Valentina L. Kouznetsova

Untargeted metabolomics identifies enterobiome metabolites and putative uremic toxins as substrates of organic anion transporter 1 (Oat1).

Untargeted metabolomics on the plasma and urine from wild-type and organic anion transporter-1 (Oat1/Slc22a6) knockout mice identified a number of physiologically important metabolites, including several not previously linked to Oat1-mediated transport. Several, such as indoxyl sulfate, derive from Phase II metabolism of enteric gut precursors and accumulate in chronic kidney disease (CKD). Other compounds included vitamins (pantothenic acid, 4-pyridoxic acid), urate, and metabolites in the tryptophan and nucleoside pathways. Three metabolites, indoxyl sulfate, kynurenine, and xanthurenic acid, were elevated in the plasma and interacted strongly and directly with Oat1 in vitro with IC50 of 18, 12, and 50 μM, respectively. A pharmacophore model based on several identified Oat1 substrates was used to screen the NCI database and candidate compounds interacting with Oat1 were validated in an in vitro assay. Together, the data suggest a complex, previously unidentified remote communication between the gut microbiome, Phase II metabolism in the liver, and elimination via Oats of the kidney, as well as indicating the importance of Oat1 in the handling of endogenous toxins associated with renal failure and uremia. The possibility that some of the compounds identified may be part of a larger remote sensing and signaling pathway is also discussed.

Analysis of Metagene Portraits Reveals Distinct Transitions During Kidney Organogenesis

Grouping microarray expression data into metagenes, followed by organization of these gene clusters into self-organizing maps, reveals distinct stages of kidney organogenesis. Revealing Kidney Formation Through Metagenes By collecting the more than 30,000 genes into 650 groups called metagenes, Tsigelny et al. uncover genes that may orchestrate the transitions between stages of kidney development. Organization of the metagenes into self-organizing maps revealed up to eight distinct stages of kidney development. Entropy calculations of the self-organizing maps allowed the metagene-defined stages to be correlated with morphometric parameters and with specific gene networks. Genes included those already known for their involvement in kidney development as well as ones previously not implicated in this process of organogenesis, thus yielding new insight. Organogenesis is a multistage process, but it has been difficult, by conventional analysis, to separate stages and identify points of transition in developmentally complex organs or define genetic pathways that regulate pattern formation. We performed a detailed time-series examination of global gene expression during kidney development and then represented the resulting data as self-organizing maps (SOMs), which reduced more than 30,000 genes to 650 metagenes. Further clustering of these maps identified potential stages of development and suggested points of stability and transition during kidney organogenesis that are not obvious from either standard morphological analyses or conventional microarray clustering algorithms. We also performed entropy calculations of SOMs generated for each day of development and found correlations with morphometric parameters and expression of candidate genes that may help in orchestrating the transitions between stages of kidney development, as well as macro- and micropatterning of the organ.

Identification of Substituted Pyrimido[5,4-b]indoles as Selective Toll-Like Receptor 4 Ligands

A cell-based high-throughput screen to identify small molecular weight stimulators of the innate immune system revealed substituted pyrimido[5,4-b]indoles as potent NFκB activators. The most potent hit compound selectively stimulated Toll-like receptor 4 (TLR4) in human and mouse cells. Synthetic modifications of the pyrimido[5,4-b]indole scaffold at the carboxamide, N-3, and N-5 positions revealed differential TLR4 dependent production of NFκB and type I interferon associated cytokines, IL-6 and interferon γ-induced protein 10 (IP-10) respectively. Specifically, a subset of compounds bearing phenyl and substituted phenyl carboxamides induced lower IL-6 release while maintaining higher IP-10 production, skewing toward the type I interferon pathway. Substitution at N-5 with short alkyl substituents reduced the cytotoxicity of the leading hit compound. Computational studies supported that active compounds appeared to bind primarily to MD-2 in the TLR4/MD-2 complex. These small molecules, which stimulate innate immune cells with minimal toxicity, could potentially be used as adjuvants or immune modulators.

Direct Recognition of Superparamagnetic Nanocrystals by Macrophage Scavenger Receptor SR-AI

Scavenger receptors (SRs) are molecular pattern recognition receptors that have been shown to mediate opsonin-independent uptake of therapeutic and imaging nanoparticles, underlying the importance of SRs in nanomedicine. Unlike pathogens, engineered nanomaterials offer great flexibility in control of surface properties, allowing addressing specific questions regarding the molecular mechanisms of nanoparticle recognition. Recently, we showed that SR-type AI/II mediates opsonin-independent internalization of dextran superparamagnetic iron oxide (SPIO) nanoparticles via positively charged extracellular collagen-like domain. To understand the mechanism of opsonin-independent SPIO recognition, we tested the binding and uptake of nanoparticles with different surface coatings by SR-AI. SPIO coated with 10 kDa dextran was efficiently recognized and taken up by SR-AI transfected cells and J774 macrophages, while SPIO with 20 kDa dextran coating or cross-linked dextran hydrogel avoided the binding and uptake. Nanoparticle negative charge density and zeta-potential did not correlate with SR-AI binding/uptake efficiency. Additional experiments and computer modeling revealed that recognition of the iron oxide crystalline core by the positively charged collagen-like domain of SR-AI is sterically hindered by surface polymer coating. Importantly, the modeling revealed a strong complementarity between the surface Fe-OH groups of the magnetite crystal and the charged lysines of the collagen-like domain of SR-AI, suggesting a specific recognition of SPIO crystalline surface. These data provide an insight into the molecular recognition of nanocrystals by innate immunity receptors and the mechanisms whereby polymer coatings promote immune evasion.

