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Context.— Measurable (minimal) residual disease (MRD) is an independent prognostic factor for survival outcomes in patients with lymphoid and plasma cell malignancies and has been incorporated into consensus criteria regarding treatment response, strategy, and clinical trial endpoints. clonoSEQ (a next-generation sequencing [NGS]-MRD assay) uses multiplex polymerase chain reaction and NGS to identify clonotypic rearrangements at the immunoglobulin (Ig) H, IgK, IgL, T-cell receptor (TCR)-β, and TCR-γ loci, as well as translocated B-cell lymphoma 1/IgH and 2/IgH sequences for MRD assessment. Additionally, it can be used to confirm diagnoses of cutaneous T-cell lymphoma (CTCL). Objective.— To review the technical aspects of our experience using the clonoSEQ Assay in routine clinical practice. Design.— In this single-center experience, 390 patients with lymphoid and plasma cell malignancies were assessed with the NGS-MRD Assay at a central laboratory. Results.— Median time from arrival of the shipment to initiation of the assay (defined as captured in Adaptive's secure tracking system) was 2.1 hours. Overall, 317 patients had 1 or more samples submitted for sequence identification. Of these, 290 (91.5%) had trackable sequences identified. The median calibration rate of samples by malignancy (where n ≥ 10 samples, excluding CTCL samples) was 88.1%, across a variety of fresh and archived sample sources (177 of 201 samples). TCR-β and/or TCR-γ clonotypes were identified in 40 of 95 samples (42.1%) from 66 patients with suspected CTCL. Conclusions.— This NGS-MRD Assay is a valuable and sensitive tool for monitoring MRD in patients with plasma cell and lymphoid malignancies and assisting in the diagnosis of CTCL.

A distinctive feature of glycans vis-à-vis proteins and nucleic acids is its structural complexity, which arises from the huge repertoire of monosaccharides, isomeric linkages and branching. A very large number of monosaccharides have so far been discovered in natural glycans. Experimentally, pathways for the biosynthesis have been characterized completely for 55 monosaccharides and partially for a few more. However, there is no single platform, which provides information about monosaccharide biosynthesis pathways and associated enzymes We have gathered 572 experimentally characterized enzymes of 66 biosynthesis pathways from literature and set up a first of its kind database called the Monosaccharide Biosynthesis Pathways Database http://www.bio.iitb.ac.in/mbpd/). Annotations such as the reaction catalyzed, substrate specificity, biosynthesis pathway and PubMed IDs are provided for all the enzymes in the database. Sequence homologs of the experimentally characterized enzymes found in nearly 13,000 completely sequenced genomes from Bacteria and Archaea have also been included in the database. This platform will help in the deduction of evolutionary relationships among enzymes such as aminotransferases, nucleotidyltransferases, acetyltransferases and SDR family enzymes. It can also facilitate experimental studies such as direct enzyme assays to validate putative annotations, establish structure–function relationship, expression profiling to determine the function, determine the phenotypic consequences of gene knock-out/knock-in and complementation studies.

A distinctive feature of glycans vis-à-vis proteins and nucleic acids is its structural complexity which arises from the huge repertoire of monosaccharides, isomeric linkages and branching. Around 70 monosaccharides have so far been discovered in natural glycans and the pathway for the biosynthesis of 57 of these have been experimentally characterized. However, there is no common platform with a comprehensive information of monosaccharide pathways and enzymes. We have gathered 542 experimentally characterized enzymes of these pathways from literature and set up a first of its kind database called GlycoPathDB (http://www.bio.iitb.ac.in/glycopathdb/). Annotations such as the reaction catalysed, substrate specificity, biosynthesis pathway and PubMed IDs are provided for all the enzymes in the database. Sequence homologs of the experimentally characterized enzymes found in nearly 13,000 completely sequenced genomes from Bacteria and Archaea have also been included in the database. This platform will help in deduction of evolutionary relationships among enzymes such as aminotransferases, nucleotidyltransferases, acetyltransferases and SDR family enzymes. It can also facilitate experimental studies such as direct enzyme assays to validate putative annotations, establish structure-function relationship, expression profiling to determine the function, determine the phenotypic consequences of gene knock-out/knock-in and complementation studies.

