Local colonisations and extinctions of European birds are poorly explained by changes in climate suitability

Climate change has been associated with both latitudinal and elevational shifts in species' ranges. The extent, however, to which climate change has driven recent range shifts alongside other putative drivers remains uncertain. Here, we use the changing distributions of 378 European breeding bird species over 30 years to explore the putative drivers of recent range dynamics, considering the effects of climate, land cover, other environmental variables, and species' traits on the probability of local colonisation and extinction. On average, species shifted their ranges by 2.4 km/year. These shifts, however, were significantly different from expectations due to changing climate and land cover. We found that local colonisation and extinction events were influenced primarily by initial climate conditions and by species' range traits. By contrast, changes in climate suitability over the period were less important. This highlights the limitations of using only climate and land cover when projecting future changes in species' ranges and emphasises the need for integrative, multi-predictor approaches for more robust forecasting.

Targeting the scaffolding role of LSD1 (KDM1A) poises acute myeloid leukemia cells for retinoic acid-induced differentiation

The histone demethylase LSD1 is deregulated in several tumors, including leukemias, providing the rationale for the clinical use of LSD1 inhibitors. In acute promyelocytic leukemia (APL), pharmacological doses of retinoic acid (RA) induce differentiation of APL cells, triggering degradation of the PML-RAR oncogene. APL cells are resistant to LSD1 inhibition or knockout, but targeting LSD1 sensitizes them to physiological doses of RA without altering of PML-RAR levels, and extends survival of leukemic mice upon RA treatment. The combination of RA with LSD1 inhibition (or knockout) is also effective in other non-APL, acute myeloid leukemia (AML) cells. Nonenzymatic activities of LSD1 are essential to block differentiation, while RA with targeting of LSD1 releases a differentiation gene expression program, not strictly dependent on changes in histone H3K4 methylation. Integration of proteomic/epigenomic/mutational studies showed that LSD1 inhibitors alter the recruitment of LSD1-containing complexes to chromatin, inhibiting the interaction between LSD1 and the transcription factor GFI1.

Inter-specific competition influences apex predator–prey populations

Abstract ContextTiger (Panthera tigris), leopard (Panthera pardus) and dhole (Cuon alpinus) represent a typical multi-predator system of species of conservation concern. Several studies have addressed this system, with heterogeneous results, and there’s a lack of information on population dynamics of multi-species assemblages. We studied a time series (1998–2009) of abundance indices for three predators and five prey species in Bor Wildlife Sanctuary (BWS), Maharashtra, India, before it was declared as Bor Tiger Reserve (BTR) in 2009. AimsTo analyse the complex relationships within a predator–prey system in a dynamic fashion, to analyse data collected in a stable and undisturbed area and to form a comparison basis for future studies within the sanctuary after its declaration as a Tiger Reserve. MethodsA 24-h effort was made annually to census the BWS. Predators were counted at waterholes from arboreal hideouts. The prey populations were censused along 353-km line-transects. For each species, we analysed the yearly growth rate, testing the effect of inter-species abundance. Key resultsTiger growth rate did not depend on any particular prey, whereas mesopredators seemed to depend on medium-sized prey. A die-out of dholes in 2001 was followed by an increase in tiger populations (from 4 to 11), which, in turn, negatively affected leopard numbers (from 6 to 2).We found no direct evidence of top-down effect, but the density dependence for three of five prey species could be linked to predation pressure. We found some evidence of interspecific competition among prey species, especially among ungulates, potentially being mediated by predation pressure. ConclusionsThe relationships among species in a predator–prey system are very complex and often could be explained only by more-than-two-species interactions. The disappearance of one predator, not necessarily the top predator, could bring multiple effects, for which it could be difficult to detect causal relationships. ImplicationsAll subsequent changes in human activities in the sanctuary, as a consequence of its designation as the BTR in 2009, should be evaluated with respect to the results of the present study. The conservation of large predators should rely on the maintenance of a rich and abundant prey base, in which different-sized prey could lessen interactive-competition among the predators.

Clinical Significance of Extracellular Vesicles in Plasma from Glioblastoma Patients

PURPOSE

Glioblastoma (GBM) is the most common primary brain tumor. The identification of blood biomarkers reflecting the tumor status represents a major unmet need for optimal clinical management of patients with GBM. Their high number in body fluids, their stability, and the presence of many tumor-associated proteins and RNAs make extracellular vesicles potentially optimal biomarkers. Here, we investigated the potential role of plasma extracellular vesicles from patients with GBM for diagnosis and follow-up after treatment and as a prognostic tool.

