Building bridges to the cortex

Innervation of the neocortex by the thalamus is dependent on the precise coordination of spatial and temporal guidance cues. In this issue of Cell, work by López-Bendito et al.(2006) reveals that tangentially migrating cells within the ventral telencephalon are essential for axonal navigation between the thalamus and the neocortex, a process apparently mediated by Neuregulin-1/ErbB4 short- and long-range signaling.     

Chemokine Receptor CCR8 Is Required for Lipopolysaccharide-Triggered Cytokine Production in Mouse Peritoneal Macrophages

Chemokine (C-C motif) receptor 8 (CCR8), the chemokine receptor for chemokine (C-C motif) ligand 1 (CCL1), is expressed in T-helper type-2 lymphocytes and peritoneal macrophages (PMφ) and is involved in various pathological conditions, including peritoneal adhesions. However, the role of CCR8 in inflammatory responses is not fully elucidated. To investigate the function of CCR8 in macrophages, we compared cytokine secretion from mouse PMφ or bone marrow-derived macrophages (BMMφ) stimulated with various Toll-like receptor (TLR) ligands in CCR8 deficient (CCR8^{- /-}) and wild-type (WT) mice. We found that CCR8^-/- PMφ demonstrated attenuated secretion of tumor necrosis factor (TNF)-α, interleukin (IL)-6, and IL-10 when stimulated with lipopolysaccharide (LPS). In particular, LPS-induced IL-10 production absolutely required CCR8. CCR8-dependent cytokine secretion was characteristic of PMφ but not BMMφ. To further investigate this result, we selected the small molecule compound R243 from a library of compounds with CCR8-antagonistic effects on CCL1-induced Ca²⁺ flux and CCL1-driven PMφ aggregation. Similar to CCR8^-/- PMφ, R243 attenuated secretion of TNF-α, IL-6, and most strikingly IL-10 from WT PMφ, but not BMMφ. CCR8^-/- PMφ and R243-treated WT PMφ both showed suppressed c-jun N-terminal kinase activity and nuclear factor-κB signaling after LPS treatment when compared with WT PMφ. A c-Jun signaling pathway inhibitor also produced an inhibitory effect on LPS-induced cytokine secretion that was similar to that of CCR8 deficiency or R243 treatment. As seen in CCR8^-/- mice, administration of R243 attenuated peritoneal adhesions in vivo. R243 also prevented hapten-induced colitis. These results are indicative of cross talk between signaling pathways downstream of CCR8 and TLR-4 that induces cytokine production by PMφ. Through use of CCR8^-/- mice and the new CCR8 inhibitor, R243, we identified a novel macrophage innate immune response pathway that involves a chemokine receptor.     

The illogical basis of phylogenetic nomenclature

The current advocacy for the so-called PhyloCode has a history rooted in twentieth-century arguments among biologists and philosophers regarding a putative distinction between classes and individuals. From this seemingly simple and innocuous discussion have come supposed distinctions between definitions and diagnosis, classification and systematization, and now Linnaean and “phylogenetic” nomenclature. Nevertheless, the metaphysical dichotomy of class versus individual, insofar as its standard applications to the issue of biological taxonomy are concerned, is an outdated remnant of early logical positivist thinking. Current views on natural kinds and their definitions under a scientific realist perspective provide grounds for rejecting the class versus individual dichotomy altogether insofar as biological entities are concerned. We review the role of natural kinds in scientific practice and the nature of definitions and scientific classifications. Although inherent instabilities of the PhyloCode are clearly sufficient to argue against the general application of this nominally phylogenetic system, our goal here is to address serious and fundamental flaws in its very foundation by exposing the unsubstantiated philosophical assumptions preceding and subtending it.