Several monosaccharides constitute naturally occurring glycans but it is uncertain if they constitute a universal set like the alphabets of proteins and DNA. Based on the available experimental observations, it is hypothesized herein that the glycan alphabet is not universal. Data on the presence / absence of pathways for the biosynthesis of 55 monosaccharides in 12939 completely sequenced archaeal and bacterial genomes are presented in support of this hypothesis. Pathways were identified by searching for homologs of biosynthesis pathway enzymes. Substantial variations are observed in the set of monosaccharides used by organisms belonging to the same phylum, genera and even species. Monosaccharides are grouped as Common, Less Common and Rare based on their prevalence in Archaea and Bacteria. It is observed that fewer enzymes suffice to biosynthesize the Common group. It appears that the Common group originated before the formation of three domains of life. In contrast, the Rare group are confined to a few species in a few phyla, suggesting that they evolved much later. Fold conservation, as observed in aminotransferases and SDR superfamily members involved in monosaccharide biosynthesis, suggests neo- and sub-functionalization of genes leading to the formation of Rare group monosaccharides. Non-universality of the glycan alphabet begets questions about the role of different monosaccharides in determining an organism’s fitness.Impact statementCarbohydrates, nucleic acids and proteins are important classes of biological macromolecules. The universality of DNA, RNA and protein alphabets has been established beyond doubt. However, the universality of glycan alphabet is unknown primarily because of the challenges associated with the elucidation of glycan structures. This has precluded a comprehensive investigation of glycan alphabet. To address this challenge, we have identified the prevalence of 55 monosaccharide biosynthesis pathways in 12939 completely sequenced archaeal and bacterial genomes by searching for homologs of biosynthesis pathway enzymes using HMM profiles, and in a few cases, BLASTp. This revealed that the glycan alphabet is highly variable; in fact, significant differences are found even among different strains of a species. Possible implications of this variability may be significant in understanding the evolution of Archaea and Bacteria in diverse and competitive environments. Factors that drive the choice of monosaccharides used by an organism need to be investigated, and will be of interest in understanding host-pathogen interactions. Additionally, the knowledge of glycan alphabet can be employed for structural characterization / validation of glycans inferred using mass spectrometry. Knowledge of unique monosaccharides and biosynthetic enzymes can also be used as novel drug targets against human pathogens.Data summaryThe curated set of proteins used in this study, with domain assignment, is listed in supplementary_data.xlsx. Corresponding 396 references with evidence of experimental characterization are included in supplementary material. Results of genome scan which include predictions of monosaccharides as well as the biosynthesis pathway enzymes is available at http://www.bio.iitb.ac.in/glycopathdb/ including the aforementioned information. Python script used to scan genomes to search for monosaccharide biosynthesis pathways are available on request.

Morphologically normal and fertile transgenic chickpea plants have been regenerated through a standardized transformation protocols. This protocol is based on the infection of apical meristem explants (AME) with Agrobacterium strain EHA105. The stain, carrying pCAMBIA2301 vector contained β-glucuronidase (uidA) gene and neomycin phosphotransferase (nptII) genes. Different explants of chickpea and Agrobacterium specific conditions were standardized with the help of transient β-glucuronidase (uidA) gene expression to further optimize the transformation protocol. Pre-conditiong of the explants, vacuum infiltration and presence of acetosyringone significantly enhanced the frequency of gus expression. Positive transformants with nptII and gus genes were confirmed by PCR and histochemical gus analysis. An overall successful chickpea transformation frequency of 1.2 was achieved. This high efficiency and easy to use method may provide opportunities for the development of transgenic lines with different useful genes in chickpea in near future.

