Diabetes Volume 70, May 2021 1117 Single Molecule–Based fliFISH Validates Radial and Heterogeneous Gene Expression Patterns in Pancreatic Islet b-Cells Fangjia Li,1 Dehong Hu,1 Cailin Dieter,2 Charles Ansong,3 Lori Sussel,2 and Galya Orr1 Diabetes 2021;70:1117–1122 | https://doi.org/10.2337/db20-0802 Single-cell RNA-sequencing (scRNA-Seq) technologies islet cell populations and enhanced our understanding of have greatly enhanced our understanding of islet cell b-cell heterogeneity with respect to their maturation and transcriptomes and have revealed the existence of functional state, as well as overall health (1–6). However, b-cell heterogeneity. However, comparison of scRNA- due to the difficulties associated with detecting lower Seq data sets from different groups have highlighted in- abundance transcripts, comparison between scRNA-Seq consistencies in gene expression patterns, primarily data sets from different groups has shown variable results due to variable detection of lower abundance tran- for genes reported to being heterogeneously expressed in scripts. Furthermore, such analyses are unable to un- b-cells (7,8). Comparing between scRNA-Seq data and ISLET STUDIES cover the spatial organization of heterogeneous gene data acquired from sorted b-cell populations has shown expression. In this study, we used fluctuation localiza- clear inconsistencies, with the identification of only few tion imaging–based fluorescence in situ hybridization markers of heterogeneity. With the exception of a small (fliFISH) to quantify transcripts in single cells inmouse number of abundant gene transcripts, most gene tran- pancreatic islet sections. We compared the expression scripts were detected in only a subset of b-cells, masking patterns of Insulin 2 (Ins2) with Mafa and Ucn3, two genes expressed in b-cells as they mature, as well as true cell heterogeneity as a result of working near the de- Rgs4, a factor with variably reported expression in the tection limit (7,8). These limitations emphasize the need islet. This approach accurately quantified transcripts to validate scRNA-Seq data using other single-cell analysis across a wide range of expression levels, from single approaches, such as quantitative mRNA fluorescence in copies to >100 copies/cell in one islet. Importantly, situ hybridization (FISH) or immunofluorescence. Single fliFISH allowed evaluation of transcript heterogeneity in molecule–based FISH approaches can provide quantitative the spatial context of an intact islet. These studies con- analysis of transcript counts without the biases imposed firm the existence of a high degree of heterogeneous by cell dissociation and destruction or cDNA amplification gene expression levels within the islet and highlight and do not require the availability of antibodies. These relative and radial expression patterns that likely reflect approaches also provide the spatial information needed to distinct b-cell maturation states along the radial axis of determine whether cell subpopulations, such as cells at the islet. different maturation or endoplasmic reticulum stress lev- els (1), and heterogeneous gene expression are spatially driven, as previously demonstrated (9,10). In this study, we used a high-accuracy single molecule– In recent years, single-cell RNA-sequencing (scRNA-Seq) based FISH approach, fluctuation localization imaging–based technologies have facilitated the identification of cell- FISH (fliFISH) (9,11), to quantify the expression of se- type-specific transcriptome signatures of the individual lected genes in single cells in pancreatic islet cryosections 1Environmental Molecular Sciences Laboratory, Pacific Northwest National This article contains supplementary material online at https://doi.org/10.2337/ Laboratory, Richland, WA figshare.14096639. 2 Barbara Davis Center for Diabetes, School of Medicine, University of Colorado © 2021 by the American Diabetes Association. Readers may use this article Anschutz Medical Campus, Aurora, CO as long as the work is properly cited, the use is educational and not for 3 Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA profit, and the work is not altered. More information is available athttps:// Corresponding authors: Galya Orr, [email protected], and Lori Sussel, www.diabetesjournals.org/content/license. [email protected] Received 8 August 2021 and accepted 23 February 2021 1118 fliFISH and Gene Expression Patterns in b-Cells Diabetes Volume 70, May 2021 to better evaluate their heterogeneity in the spatial con- one at each end. All probe sequences are listed in text of the islet. We focus on three genes that are ex- Supplementary Table 1. Hybridization followed the proto- pressed at different levels in subsets of b-cells and in col described in