Long-range power-law correlations have been reported recently for DNA sequences containing noncoding regions. We address the question of whether such correlations may be a trivial consequence of the known mosaic structure ("patchiness") of DNA. We analyze two classes of controls consisting of patchy nucleotide sequences generated by different algorithms--one without and one with long-range power-law correlations. Although both types of sequences are highly heterogenous, they are quantitatively distinguishable by an alternative fluctuation analysis method that differentiates local patchiness from long-range correlations. Application of this analysis to selected DNA sequences demonstrates that patchiness is not sufficient to account for long-range correlation properties.

DNA sequences have been analysed using models, such as an n-step Markov chain, that incorporate the possibility of short-range nucleotide correlations. We propose here a method for studying the stochastic properties of nucleotide sequences by constructing a 1:1 map of the nucleotide sequence onto a walk, which we term a 'DNA walk'. We then use the mapping to provide a quantitative measure of the correlation between nucleotides over long distances along the DNA chain. Thus we uncover in the nucleotide sequence a remarkably long-range power law correlation that implies a new scale-invariant property of DNA. We find such long-range correlations in intron-containing genes and in nontranscribed regulatory DNA sequences, but not in complementary DNA sequences or intron-less genes.

Vascular endothelial growth factors (VEGFs) and their receptors (VEGFRs) are uniquely required to balance the formation of new blood vessels with the maintenance and remodelling of existing ones, during development and in adult tissues. Recent advances have greatly expanded our understanding of the tight and multi-level regulation of VEGFR2 signalling, which is the primary focus of this Review. Important insights have been gained into the regulatory roles of VEGFR-interacting proteins (such as neuropilins, proteoglycans, integrins and protein tyrosine phosphatases); the dynamics of VEGFR2 endocytosis, trafficking and signalling; and the crosstalk between VEGF-induced signalling and other endothelial signalling cascades. A clear understanding of this multifaceted signalling web is key to successful therapeutic suppression or stimulation of vascular growth.

SUMMARY A key function of blood vessels, to supply oxygen, is impaired in tumors because of abnormalities in their endothelial lining. PHD proteins serve as oxygen sensors and may regulate oxygen delivery. We therefore studied the role of endothelial PHD2 in vessel shaping by implanting tumors in PHD2+/− mice. Haplodeficiency of PHD2 did not affect tumor vessel density or lumen size, but normalized the endothelial lining and vessel maturation. This resulted in improved tumor perfusion and oxygenation and inhibited tumor cell invasion, intravasation, and metastasis. Haplodeficiency of PHD2 redirected the specification of endothelial tip cells to a more quiescent cell type, lacking filopodia and arrayed in a phalanx formation. This transition relied on HIF-driven upregulation of (soluble) VEGFR-1 and VE-cadherin. Thus, decreased activity of an oxygen sensor in hypoxic conditions prompts endothelial cells to readjust their shape and phenotype to restore oxygen supply. Inhibition of PHD2 may offer alternative therapeutic opportunities for anticancer therapy.

Summary Chemical or traumatic damage to the liver is frequently associated with aberrant healing(fibrosis) that overrides liver regeneration1–5. The mechanism by which hepatic niche cells differentially modulate regeneration and fibrosis during liver repair remains to be defined6–8. Hepatic vascular niche predominantly represented by liver sinusoidal endothelial cells (LSECs), deploys paracrine trophogens, known as angiocrine factors, to stimulate regeneration9–15. Nevertheless, it remains unknown how pro-regenerative angiocrine signals from LSECs is subverted to promote fibrosis16,17. Here, by combining inducible endothelial cell (EC)-specific mouse gene deletion strategy and complementary models of acute and chronic liver injury, we revealed that divergent angiocrine signals from LSECs elicit regeneration after immediateinjury and provoke fibrosis post chronic insult. The pro-fibrotic transition of vascular niche results from differential expression of stromal derived factor-1 (SDF-1) receptors, CXCR7 and CXCR418–21in LSECs. After acute injury, CXCR7 upregulation in LSECs acts in conjunction with CXCR4 to induce transcription factor Id1, deploying pro-regenerative angiocrine factors and triggering regeneration. Inducible deletion of Cxcr7 in adult mouse LSECs (Cxcr7iΔEC/iΔEC) impaired liver regeneration by diminishing Id1-mediated production of angiocrine factors9–11. By contrast, after chronic injury inflicted by iterative hepatotoxin (carbon tetrachloride) injection and bile duct ligation, constitutive FGFR1 signaling in LSECs counterbalanced CXCR7-dependent pro-regenerative response and augmented CXCR4 expression. This predominance of CXCR4 over CXCR7 expression shifted angiocrine response of LSECs, stimulating proliferation of desmin+hepatic stellate-like cells22,23 and enforcing a pro-fibrotic vascular niche. EC-specific ablation of either Fgfr1 (Fgfr1iΔEC/iΔEC) or Cxcr4 (Cxcr4iΔEC/iΔEC) in mice restored pro-regenerative pathway and prevented FGFR1-mediated maladaptive subversion of angiocrine factors. Similarly, selective CXCR7 activation in LSECs abrogated fibrogenesis. Thus, we have demonstrated that in response to liver injury, differential recruitment of pro-regenerative CXCR7/Id1 versus pro-fibrotic FGFR1/CXCR4 angiocrine pathways in vascular niche balances regeneration and fibrosis. These results provide a therapeutic roadmap to achieve hepatic regeneration without provoking fibrosis1,2,4.