The proline-rich Akt (v-akt murine thymoma viral oncogene homolog 1) substrate of 40 kDa (PRAS40), an inhibitory component of the mTORC1 complex, was identified as an Akt substrate through phosphorylation at Thr246. Phosphorylation at this site releases PRAS40 from the mammalian/mechanistic target of rapamycin complex 1 (mTORC1) complex allowing increased activity. Targeted expression of a mutant form of PRAS40 (PRAS40 T246A ) in basal keratinocytes of mouse epidermis (BK5.PRAS40 T246A mice) has allowed further examination of mTORC1-specific signaling in epithelial carcinogenesis. BK5.PRAS40 T246A mice were resistant to 12- O -tetradecanoylphorbol-13-acetate (TPA)-induced epidermal hyperproliferation and skin tumor development. In transgenic mice, PRAS40 T246A remained bound to raptor in keratinocytes even after treatment with TPA, consistent with reduced mTORC1 signaling and altered levels of cell cycle proteins. BK5.PRAS40 T246A mice also displayed attenuated skin inflammation in response to TPA. Inhibition of mTORC1 in keratinocytes significantly inhibited their migration in vitro and, in addition, inhibited 12- O -tetradecanoylphorbol-13-acetate-induced proliferation and migration of bulge-region stem cells in vivo. Furthermore, targeted inhibition of mTORC1 in BK5.PRAS40 T246A mice resulted in delayed wound healing. Decreased keratinocyte migration and impaired wound healing correlated with altered expression of epithelial-mesenchymal transition (EMT) markers and reduced smad signaling. Collectively, the current data using this unique mouse model provide further evidence that mTORC1 signaling in keratinocytes regulates key events in keratinocyte function and epithelial cancer development.

Stat3 is a member of the signal transducers and activators of transcription family and is a known regulator of essential biologic processes including angiogenesis, apoptosis, cell cycle progression, and cell migration. Canonical Stat3-mediated signaling involves tyrosine phosphorylation on specific residues that leads to homodimerization and translocation to the nucleus. For many years it was presumed that most, if not all, of the functions of Stat3, both normal and aberrant, were due to the canonical cytokine and growth factor signaling mechanisms. Recent studies suggest that Stat3 functions through alternate non-canonical pathways to bring about some of these biological functions both in normal cells as well as during cancer development and progression. A number of studies have now shown that Stat3 has a function in mitochondria and that unphosphorylated Stat3 (uStat3) can also function as a transcription factor broadening the potential mechanisms involved in Stat3 action. In this review article, we discuss these two main non-canonical functions of Stat3 and their potential roles in oncogenesis. Given the many facets of Stat3 signaling, additional comprehensive investigations are required to fully understand the role of non-canonical Stat3 signaling in cancer and whether these pathways can be targeted for cancer prevention and treatment. © 2015 Wiley Periodicals, Inc.

In the present study, we evaluated the effect of deleting Twist1 on keratinocyte proliferation and on skin tumor development using the two-stage chemical carcinogenesis model. BK5.Cre × Twist1(flox/flox) mice, which have a keratinocyte-specific Twist1 knockout (Twist1 KO), developed significantly reduced numbers of papilloma (70% reduction) and squamous cell carcinoma (75% reduction) as well as delayed tumor latency compared to wild-type (WT) mice. Interestingly, knockdown of Twist1 in primary keratinocytes impeded cell cycle progression at the G1/S transition that coincided with reduced levels of the cell cycle proteins c-Myc, Cyclin E1, and E2F1 and increased levels of p53 and p21. Furthermore, ChIP analyses revealed that Twist1 bound to the promoter regions of Cyclin E1, E2F1, and c-Myc at the canonical E-box binding motif suggesting a direct transcriptional regulation. Further analyses of Twist1 KO mice revealed a significant reduction in the number of label-retaining cells as well as the number of α6-integrin(+) /CD34(+) cells in the hair follicles of untreated mice compared to WT mice. These mice also exhibited significantly reduced epidermal proliferation in response to TPA treatment that again correlated with reduced levels of cell cycle regulators and increased levels of p53 and p21. Finally, Twist1 deficiency in keratinocytes led to an upregulation of p53 via its stabilization and nuclear localization, which is responsible for the increased expression of p21 in these cells. Collectively, these findings indicate that Twist1 has a novel role in epithelial carcinogenesis by regulating proliferation of keratinocytes, including keratinocyte stem cells during tumor promotion.

