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The present article deals with the diffusiophoresis of hydrophobic rigid colloids bearing arbitrary ζ-potential. We derived the generic expression for the diffusiophoretic velocity of such a colloid exposed in an externally applied concentration gradient of the general electrolyte solution. The derived expression takes into account the relaxation effect and is applicable for all values of surface ζ-potential and hydrodynamic slip length at large κa ([Formula: see text]), where [Formula: see text] is the thickness of the electric double layer and a is the particle radius. We further derived several closed-form expressions for particle velocity derived under various electrostatic and hydrodynamic conditions when the particle is exposed in an applied concentration gradient of binary symmetric (e.g., [Formula: see text]), asymmetric (1:2, 2:1, 3:1, 1:3), and a mixed electrolyte (mixture of 1:1 and 2:1 electrolytes). The results for diffusiophoretic velocity are further illustrated graphically to indicate the mutual interaction of chemiphoresis, induced electrophoresis due to unequal mobilities of cations and anions of the electrolyte, and the mechanism by which the sufficiently charged particle migrates opposite to the direction of the applied concentration gradient. The impact of hydrophobicity is further discussed.

This paper aims to develop a strategic decision support system for logistics and supply chain network design of a multi-stage, multi-commodity, and multi-period distribution and transportation system. A mixed integer linear programming model is proposed to tackle the problem while minimizing the operating, transportation and handling cost through all tiers of the supply chain network. A genetic algorithm based method has been proposed to solve the problem in a large scale realistic environment. The efficacy of the developed strategic decision support model in achieving better utilization of network and resources to fulfil the customer demand is demonstrated using illustrative scenarios inspired from the real case of a logistics company.

The precise molecular alterations driving castration-resistant prostate cancer (CRPC) are not clearly understood. Using a novel network-based integrative approach, here, we show distinct alterations in the hexosamine biosynthetic pathway (HBP) to be critical for CRPC. Expression of HBP enzyme glucosamine-phosphate N-acetyltransferase 1 (GNPNAT1) is found to be significantly decreased in CRPC compared with localized prostate cancer (PCa). Genetic loss-of-function of GNPNAT1 in CRPC-like cells increases proliferation and aggressiveness, in vitro and in vivo. This is mediated by either activation of the PI3K-AKT pathway in cells expressing full-length androgen receptor (AR) or by specific protein 1 (SP1)-regulated expression of carbohydrate response element-binding protein (ChREBP) in cells containing AR-V7 variant. Strikingly, addition of the HBP metabolite UDP-N-acetylglucosamine (UDP-GlcNAc) to CRPC-like cells significantly decreases cell proliferation, both in-vitro and in animal studies, while also demonstrates additive efficacy when combined with enzalutamide in-vitro. These observations demonstrate the therapeutic value of targeting HBP in CRPC., The molecular alterations driving anti-androgen resistance in prostate cancer are unclear. Here, the authors show, using a network-based approach, that inhibition of the hexosamine biosynthetic pathway is necessary to develop resistance and that increasing the activity of the pathway enhances the anti-androgen response.

We used human bladder cancer as a model system and the whole-organ histologic and genetic mapping strategy to identify clonal genetic hits associated with growth advantage, tracking the evolution of bladder cancer from intraurothelial precursor lesions. Six putative chromosomal regions critical for clonal expansion of intraurothelial neoplasia and development of bladder cancer were identified by using this approach. Focusing on one of the regions, which includes the model tumor suppressor RB1 , we performed allelotyping of single-nucleotide polymorphic sites and identified a 1.34-Mb segment around RB1 characterized by a loss of polymorphism associated with the initial expansion of in situ neoplasia. This segment contains several positional candidate genes referred to by us as forerunner genes that may contribute to such expansion. We subsequently concentrated our efforts on the two neighbor genes flanking RB1 , namely ITM2B and CHC1L , as well as P2RY5 , which is located inside RB1 . Here, we report that ITM2B and P2RY5 modulated cell survival and were silenced by methylation or point mutations, respectively, and thus by functional loss may contribute to the growth advantage of neoplasia. We also show that homozygous inactivation of P2RY5 was antecedent to the loss of RB1 during tumor development, and that nucleotide substitutions in P2RY5 represent a cancer predisposing factor.

