High-resolution spatial RNA profiling of tissues with immuno-labeling based LCM
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ABSTRACT: We report a robust protocol to effectively maintain high RNA quality for immuno-fluorescence-based laser capture microdissection (LCM), enabling finely resolved spatial transcriptome acquisition with only tens of cells from snap-frozen or RNAlater-treated tissues. With the repertoire of readily-available antibodies, this method fulfils the potential of LCM to determine native transcriptomic landscapes, as exemplified here with the characterization of mouse lacteal tip and tube cells. Methods: mRNA profiles of mouse small intestine epithelial cells (labeled by panCK) and lateal tip and tube cells (labele by Lyve1), as well as human jejunum lymphatic vessel cells were generated by deep sequencing, lacteal tip and tube samples in triplicate, using Illumina hiseq2000. The sequence reads that passed quality filters were analyzed at both the gene expression level and transcript isoform level with Stringtie. Results: Using an optimized data analysis workflow, we mapped about 15 million sequence reads per epithelial sample and about 50 million reads per lymphatic vessel cells (in cluding lacteal) to the mouse genome (GRCm38,mm10) and identified average more than 12,000 genes for each sample. RNA-seq data had a average pearson correlation higher than 0.88 for same type samples. Approximately 1.3% of the expressed genes showed differential expression between the lacteal tip and tube samples, with a log2(fold change) ≥2 or ≤-2 and padj value <0.01. This also indicate the overall sameness of lacteal tip and tube cells (the small difference is that tip cells exist filopodia structrue). Differentially expressed genes uncovered several intersting genes that reflected the potential mechanism responsible for the filopodia stucture difference. Conclusions: We have developed an easily adaptable approach that enables high-quality RNA analysis from a few 10s of cells using IF/LCM from tissues either snap-frozen or preserved with RNAlater. Such methods are uniquely required for the comprehensive delineation of spatial transcriptomic landscapes of complex tissues under near-native conditions. Only with this information can we start to unravel the basic principles that underlie the physiological and pathophysiological processes within these tissues as well as the identity and fundamental characteristics of the resident cells contained therein.
Project description:Banking of high-quality placental tissue specimens will enable biomarker discovery and molecular studies on diseases involving placental dysfunction. Systematic studies aimed at developing feasible standardized methodology for placental collection for genomic analyses are lacking. To determine the acceptable timeframe for placental collection, we collected multiple samples from first and third trimester placentas at serial time points 0-120 minutes after delivery, simultaneously comparing the traditional snap-freeze technique to collection in commercial solutions designed to preserve RNA (RNAlaterTM, Ambion), and DNA (DNAgard®, Biomatrica). The performance of RNAlater for preserving DNA was also tested. Nucleic acid quality was assessed by determining the RNA integrity number (RIN) and genome-wide expression and DNA methylation microarray profiling. We found that samples collected in RNAlater had higher and more consistent RINs compared to snap frozen tissue, with similar RINs obtained for tissue collected in RNAlater as large (1 cm3) and small (~0.1 cm3) tissue pieces. RNAlater appeared to better stabilize the time zero gene expression pattern compared to snap freezing for first trimester placenta. Microarray DNA methylation analysis showed that overall the DNA methylation profiles remained quite stable over a two hour time period after removal of the placenta from the uterus, with the DNAgard condition being superior to both snap freezing and RNAlater. The collection of placental samples in RNAlater and DNAgard is simple, and eliminates the need for liquid nitrogen or a freezer on-site. Moreover, the quality of the nucleic acids and the resulting data from samples collected in these preservation solutions is actually higher than that from samples collected using the traditional snap-freeze method. Thus, this new approach to placental sample collection is both easier to implement in busy clinical environments and yields higher quality data. 48 samples
Project description:Banking of high-quality placental tissue specimens will enable biomarker discovery and molecular studies on diseases involving placental dysfunction. Systematic studies aimed at developing feasible standardized methodology for placental collection for genomic analyses are lacking. To determine the acceptable timeframe for placental collection, we collected multiple samples from first and third trimester placentas at serial time points 0-120 minutes after delivery, simultaneously comparing the traditional snap-freeze technique to collection in commercial solutions designed to preserve RNA (RNAlaterTM, Ambion), and DNA (DNAgard®, Biomatrica). The performance of RNAlater for preserving DNA was also tested. Nucleic acid quality was assessed by determining the RNA integrity number (RIN) and genome-wide expression and DNA methylation microarray profiling. We found that samples collected in RNAlater had higher and more consistent RINs compared to snap frozen tissue, with similar RINs obtained for tissue collected in RNAlater as large (1 cm3) and small (~0.1 cm3) tissue pieces. RNAlater appeared to better stabilize the time zero gene expression pattern compared to snap freezing for first trimester placenta. Microarray DNA methylation analysis showed that overall the DNA methylation profiles remained quite stable over a two hour time period after removal of the placenta from the uterus, with the DNAgard condition being superior to both snap freezing and RNAlater. The collection of placental samples in RNAlater and DNAgard is simple, and eliminates the need for liquid nitrogen or a freezer on-site. Moreover, the quality of the nucleic acids and the resulting data from samples collected in these preservation solutions is actually higher than that from samples collected using the traditional snap-freeze method. Thus, this new approach to placental sample collection is both easier to implement in busy clinical environments and yields higher quality data. 72 samples