EXPERIMENTAL DESIGN

Plasma from healthy controls (n = 33), patients with GBM (n = 43), and patients with different central nervous system malignancies (n = 25) were collected. Extracellular vesicles were isolated by ultracentrifugation and characterized in terms of morphology by transmission electron microscopy, concentration, and size by nanoparticle tracking analysis, and protein composition by mass spectrometry. An orthotopic mouse model of human GBM confirmed human plasma extracellular vesicle quantifications. Associations between plasma extracellular vesicle concentration and clinicopathologic features of patients with GBM were analyzed. All statistical tests were two-sided.

RESULTS

GBM releases heterogeneous extracellular vesicles detectable in plasma. Plasma extracellular vesicle concentration was higher in GBM compared with healthy controls (P < 0.001), brain metastases (P < 0.001), and extra-axial brain tumors (P < 0.001). After surgery, a significant drop in plasma extracellular vesicle concentration was measured (P < 0.001). Plasma extracellular vesicle concentration was also increased in GBM-bearing mice (P < 0.001). Proteomic profiling revealed a GBM-distinctive signature.

CONCLUSIONS

Higher extracellular vesicle plasma levels may assist in GBM clinical diagnosis: their reduction after GBM resection, their rise at recurrence, and their protein cargo might provide indications about tumor, therapy response, and monitoring.

Extensive and systematic rewiring of histone post-translational modifications in cancer model systems

Histone post-translational modifications (PTMs) generate a complex combinatorial code that regulates gene expression and nuclear functions, and whose deregulation has been documented in different types of cancers. Therefore, the availability of relevant culture models that can be manipulated and that retain the epigenetic features of the tissue of origin is absolutely crucial for studying the epigenetic mechanisms underlying cancer and testing epigenetic drugs. In this study, we took advantage of quantitative mass spectrometry to comprehensively profile histone PTMs in patient tumor tissues, primary cultures and cell lines from three representative tumor models, breast cancer, glioblastoma and ovarian cancer, revealing an extensive and systematic rewiring of histone marks in cell culture conditions, which includes a decrease of H3K27me2/me3, H3K79me1/me2 and H3K9ac/K14ac, and an increase of H3K36me1/me2. While some changes occur in short-term primary cultures, most of them are instead time-dependent and appear only in long-term cultures. Remarkably, such changes mostly revert in cell line- and primary cell-derived in vivo xenograft models. Taken together, these results support the use of xenografts as the most representative models of in vivo epigenetic processes, suggesting caution when using cultured cells, in particular cell lines and long-term primary cultures, for epigenetic investigations.

RNAi screens identify CHD4 as an essential gene in breast cancer growth

Epigenetic regulation plays an essential role in tumor development and epigenetic modifiers are considered optimal potential druggable candidates. In order to identify new breast cancer vulnerabilities and improve therapeutic chances for patients, we performed in vivo and in vitro shRNA screens in a human breast cancer cell model (MCF10DCIS.com cell line) using epigenetic libraries. Among the genes identified in our screening, we deeply investigated the role of Chromodomain Helicase DNA binding Protein 4 (CHD4) in breast cancer tumorigenesis. CHD4 silencing significantly reduced tumor growth in vivo and proliferation in vitro of MCF10DCIS.com cells. Similarly, in vivo breast cancer growth was decreased in a spontaneous mouse model of breast carcinoma (MMTV-NeuT system) and in metastatic patient-derived xenograft models. Conversely, no reduction in proliferative ability of non-transformed mammary epithelial cells (MCF10A) was detected. Moreover, we showed that CHD4 depletion arrests proliferation by inducing a G0/G1 block of cell cycle associated with up-regulation of CDKN1A (p21). These results highlight the relevance of genetic screens in the identification of tumor frailties and the role of CHD4 as a potential pharmacological target to inhibit breast cancer growth.

Retrospective biomonitoring of mercury and other elements in museum feathers of common kestrel Falco tinnunculus using instrumental neutron activation analysis (INAA)

This study examines the potential to use instrumental neutron activation analysis (INAA) to explore temporal and geographical variation in exposure to heavy metals and other selected elements in common kestrel Falco tinnunculus using feathers from a natural history collection. The study gathered samples of two breast feathers from each of 16 adult male kestrel specimens from Naturalis Biodiversity Centre, collected in The Netherlands between 1901 and 2001. Feather samples were analysed for more than 50 elements, using INAA at the Reactor Institute Delft. Results (in mg/kg dw) were transformed into ratios of milligram of element per millimetre of feather length. The distribution of the mass fractions and ratios was plotted for each element against time and by geographical area. Observed mass fractions and/or ratios are discussed for selected elements (Hg, Cd, Zn, Pt, Pd, Se, Al, Rb, As, Sb, Cr, V, Cl, Br) known to have, at certain concentrations, adverse effects on raptors. Some samples show mass fractions of certain elements (Cr, Cd, Se, As) above levels known to have adverse effects. We conclude that the analysis of museum feathers using INAA provides reference values for concentrations of selected elements, including those of high societal concern such as Hg and Cd, against which to assess concentrations of these elements in feathers of present-day living raptor populations.