Understanding the structure and function of the ATP-binding cassette (ABC) transporters is very important because defects in ABC transporters lie at the root of several serious diseases including cystic fibrosis. MalK, the ATP-binding cassette of the maltose transporter of Escherichia coli, is distinct from most other ATP-binding cassettes in that it contains an additional C-terminal regulatory domain. The published structure of a MalK dimer is elongated with C-terminal domains at opposite poles (Diederichs, K., Diez, J., Greller, G., Muller, C., Breed, J., Schnell, C., Vonrhein, C., Boos, W., and Welte, W. (2000) EMBO J. 19, 5951-5961). Some uncertainty exists as to whether the orientation of MalK in the dimer structure is correct. Superpositioning of the N-terminal domains of MalK onto the ATP-binding domains of an alternate ABC dimer, in which ATP is bound along the dimer interface between Walker A and LSGGQ motifs, places both N- and C-terminal domains of MalK along the dimer interface. Consistent with this model, a cysteine substitution at position 313 in the C-terminal domain of an otherwise cysteine-free MalK triggered disulfide bond formation between two MalK subunits in an intact maltose transporter. Disulfide bond formation did not inhibit the function of the transporter, suggesting that the C-terminal domains of MalK remain in close proximity throughout the transport cycle. Enzyme IIAglc still inhibited the ATPase activity of the disulfide-linked transporter indicating that the mechanism of inducer exclusion was unaffected. These data support a model for ATP hydrolysis in which the C-terminal domains of MalK remain in contact whereas the N-terminal domains of MalK open and close to allow nucleotide binding and dissociation.

Metabolic profiling of cancer cells has recently been established as a promising tool for the development of therapies and identification of cancer biomarkers. Here we characterized the metabolomic profile of human breast tumors and uncovered intrinsic metabolite signatures in these tumors using an untargeted discovery approach and validation of key metabolites. The oncometabolite 2-hydroxyglutarate (2HG) accumulated at high levels in a subset of tumors and human breast cancer cell lines. We discovered an association between increased 2HG levels and MYC pathway activation in breast cancer, and further corroborated this relationship using MYC overexpression and knockdown in human mammary epithelial and breast cancer cells. Further analyses revealed globally increased DNA methylation in 2HG-high tumors and identified a tumor subtype with high tissue 2HG and a distinct DNA methylation pattern that was associated with poor prognosis and occurred with higher frequency in African-American patients. Tumors of this subtype had a stem cell-like transcriptional signature and tended to overexpress glutaminase, suggestive of a functional relationship between glutamine and 2HG metabolism in breast cancer. Accordingly, 13C-labeled glutamine was incorporated into 2HG in cells with aberrant 2HG accumulation, whereas pharmacologic and siRNA-mediated glutaminase inhibition reduced 2HG levels. Our findings implicate 2HG as a candidate breast cancer oncometabolite associated with MYC activation and poor prognosis.

Prostate Cancer (PCa) is the second highest cause of cancer-related death in men in the US. PCa is androgen dependent when organ-confined and is conventionally treated using surgery or using a combination of anti-androgens and radiation therapy. However, in about 30% of the patients tumor recurs and are initially administered androgen deprivation therapy (ADT). Majority of the patients become resistant to ADT and develop hormone-refractory disease also termed castration-resistant prostate cancer (CRPC), which is lethal. Currently, the molecular and biochemical alterations driving CRPC are not well understood. Using a novel network-based integrative approach, we show distinct alterations in the Hexosamine Biosynthetic Pathway (HBP) to be critical for sustaining the castrate resistant state. Our data suggests expression of key HBP enzymes to be significantly elevated in androgen dependent (AD) PCa while interestingly enough, relatively diminished in CRPC. Genetic loss of function experiments for these HBP enzymes in CRPC-like cells had tumor promoting effect both in vitro and in vivo. This was mediated by alterations in either PI3K-AKT pathway or SP1-ChREBP (SP1- carbohydrate response element binding protein) network in CRPC cells containing full length androgen receptor (AR) or its splice variant AR-V7, respectively. Strikingly, addition of HBP metabolite UDP-N-acetylglucosamine (UDP-GlcNAc) or glucosamine (GlcN) to CRPC-like cells attenuated tumor cell proliferation, both in vitro and in animal studies. Interestingly, these metabolites demonstrated additive efficacy when combined with enzalutamide in vitro. These findings are particularly significant given that the CRPC-like cells tested, inclusive of those containing AR-V7 variant, are inherently resistant to enzalutamide. These observations demonstrate the therapeutic value of targeting altered HBP in CRPC. Citation Format: Akash K. Kaushik, Ali Shojaie, Katrin Panzitt, Rajni Sonavane, Harene Venghatakrishnan, Mohan Manikkam, Alexander Zaslavsky, Vasanta Putluri, Vihas Vasu, Yiqing Zhang, Ayesha Khan, Stacy Lloyd, Adam Szafran, Subhamoy Dasgupta, David Bader, Fabio Stossi, Hangwen Li, Susmita Samanta, Xuhong Cao, Efrosini Tsouko, Shixia Huang, Daniel Frigo, Lawrence Chan, Dean Edwards, Benny Kaipparettu, Nicholas Mitsiades, Nancy Weigel, Michael Mancini, Michael Ittmann, Arul Chinnaiyan, Nagireddy Putluri, Ganesh Palapattu, George Michailidis, Arun Sreekumar. Inhibition of hexose monophosphate pathway promotes castration resistant prostate cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1056.

