Unraveling the Human Bone Microenvironment beyond the Classical Extracellular Matrix Proteins: A Human Bone Protein Library

Abstract

A characteristic feature of bone, differentiating it from other connective tissues, is the mineralized extracellular matrix (ECM). Mineral accounts for the majority of the bone tissue volume, being the remainder organic material mostly derived from collagen. This, and the fact that only a limited number of noncollagenous ECM proteins are described, provides a limited view of the bone tissue composition and bone metabolism, the more so considering the increasing understanding of ECM significance for cellular form and function. For this reason, we set out to analyze and extensively characterize the human bone proteome using large-scale mass spectrometry-based methods. Bone samples of four individuals were analyzed identifying 3038 unique proteins. A total of 1213 of these were present in at least 3 out of 4 bone samples. For quantification purposes, we were limited to noncollagenous proteins (NCPs) and we could quantify 1051 NCPs. Most classical bone matrix proteins mentioned in literature were detected but were not among the highly abundant ones. Gene ontology analyses identified high-abundance groups of proteins with a functional link to mineralization and mineral metabolism such as transporters, pyrophosphatase activity, and Ca(2+)-dependent phospholipid binding proteins. ECM proteins were as well overrepresented together with nucleosome and antioxidant activity proteins, which have not been extensively characterized as being important for bone. In conclusion, our data clearly demonstrates that human bone tissue is a reservoir of a wide variety of proteins. In addition to the classical osteoblast-derived ECM, we have identified many proteins from different sources and of unknown function in bone. Thus, this study represents an informative library of bone proteins forming a source for novel bone formation modulators as well as biomarkers for bone diseases such as osteoporosis.

Proteomics Analysis of the Zebrafish Skeletal Extracellular Matrix

“…collagen type I isoforms, extracellular matrix protein 2) and cartilage proteins (e.g. collagen type II, matrilin 1, apolipoprotein A-I, epyphican), previously described in MS based analyses of these tissues/structures in other vertebrate species, including humans [29], [30], [31], [32]. Also the serum-derived protein alpha-2-HS-glycoprotein (Ahsg), reported to bind to the mineral content of bone, was found among the most abundant proteins (Fig.…”

Nuclear Lamin-A Scales with Tissue Stiffness and Enhances Matrix-Directed Differentiation

“…Differentiation might also be sensitive to splice-forms because AGN increased the A splice-form of LMNA , as did forced overexpression, and tissue profiling showed bone has more A than C splice-form, all of which motivates further study. In human bone tissue, lamin-A is among the 20 most abundant proteins detected by MS, together with several SRF-regulated gene products (ACTB, ACTA2, and MYL9) (71), and whereas SRF positively regulates a key transcription factor (RUNX2) in osteogenesis (45), chromatin-IP has thus far identified the RUNX2 gene to be a direct target of RA transcription factors and not of SRF. Lamin-A overexpression in MSCs on stiff matrix not only enhanced osteogenesis but also produced a modest decrease in nuclear YAP1 consistent with the measured nonmonotonic responses of YAP1 across tissues.…”

Proteomic profiling of archaeological human bone

“…In this study we used rib samples, which may explain why we could detect ample leucocyte-derived proteins. For instance, these proteins are scarcely detected in the femur [59]. …”