Clustering Coefficients of Protein-Protein Interaction Networks

The properties of certain networks are determined by hidden variables that are not explicitly measured. The conditional probability (propagator) that a vertex with a given value of the hidden variable is connected to k of other vertices determines all measurable properties. We study hidden variable models and find an averaging approximation that enables us to obtain a general analytical result for the propagator. Analytic results showing the validity of the approximation are obtained. We apply hidden variable models to protein-protein interaction networks (PINs) in which the hidden variable is the association free-energy, determined by distributions that depend on biochemistry and evolution. We compute degree distributions as well as clustering coefficients of several PINs of different species; good agreement with measured data is obtained. For the human interactome two different parameter sets give the same degree distributions, but the computed clustering coefficients differ by a factor of about two. This shows that degree distributions are not sufficient to determine the properties of PINs.Comment: 16 pages, 3 figures, in Press PRE uses pdflate

Amyloidosis and the lungs and airways

Amyloidosis can both complicate long-standing respiratory conditions and be deposited within the respiratory system itself. In acquired systemic amyloidosis, control of the underlying condition that is producing the circulating amyloid precursor protein is paramount. Systemic AA amyloidosis can result from unremitting chronic inflammation or infection such as in bronchiectasis. Control of the inflammation is paramount to amyloid regression. For systemic AL amyloidosis, treatment requires the use of chemotherapy or novel immunotherapies targeting the underlying plasma cell dyscrasia or lymphoproliferative disease that produce the abnormal amyloidogenic light chain. Localised amyloidosis can occur anywhere along the respiratory tract and can present with marked heterogeneity. In localised amyloidosis, management generally involves resection or ablation of symptomatic deposits. On occasion, localised pulmonary amyloidosis can be a manifestation of underlying Sjögren syndrome. Novel treatments are beginning to become available, including specific drug therapies to prevent translation of amyloidogenic proteins, stabilise amyloid precursor proteins and interfere with amyloid fibrillogenesis

Recent guidelines for high-dose chemotherapy and autologous stem cell transplant for systemic AL amyloidosis: a practitioner's perspective

INTRODUCTION: High-dose melphalan followed by autologous stem cell transplant (ASCT) has been transformative in treating AL amyloidosis since the early nineties. Recently, the European Hematology Association (EHA) and International Society of Amyloidosis (ISA) have developed a combined guideline for the management of patients undergoing an ASCT for AL amyloidosis. AREAS COVERED: In this practitioner's perspective, we review the guideline, focusing on 6 major areas and offer practical advice for its application. We provide a perspective on the optimal use of ASCT and its potential application in the future. EXPERT OPINION: The EHA-ISA guideline comprehensively outlines the practicalities of performing an ASCT in AL amyloidosis. The critical aspect is careful patient selection. Vigilant fluid balance assessments are crucial as associated complications are common and dangerous. The role of ASCT is changing with improving hematological responses associated with novel agents. Evidence is limited for the use of ASCT in patients who achieve a complete hematological response (CR). Therefore, ASCT should be considered for those who only achieve a very good partial response (VGPR)/partial response (PR) and fulfil the strict selection criteria. Future research identifying the cohort who would benefit most from ASCT in the era of novel therapies is warranted

Fast chromatin immunoprecipitation assay

Chromatin immunoprecipitation (ChIP) is a widely used method to explore in vivo interactions between proteins and DNA. The ChIP assay takes several days to complete, involves several tube transfers and uses either phenol–chlorophorm or spin columns to purify DNA. The traditional ChIP method becomes a challenge when handling multiple samples. We have developed an efficient and rapid Chelex resin-based ChIP procedure that dramatically reduces time of the assay and uses only a single tube to isolate PCR-ready DNA. This method greatly facilitates the probing of chromatin changes over many time points with several antibodies in one experiment

Free-energy distribution of binary protein-protein binding suggests cross-species interactome differences

Major advances in large-scale yeast two hybrid (Y2H) screening have provided a global view of binary protein-protein interactions across species as dissimilar as human, yeast, and bacteria. Remarkably, these analyses have revealed that all species studied have a degree distribution of protein-protein binding that is approximately scale-free (varies as a power law) even though their evolutionary divergence times differ by billions of years. The universal power-law shows only the surface of the rich information harbored by these high-throughput data. We develop a detailed mathematical model of the protein-protein interaction network based on association free energy, the biochemical quantity that determines protein-protein interaction strength. This model reproduces the degree distribution of all of the large-scale Y2H data sets available and allows us to extract the distribution of free energy, the likelihood that a pair of proteins of a given species will bind. We find that across-species interactomes have significant differences that reflect the strengths of the protein-protein interaction. Our results identify a global evolutionary shift: more evolved organisms have weaker binary protein-protein binding. This result is consistent with the evolution of increased protein unfoldedness and challenges the dogma that only specific protein-protein interactions can be biologically functional..Comment: 31 pages, 5 figure

