Towards a phylogeny and evolution of Acochlidia (Mollusca: Gastropoda: Opisthobranchia)

The Acochlidia are unique among opisthobranch gastropods in combining extremely high morphological and ecological diversity with modest species diversity. The phylogeny of acochlidians has never been addressed by cladistic means, as their evolution has remained unknown. This study gives a first overview on more than 150 biological and morphological characters that are potentially useful for phylogenetic analysis. Based on 107 characters, a parsimony analysis (PAUP) was performed for all 27 valid acochlidian species together with 11 (plus two) outgroup taxa. The resulting strict consensus tree shows a moderate overall resolution, with at least some bootstrap support for most resolved nodes. The Acochlidia are clearly monophyletic, and originate from an unresolved basal opisthobranch level. The Acochlidia split into the Hedylopsacea (Tantulum (Hedylopsis (Pseudunela (Strubellia (‘Acochlidium’, ‘Palliohedyle’))))) and Microhedylacea (Asperspina (Pontohedyle, ‘Parhedyle’, ‘Microhedyle’, (Ganitus, Paraganitus))). The formerly enigmatic Ganitidae, resembling sacoglossan opisthobranchs by having dagger‐like rachidian radular teeth, are likely to be highly derived microhedylids. The paraphyly of some of the traditionally recognized family level taxa induced a preliminary reclassification. From the phylogenetic hypothesis obtained, we conclude that the acochlidian ancestor was marine mesopsammic. The colonization of limnic systems occurred twice, independently: first in the Caribbean (with the development of the small interstitial Tantulum elegans), and second in the Indo‐Pacific, with a radiation of large‐sized benthic acochlidian species. The evolution of extraordinary reproductive features, such as hypodermic impregnation by a complex copulative aparatus in hedylopsaceans, cutaneous insemination via spermatophores in microhedylaceans, and gonochorism in Microhedylidae s.l. (including Ganitidae), is discussed. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 158 , 124–154.     

The pharmacophore of a peptoid VEGF receptor 2 antagonist includes both side chain and main chain residues

Here we identify the pharmacophore in a peptoid that antagonizes Vascular Endothelial Growth Factor Receptor-2 (VEGFR2) in vitro and in vivo. Only three of the side chains in the peptoid are required for activity. Surprisingly, however, main chain atoms also form critical interactions with the receptor.     

Introns and reading frames: correlation between splicing sites and their codon positions

Computer analyses of the entire GenBank database were conducted to examine correlation between splicing sites and codon positions in reading frames. Intron insertion patterns (i.e., splicing site locations with respect to codon positions) have been analyzed for all of the 74 codons of all the eukaryote taxonomic groups: primates, rodents mammals, vertebrates, invertebrates, and plants. We found that reading frames are interrupted by an intron at a codon boundary (as opposed to the middle of a codon) significantly more often than expected. This observation is consistent with the exon shuffling hypothesis, because exons that end at codon boundaries can be concatenated without causing a frame shift and thus are evolutionarily advantageous. On the other hand, when introns interrupt at the middles of codons, they exist in between the first and second bases much more frequently than between the second and third bases, despite the fact that boundaries between the first and second bases of codons are generally far more important than those between the second and third bases. The reason for this is not clear and yet to be explained. We also show that the length of an exon is a multiple of 3 more frequently than expected. Furthermore, the total length of two consecutive exons is also more frequently a multiple of 3. All the observations above are consistent with results recently published by Long, Rosenberg, and Gilbert (1995).      