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Resumen  Las propuestas actuales en favor del llamado Código de Nomenclatura Filogenética (Phylo-Code) tienen una historia basada en argumentos desarrollados, durante el siglo veinte, por biólogos y filósofos sobre una distinción putativa entre clases e individuos. De esta simple y aparentemente inocua discusión han surgido supuestas distinciones entre definición y diagnosis, clasificación y sistematización, y ahora entre nomenclatura Lineana y “filogenética.” Sin embargo, la dicotomía metafísica clase contra individuo, al menos en lo concerniente a su aplicación estándar al tema de taxonomía biológica, es un remanente obsoleto del pensamiento positivista lógico. Opiniones actuales sobre categorías naturales y sus definiciones bajo la perspectiva del realismo científico proveen bases para rechazar por completo dicha dicotomía, al menos en lo que concierne a las entidades biológicas. En este artículo se revisa el papel de las categorías naturales en la práctica científica, y la naturaleza de las definiciones y la clasificación científica. Aún cuando la inestabilidad inherente en el Código de Nomenclatura Filogenética es claramente suficiente para argumentar contra la aplicación general de este sistema nominal filogenético, el objetivo de este artículo es mostrar las serias y fundamentales deficiencias en sus propias bases al exponer las suposiciones filosóficas sin fundamento que le preceden y sustentan.

     

Cover Picture: Protein folding in vivo

Cover illustration: Protein folding in vivo. This special issue, edited by Marc Blondel (Brest, France) and Mónica Marín (Montevideo, Uruguay) includes review and original articles on co-translational folding, alternative codon usage and the impacts of protein folding on protein production. The drawing on the cover illustrates the ribosome as a platform for co-translational folding of newly synthesized proteins. © HRATCH ARBACH 2011     

GRP78 determines glioblastoma sensitivity to UBA1 inhibition-induced UPR signaling and cell death

Glioblastoma multiforme (GBM) is an extremely aggressive brain tumor for which new therapeutic approaches are urgently required. Unfolded protein response (UPR) plays an important role in the progression of GBM and is a promising target for developing novel therapeutic interventions. We identified ubiquitin-activating enzyme 1 (UBA1) inhibitor TAK-243 that can strongly induce UPR in GBM cells. In this study, we evaluated the functional activity and mechanism of TAK-243 in preclinical models of GBM. TAK-243 significantly inhibited the survival, proliferation, and colony formation of GBM cell lines and primary GBM cells. It also revealed a significant anti-tumor effect on a GBM PDX animal model and prolonged the survival time of tumor-bearing mice. Notably, TAK-243 more effectively inhibited the survival and self-renewal ability of glioblastoma stem cells (GSCs) than GBM cells. Importantly, we found that the expression level of GRP78 is a key factor in determining the sensitivity of differentiated GBM cells or GSCs to TAK-243. Mechanistically, UBA1 inhibition disrupts global protein ubiquitination in GBM cells, thereby inducing ER stress and UPR. UPR activates the PERK/ATF4 and IRE1α/XBP signaling axes. These findings indicate that UBA1 inhibition could be an attractive strategy that may be potentially used in the treatment of patients with GBM, and GRP78 can be used as a molecular marker for personalized treatment by targeting UBA1.Subject terms: CNS cancer, Cancer stem cells     

A Numeric Index to Establish Conservation Priorities for Medicinal Plants in the Paravachasca Valley, Córdoba, Argentina

Medicinal plant extraction is a relevant issue in the province of Córdoba, Argentina. A quantitative methodology is proposed for the evaluation of conservation priorities for species used in popular medicine in the Paravachasca Valley, Córdoba. Qualitative attributes were surveyed through the knowledge and perception of local communities. Species are ranked by their index of conservation priority (ICP) values. This index takes into consideration the following data: harvest, abundance, propagation method, origin and commercial demand of species in the area. Among the native species prioritized for conservation are Minthostachys mollis, Hedeoma multiflora, Julocroton argenteus, Baccharis crispa, Trixis divaricata subsp. discolor, Passiflora caerulea, Usnea spp. and Equisetum giganteum.     

Ligation of IFN-gamma-induced HLA-DR molecules on fibroblasts induces RANTES expression via c-Jun N-terminal kinase (JNK) pathway

The role of human leukocyte antigen (HLA) class II molecules on non-antigen presenting cells has been a matter of controversy. We recently reported that ligation of HLA-DR molecule with anti-HLA-DR antibodies (L243) and/or antigenic peptide/T cell receptor complex resulted in a secretion of several chemokines such as RANTES. In the present study, we aimed to detect putative signal transduction pathway leading to RANTES production from fibroblasts when the DR molecules were ligated with L243. Protein tyrosine kinase inhibitor (GF109203X) suppressed RANTES expression in a dose dependent manner for up to 50% from gingival fibroblasts (GF), while protein kinase C inhibitor (genistein) had no inhibitory effect. Ligation of DR molecules with L243 resulted in tyrosine phosphorylation of 54 kDa cellular protein. Thus, we suspected that either Jun N-terminal kinase-2 (JNK-2) or Src family proteins were involved in HLA-DR-mediated signaling. JNK inhibitor (SP600125), but not Src inhibitor (PP2), suppressed both L243 stimulated RANTES mRNA expression and protein secretion. The maximum inhibition for RANTES production by SP600125 was more than 80%. Additionally, JNK inhibitor nearly completely blocked tumor necrosis factor-alpha (TNF-alpha)-induced RANTES production in GF. Furthermore, ligation of GF HLA-DR with L243 induced selective phosphorylation of JNK-2. We concluded that JNK-2 was one of the HLA-DR-mediated signal transduction pathways.     

