Region and cell-type resolved quantitative proteomic map of the human heart

Abstract

The heart is a central human organ and its diseases are the leading cause of death worldwide, but an in-depth knowledge of the identity and quantity of its constituent proteins is still lacking. Here, we determine the healthy human heart proteome by measuring 16 anatomical regions and three major cardiac cell types by high-resolution mass spectrometry-based proteomics. From low microgram sample amounts, we quantify over 10,700 proteins in this high dynamic range tissue. We combine copy numbers per cell with protein organellar assignments to build a model of the heart proteome at the subcellular level. Analysis of cardiac fibroblasts identifies cellular receptors as potential cell surface markers. Application of our heart map to atrial fibrillation reveals individually distinct mitochondrial dysfunctions. The heart map is available at maxqb.biochem.mpg.de as a resource for future analyses of normal heart function and disease.

Unveiling the molecular crosstalk in a human induced pluripotent stem cell‐derived cardiac model

“…The expression of matrix metalloproteinase‐2 and tissue inhibitor of metalloproteinases‐1, which are involved in the regulation of collagen degradation, did not change significantly between monoculture and coculture (Figure c). Altogether, our results show that the heterotypic cell communication induces the formation of a more intricate ECM that better resemble the composition of the human myocardial ECM (Doll et al, ).…”

“…We observed upregulation of brain natriuretic peptide (Figure 3d) and no changes in expression atrial natriuretic peptide, (which are both cardiac hormones predominantly secreted by the ventricles and atria, respectively). Increased expression of several factors involved in ECM remodeling (CTGF, PAI1/2, CRTAP, SPRC, FETUA, NPC2, and THBS4) was also observed in coculture conditions(Figure 3e), which together with the previously described upregulation of fibrillar forms of collagen (I and III) and fibronectin(Figure 3a), seem to indicate an activation of the stromal population in coculture namely, smooth muscle cells and cardiac fibroblasts(Doll et al, 2017). We hypothesize that the previously mentioned SMA pos cells may have appeared through phenotypic conversion of hiPSC-EC by EndoMT(James et al, 2010;Welch-Reardon, Wu, & Hughes, 2015), as EndoMT is described to be TGF-β signaling-dependent(Welch-Reardon et al, 2015) and the composition of the medium used in coculture is depleted of TGF-β inhibitor (SB431542) and vascular endothelial growth factor (VEGF) supplements and may be partly responsible for the ECM remodeling.…”

Efficient mitotic checkpoint signaling depends on integrated activities of Bub1 and the RZZ complex

“…This was done essentially as in Doll et al (2017). Nanoflow LC-MS/MS analysis of tryptic peptides was conducted on a quadrupole Orbitrap mass spectrometer (Q Exactive HF-X, Thermo Fisher Scientific, Rockford, IL, USA; Kelstrup et al, 2018) coupled to an EASYnLC 1200 ultra-high-pressure system (Thermo Fisher Scientific) via a nano-electrospray ion source.…”

Rapid proteomic analysis for solid tumors revealsLSD1 as a drug target in an end‐stage cancer patient

“…Our group has already established proteomic workflows enabling processing of clinically relevant tissue samples to great depth, even for formalin-fixed paraffin-embedded (FFPE) material (Wi sniewski et al, 2011(Wi sniewski et al, , 2013. Recently, we have combined nearly all sample processing steps in a single reaction tube, thereby reducing preparation time, contamination, and loss, while increasing quantification accuracy in tissues (inStageTip or iST method) (Kulak et al, 2014;Doll et al, 2017). We reasoned that these advances would now enable rapid analysis of individual tumor tissues to inform treatment decisions, especially in patients with rare and end-stage cancer, where evidence for therapeutic strategies and clinical trials are often lacking.…”