Metabolome and metaboproteome remodeling in nuclear reprogramming

Nuclear reprogramming resets differentiated tissue to generate induced pluripotent stem (iPS) cells. While genomic attributes underlying reacquisition of the embryonic-like state have been delineated, less is known regarding the metabolic dynamics underscoring induction of pluripotency. Metabolomic profiling of fibroblasts vs. iPS cells demonstrated nuclear reprogramming-associated induction of glycolysis, realized through augmented utilization of glucose and accumulation of lactate. Real-time assessment unmasked downregulated mitochondrial reserve capacity and ATP turnover correlating with pluripotent induction. Reduction in oxygen consumption and acceleration of extracellular acidification rates represent high-throughput markers of the transition from oxidative to glycolytic metabolism, characterizing stemness acquisition. The bioenergetic transition was supported by proteome remodeling, whereby 441 proteins were altered between fibroblasts and derived iPS cells. Systems analysis revealed overrepresented canonical pathways and interactome-associated biological processes predicting differential metabolic behavior in response to reprogramming stimuli, including upregulation of glycolysis, purine, arginine, proline, ribonucleoside and ribonucleotide metabolism, and biopolymer and macromolecular catabolism, with concomitant downregulation of oxidative phosphorylation, phosphate metabolism regulation, and precursor biosynthesis processes, prioritizing the impact of energy metabolism within the hierarchy of nuclear reprogramming. Thus, metabolome and metaboproteome remodeling is integral for induction of pluripotency, expanding on the genetic and epigenetic requirements for cell fate manipulation.     

NAMPT inhibition sensitizes pancreatic adenocarcinoma cells to tumor-selective,PAR-independent metabolic catastrophe and cell death induced by β-lapachone