The development of drugs to counter diseases related to cell migration has resulted in a multi-billion dollar endeavor. Unfortunately, few drugs have emerged from this effort highlighting the need for new methods to enhance assays to study, analyze and control cell migration. In response to this complex process, computational models have emerged as potent tools to describe migration providing a high throughput and low cost method. However, most models are unable to predict migration response to drug with direct application to in vitro experiments. In addition to this, no model to date has attempted to describe migration in response to drugs while incorporating simultaneously protein signaling, proteolytic activity, and 3D culture. In this paper, we describe an integrated computational approach, in conjunction with in vitro observations, to serve as a platform to accurately predict migration in 3D matrices incorporating the function of matrix metalloproteinases (MMPs) and their interaction with the Extracellular signal-related kinase (ERK) signaling pathway. Our results provide biological insight into how matrix density, MMP activity, integrin adhesions, and p-ERK expression all affect speed and persistence in 3D. Predictions from the model provide insight toward improving drug combinations to more effectively reduce both speed and persistence during migration and the role of integrin adhesions in motility. In this way our integrated platform provides future potential to streamline and improve throughput toward the testing and development of migration targeting drugs with tangible application to current in vitro assays.

Although very few studies have addressed the molecular and cellular mechanisms underlying the development of biliary tract cancer (BTC), several lines of evidence suggest a role for the erbB receptor family. Overexpression and activation of erbB2 has been reported in a significant percentage of human BTC. Further, we previously reported that overexpression of erbB2 basal epithelial cells of the biliary tract (BK5.erbB2 mouse) led to the development of BTC. However, the mechanisms by which erbB2 overexpression led to the spontaneous development of tumors specifically in the biliary tract are not completely understood. The goals of the current study were to (1) determine whether a cooperative relationship between bile acid exposure and erbB2 activation exists during biliary tract carcinogenesis and (2) to characterize the mechanism(s) underlying bile acid-mediated biliary tract carcinogenesis in cells with activated erbB2. In this study, we demonstrated that the secondary conjugated bile acid, taurochenodeoxycholic acid (TCDC), increased proliferation of primary cultured gallbladder epithelial cells from BK5.erbB2 mice and human BTC cells. TCDC treatment activated EGFR/erbB2 and downstream signaling molecules in both primary cultured cells and human BTC cells. TCDC also increased the expression of epidermal growth factor receptor (EGFR) ligands and TACE activity in human BTC cells. Inhibition of src activation led to attenuation of bile-induced upregulation of TACE activity as well as signaling through the EGFR/erbB2, suggesting that during the development of BTC erbB2 overexpression/activation accelerates the bile acid-induced signaling cascade: bile acid src TACE EGFR/erbB2 downstream signaling. We also provide direct evidence that bile acids possess tumor promoting capacity in epithelial cells overexpressing erbB2 using the two-stage skin carcinogenesis model. Collectively these findings suggest cooperative roles for bile acid and erbB2 activation in epithelial cell proliferation; bile acid appears to accelerate erbB2-induced pro-tumorigenic activities in the biliary tract and skin. © 2013 Wiley Periodicals, Inc.

Chickpea (Cicer arietinum L.) is a major food legume crops for the tropics and sub-tropical regions and is the main dietary protein source for vegetarians in developing countries. Besides several abiotic factors, its production is constrained by insect pests, as well as many fungal diseases. The success of any attempt to produce resistant varieties through genetic engineering to a large extent depends on the availability of efficient and reproducible regeneration and transformation procedures. Further, the transformation techniques can be more successfully applied if the ontogeny of shoot development is well understood. Ontogeny of shoot development from axillary meristem explants (AME) in chickpea has been studied with the optimization of conditions for high-frequency multiple shoot induction. Preculture of seeds in TDZ significantly enhances the frequency of multiple shoot induction from the explants. Ontogeny and early events of multiple shoot induction revealed direct adventitious origin of the shoots. The understanding of the regeneration process could be further utilized in the designing of efficient transformation methods.