Project description:We used quantitative RNA expression profiling on the Affymetrix U133 human expression array to validate quantitative expression results obtained with the tissue preservative RNALater against snap frozen and fresh tissues as a means of routine tissue collection and temporary storage. By using split samples from a homogenous tissue (uterine myometrium), and including duplicates within each processing group compared, we were able to undertake a formal ANOVA analysis comparing the magnitude of result variation contributed by sample source (different patients), processing protocol (fresh vs. frozen vs. 24 or 72 hours RNALater), and random background (duplicates). The dataset was randomly permuted to define a baseline pattern of test statistic values against which the observed results could be interpreted. Ambient storage of tissues for 24 or 72 hours in RNALater did not contribute any systematic shift in quantitative RNA expression results relative to the alternatives of fresh or frozen tissue. Keywords: parallel sample
Project description:The functional shift of quiescent endothelial cells into tip cells that migrate and stalk cells that proliferate is a key event during sprouting angiogenesis. We previously showed that the sialomucin CD34 is expressed in a small subset of cultured endothelial cells and that these cells extend filopodia: a hallmark of tip cells in vivo. In the present study, we characterized endothelial cells expressing CD34 in endothelial monolayers in vitro. We found that CD34-positive human umbilical vein endothelial cells show low proliferation activity and increased mRNA expression of all known tip cell markers, as compared to CD34- negative cells. Genome-wide mRNA profiling analysis of CD34-positive endothelial cells demonstrated enrichment for biological functions related to angiogenesis and migration, whereas CD34-negative cells were enriched for functions related to proliferation. In addition, we found an increase or decrease of CD34-positive cells in vitro upon exposure to stimuli that enhance or limit the number of tip cells in vivo, respectively. Our findings suggest cells with virtually all known properties of tip cells are present in vascular endothelial cell cultures and that they can be isolated based on expression of CD34. This novel strategy may open alternative avenues for future studies of molecular processes and functions in tip cells in angiogenesis.
Project description:Compare luteal and follicular phases of fimbria and ampulla tissue Fallopian tube epithelial cells for gene expression analysis of fimbria and ampulla specimens were obtained using LCM
Project description:Gene expression analyses of pancreatic adenocarcinoma and adjacent ductal epithelia from the same patient using bulk vs LCM dissected samples. Our results indicate that laser capture microdissection (LCM) is necessary to identify differentially expressed genes that discriminate between PDAC and healthy pancreatic ductal tissue. Pancreatic tissues were collected at time of surgery and snap frozen in liquid nitrogen for RNA extraction and Affymetrix GeneChip Expression analyses.
Project description:Mouse distal colons were preserved snap frozen in RNAlater, homogenized in Trizol Reagent. A total of 100 ng of RNA per sample were used for hybridization and run on the XT_PGX_MmV2_Inflammation_CSO 248 gene panel for multiplexed semi-quantitative analysis of colonic RNA markers of inflammation.
Project description:The functional shift of quiescent endothelial cells into tip cells that migrate and stalk cells that proliferate is a key event during sprouting angiogenesis. We previously showed that the sialomucin CD34 is expressed in a small subset of cultured endothelial cells and that these cells extend filopodia: a hallmark of tip cells in vivo. In the present study, we characterized endothelial cells expressing CD34 in endothelial monolayers in vitro. We found that CD34-positive human umbilical vein endothelial cells show low proliferation activity and increased mRNA expression of all known tip cell markers, as compared to CD34- negative cells. Genome-wide mRNA profiling analysis of CD34-positive endothelial cells demonstrated enrichment for biological functions related to angiogenesis and migration, whereas CD34-negative cells were enriched for functions related to proliferation. In addition, we found an increase or decrease of CD34-positive cells in vitro upon exposure to stimuli that enhance or limit the number of tip cells in vivo, respectively. Our findings suggest cells with virtually all known properties of tip cells are present in vascular endothelial cell cultures and that they can be isolated based on expression of CD34. This novel strategy may open alternative avenues for future studies of molecular processes and functions in tip cells in angiogenesis. Four HUVEC donors were FACS-sorted by CD34 and divided in CD34-positive and CD34-negative fractions.
Project description:Time series of eleven breast cancer samples subjected to different cold ischemic stress of up to 3 hr post tumor excision. A different 2x2 factorial within this study evaluated the effect of stabilization method (RNAlater vs snap freezing) and stablization delay (0 and 40 min) at room temperature.
Project description:We used quantitative RNA expression profiling on the Affymetrix U133 human expression array to validate quantitative expression results obtained with the tissue preservative RNALater against snap frozen and fresh tissues as a means of routine tissue collection and temporary storage. By using split samples from a homogenous tissue (uterine myometrium), and including duplicates within each processing group compared, we were able to undertake a formal ANOVA analysis comparing the magnitude of result variation contributed by sample source (different patients), processing protocol (fresh vs. frozen vs. 24 or 72 hours RNALater), and random background (duplicates). The dataset was randomly permuted to define a baseline pattern of test statistic values against which the observed results could be interpreted. Ambient storage of tissues for 24 or 72 hours in RNALater did not contribute any systematic shift in quantitative RNA expression results relative to the alternatives of fresh or frozen tissue.