Nicotinamide phosphoribosyltransferase (NAMPT) inhibitors (e.g., FK866) target the most active pathway of NAD⁺ synthesis in tumor cells, but lack tumor-selectivity for use as a single agent. Reducing NAD⁺ pools by inhibiting NAMPT primed pancreatic ductal adenocarcinoma (PDA) cells for poly(ADP ribose) polymerase (PARP1)-dependent cell death induced by the targeted cancer therapeutic, β-lapachone (β-lap, ARQ761), independent of poly(ADP ribose) (PAR) accumulation. β-Lap is bioactivated by NADPH:quinone oxidoreductase 1 (NQO1) in a futile redox cycle that consumes oxygen and generates high levels of reactive oxygen species (ROS) that cause extensive DNA damage and rapid PARP1-mediated NAD⁺ consumption. Synergy with FK866+β-lap was tumor-selective, only occurring in NQO1-overexpressing cancer cells, which is noted in a majority (∼85%) of PDA cases. This treatment strategy simultaneously decreases NAD⁺ synthesis while increasing NAD⁺ consumption, reducing required doses and treatment times for both drugs and increasing potency. These complementary mechanisms caused profound NAD(P)⁺ depletion and inhibited glycolysis, driving down adenosine triphosphate levels and preventing recovery normally observed with either agent alone. Cancer cells died through an ROS-induced, μ-calpain-mediated programmed cell death process that kills independent of caspase activation and is not driven by PAR accumulation, which we call NAD⁺-Keresis. Non-overlapping specificities of FK866 for PDA tumors that rely heavily on NAMPT-catalyzed NAD⁺ synthesis and β-lap for cancer cells with elevated NQO1 levels affords high tumor-selectivity. The concept of reducing NAD⁺ pools in cancer cells to sensitize them to ROS-mediated cell death by β-lap is a novel strategy with potential application for pancreatic and other types of NQO1+ solid tumors.An emerging metabolic target for the treatment of recalcitrant cancers, such as pancreatic adenocarcinoma (PDA), is their reliance on NAD⁺ synthesis, particularly through the nicotinamide-recycling pathway.^{1, 2, 3} Rapid and efficient NAD⁺ synthesis is critical to sustain signaling processes, such as deacetylation by sirtuins and adenosine diphosphate (ADP) ribosylation by poly(ADP ribose) polymerase 1 (PARP1). NAD(P)⁺ pools are also necessary to support anabolic metabolism and proliferation of cancer cells. In an attempt to leverage increased tumor-cell reliance on NAD⁺ synthesis, small molecule inhibitors of nicotinamide phosphoribosyltransferase (NAMPT) were developed (e.g., FK866).⁴ NAMPT catalyzes the rate-limiting step of the most active pathway of NAD⁺ synthesis. Inhibitors of NAMPT, such as FK866, reduce NAD⁺ levels, induce canonical apoptosis preferentially in cancer cells in vitro, inhibit tumor growth, and increase overall survival in preclinical cancer models.^{1, 5, 6, 7} FK866 (APO866) was relatively well tolerated in humans and advanced to phase II clinical trials. However, owing to its short half-life in circulation, prolonged treatment regimens were required and toxicity to normal, rapidly proliferating hematopoietic cells was noted. Accordingly, FK866 and other NAMPT inhibitors did not demonstrate sufficient tumor-selectivity to achieve clinical success as single agents.⁸To increase the specificity and efficacy of NAMPT inhibition, we combined FK866 with β-lapachone (β-lap), a targeted cancer therapeutic that causes tumor-selective PARP1 hyperactivation and NAD⁺ depletion in an NADPH:quinone oxidoreductase 1 (NQO1)-specific manner.⁹ β-Lap is a substrate for two-electron oxidoreduction by NQO1, a Phase II quinone-detoxifying enzyme.⁹ The resulting hydroquinone form of β-lap is highly unstable and spontaneously reacts with oxygen to revert back to the parent compound, generating two moles of superoxide per mole of NAD(P)H used in the process. This results in a futile cycle that occurs rapidly in NQO1-overexpressing cells, causing marked NADH/NADPH oxidation. DNA damage in the form of base oxidation and DNA single-strand breaks results from H₂O₂ generated from the futile redox cycle. In an attempt to repair this damage, PARP1 becomes hyperactivated, generating extensive branched poly(ADP ribose) (PAR) polymer. Hyperactivated PARP1 substantially depletes NAD⁺ and ultimately adenosine triphosphate (ATP) levels, thereby inhibiting subsequent repair of β-lap-induced DNA lesions. The observed cell death is caspase-independent and driven by nuclear translocation of apoptosis-inducing factor (AIF), activation of μ-calpain, and post-translational modification of GAPDH.^{10, 11, 12, 13} NQO1 is highly expressed in many types of cancer, and the therapeutic window provided by NQO1 bioactivation of β-lap has advanced its use to phase I clinical trials (ARQ761).¹⁴ Elevated NQO1 expression (≥10-fold) has been identified in ~85% of patient tissue from pancreatic ductal adenocarcinoma (PDA), making pancreatic cancer an especially appealing target for therapy using NQO1 bioactivatable drugs, such as β-lap.^{15, 16, 17, 18} However, dose-limiting methemoglobinemia caused by nonspecific reactive oxygen species (ROS) generation at high β-lap doses may limit the efficacy of β-lap as monotherapy.¹⁹ Strategies for increasing cancer cell cytotoxicity while maintaining NQO1 specificity could enhance use of β-lap for therapy against PDAs, as well as other solid cancers that overexpress NQO1.We found that examining cell death pathways induced by β-lap, with or without FK866 treatment, is a novel means to elucidate general mechanisms of lethality mediated by NAD⁺ loss, as cell death by PARP1 hyperactivation occurs in other contexts. Notably, cell death induced by ischemia/reperfusion shares many of the same characteristics: ROS induction, PARP1 hyperactivation, calcium release, AIF translocation, and caspase-independence.^{20, 21} Similarly, treatment with methylnitronitrosoguanidine (MNNG; a DNA alkylating agent) or induction of neuronal excitotoxicty induces PARP1 hyperactivation and cell death, but without futile cycle-induced ROS production.^{22, 23, 24} Recent studies suggest an important role for accumulated free PAR polymer that can directly activate μ-calpain, activate and release AIF, and inhibit glycolysis.^{22, 25, 26, 27, 28} By combining β-lap and FK866, we uncouple NAD⁺ and ATP depletion from the robust formation of PAR noted with β-lap alone, allowing us to define the function of PAR formation in β-lap-induced cell death.β-Lap and FK866 have distinct, but highly complementary mechanisms of action. β-Lap induces tumor-selective NAD⁺ depletion specifically in cancer cells that express high levels of NQO1. FK866 primes cancer cells for cell death by lowering NAD⁺/NADH pools and prevents recovery by inhibiting NAD⁺ synthesis from nicotinamide liberated by activated PARP1. We show that the increased dependence of PDA cells on glycolysis is specifically targeted by ROS-induced, NAD⁺ depletion caused by exposure to both drugs. Glycolytic inhibition, ATP depletion, and cell death is independent of PAR formation, strongly suggesting that PAR accumulation is not directly involved. The use of β-lap with NAMPT inhibitors results in synergistic NQO1- and PARP1-dependent cancer cell death, allowing the use of lower doses and shorter treatment times for both therapeutics.     