Mitochondrial toxicity results from pyrimidine nucleoside reverse transcriptase inhibitors (NRTIs) for HIV/AIDS. In the heart, this can deplete mitochondrial (mt) DNA and cause cardiac dysfunction (eg, left ventricle hypertrophy, LVH). Four unique transgenic, cardiac-targeted overexpressors (TGs) were generated to determine their individual impact on native mitochondrial biogenesis and effects of NRTI administration on development of mitochondrial toxicity. TGs included cardiac-specific overexpression of native thymidine kinase 2 (TK2), two pathogenic TK2 mutants (H121N and I212N), and a mutant of mtDNA polymerase, pol-gamma (Y955C). Each was treated with antiretrovirals (AZT-HAART, 3 or 10 weeks, zidovudine (AZT) + lamivudine (3TC) + indinavir, or vehicle control). Parameters included left ventricle (LV) performance (echocardiography), LV mtDNA abundance (real-time PCR), and mitochondrial fine structure (electron microscopy, EM) as a function of duration of treatment and presence of TG. mtDNA abundance significantly decreased in Y955C TG, increased in TK2 native and I212N TGs, and was unchanged in H121N TGs at 10 weeks regardless of treatment. Y955C and I212N TGs exhibited LVH during growth irrespective of treatment. Y955C TGs exhibited cardiomyopathy (CM) at 3 and 10 weeks irrespective of treatment, whereas H121N and I212N TGs exhibited CM only after 10 weeks AZT-HAART. EM features were consistent with cardiac dysfunction. mtDNA abundance and cardiac functional changes were related to TG expression of mitochondrially related genes, mutations thereof, and NRTIs.

Mitochondrial (mt) DNA biogenesis is critical to cardiac contractility. DNA polymerase gamma (Pol gamma) replicates mtDNA, whereas thymidine kinase 2 (TK2) monophosphorylates pyrimidines intramitochondrially. Point mutations in POLG and TK2 result in clinical diseases associated with mtDNA depletion and organ dysfunction. Pyrimidine analogs (NRTIs) inhibit Pol gamma and mtDNA replication. Cardiac "dominant negative" murine transgenes (TGs; Pol gamma Y955C, and TK2 H121N or I212N) defined the role of each in the heart. mtDNA abundance, histopathological features, histochemistry, mitochondrial protein abundance, morphometry, and echocardiography were determined for TGs in "2 x 2" studies with or without pyrimidine analogs. Cardiac mtDNA abundance decreased in Y955C TGs ( approximately 50%) but increased in H121N and I212N TGs (20-70%). Succinate dehydrogenase (SDH) increased in hearts of all mutants. Ultrastructural changes occurred in Y955C and H121N TGs. Histopathology demonstrated hypertrophy in H121N, LV dilation in I212N, and both hypertrophy and dilation in Y955C TGs. Antiretrovirals increased LV mass ( approximately 50%) for all three TGs which combined with dilation indicates cardiomyopathy. Taken together, these studies demonstrate three manifestations of cardiac dysfunction that depend on the nature of the specific mutation and antiretroviral treatment. Mutations in genes for mtDNA biogenesis increase risk for defective mtDNA replication, leading to LV hypertrophy.