Organic Anion and Cation SLC22 “Drug” Transporter (Oat1, Oat3, and Oct1) Regulation during Development and Maturation of the Kidney Proximal Tubule

Proper physiological function in the pre- and post-natal proximal tubule of the kidney depends upon the acquisition of selective permeability, apical-basolateral epithelial polarity and the expression of key transporters, including those involved in metabolite, toxin and drug handling. Particularly important are the SLC22 family of transporters, including the organic anion transporters Oat1 (originally identified as NKT) and Oat3 as well as the organic cation transporter Oct1. In ex vivo cultures of metanephric mesenchyme (MM; the embryonic progenitor tissue of the nephron) Oat function was evident before completion of nephron segmentation and corresponded with the maturation of tight junctions as measured biochemically by detergent extractability of the tight junction protein, ZO-1. Examination of available time series microarray data sets in the context of development and differentiation of the proximal tubule (derived from both in vivo and in vitro/ex vivo developing nephrons) allowed for correlation of gene expression data to biochemically and functionally defined states of development. This bioinformatic analysis yielded a network of genes with connectivity biased toward Hnf4α (but including Hnf1α, hyaluronic acid-CD44, and notch pathways). Intriguingly, the Oat1 and Oat3 genes were found to have strong temporal co-expression with Hnf4α in the cultured MM supporting the notion of some connection between the transporters and this transcription factor. Taken together with the ChIP-qPCR finding that Hnf4α occupies Oat1, Oat3, and Oct1 proximal promoters in the in vivo differentiating rat kidney, the data suggest a network of genes with Hnf4α at its center plays a role in regulating the terminal differentiation and capacity for drug and toxin handling by the nascent proximal tubule of the kidney.

An All-Atom Model of the Structure of Human Copper Transporter 1

Human copper transporter 1 (hCTR1) is the major high affinity copper influx transporter in mammalian cells that also mediates uptake of the cancer chemotherapeutic agent cisplatin. A low resolution structure of hCTR1 determined by cryoelectron microscopy was recently published. Several protein structure simulation techniques were used to create an all-atom model of this important transporter using the low resolution structure as a starting point. The all-atom model provides new insights into the roles of specific residues of the N-terminal extracellular domain, the intracellular loop, and C-terminal region in metal ion transport. In particular, the model demonstrates that the central region of the pore contains four sets of methionine triads in the intramembranous region. The structure confirms that two triads of methionine residues delineate the intramembranous region of the transporter, and further identifies two additional methionine triads that are located in the extracellular N-terminal part of the transporter. Together, the four triads create a structure that promotes stepwise transport of metal ions into and then through the intramembranous channel of the transporter via transient thioether bonds to methionine residues. Putative copper-binding sites in the hCTR1 trimer were identified by a program developed by us for prediction of metal-binding sites. These sites correspond well with the known effects of mutations on the ability of the protein to transport copper and cisplatin.

Automated registration of digital ocular fundus images for comparison of lesions

In the STARE project (structured analysis of the retina) we are developing a system that will automatically diagnose images of the ocular fundus, compare sequential images for change, and make clinically significant measurements of lesions and anatomical structures in the images. Ophthalmologists need to compare color images, fluorescein angiograms, indocyanine angiograms, and scanning laser ophthalmoscopy for onset of disease and changes in lesions. The images are made from fundus cameras of different manufacture and at different magnification. Consequently we designed our system to register images of different magnification or appearance automatically.

A Protein Kinase A and Wnt-dependent network regulating an intermediate stage in epithelial tubulogenesis during kidney development

Genetic interactions regulating intermediate stages of tubulogenesis in the developing kidney have been difficult to define. A systems biology strategy using microarray was combined with in vitro/ex vivo and genetic approaches to identify pathways regulating specific stages of tubulogenesis. Analysis of the progression of the metanephric mesenchyme (MM) through four stages of tubule induction and differentiation (i.e., epithelialization, tubular organization and elongation and early differentiation) revealed signaling pathways potentially involved at each stage and suggested key roles for a number of signaling molecules. A screen of the signaling pathways on in vitro/ex vivo nephron formation implicated a unique regulatory role for protein kinase A (PKA), through PKA-2, in a specific post-epithelialization morphogenetic step (conversion of the renal vesicle to the S-shaped body). Microarray analysis not only confirmed this stage-specificity, but also highlighted the upregulation of Wnt genes. Addition of PKA agonists to LIF-induced nephrons (previously shown to be a Wnt/beta-catenin dependent pathway) disrupted normal tubulogenesis in a manner similar to PKA-agonist treated MM/spinal-cord assays, suggesting that PKA regulates a Wnt-dependent tubulogenesis step. PKA induction of canonical Wnt signaling during tubulogenesis was confirmed genetically using MM from Batgal-reporter mice. Addition of a Wnt synthesis inhibitor to activated PKA cultures rescued tubulogenesis. By re-analysis of existing microarray data from the FGF8, Lim1 and Wnt4 knockouts, which arrest in early tubulogenesis, a network of genes involving PKA, Wnt, Lhx1, FGF8, and hyaluronic acid signaling regulating the transition of nascent epithelial cells to tubular epithelium was derived, helping to reconcile in vivo and in vitro/ex vivo data.