Mre11 ATLD17/18 mutation retains Tel1/ATM activity but blocks DNA double-strand break repair

The Mre11 complex (Mre11-Rad50-Nbs1 or MRN) binds double-strand breaks where it interacts with CtIP/Ctp1/Sae2 and ATM/Tel1 to preserve genome stability through its functions in homology-directed repair, checkpoint signaling and telomere maintenance. Here, we combine biochemical, structural and in vivo functional studies to uncover key properties of Mre11-W243R, a mutation identified in two pediatric cancer patients with enhanced ataxia telangiectasia-like disorder. Purified human Mre11-W243R retains nuclease and DNA binding activities in vitro. X-ray crystallography of Pyrococcus furiosus Mre11 indicates that an analogous mutation leaves the overall Mre11 three-dimensional structure and nuclease sites intact but disorders surface loops expected to regulate DNA and Rad50 interactions. The equivalent W248R allele in fission yeast allows Mre11 to form an MRN complex that efficiently binds double-strand breaks, activates Tel1/ATM and maintains telomeres; yet, it causes hypersensitivity to ionizing radiation and collapsed replication forks, increased Rad52 foci, defective Chk1 signaling and meiotic failure. W248R differs from other ataxia telangiectasia-like disorder analog alleles by the reduced stability of its interaction with Rad50 in cell lysates. Collective results suggest a separation-of-function mutation that disturbs interactions amongst the MRN subunits and Ctp1 required for DNA end processing in vivo but maintains interactions sufficient for Tel1/ATM checkpoint and telomere maintenance functions.     

Not all colors are equal: predation and color polytypism in the aposematic poison frog Oophaga pumilio

Aposematic organisms are not predicted to show high levels of warning signal diversity because they are expected to be under stabilizing selection to decrease costs of ‘educating’ predators about their unpalatability. However, systematic changes in warning signals (polytypism) can be expected if they represent adaptations to local predators. The aposematic strawberry poison frog (Oophaga pumilio) is red throughout its mainland distribution in Costa Rica and Panamá, but displays high levels of warning signal diversity in the Bocas del Toro Archipelago of Panamá. Both coloration and spot pattern vary in a polytypic sense. Sexual selection contributes to maintaining the polytypism, but little work has investigated the potential influence of predation. We used unspotted models of O. pumilio to determine if predation might help explain the color polytypism on Isla Colón in the Bocas del Toro Archipelago of Panamá. We tested whether attack rates differed among the red mainland morph, green/yellow Isla Colón morph, and the brown control. We found that frog color significantly predicted being attacked. The local green Isla Colón models were attacked more than foreign red or brown models. No difference in attack rate existed between red and brown control models. Our results suggest that the red mainland morph possesses a more effective warning signal, even when it is not the local morph. Honest signaling of unpalatability, neophobia, and the use of search images by local predators are potential explanations. Similarity of the brown model to other local poison frogs might explain the lower attack rate compared to previous work. The attack rate was lower on Isla Colón compared to mainland Costa Rica, which supports the hypothesis that less overall predation in the Bocas del Toro Archipelago may contribute to the overall warning signal diversity in O. pumilio there by relaxing selection for aposematic traits.     

Determination of strongly overlapping signaling activity from microarray data

Background  

As numerous diseases involve errors in signal transduction, modern therapeutics often target proteins involved in cellular signaling. Interpretation of the activity of signaling pathways during disease development or therapeutic intervention would assist in drug development, design of therapy, and target identification. Microarrays provide a global measure of cellular response, however linking these responses to signaling pathways requires an analytic approach tuned to the underlying biology. An ongoing issue in pattern recognition in microarrays has been how to determine the number of patterns (or clusters) to use for data interpretation, and this is a critical issue as measures of statistical significance in gene ontology or pathways rely on proper separation of genes into groups.     