Extracellular vesicle-mediated transfer of CLIC1 protein is a novel mechanism for the regulation of glioblastoma growth

Little progresses have been made in the treatment of glioblastoma (GBM), the most aggressive and lethal among brain tumors. Recently we have demonstrated that Chloride Intracellular Channel-1 (CLIC1) is overexpressed in GBM compared to normal tissues, with highest expression in patients with poor prognosis. Moreover, CLIC1-silencing in cancer stem cells (CSCs) isolated from human GBM patients negatively influences proliferative capacity and self-renewal properties in vitro and impairs the in vivo tumorigenic potential. Here we show that CLIC1 exists also as a circulating protein, secreted via extracellular vesicles (EVs) released by either cell lines or GBM-derived CSCs. Extracellular vesicles (EVs), comprising exosomes and microvesicles based on their composition and biophysical properties, have been shown to sustain tumor growth in a variety of model systems, including GBM. Interestingly, treatment of GBM cells with CLIC1-containing EVs stimulates cell growth both in vitro and in vivo in a CLIC1-dose dependent manner. EVs derived from CLIC1-overexpressing GBM cells are strong inducers of proliferation in vitro and tumor engraftment in vivo. These stimulations are significantly attenuated by treatment of GBM cells with EVs derived from CLIC1-silenced cells. However, CLIC1 modulation appears to have no direct role in EV structure, biogenesis and secretion. These findings reveal that, apart from the function of CLIC1 cellular reservoir, CLIC1 contained in EVs is a novel regulator of GBM growth.

A new female-like morph of juvenile male Levant Sparrowhawk (Accipiter brevipes) – sexual mimicry to avoid intra-specific predation?

In migrant Levant Sparrowhawk (Accipiter brevipes) at Eilat, Israel, we noted that juvenile males had two different morphs – the one described to date in literature; and a second, previously undescribed morph, with femalelike barring on the chest and flanks interspersed with tear-shaped elongated spots, giving an overall female-like appearance. Here we forward the hypothesis that explain the evolutionary consequences for the female-like plumage of juvenile males as that of intra-specific sex mimicry developed to avoid intra-specific predation by the larger females.

Redox-Mediated Suberoylanilide Hydroxamic Acid Sensitivity in Breast Cancer

AIMS

Vorinostat (suberoylanilide hydroxamic acid; SAHA) is a histone deacetylase inhibitor (HDACi) approved in the clinics for the treatment of T-cell lymphoma and with the potential to be effective also in breast cancer. We investigated the responsiveness to SAHA in human breast primary tumors and cancer cell lines.

RESULTS

We observed a differential response to drug treatment in both human breast primary tumors and cancer cell lines. Gene expression analysis of the breast cancer cell lines revealed that genes involved in cell adhesion and redox pathways, especially glutathione metabolism, were differentially expressed in the cell lines resistant to SAHA compared with the sensitive ones, indicating their possible association with drug resistance mechanisms. Notably, such an association was also observed in breast primary tumors. Indeed, addition of buthionine sulfoximine (BSO), a compound capable of depleting cellular glutathione, significantly enhanced the cytotoxicity of SAHA in both breast cancer cell lines and primary breast tumors.

INNOVATION

We identify and validate transcriptional differences in genes involved in redox pathways, which include potential predictive markers of sensitivity to SAHA.

CONCLUSION

In breast cancer, it could be relevant to evaluate the expression of antioxidant genes that may favor tumor resistance as a factor to consider for potential clinical application and treatment with epigenetic drugs (HDACis).

CD133 is essential for glioblastoma stem cell maintenance

The role of the cell surface CD133 as a cancer stem cell marker in glioblastoma (GBM) has been widely investigated, since it identifies cells that are able to initiate neurosphere growth and form heterogeneous tumors when transplanted in immune-compromised mice. However, evidences of CD133-negative cells exhibiting similar properties have also been reported. Moreover, the functional role of CD133 in cancer stem/progenitor cells remains poorly understood. We studied the biological effects of CD133 downregulation in GBM patient-derived neurospheres. Our results indicate that there is not a hierarchical relation between CD133-positive and CD133-negative cells composing the neurospheres. Indeed, CD133 appears in an interconvertible state, changing its subcellular localization between the cytoplasm and the plasmamembrane of neurosphere cells. Silencing of CD133 in human GBM neurospheres using lentivirus-mediated short hairpin RNA impairs the self-renewal and tumorigenic capacity of neurosphere cells. These results imply that CD133 could be used as a therapeutic target in GBMs.