Background Sequence variation in the human 12/15 lipoxygenase (ALOX15) has been associated with atherosclerotic disease. We functionally characterized an ALOX15 promoter polymorphism, rs2255888, previously associated with carotid plaque burden. Methodology/Principal Findings We demonstrate specific in vitro and in vivo binding of the cytoskeletal protein, vimentin, to the ALOX15 promoter. We show that the two promoter haplotypes carrying alternate alleles at rs2255888 exhibit significant differences in promoter activity by luciferase reporter assay in two cell lines. Differences in in-vitro vimentin-binding to and formation of DNA secondary structures in the polymorphic promoter sequence are also detected by electrophoretic mobility shift assay and biophysical analysis, respectively. We show regulation of ALOX15 protein by vimentin. Conclusions/Significance This study suggests that vimentin binds the ALOX15 promoter and regulates its promoter activity and protein expression. Sequence variation that results in changes in DNA conformation and vimentin binding to the promoter may be relevant to ALOX15 gene regulation.

Human 12/15-lipoxygenase (ALOX15) catalyzes the oxidation of polyunsaturated fatty acids and has been implicated in the pathogenesis of atherosclerosis. We previously reported that a common haplotype of the ALOX15 gene is associated with higher prevalence of coronary artery calcification in a cohort of middle-aged African-Americans. This haplotype was uniquely tagged by a promoter variant (rs2255888). We carried out an in vitro characterization of this promoter variant to further investigate regulatory mechanisms of the ALOX15 gene. We evaluated the activity of ALOX15 variant A-carrying and wild type G-carrying promoter haplotypes using a luciferase assay. We demonstrated a 65% higher activity of the A-carrying promoter haplotype as compared to the G-carrying promoter haplotype. Using mass-spectrometry and electrophoretic mobility shift assay we showed that vimentin, a structural protein, specifically binds to both A-carrying and G-carrying promoter haplotypes in vitro. However, the A allele-carrying promoter haplotype had an 83% increased in vitro binding of vimentin compared to the G allele-carrying promoter haplotype. In vivo binding of vimentin to this particular promoter region has also been detected by chromatin immunoprecipitation. Using non-denaturing polyacrylamide gel electrophoresis and UV thermal melting we showed evidence of the formation of intramolecular G-quadruplex structure in the DNA sequence of the G-carrying promoter haplotype. However, for the A-carrying promoter haplotype, formation of intramolecular G-quadruplex structure was reduced and intermolecular G-quadruplex was increased. We also observed that vimentin increased ALOX15 gene expression. The current studies indicate that sequence variant of the rs2255888 polymorphism is associated with a structural change of ALOX15 promoter region. This change may be responsible for the increased binding of vimentin to the promoter region. Our study is the first to show that vimentin may act as a transcription regulator of ALOX15. It has been reported that vimentin is secreted by activated macrophages. Thus, the novel function identified here may be relevant to ALOX15 pathogenesis mechanisms in atherosclerosis.