TBK1 directly engages Akt/PKB survival signaling to support oncogenic transformation

The innate immune-signaling kinase, TBK1, couples pathogen surveillance to induction of host defense mechanisms. Pathological activation of TBK1 in cancer can overcome programmed cell death cues, enabling cells to survive oncogenic stress. The mechanistic basis of TBK1 prosurvival signaling, however, has been enigmatic. Here, we show that TBK1 directly activates AKT by phosphorylation of the canonical activation loop and hydrophobic motif sites independently of PDK1 and mTORC2. Upon mitogen stimulation, triggering of the innate immune response, re-exposure to glucose, or oncogene activation, TBK1 is recruited to the exocyst, where it activates AKT. In cells lacking TBK1, insulin activates AKT normally, but AKT activation by exocyst-dependent mechanisms is impaired. Discovery and characterization of a 6-aminopyrazolopyrimidine derivative, as a selective low-nanomolar TBK1 inhibitor, indicates that this regulatory arm can be pharmacologically perturbed independently of canonical PI3K/PDK1 signaling. Thus, AKT is a direct TBK1 substrate that connects TBK1 to prosurvival signaling.     

Enhanced growth of pancreatic tumors in SPARC-null mice is associated with decreased deposition of extracellular matrix and reduced tumor cell apoptosis

SPARC, a matricellular glycoprotein, modulates cellular interaction with the extracellular matrix (ECM). Tumor growth and metastasis occur in the context of the ECM, the levels and deposition of which are controlled in part by SPARC. Tumor-derived SPARC is reported to stimulate or retard tumor progression depending on the tumor type, whereas the function of host-derived SPARC in tumorigenesis has not been explored fully. To evaluate the function of endogenous SPARC, we have examined the growth of pancreatic tumors in SPARC-null (SP(-/-)) mice and their wild-type (SP(+/+)) counterparts. Mouse pancreatic adenocarcinoma cells injected s.c. grew significantly faster in SP(-/-) mice than cells injected into SP(+/+) animals, with mean tumor weights at sacrifice of 0.415 +/- 0.08 and 0.086 +/- 0.03 g (P < 0.01), respectively. Lack of endogenous SPARC resulted in decreased collagen deposition and fiber formation, alterations in the distribution of tumor-infiltrating macrophages, and decreased tumor cell apoptosis. There was no difference in microvessel density of tumors from SP(-/-) or SP(+/+) mice. However, tumors grown in SP(-/-) had a lower percentage of blood vessels that expressed smooth muscle alpha-actin, a marker of pericytes. These data reflect the importance of ECM deposition in regulating tumor growth and demonstrate that host-derived SPARC is a critical factor in the response of host tissue to tumorigenesis.     

Phylogenetic analysis using insertion sequence fingerprinting in Escherichia coli

Chromosomal DNA from 23 closely related, pathogenic strains of Escherichia coli was digested and probed for the insertion sequences IS1, IS2, IS4, IS5, and IS30. Under the assumption that elements residing in DNA restriction fragments of the same apparent length are identical by descent, parsimony analysis of these characters yielded a unique phylogenetic tree. This analysis not only distinguished among bacterial strains that were otherwise identical in their biochemical characteristics and enzyme electrophoretic mobilities, but certain aspects of the topology of the tree were consistent across several unrelated insertion elements. The distribution of IS elements was then reexamined in light of the inferred phylogenetic relationships to investigate the biological properties of the elements, such as rates of insertion and deletion, and to discover apparent recombinational events. The analysis shows that the pattern of distribution of insertion elements in the bacterial genome is sufficiently stable for epidemiological studies. Although the rate of recombination by conjugation has been postulated to be low, at least two such events appear to have taken place.