Laser capture microdissection for gene expression analysis of inner cell mass and trophectoderm from blastocysts

Histological cut of a paraffin-embedded blastocyst: Optimized protocol for murine blastocysts

Paraffin-embedded tissues have been used for research and therapeutic applications for decades, as they represent a valuable tool in histology and for molecular analysis, as well as being a way to preserve tissue samples for long periods at a low cost. For tissues such as the liver, lungs, kidney, heart or brain, there are many protocols available, already optimized. The purpose of this work is to optimize and simplify the protocols already available to take a single blastocyst from a mouse, fix it and embed it into a paraffin block without using gelatin, to then perform histological cuts using a microtome, with no need of sophisticated equipment or trained personnel. •The protocol presented here preserves well the morphology of the blastocyst.•Paraffin-embedded sections of the sample can be used for studies such as in situ hybridization, immunohistochemistry, enzyme histochemistry, DNA, RNA or protein extractions, analysis of biomarkers, characterization of surface markers of stem cells integrated into the embryo, to prepare histological material for educational purposes, etc.•Some of these studies could represent a valuable source of new information for the field of reproductive biology.

Laser capture microdissection of intestinal tissue from sea bass larvae using an optimized RNA integrity assay and validated reference genes

The increasing demand for a sustainable larviculture has promoted research regarding environmental parameters, diseases and nutrition, intersecting at the mucosal surface of the gastrointestinal tract of fish larvae. The combination of laser capture microdissection (LCM) and gene expression experiments allows cell specific expression profiling. This study aimed at optimizing an LCM protocol for intestinal tissue of sea bass larvae. Furthermore, a 3′/5′ integrity assay was developed for LCM samples of fish tissue, comprising low RNA concentrations. Furthermore, reliable reference genes for performing qPCR in larval sea bass gene expression studies were identified, as data normalization is critical in gene expression experiments using RT-qPCR. We demonstrate that a careful optimization of the LCM procedure allows recovery of high quality mRNA from defined cell populations in complex intestinal tissues. According to the geNorm and Normfinder algorithms, ef1a, rpl13a, rps18 and faua were the most stable genes to be implemented as reference genes for an appropriate normalization of intestinal tissue from sea bass across a range of experimental settings. The methodology developed here, offers a rapid and valuable approach to characterize cells/tissues in the intestinal tissue of fish larvae and their changes following pathogen exposure, nutritional/environmental changes, probiotic supplementation or a combination thereof.

Laser micro-dissection and qPCR for identifying specific HPV types responsible for malignancy in penile lesions

The aim of the study was to identify specific human papillomavirus (HPV) type responsible for malignancy in penile tissue samples using laser micro-dissection and TaqMan quantitative real-time PCR (qPCR). The study was based on two pre-malignant and seven malignant penile tissue samples and laser micro-dissection was performed on all. Genotyping was performed on whole tissue sections and laser micro-dissection samples using qPCR. Two whole tissue section samples were HPV negative while seven were HPV positive. In four samples that were single HPV infections with whole tissue section PCR, identical HPV types were confirmed with laser micro-dissection PCR. Clearly confirming that the single HPV type detected is responsible for malignancy. In two samples that had multiple HPV infections with whole tissue section PCR, only one HPV type with the highest viral load was detected with laser micro-dissection PCR, suggesting that the HPV type with the highest viral load is most likely the cause of that particular lesion. HPV 11 and/or HPV 16 were the only types detected with laser micro-dissection PCR in these cases, compared to multiple HPV types (HPV 11, HPV 16, HPV 18, HPV 31, HPV 33, HPV 35, and HPV 39) initially detected with whole tissue section PCR. HPV 11 was associated with verrucous lesions while HPV 16 was associated with squamous cell carcinoma and PIN 3 lesions. This study confirms that laser micro-dissection and qPCR are essential tools in identifying the HPV types responsible for malignancy in penile lesions, particularly in samples with multiple infections.

A simple and effective method for the isolation of inner cell mass samples from human blastocysts for gene expression analysis

The isolation of pure inner cell mass (ICM) and trophectoderm (TE) cells from a single human blastocyst is necessary to obtain accurate gene expression patterns of these cells, which will aid in the understanding of the primary steps of embryo differentiation. However, previously developed pure ICM isolation methods are either time-consuming or alter the normal gene expression patterns of these cells. Here, we demonstrate a simple and effective method of ICM samples isolation from human blastocysts. In total, 35 human blastocysts of all stages with expanded and good morphology were incubated in calcium/magnesium-free HEPES medium for 5 min before micromanipulation. With the aid of a laser, a biopsy pipette was inserted directly into the blastocoel for the suction-based removal of ICM samples. The ICM samples were obtained through simple mechanical pulling force or laser assistance, and each isolation process required 3-4 min. The isolated ICM and TE fractions were subjected to single-cell real-time quantitative RT-PCR to evaluate keratin 18 (KRT18) expression. Finally, 33 paired ICM and TE samples were verified using gene expression analysis. KRT18 was readily detectable in all TE cells but absent in 30 ICM counterparts, indicating a pure ICM isolation rate of 90.9% (30/33). The relative KRT18 expression of three TE samples compared with their three contaminated ICM counterparts was 19-fold (P < 0.001), indicating that the contamination was very weak. These results demonstrate that our ICM isolation method is simple and effective.

Introduction: why analyze single cells?

Powerful methods in molecular biology are abundant; however, in many fields including hematology, stem cell biology, tissue engineering, and cancer biology, data from tools and assays that analyze the average signals from many cells may not yield the desired result because the cells of interest may be in the minority-their behavior masked by the majority-or because the dynamics of the populations of interest are offset in time. Accurate characterization of samples with high cellular heterogeneity may only be achieved by analyzing single cells. In this chapter, we discuss the rationale for performing analyses on individual cells in more depth, cover the fields of study in which single-cell behavior is yielding new insights into biological and clinical questions, and speculate on how single-cell analysis will be critical in the future.

Laser capture microdissection for gene expression analysis of specific cell populations in single blastocysts

Laser capture microdissection (LCM) allows for the isolation of small tissue fractions from heterogeneous tissue sections, for downstream genetic or proteomic analysis without contamination by the surrounding tissue. This technique can also be successfully used for the isolation of small tissue fractions from developing embryos, such as expanding blastocysts. However, the small size of early-stage embryos hampers tissue processing prior to LCM. The present protocol describes the application of LCM to isolate specific cell fractions from blastocysts for downstream gene expression analysis with RT-PCR.