Prostate Cancer is the second most common cause of cancer-related death in men in the US. Like other tumors, prostate cancer development and progression is dictated by multiple molecular events that include changes in levels of genes, transcripts, proteins and metabolites. To better understand the biology of prostate cancer development it is essential to integrate these disparate yet related datasets. Our laboratory has identified matched transcriptomic, proteomic and metabolomic changes in localized prostate cancer relative to adjacent benign tissue as well in metastatic disease compared to organ-confined tumor. To study this using a System's Biology approach we have recently embarked on a pilot study aimed at integrating transcriptomic and metabolomic data to obtain biochemical pathways that key to prostate cancer development. Using an in-house network-based enrichment strategy, amino sugar metabolism was found to be significantly enriched in organ-confined prostate cancer but not in metastatic disease. Amino sugar metabolism describes the utilization of glucose-derived carbon and amino acid (mostly glutamine)-derive nitrogen to produce glucosamines. These amino sugars participate in synthesis of immune modulatory compounds as well as in glycosylation cascades. In this study, we describe the molecular analyses of Glucosamine-6 phosphate-N-acetyl Transferase (GNPNAT1), a key enzyme that converts D-glucosamine 6-phosphate to N-acetyl-D-glucosamine 6-phosphate, in prostate cancer. Our results indicate upregulation of GNPNAT1 in organ-confined prostate cancer as compared to benign adjacent tissue as well as metastatic tissue and regulation of the pathway by androgen. Stable knockdown of GNPNAT1 in androgen dependent LNCap cells leads to diminished cell growth and cell cycle arrest. In contrast, growth and cell cycle are not affected by the knockdown of GNPNAT1 in androgen independent C4-2 cells. Knockdown of GNPNAT1 in C4-2 cells enhances invasiveness which is not observed in LNCap knockdown cells. In this work we show that GNPNAT1 is linked to androgen receptor (AR) action and thus is a critical enzyme for the survival of androgen dependent prostate cancer cells. Citation Format: Katrin Panzitt, Ali Shojaie, Nagireddy Putluri, Sumanta Basu, Vasanta Putluri, Susmita Samanta, Michael Ittmann, Ismael Vergara, George Michailidis, Ganesh Palapattu, Arun Sreekumar. Integrative analysis of transcriptomic and metabolomic data reveals a critical role for aminosugar metabolism in prostate cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5387. doi:10.1158/1538-7445.AM2013-5387

In chronic myelogenous leukemia (CML), treatment of early stage disease has been significantly improved with the discovery of imatinib mesylate (IM, Gleevec), but with the progression of the disease, drug resistance develops which is due to mutation of the ATP binding site domain within the Bcr-Abl tyrosine kinase, the activation of Lyn kinase (a Src-related tyrosine kinase) and other mutations that produce a more aggressive disease. Thus, patients relapse and the disease progresses to blast crisis (BC) stage where survival is limited to only several months. No suitable drug treatment for BC is available, and the mechanism of drug resistance for BC is unclear. A new synthesized small molecule, WP1193, a caffeic acid derivative, induced apoptosis in all types of drug-resistant CML cells including IM-resistant T315I BCR-ABL+ cells, IM-resistant CML cells with up-regulated Lyn tyrosine kinase (K562-R) and cells from blast crisis CML patients. Treatment of BCR-ABL+ cells with WP1193 inhibited Janus kinase activities, leading to strong reduction of Bcr-Abl; this treatment also reduced STAT3 and pTyr 705 STAT3 protein levels. CML cell lines contain a large signaling network complex composed of Bcr-Abl, Jak2, HSP90 and its client proteins. HSP90 is a molecular chaperone that plays an important role in conformational maturation and stabilization of client proteins (Bcr- Abl, Jak2, STAT3, etc.), which are physically associated in the signaling network complex. This network complex (estimated to be between 2–5 million daltons) has been characterized by gel filtration column chromatography. This complex is disassembled by treatment of Bcr-Abl+ cells with WP1193 (10 μM for 3–6 h). Treatment of the cells with WP1193 also inhibited binding of STAT3 to its consensus DNA sequence and reduced levels of HSP90α transcripts, HSP90α protein and its client proteins, which include Bcr-Abl, Jak2 and Akt. WP1193 also reduced solid tumors in mice inoculated with IM-resistant K562-R cells, and inhibited leukemic effects caused by T315I BCR-ABL+ cells. These results indicate that disruption of the Bcr-Abl/Jak2/HSP90 network complex by WP1193 overcomes drug resistance in advanced stage CML cells. Since disruption of this network complex causes apoptosis induction in all IM-resistant and late stage CML patient cells tested so far, and since no significant toxicity was observed in short-term mouse experiments, WP1193 may have medical utility for the treatment of IM-resistant forms of CML and late stage CML where other drugs fail. One novel feature of WP1193 is its ability to reduce the activity of several important components of the network, namely Bcr-Abl, Jak2 and STAT3 activities and reduction of HSP90α, which then causes a high level of apoptosis in IM-resistant cells and late-stage CML cells.