Microplate-based platform for combined chromatin and DNA methylation immunoprecipitation assays

<p>Abstract</p> <p>Background</p> <p>The processes that compose expression of a given gene are far more complex than previously thought presenting unprecedented conceptual and mechanistic challenges that require development of new tools. Chromatin structure, which is regulated by DNA methylation and histone modification, is at the center of gene regulation. Immunoprecipitations of chromatin (ChIP) and methylated DNA (MeDIP) represent a major achievement in this area that allow researchers to probe chromatin modifications as well as specific protein-DNA interactions <it>in vivo </it>and to estimate the density of proteins at specific sites genome-wide. Although a critical component of chromatin structure, DNA methylation has often been studied independently of other chromatin events and transcription.</p> <p>Results</p> <p>To allow simultaneous measurements of DNA methylation with other genomic processes, we developed and validated a simple and easy-to-use high throughput microplate-based platform for analysis of DNA methylation. Compared to the traditional beads-based MeDIP the microplate MeDIP was more sensitive and had lower non-specific binding. We integrated the MeDIP method with a microplate ChIP assay which allows measurements of both DNA methylation and histone marks at the same time, Matrix ChIP-MeDIP platform. We illustrated several applications of this platform to relate DNA methylation, with chromatin and transcription events at selected genes in cultured cells, human cancer and in a model of diabetic kidney disease.</p> <p>Conclusion</p> <p>The high throughput capacity of Matrix ChIP-MeDIP to profile tens and potentially hundreds of different genomic events at the same time as DNA methylation represents a powerful platform to explore complex genomic mechanism at selected genes in cultured cells and in whole tissues. In this regard, Matrix ChIP-MeDIP should be useful to complement genome-wide studies where the rich chromatin and transcription database resources provide fruitful foundation to pursue mechanistic, functional and diagnostic information at genes of interest in health and disease.</p

IgM paraprotein-associated peripheral neuropathy: small CD20-positive B-cell clones may predict a monoclonal gammopathy of neurological significance and rituximab responsiveness

IgM paraprotein‐associated peripheral neuropathy (PN) in patients without overt evidence of lymphoma is a recognised clinical entity of unknown aetiology. Interrogating the bone marrow B‐cell or plasma cell clones underlying paraproteinemic neuropathies may improve our understanding of both pathogenesis and treatment options. This retrospective observational analysis of IgM paraprotein‐associated PN identified five patients with small pathological MYD88 L265P and CD20‐positive B‐cell clones in their bone marrow using multi‐parametric flow cytometry, who have shown durable neurological response to rituximab. We posit that multi‐parametric flow cytometry may be instrumental in identifying the cellular source of the paraprotein in IgM paraprotein‐associated PN, and thus directing appropriate immunomodulatory therapy. Further understanding of these small pathological B‐cell clones may also provide additional insight into mechanisms of monoclonal gammopathy of clinical significance overall

Halogenated imidazole derivatives block RNA polymerase II elongation along mitogen inducible genes

<p>Abstract</p> <p>Background</p> <p>Aberrant activation of protein kinases is one of the essential oncogenic driving forces inherent to the process of tumorigenesis. The protein kinase CK2 plays an important role in diverse biological processes, including cell growth and proliferation as well as in the governing and transduction of prosurvival signals. Increased expression of CK2 is a hallmark of some cancers, hence its antiapoptotic properties may be relevant to cancer onset. Thus, the designing and synthesis of the CK2 inhibitors has become an important pursuit in the search for cancer therapies.</p> <p>Results</p> <p>Using a high-throughput microarray approach, we demonstrate that two potent inhibitors of CK2, 4,5,6,7-tetrabromo-benzimidazole (TBBz) and 2-Dimethyloamino-4,5,6,7-tetrabromo-1H-benzimidazole (DMAT), blocked mitogen induced mRNA expression of immediate early genes. Given the impact of these inhibitors on the process of transcription, we investigated their effects on RNA Polymerase II (RNAPII) elongation along the mitogen inducible gene, <it>EGR1 </it>(early growth response 1), using chromatin immunoprecipitation (ChIP) assay. ChIP analysis demonstrated that both drugs arrest RNAPII elongation. Finally, we show that CDK9 kinase activity, essential for the triggering of RNAPII elongation, was blocked by TBBz and to lesser degree by DMAT.</p> <p>Conclusions</p> <p>Our approach revealed that small molecules derived from halogenated imidazole compounds may decrease cell proliferation, in part, by inhibiting pathways that regulate transcription elongation.</p