the mRNA in a reference sample.
3. The method of claim 2 , wherein the reference sample comprises a non-cancerous sample from a different subject, a cancerous sample from a different subject, a non-cancerous sample from the subject, or a cancerous sample from the subject.
4. The method of claim 2 , wherein the reference sample is an immune cell sample from a different subject or a non-immune cell sample from the subject.
5. The method of claim 4 , wherein the immune cell sample comprises an M0 macrophage.
6. The method of claim 1 , wherein the capture probe further comprises one or more functional domains, a unique molecular identifier, a cleavage domain, or combinations thereof.
7. The method of claim 1 , further comprising generating a nucleic acid that is complementary to all or a part of the extended capture probe.
8. The method of claim 1 , wherein the capture domain comprises a poly-uridine sequence or a poly-thymidine sequence.
9. The method of claim 1 , further comprising determining a location of one or more additional mRNAs expressed by one or more additional immune cells or one or more additional cancer cells in the tissue section.
10. The method of claim 1 , wherein the mRNA expressed by the infiltrating M0 macrophage comprises at least one genomic mutation.
11. The method of claim 1 , wherein the tissue section is a frozen tissue sample, a fresh tissue sample, or a fixed tissue sample.
12. The method of claim 1 , wherein the tissue section is stained by hematoxylin, eosin, immunohistochemistry, and/or immunofluorescence.
13. The method of claim 1 , further comprising imaging the tissue section.