IntroductionAtherosclerosis is a progressive disorder initiated by biomechanical forces in areas of the vascular tree subjected to disturbed blood flow and a number of systemic factors, including hyperlipidemia, smoking, and diabetes (1, 2). Lipid uptake by the vascular wall leads over time to a gradual buildup of atherosclerotic plaques. Once formed, the plaque continues to expand, leading to a gradual restriction in lumen diameter and compromise of blood flow. Under certain conditions, plaque rupture can precipitate intravascular thrombosis, resulting in complete and sudden interruption of the arterial blood supply. The buildup, growth, and rupture of the plaque have all been associated with the presence of systemic and vascular wall inflammation (3-5). Despite strong data linking vessel wall inflammation to atherosclerosis progression, the mechanism(s) of inflammation-induced atherosclerotic disease progression remains obscure (4), while efforts to halt disease progression by antiinflammatory therapies have failed in clinical trial (3).Recent studies have documented a high incidence of endothelial-to-mesenchymal transition (EndMT) in a number of pathological conditions associated with inflammation, such as myocardial infarction (6), cerebral cavernous malformations (7), portal hypertension (8), pulmonary hypertension (9), and vascular graft failure (10, 11) among others. EndMT is characterized by a change in phenotype of normal endothelial cells (ECs) that assume the shape and properties of mesenchymal cells (fibroblasts, smooth muscle cells [SMCs]), including enhanced proliferation and migration; secretion of extracellular matrix proteins, such as fibronectin and collagen; and expression of various leukocyte adhesion molecules.TGF-β has been identified as the central player in driving EndMT progression (12, 13), but the processes leading to activation of its signaling remain poorly defined. We have previously reported that a reduction in endothelial FGF-mediated signaling induced by knockout of either the key intracellular signal mediator FGF receptor substrate 2 α (FRS2α) (10) or the primary FGF receptor in the endothelium (FGF receptor 1 [FGFR1]) (14) activates TGF-β signaling, leading to EndMT.The unusual feature of FGFR1 biology is that FGFR1's expression in ECs is affected by certain inflammatory stimuli, including IFN-γ, TNF-α, and IL-1β, that induce a profound reduction in its expression (10). Since these are precisely the inflammatory mediators found in atherosclerotic plaques, we set out to investigate the occurrence and role of EndMT in atherosclerosis.Studies in cell culture and mouse models demonstrated that both oscillatory fluid shear stress and soluble inflammatory mediators reduced FGFR1 expression and signaling and promoted TGF-β signaling and EndMT. In addition, analysis of human coronary arteries demonstrated a strong correlation among endothelial FGFR1 expression, increased TGF-β signaling, and the appearance of EndMT with the severity of atherosclerosis. Together, these findings point to...

Summary To identify the pathways involved in adult lung regeneration, we have employed left unilateral pneumonectomy (PNX) model that promotes regenerative alveolarization in the remaining intact right lung lobes. Here, we show that PNX stimulates pulmonary capillary endothelial cells (PCECs) to produce paracrine (angiocrine) growth factors that induce proliferation of epithelial progenitor cells supporting alveologenesis. After PNX, endothelial-specific inducible genetic ablation of Vegfr2 and Fgfr1 in mice inhibited production of MMP14 impairing alveolarization. MMP14 via unmasking cryptic EGF-like ectodomain and activation of EGF-receptor (EGFR) expands epithelial progenitor cells. Neutralization of MMP14 impaired EGFR-ligand mediated alveolar regeneration. By contrast, administration of recombinant EGF, or intravascular transplantation of MMP14+ PCECs from wild-type mice, into pneumonectomized Vegfr2/Fgfr1 deficient mice restored alveologenesis and lung inspiratory volume and compliance function. This study shows that VEGFR2 and FGFR1 activation in PCECs by increasing MMP14-dependent bioavailability of EGFR-ligands initiates and sustains alveologenesis and holds promise to develop therapeutic strategies to promote lung regeneration.

Higher organisms rely on a closed cardiovascular circulatory system with blood vessels supplying vital nutrients and oxygen to distant tissues. Not surprisingly, vascular pathologies rank among the most life-threatening diseases. At the crux of most of these vascular pathologies are (dysfunctional) endothelial cells (ECs), the cells lining the blood vessel lumen. ECs display the remarkable capability to switch rapidly from a quiescent state to a highly migratory and proliferative state during vessel sprouting. This angiogenic switch has long been considered to be dictated by angiogenic growth factors (eg vascular endothelial growth factor; VEGF) and other signals (eg Notch) alone, but recent findings show that it is also driven by a metabolic switch in ECs. Furthermore, these changes in metabolism may even override signals inducing vessel sprouting. Here, we review how EC metabolism differs between the normal and dysfunctional/diseased vasculature and how it relates to or impacts the metabolism of other cell types contributing to the pathology. We focus on the biology of ECs in tumor blood vessel and diabetic ECs in atherosclerosis as examples of the role of endothelial metabolism in key pathological processes. Finally, current as well as unexplored ‘EC metabolism’-centric therapeutic avenues are discussed.