Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/019794

Mining the archives: a cross-platform analysis of gene expression profiles in archival formalin-fixed paraffin-embedded (FFPE) tissue

Anna Francina Webster·Paul Zumbo·Jennifer Fostel·Jorge Gandara·Susan D Hester·Leslie Recio·Andrew Williams·Chales Wood·Carole Yauk·Christopher E Mason
View original source ↗Export metadata ↓

Abstract

Formalin-fixed paraffin-embedded (FFPE) tissue samples represent a potentially invaluable resource for transcriptomic-based research into the molecular basis of disease. However, use of FFPE samples in gene expression studies has been limited by technical challenges resulting from degradation of nucleic acids. Here we evaluated gene expression profiles derived from fresh-frozen (FRO) and FFPE mouse liver tissues using two DNA microarray protocols and two whole transcriptome sequencing (RNA-seq) library preparation methodologies. The ribo-depletion protocol outperformed the other three methods by having the highest correlations of differentially expressed genes (DEGs) and best overlap of pathways between FRO and FFPE groups. We next tested the effect of sample time in formalin (18 hours or 3 weeks) on gene expression profiles. Hierarchical clustering of the datasets indicated that test article treatment, and not preservation method, was the main driver of gene expression profiles. Meta- and pathway analyses indicated that biological responses were generally consistent for 18-hour and 3-week FFPE samples compared to FRO samples. However, clear erosion of signal intensity with time in formalin was evident, and DEG numbers differed by platform and preservation method. Lastly, we investigated the effect of age in FFPE block on genomic profiles. RNA-seq analysis of 8-, 19-, and 26-year-old control blocks using the ribo-depletion protocol resulted in comparable quality metrics, including expected distributions of mapped reads to exonic, UTR, intronic, and ribosomal fractions of the transcriptome. Overall, our results suggest that FFPE samples are appropriate for use in genomic studies in which frozen samples are not available, and that ribo-depletion RNA-seq is the preferred method for this type of analysis in archival and long-aged FFPE samples.\n\nAuthor contributions\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@124589eorg.highwire.dtl.DTLVardef@1361ddeorg.highwire.dtl.DTLVardef@1e30065org.highwire.dtl.DTLVardef@2f0ed5org.highwire.dtl.DTLVardef@176fc83_HPS_FORMAT_FIGEXP M_TBL C_TBL

Source connections

Explore related subjects

GeneticsPreprint

Keep this discovery

BibTeXRIS

Anna Francina Webster, Paul Zumbo, Jennifer Fostel, Jorge Gandara, Susan D Hester, Leslie Recio, Andrew Williams, Chales Wood, Carole Yauk, Christopher E Mason. 2015-05-24. Mining the archives: a cross-platform analysis of gene expression profiles in archival formalin-fixed paraffin-embedded (FFPE) tissue. https://doi.org/10.1101/019794

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2016

Rapid evolution of primate type 2 immune response factors linked to asthma susceptibility

Host immunity pathways evolve rapidly in response to antagonism by pathogens. Microbial infections can also trigger excessive inflammation that contributes to diverse autoimmune disorders including asthma, lupus, diabetes, and arthritis. Definitive links between immune system evolution and human autoimmune disease remain unclear. Here we provide evidence that several components of the type 2 immune response pathway have been subject to recurrent positive selection in the primate lineage. Notably, rapid evolution of the central immune regulator IL13 corresponds to a polymorphism linked to asthma susceptibility in humans. We also find evidence of accelerated amino acid substitutions as well as repeated gene gain and loss events among eosinophil granule proteins, which act as toxic antimicrobial effectors that promote asthma pathology by damaging airway tissues. These results support the hypothesis that evolutionary conflicts with pathogens promote tradeoffs for increasingly robust immune responses during animal evolution. Our findings are also consistent with the view that natural selection has contributed to the spread of autoimmune disease alleles in humans.

Genetics↗
bioRxiv2016

Single Cell Expression Data Reveal Human Genes that Escape X-Chromosome Inactivation

Sex chromosomes pose an inherent genetic imbalance between genders. In mammals, one of the females X-chromosomes undergoes inactivation (Xi). Indirect measurements estimate that about 20% of Xi genes completely or partially escape inactivation. The identity of these escapee genes and their propensity to escape inactivation remain unsolved. A direct method for identifying escapees was applied by quantifying differential allelic expression from single cells. RNA-Seq fragments were assigned to informative SNPs which were labeled by the appropriate parental haplotype. This method was applied for measuring allelic specific expression from Chromosome-X (ChrX) and an autosomal chromosome as a control. We applied the protocol for measuring biallelic expression from ChrX to 104 primary fibroblasts. Out of 215 genes that were considered, only 13 genes (6%) were associated with biallelic expression. The sensitivity of escapees' identification was increased by combining SNP mapping for parental diploid genomes together with RNA-Seq from clonal single cells (25 lymphoblasts). Using complementary protocols, referred to as strict and relaxed, we confidently identified 25 and 31escapee genes, respectively. When pooled versions of 30 and 100 cells were used, <50% of these genes were revealed. We assessed the generality of our protocols in view of an escapee catalog compiled from indirect methods. The overlap between the escapee catalog and the genes list from this study is statistically significant (P-value of E-07). We conclude that single cells expression data are instrumental for studying X-inactivation with an improved sensitivity. Finally, our results support the emerging notion of the non-deterministic nature of genes that escape X-chromosome inactivation.

Genetics↗
bioRxiv2016

Frequency of mosaicism points towards mutation-prone early cleavage cell divisions.

It has recently become possible to directly estimate the germ-line de novo mutation (dnm) rate by sequencing the whole genome of father-mother-offspring trios, and this has been conducted in human1-5, chimpanzee6, mice7, birds8 and fish9. In these studies dnms are typically defined as variants that are heterozygous in the offspring while being absent in both parents. They are assumed to have occurred in the germ-line of one of the parents and to have been transmitted to the offspring via the sperm cell or oocyte. This definition assumes that detectable mosaicism in the parent in which the mutation occurred is negligible. However, instances of detectable mosaicism or premeiotic clusters are well documented in humans and other organisms, including ruminants10-12. We herein take advantage of cattle pedigrees to show that as much as [~]30% to [~]50% of dnms present in a gamete may occur during the early cleavage cell divisions in males and females, respectively, resulting in frequent detectable mosaicism and a high rate of sharing of multiple dnms between siblings. This should be taken into account to accurately estimate the mutation rate in cattle and other species.

Genetics↗