Journal Article

The Transcriptomic and Proteomic Landscapes of Bone Marrow and Secondary Lymphoid Tissues

Nilsson, Kenneth, Andersson, Sandra, Sundström, Christer, Uhlen, Mathias, Edlund, Karolina, Hallström, Björn M., Danielsson, Angelika, Asplund, Anna, Fagerberg, Linn

2014

Overview

The sequencing of the human genome has opened doors for global gene expression profiling, and the immense amount of data will lay an important ground for future studies of normal and diseased tissues. The Human Protein Atlas project aims to systematically map the human gene and protein expression landscape in a multitude of normal healthy tissues as well as cancers, enabling the characterization of both housekeeping genes and genes that display a tissue-specific expression pattern. This article focuses on identifying and describing genes with an elevated expression in four lymphohematopoietic tissue types (bone marrow, lymph node, spleen and appendix), based on the Human Protein Atlas-strategy that combines high throughput transcriptomics with affinity-based proteomics. An enriched or enhanced expression in one or more of the lymphohematopoietic tissues, compared to other tissue-types, was seen for 693 out of 20,050 genes, and the highest levels of expression were found in bone marrow for neutrophilic and erythrocytic genes. A majority of these genes were found to constitute well-characterized genes with known functions in lymphatic or hematopoietic cells, while others are not previously studied, as exemplified by C19ORF59. In this paper we present a strategy of combining next generation RNA-sequencing with in situ affinity-based proteomics in order to identify and describe new gene targets for further research on lymphatic or hematopoietic cells and tissues. The results constitute lists of genes with enriched or enhanced expression in the four lymphohematopoietic tissues, exemplified also on protein level with immunohistochemical images.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Affinity / Appendix / Appendix - metabolism / Bioinformatics / Biology / Biology and life sciences / Bone marrow / Bone Marrow - metabolism / comparative study / controlled study / erythrocyte / Gene expression / gene expression profiling / Gene Expression Profiling - methods / gene function / gene identification / gene location / Gene sequencing / gene targeting / Genes / genetic analysis / genetic transcription / Genome, Human / Genomes / Genomics / High-Throughput Nucleotide Sequencing - methods / human / human cell / human tissue / Humans / immunohistochemistry / Immunology / Laboratories / Leukemia / Leukocytes (neutrophilic) / Lists / Localization / lymph node / Lymph nodes / Lymph Nodes - metabolism / Lymphatic system / lymphoid cell / Lymphoid tissue / neutrophil / Ontology / Pathology / Patologi / Proteins / Proteome - analysis / Proteome - genetics / Proteomics / Proteomics - methods / Research and Analysis Methods / Ribonucleic acid / RNA / RNA sequence / Rodents / Science / Spleen / Spleen - metabolism / Tissues / Transcriptome