detail earlier (9,11). fliFISH analysis was non–b-cell islet populations in comparison with Insulin 2 done as described earlier (9,11), with the following excep- (Ins2) expression. v-maf musculoaponeurotic fibrosarcoma tion. After finding the centroid for each photo-switching oncogene family, protein A (MafA) and Urocortin 3 fluorescent spot showing on-off emission or blinking pat- (Ucn3) are both believed to be expressed in b-cells as they tern (18), a blinking density map was generated in which mature (12–14). Similar to most transcription factor the value of each pixel indicates the number of blinking genes, MafA is expressed at relatively low levels. Regulator events within distance R of that pixel. Such map was used of G protein signaling 4 (Rgs4) has been functionally ana- to group blinking events into clusters (or transcripts). R lyzed in the developing pancreas and in b-cells (15,16), was determined by the length of the target mRNAs and yet a recent single-cell study identified it as primarily an the probe localization error upon hybridization, which in a-cell marker (2). fliFISH analysis clearly demonstrates our study was determined to be �30 nm. To evaluate the that there is a wide range of transcript copies for each of transcript numbers per cell, the cell boundaries were out- these genes in b-cells. For all four genes, we found that lined, guided by the insulin immunofluorescence signal, cells with highest transcript copies are located near the and the nuclei stained with DAPI. The analysis was per- center of the islet, while cells with low copies are located formed using MATLAB routines available upon request. along the periphery. This radial pattern is especially obvi- ous for Ins2, consistent with the idea that more mature Fluorescence Microscopy b-cells are found near the center of the islet, while b-cells Imaging was performed using an Olympus IX-71 inverted at the periphery are likely to be at an earlier maturation microscope with a 100 times oil immersion objective, five stage (17). Rgs4 transcripts are found in nearly all islet solid-state lasers (405, 488, 542, 594, and 640 nm), and cells, with a similar radial expression pattern as Ins2. The an Electron Multiplying CCD camera (iXon Ultra 897; An- radial expression pattern is less obvious for Mafa and dor). The camera’s pixel size was 16 mm, and the micro- Ucn3, which tend to have a narrower range of transcript scope magnification was �100. Thus, the scale factor was numbers in adult b-cells. However, similar relative expres- 160 nm/pixel. A total of 10,000 images of 512 � 512 sion levels are often found for all four genes, in which a pixels were collected within 400 s and stored as 16-bit single cell expresses either higher or lower levels of all FITS files. Imaging was done in oxygen-depleting buffer (9). four transcripts. The similar relative and radial expression patterns, together with the heterogeneous expression lev- Data and Resource Availability els, likely reflect distinct b-cell maturation states along The data sets generated and analyzed during the current the radial axis of the islet. study are available from the corresponding authors upon reasonable request. RESEARCH DESIGN AND METHODS Mouse Pancreatic Tissue Sections RESULTS AND DISCUSSION Animal studies were approved by the Institutional Animal In this study, we used fliFISH to quantify gene expression in Care and Use Committee at University of Colorado. Pan- islet cells in mouse pancreatic tissue sections. fliFISH is built creata were isolated from 8-week-old wild-type C57BL/6J on principles used in single molecule–based super-resolution mice, washed in PBS, fixed in 4% paraformaldehyde/PBS fluorescence imaging, such as stochastic optical reconstruc- overnight, and then transferred to 30% sucrose/PBS over- tion microscopy or photo-activation localization microscopy, night at 4�C. Samples were embedded in OCT and sec- in which photo-switching fluorophores are used. By tagging tioned at 8–10-mm thickness. To identify the islets, the the FISH probes with photo-switching fluorescent dyes, fli- sections were subjected to immunostaining using primary FISH enables the detection and counting of individual tran- antibody against insulin (#3014; Cell Signaling Technol- scripts with high resolution and accuracy (9). Figure 1 shows ogy), followed with a secondary antibody tagged with an example of an islet in which the transcripts for Ins2, Alexa 800, as previously described (9). MafA, Ucn3, and Rgs4 are presented as dots in green, red, blue, and magenta, respectively. The islets were identified by fliFISH Probe Design and Analysis immunofluorescence targeting insulin (grayscale), and the fliFISH was used following the approach describe earlier nuclei were stained using