Considerable evidence indicates a crucial role for Akt and mTORC1 signaling in cancer. Previously, we discovered that the Akt and mTORC1 signaling pathways play an important role in epithelial multistage carcinogenesis using the mouse skin model, especially during the tumor promotion stage. The proline-rich Akt substrate of 40 kDa (PRAS40), a subunit of mTORC1 was originally identified as a novel Akt substrate through Akt-mediated phosphorylation at Thr246 and this phosphorylation is critical for mTORC1 activity. Moreover, PRAS40 has been identified to negatively regulate mTORC1 signaling. In this study, transgenic mice were generated that overexpress a mutant form of PRAS40 [PRAS40(T246A)] using the bovine keratin 5 (BK5) promoter to further examine the importance of mTORC1 signaling in epithelial carcinogenesis. BK5.PRAS40(T246A) transgenic mice did not have a discernable gross skin phenotype. However, these mice were significantly less sensitive to TPA-induced epidermal hyperproliferation and hyperplasia. Overexpression of PRAS40(T246A) in the epidermis led to significant suppression of skin tumor development and significant reductions in tumor weight and tumor size compared to wild-type mice. Immunoprecipitation analysis of epidermal protein lysates from BK5.PRAS40(T246A) mice showed that PRAS40(T246A) remained bound to raptor even after TPA treatment. BK5.PRAS40(T246A) mice also displayed reduced mTORC1 signaling, reduced levels of cell cycle proteins and increased autophagy signaling as well as the skin inflammatory response in the epidermis following treatment with TPA. Notably, TPA-induced proliferation and migration of bulge-region label retaining cells were also significantly inhibited in BK5.PRAS40(T246A) mice. In addition, expression of PRAS40(T246A) in basal keratinocytes significantly inhibited keratinocyte migration both in vivo and in vitro and led to delayed wound healing. Decreased migration and impaired wound healing may be attributed to altered expression of EMT markers as identified in PRAS40(T246A) epidermal cells. The current data using this novel mouse model provides further evidence that mTORC1 specific signaling in keratinocytes contributes significantly to the process of skin tumor promotion by regulating proliferation and migration of keratinocyte stem cells. In addition, the data demonstrate an important role for mTORC1 specific signaling in keratinocytes in regulating skin inflammation. Collectively, using this novel mouse model where mTORC1 signaling is selectively suppressed in keratinocytes has provided further evidence that this signaling pathway regulates several important mechanistic events involved in the process of skin tumor promotion. Research supported by NIH Grants CA129409, CA037111, and American Cancer Research Center and Foundation Citation Format: Okkyung Rho, Jaya Srivastava, Jiyoon Cho, John DiGiovanni. Targeting mTORC1 by overexpression of PRAS40(T246A) in basal keratinocytes suppresses proliferation and migration of keratinocyte stem cells and skin inflammation during tumor promotion. [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 4617.

Nonmelanoma skin cancer (NMSC) is the most common cancer and consists of basal cell carcinoma (BCC) and squamous cell carcinoma (SCC). SCC metastases account for up to 20% of all deaths from skin cancer. The major risk factor for the development of NMSC is solar ultraviolet radiation (UV). UVA and UVB both function as initiators and promoters in carcinogenesis and possess immunosuppressive activity. Given the prevalence of this disease, there remains a pressing need for the development of novel prevention and treatment strategies for NMSC. In a recent study (Srivastava et al. 2015. Mol. Carcinog. doi:10.1002/mc.22335), we evaluated the effect of Twist1, a transcription factor that is known to play a role in tumor progression, during epithelial carcinogenesis. Using the two-stage chemical carcinogenesis model, we identified that BK5.Cre x Twist1flox/flox mice, which have a keratinocyte-specific Twist1 knockout (Twist1 KO), developed significantly reduced numbers of papillomas (70% reduction) and SCCs (75% reduction) as well as delayed tumor latency compared to wild-type (WT) mice. Twist1 KO mice also exhibited significantly reduced epidermal proliferation in response to chemical promotion that correlated with reduced levels of cell cycle regulators and increased levels of p53 and p21. In further studies, we have begun analyzing the effects of UVB irradiation in Twist1 KO mice. Specifically, Twist1 KO mice exhibited heightened sensitivity to UVB-induced apoptosis and decreased epidermal proliferation as compared to similarly exposed WT mice. In addition, the accumulation of mast cells in the skin was significantly decreased in Twist1 KO mice as compared to WT mice. Further preliminary experiments showed that the protein expression levels of c-Myc, phospho-p65 (S536) and phospho-p50 (S337) decreased following UVB irradiation whereas levels of the cell cycle inhibitors p21 and p27 exhibited an increased expression in Twist1 KO mice as compared to WT mice. Further experiments have suggested that Twist1 may play a pivotal role in the proliferation/migration of bulge region keratinocyte stem cells (KSCs) following exposure to UVB. These and other results from ongoing experiments will be presented. Collectively, these findings suggest that Twist1 may have a novel role in UVB-induced epithelial carcinogenesis by regulating proliferation and migration of keratinocytes and KSCs. Research supported by CPRIT RP150346, CPRIT RP140108, and NIH T32 ES007247. Citation Format: Jaya Srivastava, Okkyung Rho, John DiGiovanni. Twist1 regulates UVB-induced epidermal cell proliferation in non-melanoma skin 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 2022.