MAPAS: a tool for predicting membrane-contacting protein surfaces.

To the editor: Many important biological processes, from serum phospholipid metabolism to amyloid disease, involve formation of protein-membrane complexes. Thus, tools for identifying membranecontacting features in a protein structure are very important. However, few algorithmic approaches for membrane-contacting surface prediction have yet been reported1,2. We developed a program and web-based tool called MAPAS, or membrane-associated-proteins assessment (http://cancertools.sdsc.edu/MAPAS/pro2.html). MAPAS uses a set of algorithmic scoring functions to predict whether a given protein structure can form strong membrane contacts and to define the regions of the protein surface that most likely form such contacts (Supplementary Methods online). The MAPAS input window (Supplementary Fig. 1 online) accepts Protein Data Bank (PDB) protein identifiers or a pasted file in pdb format. The MAPAS algorithm is based on the assumption that membrane-contacting protein surfaces have a specific distribution of membranephilic surface residues in a plane. This planar region would contact the membrane (the explicit assumption is that, on the scale of proteins, the cell membrane can be considered as a plane). These residues must provide the necessary binding energy to keep the protein at the membrane surface. MAPAS (i) identifies the planar surfaces that encompass a given protein, and (ii) scores them according to their membranephilic properties. To provide a measure of membranephilicity, we estimated the relative tendency of individual residues to bind to a phospholipid bilayer. We calculated scoring functions using a semi-empiric approach based on steered molecular dynamics (Supplementary Figs. 2–4 and Supplementary Table 1 online) and Poisson-Boltzmann calculations (Supplementary Methods). MAPAS accepts a protein’s three-dimensional structure as input and identifies all planes encompassing the protein structure (Fig. 1a) then calculates all residues that lie in the layer of a given thickness (Supplementary Fig. 5 online). Then MAPAS sorts the planar protein surfaces based on their membranephilic character. The output window displays rotatable three-dimensional presentations of submitted proteins with their possible membrane–contacting surfaces indicated (see for example, Supplementary Figs. 6 and 7 online). We validated the performance of MAPAS with several known membrane-contacting proteins (Fig. 1b and Supplementary Tables 2 and 3 online). MAPAS can predict membrane-contacting proteins, membrane-associated proteins and the membrane-contacting surfaces of proteins including transmembrane proteins (Supplementary Discussion online). Nevertheless, as with all prediction programs, MAPAS can yield false positive and false negative predictions. One possible source of error is the fact that coordinates of proteins listed in PDB as membrane-contacting do not include the membrane–contacting regions, either because they are disordered or because they are engineered out of the protein to permit crystallization. Another problem is the relatively small area of membrane contact found in some proteins. Our tests show that MAPAS is reliable when the number of membrane-contacting residues is at least 5 (data not shown). With fewer residues in the membrane-contacting zone the statistical error increases. Note: Supplementary information is available on the Nature Methods website.

Structural Diversity of Alzheimer's Disease Amyloid-β Dimers and Their Role in Oligomerization and Fibril Formation

Alzheimers disease (AD) is associated with the formation of toxic amyloid-β (Aβ)42 oligomers, and recent evidence supports a role for Aβ dimers as building blocks for oligomers. Molecular dynamics simulation studies have identified clans for the dominant conformations of Aβ42 forming dimers; however, it is unclear if a larger spectrum of dimers is involved and which set(s) of dimers might evolve to oligomers verse fibrils. Therefore, for this study we generated multiple structural conformations of Aβ42, using explicit all-atom molecular dynamics, and then clustering the different structures based on key conformational similarities. Those matching a selection threshold were then used to model a process of oligomerization. Remarkably, we showed a greater diversity in Aβ dimers than previously described. Depending on the clan family, different types of Aβ dimers were obtained. While some had the tendency to evolve into oligomeric rings, others formed fibrils of diverse characteristics. Then we selected the dimers that would evolve to membranephilic annular oligomers. Nearly one third of the 28 evaluated annular oligomers had the dimer interfaces between the neighboring Aβ42 monomers with possible salt bridges between the residue K28 from one side and either residue E22 or D23 on the other. Based on these results, key amino acids were identified for point mutations that either enhanced or suppressed the formation and toxicity of oligomer rings. Our studies suggest a greater diversity of Aβ dimers. Understanding the structure of Aβ dimers might be important for the rationale design of small molecules that block formation of toxic oligomers.