Mol. Syst. Biol.

We report a proteomic analysis of microdissected material from formalin-fixed and paraffin-embedded colorectal cancer, quantifying >7500 proteins between patient matched normal mucosa, primary carcinoma, and nodal metastases. Expression levels of 1808 proteins changed significantly between normal and cancer tissues, a much larger fraction than that reported in transcript-based studies. Tumor cells exhibit extensive alterations in the cell-surface and nuclear proteomes. Functionally similar changes in the proteome were observed comparing rapidly growing and differentiated CaCo-2 cells. In contrast, there was minimal proteomic remodeling between primary cancer and metastases, suggesting that no drastic proteome changes are necessary for the tumor to propagate in a different tissue context. Additionally, we introduce a new way to determine protein copy numbers per cell without protein standards. Copy numbers estimated in enterocytes and cancer cells are in good agreement with CaCo-2 and HeLa cells and with the literature data. Our proteomic data set furthermore allows mapping quantitative changes of functional protein classes, enabling novel insights into the biology of colon cancer

Thermodynamics of entropy-driven phase transformations

Thermodynamic properties of one-dimensional lattice models exhibiting entropy-driven phase transformations are discussed in quantum and classical regimes. Motivated by the multistability of compounds exhibiting photoinduced phase transitions, we consider systems with asymmetric, double, and triple well on-site potential. One finds that among a variety of regimes, quantum versus classical, discrete versus continuum, a key feature is asymmetry distinguished as a "shift" type and "shape" type in limiting cases. The behavior of the specific heat indicates one phase transformation in a "shift" type and a sequence of two phase transformations in "shape"-type systems. Future analysis in higher dimensions should allow us to identify which of these entropy-driven phase transformations would evolve into phase transitions of the first order

One-Step Preservation of Phosphoproteins and Tissue Morphology at Room Temperature for Diagnostic and Research Specimens

BACKGROUND: There is an urgent need to measure phosphorylated cell signaling proteins in cancer tissue for the individualization of molecular targeted kinase inhibitor therapy. However, phosphoproteins fluctuate rapidly following tissue procurement. Snap-freezing preserves phosphoproteins, but is unavailable in most clinics and compromises diagnostic morphology. Formalin fixation preserves tissue histomorphology, but penetrates tissue slowly, and is unsuitable for stabilizing phosphoproteins. We originated and evaluated a novel one-step biomarker and histology preservative (BHP) chemistry that stabilizes signaling protein phosphorylation and retains formalin-like tissue histomorphology with equivalent immunohistochemistry in a single paraffin block. RESULTS: Total protein yield extracted from BHP-fixed, routine paraffin-embedded mouse liver was 100% compared to snap-frozen tissue. The abundance of 14 phosphorylated proteins was found to be stable over extended fixation times in BHP fixed paraffin embedded human colon mucosa. Compared to matched snap-frozen tissue, 8 phosphoproteins were equally preserved in mouse liver, while AMPKβ1 Ser108 was slightly elevated after BHP fixation. More than 25 tissues from mouse, cat and human specimens were evaluated for preservation of histomorphology. Selected tissues were evaluated in a multi-site, independent pathology review. Tissue fixed with BHP showed equivalent preservation of cytoplasmic and membrane cytomorphology, with significantly better nuclear chromatin preservation by BHP compared to formalin. Immunohistochemical staining of 13 non-phosphorylated proteins, including estrogen receptor alpha, progesterone receptor, Ki-67 and Her2, was equal to or stronger in BHP compared to formalin. BHP demonstrated significantly improved immunohistochemical detection of phosphorylated proteins ERK Thr202/Tyr204, GSK3-α/β Ser21/Ser9, p38-MAPK Thr180/Tyr182, eIF4G Ser1108 and Acetyl-CoA Carboxylase Ser79. CONCLUSION: In a single paraffin block BHP preserved the phosphorylation state of several signaling proteins at a level comparable to snap-freezing, while maintaining the full diagnostic immunohistochemical and histomorphologic detail of formalin fixation. This new tissue fixative has the potential to greatly facilitate personalized medicine, biobanking, and phospho-proteomic research

Chapter Ten - A Protocol for Large-Scale Proteomic Analysis of Microdissected Formalin Fixed and Paraffin Embedded Tissue

Extensive use of biomarkers in diagnostic and therapeutic procedures is probably the hallmark of future medicine. Biomarkers can be of different chemical nature-most frequently DNA, RNA, and proteins are considered as molecules of interest. As the most rational approach appears analysis of proteins, because these are the "effector" molecules directly involved for cell homeostasis. There is no commonly accepted standard procedure in proteomic-based biomarker search. In this chapter, we described a protocol for proteomic analysis of formalin-fixed and paraffin-embedded tissue, which has been proven to be highly effective for proteomics-based biomarker discovery

How Nodes and Groups Properties Influence Assortativity in Social Networks?

A model of social network construction taking into account both social and individual influences on the distribution of links is proposed. The balance between social and individual factors is regulated through a "flexibility" parameter, reflecting how strong the initial individual sociability is altered by groups structure. The main interest is focused on the effect of groups on degree-degree correlation. Both numerical and analytical results on the relationship between assortativity and flexibility are presented