Molecular networks in melanoma invasion and metastasis

Metastatic melanoma accounts for approximately 80% of skin cancer-related deaths. Up to now there has been no effective treatment for stage IV melanoma patients due to the complexity and dissemination potential of this disease. Melanomas are heterogeneous tumors in which conventional therapies fail to improve overall survival. Targeted therapies are being developed, but the final outcome can be hampered by the incomplete knowledge of the process of melanoma progression. Even if the intracellular pathways are similar, the interaction of the cells with the surrounding environment should be taken into consideration. This article seeks to highlight some of the advances in the understanding of the molecular mechanisms underlying melanoma dissemination.

Functional role of CLIC1 ion channel in glioblastoma-derived stem/progenitor cells

Background

Chloride channels are physiologically involved in cell division and motility. Chloride intracellular channel 1 (CLIC1) is overexpressed in a variety of human solid tumors compared with normal tissues, suggesting a potential involvement of CLIC1 in the regulation of tumorigenesis. This led us to investigate the role of CLIC1 in gliomagenesis.

Methods

We used the neurosphere system to isolate stem/progenitor cells from human glioblastomas (GBMs). CLIC1 targeting in GBM neurospheres was achieved by both lentiviral-mediated short-hairpin RNA transduction and CLIC1 antibody treatment, and its effect on stem-like properties was analyzed in vitro by proliferation and clonogenic assays and in vivo by orthotopic injection in immunocompromised mice. Channel activity was studied by perforated patch clamp technique. Differences in expression were analyzed by analysis of variance with Tamhane’s multiple comparison test. Kaplan–Meier analyses and log-rank test were used to assess survival. All statistical tests were two-sided.

Results

CLIC1 was statistically significantly overexpressed in GBMs compared with normal brain tissues (P < .001) with a better survival of patients with CLIC1 low-expressing tumors (CLIC1^low vs CLIC1^high survival: χ² = 74.35; degrees of freedom = 1; log-rank P < .001). CLIC1 was variably expressed in patient-derived GBM neurospheres and was found enriched in the stem/progenitor compartment. CLIC1 silencing reduced proliferative (P < .01), clonogenic (P < .01), and tumorigenic capacity (P < .05) of stem/progenitor cells. The reduction of CLIC1 chloride currents with a specific CLIC1 antibody mirrored the biological effects of CLIC1 silencing in GBM patient–derived neurospheres.

Conclusions

Reduced gliomagenesis after CLIC1 targeting in tumoral stem/progenitor cells and the finding that CLIC1 expression is inversely associated with patient survival suggest CLIC1 as a potential target and prognostic biomarker.

Field-induced clearing in sphere-sphere and rod-sphere binary mixtures of charged colloidal particles

Binary mixtures of larger and smaller colloids having charges of equal sign display unusual response to low-frequency electric fields. We show here that the previously reported negative torque acting on rodlike particles when in presence of a sea of smaller particles is accompanied by a field-induced clearing of the suspension. Measurements of transmitted intensity performed on mixtures of large (dilute) and small (semidilute) spherical particles indicate that such a clearing effect is universal and due to an anisotropic E2 -dependent redistribution of the small spheres around the large ones. We interpret this behavior as resulting from O(E2) electro-osmotic flows whose magnitude is greatly enhanced by the presence of the small particles.

NA-Seq: a discovery tool for the analysis of chromatin structure and dynamics during differentiation

It is well established that epigenetic modulation of genome accessibility in chromatin occurs during biological processes. Here we describe a method based on restriction enzymes and next-generation sequencing for identifying accessible DNA elements using a small amount of starting material, and use it to examine myeloid differentiation of primary human CD34+ cells. The accessibility of several classes of cis-regulatory elements was a predictive marker of in vivo DNA binding by transcription factors, and was associated with distinct patterns of histone posttranslational modifications. We also mapped large chromosomal domains with differential accessibility in progenitors and maturing cells. Accessibility became restricted during differentiation, correlating with a decreased number of expressed genes and loss of regulatory potential. Our data suggest that a permissive chromatin structure in multipotent cells is progressively and selectively closed during differentiation, and illustrate the use of our method for the identification of functional cis-regulatory elements.