The human gastrointestinal tract-specific transcriptome and proteome as defined by RNA sequencing and antibody-based profiling

  title={The human gastrointestinal tract-specific transcriptome and proteome as defined by RNA sequencing and antibody-based profiling},
  author={Gabriela Gremel and Alkwin Wanders and Jonathan Cedernaes and Linn Fagerberg and Bj{\"o}rn M. Hallstr{\"o}m and Karolina Edlund and Evelina Sj{\"o}stedt and Mathias Uhl{\'e}n and Fredrik Pont{\'e}n},
  journal={Journal of Gastroenterology},
BackgroundThe gastrointestinal tract (GIT) is subdivided into different anatomical organs with many shared functions and characteristics, but also distinct differences. We have combined a genome-wide transcriptomics analysis with immunohistochemistry-based protein profiling to describe the gene and protein expression patterns that define the human GIT.MethodsRNA sequencing data derived from stomach, duodenum, jejunum/ileum and colon specimens were compared to gene expression levels in 23 other… 
Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium
The results show that RNA-Seq and CAGE tissue transcriptome data sets are highly complementary for improving gene model annotations and highlight biological complexities within tissue transcriptomes.
Tissue-based map of the human proteome
A genome-wide analysis of the tissue specificity of RNA and protein expression covering more than 90% of the putative protein-coding genes is reported, complemented with analyses of various subproteomes, such as predicted secreted proteins and membrane-bound proteins.
Defining the Human Brain Proteome Using Transcriptomics and Antibody-Based Profiling with a Focus on the Cerebral Cortex
This multi-angle approach uncovered the brain-enriched transcriptome and linked genes to cell types and functions, providing novel insights into the molecular foundation of this highly specialized organ.
Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines
Analysis of RNA-seq data from 139 different individuals across the 5 tissues revealed substantial variation in both expression levels and splicing across samples and tissue types, and revealed 183 splicing events in pharmacogenes that were previously not annotated.
Comparative RNA-Seq analysis reveals pervasive tissue-specific alternative polyadenylation in Caenorhabditis elegans intestine and muscles
A new method, polyA-tagging and sequencing (PAT-Seq), is developed to isolate high-quality tissue-specific mRNA from Caenorhabditis elegans intestine, pharynx and body muscle tissues and study changes in their tissue- Specific transcriptomes and 3’UTRomes, suggesting novel and unexplored tissue- specific post-transcriptional regulatory networks in somatic cells.
Cells of the human intestinal tract mapped across space and time
This work reveals the presence of BEST4+ absorptive cells throughout the human intestinal tract, demonstrating the existence of this cell type beyond the colon for the first time, and identifies key cell players across multiple cell lineages driving secondary lymphoid tissue formation in early human development.
The Human Protein Atlas—Spatial localization of the human proteome in health and disease
The HPA constitutes an important resource for further understanding of human biology, and the publicly available datasets hold much promise for integration with other emerging efforts focusing on single cell analyses, both at transcriptomic and proteomic level.
Carausius morosus (Phasmatodea) Homologues of Human Genes with Elevated Expression in the Colon
  • M. Shelomi
  • Biology, Medicine
    Annals of Colorectal Research
  • 2019
C. morosus can be used as model insect for human medical research applications, including colorectal drug testing, and several genes were identified with prognostic value for renal, pancreatic, endometrial, liver, skin, and urothelial cancers.
Intestinal region-specific Wnt signalling profiles reveal interrelation between cell identity and oncogenic pathway activity in cancer development
It is observed that the region-specific cell identity has a substantial effect on the reaction to Wnt activation in a simple intestinal adenoma model, which provides a way forward in resolving the distinct biology between left- and right-sided human colon cancers with potential clinical relevance.
Quantitative analysis of Y-Chromosome gene expression across 36 human tissues.
Divergence between the X and Y Chromosomes in regulatory sequence can lead to tissue-specific, Y-Chromosome-driven sex biases in expression of critical, dosage-sensitive regulatory genes.


Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics*
A quantitative transcriptomics analysis (RNA-Seq) is used to classify the tissue-specific expression of genes across a representative set of all major human organs and tissues and combined this analysis with antibody-based profiling of the same tissues.
Biomarkers of human gastrointestinal tract regions
This study furnishes the first map of gene expression along the healthy human gastrointestinal tract and implements a procedure for microarray data analysis that would allow its use as a reference when screening for pathological deviations.
A DNA microarray survey of gene expression in normal human tissues
A systematic survey of gene expression in 115 human tissue samples representing 35 different tissue types, using cDNA microarrays representing approximately 26,000 different human genes provides a baseline for comparison to diseased tissues, and will aid in the identification of tissue-specific functions.
A global map of human gene expression
A global gene expression map is constructed by integrating microarray data from 5,372 human samples representing 369 different cell and tissue types, disease states and cell lines and reveals that it can be described by a small number of distinct expression profile classes.
Antibody-based tissue profiling as a tool for clinical proteomics
The data presented here suggest that antibody-based profiling of protein expression in tissues can be used as a valuable tool in clinical proteomics.
Expression profiling identifies novel gene targets and functions for Pdx1 in the duodenum of mature mice.
  • Chin Chen, E. Sibley
  • Biology
    American journal of physiology. Gastrointestinal and liver physiology
  • 2012
Transcription factor pancreatic and duodenal homeobox 1 (Pdx1) plays an essential role in the pancreas to regulate its development and maintain proper islet function. However, the functions of Pdx1
The Human Protein Atlas—a tool for pathology
An immunohistochemistry‐based map of protein expression profiles in normal tissues, cancer and cell lines is generated and the presented Human Protein Atlas provides a resource for pathology‐based biomedical research, including protein science and biomarker discovery.
A compendium of gene expression in normal human tissues.
A compendium of gene expression in normal human tissues suitable as a reference for defining basic organ systems biology is created and subsets of tissue-selective genes are identified that define key biological processes characterizing each organ.
RNA sequencing reveals two major classes of gene expression levels in metazoan cells
RNA sequencing of mouse Th2 cells is used, coupled with a range of other techniques, to show that all genes can be separated, based on their expression abundance, into two distinct groups: one group comprised of lowly expressed and putatively non‐functional mRNAs, and the other of highly expressed m RNAs with active chromatin marks at their promoters.
SATB2 in Combination With Cytokeratin 20 Identifies Over 95% of all Colorectal Carcinomas
The specific expression of SATB2 in a large majority of CRCs suggests that SATB 2 can be used as an important complementary tool for the differential diagnosis of carcinoma of unknown primary origin.