The carboxy‐terminal tail of connexin43 gap junction protein is sufficient to mediate cytoskeleton changes in human glioma cells

Connexin43 (Cx43) is a ubiquitously expressed member of the gap junction protein family that mediates gap junction intercellular communication (GJIC) by allowing exchange of cytosolic materials. Previous studies have used Cx43 truncated at the cytoplasmic tail (C‐tail) to demonstrate that the C‐tail is essential to regulate cell growth and motility. Therefore, the aim of our study was to delineate the respective role of the truncated Cx43 and the C‐tail in mediating Cx43‐dependent signaling. A truncated Cx43 expressing the channel part of the protein (TrCx43, amino acid 1–242) and a construct encompassing only the C‐tail from amino acid 243 (243Cx43) were transduced into LN18 human glioma cells. Our results showed that the ability of Cx43 to suppress growth was independent of GJIC as assessed by dye transfer, but was dependent on the presence of a rigid extracellular matrix. We further demonstrated that the C‐tail alone is sufficient to promote motility. Surprisingly, Cx43 is also able to increase migration in the absence of the C‐tail, suggesting the presence of at least two distinct signaling mechanisms utilized by Cx43 to affect motility. Finally, we used time‐lapse imaging to examine the behavior of migrating cells and it was apparent that the C‐tail was associated with a lamellipodia‐based migration not observed in either mock or TrCx43 expressing LN18 cells. Our study shows for the first time that a free C‐tail is sufficient to induce Cx43‐dependent changes in cell morphology and that Cx43 signaling is linked to the regulation of the actin cytoskeleton. J. Cell. Biochem. 110: 589–597, 2010. © 2010 Wiley‐Liss, Inc.     

The physiology and pathology of inositide signaling in the nucleus

Nuclear inositide signaling is nowadays a well‐established issue and a growing field of investigation, even though the very first evidence came out at the end of the 1980's. The understanding of its biological role is supported by the recent acquisitions dealing with pathology and namely hematological malignancies. Here, we review this issue highlighting the main achievements in the last years. J. Cell. Physiol. 226: 14–20, 2010. © 2010 Wiley‐Liss, Inc.     

Tiki casts a spell on Wnt

Negative feedback is a widespread feature of signaling pathways. In an unexpected twist described in this issue, He and colleagues identify a membrane-tethered metalloprotease named Tiki that inhibits Wnt signaling by removing an essential eight-residue fragment from Wnt itself.     

And Akt-ion! IQGAP1 in control of signaling pathways

ERK signaling and Akt signaling are inversely correlated in some cancers. Yet, the precise molecular mechanism for cross-inhibition remains unclear. In this issue of The EMBO Journal, Pan et al ( 2017 ) show that when Akt is on, its phosphorylated cytoplasmic substrate FOXO1 turns off ERK activity by reshaping the Ras-ERK scaffold IQGAP1.     

Cancer: leaping the E‐cadherin hurdle

Aberrant activation of the Wnt signaling pathway is a common cause of colon cancer and other tumor types, accomplishing many of the hallmarks of cancer including sustained proliferative signaling, replicative immortality, reprogrammed metabolism, angiogenesis, and invasion. Yet, the dominant mutation that leads to chronic Wnt signaling in colon cancer is quite different from the spectrum of mutations that activate Wnt signaling in other tumor types. In this issue of The EMBO Journal, Huels et al ( 2015 ) focus on the influential role E‐cadherin plays in shaping these differences.     

Protein evolution on a human signaling network

Background  

The architectural structure of cellular networks provides a framework for innovations as well as constraints for protein evolution. This issue has previously been studied extensively by analyzing protein interaction networks. However, it is unclear how signaling networks influence and constrain protein evolution and conversely, how protein evolution modifies and shapes the functional consequences of signaling networks. In this study, we constructed a human signaling network containing more than 1,600 nodes and 5,000 links through manual curation of signaling pathways, and analyzed the d _N/d _S values of human-mouse orthologues on the network.     

Journal of Cellular Physiology: Volume 228, Number 2, February 2013

Cover: Fluoresecent image showing PDBu‐induced phosphorylation and translocation of Src and MAPK signaling proteins. See the article by Xiao et al on pages 416–427, in this issue.