Significant progress has been achieved toward elucidating the molecular mechanisms that underlie breast cancer progression; yet, much less is known about the associated cellular biophysical traits. To this end, we use time-lapsed confocal microscopy to investigate the interplay among cell motility, three-dimensional (3D) matrix stiffness, matrix architecture, and transforming potential in a mammary epithelial cell (MEC) cancer progression series. We use a well characterized breast cancer progression model where human-derived MCF10A MECs overexpress either ErbB2, 14-3-3ζ, or both ErbB2 and 14-3-3ζ, with empty vector as a control. Cell motility assays showed that MECs overexpressing ErbB2 alone exhibited notably high migration speeds when cultured atop two-dimensional (2D) matrices, while overexpression of 14-3-3ζ alone most suppressed migration atop 2D matrices (as compared to non-transformed MECs). Our results also suggest that co-overexpression of the 14-3-3ζ and ErbB2 proteins facilitates cell migratory capacity in 3D matrices, as reflected in cell migration speed. Additionally, 3D matrices of sufficient stiffness can significantly hinder the migratory ability of partially transformed cells, but increased 3D matrix stiffness has a lesser effect on the aggressive migratory behavior exhibited by fully transformed cells that co-overexpress both ErbB2 and 14-3-3ζ. Finally, this study shows that for MECs possessing partial or full transforming potential, those overexpressing ErbB2 alone show the greatest sensitivity of cell migration speed to matrix architecture, while those overexpressing 14-3-3ζ alone exhibit the least sensitivity to matrix architecture. Given the current knowledge of breast cancer mechanobiology, these findings overall suggest that cell motility is governed by a complex interplay between matrix mechanics and transforming potential.

Without efficient communication, a cell’s ability to survive in a system would be improbable. Moreover, the efficiency with which cancer cells metastasize is attributed to the proficiency with which tumorigenic cells integrate signals from both their surrounding environment and intracellular processes. The mechanosensing ability of a cell is such a process that impacts cellular differentiation, migration, proliferation, and apoptosis. The migratory ability of a cell requires rearrangement of cellular actin scaffolds for the formation of protrusive structures, such as pseudopodia, and secretion of proteolytic enzymes that degrade the extracellular environment. Adhesive structures, such as cadherins and integrins, are tightly regulated processes to efficiently mediate cell migration and apoptosis. In order to properly investigate the behavior of molecular level interactions, scientific research has begun to probe into such dynamic processes at the systems level. This chapter explores the signaling cascades associated with cancer cell migration and those known to be influenced by the mechanical variations of the extracellular matrix.

India is the largest chickpea producing country. Several biotic and abiotic constraints limit its productivity. Production of resistant/tolerant chickpea varieties through conventional breeding is limited due to unavailability of sufficient level of resistance in the gene pool. The success of gene transfer technologies largely depends on availability of a rapid, efficient and reliable in vitro plant regeneration protocol. In the present study, an efficient, short and reproducible regeneration protocol has been standardized for chickpea. For preparation of the ex-plants, de-coated mature seeds of chickpea were germinated on a medium fortified with TDZ for seven days. The explants were then cultured on MS medium supplemented with different combinations of benzylaminopurine (BAP), thidiazuron (TDZ) and indole butyric acid (IBA) for multiple shoot regeneration. Pre-culture of seeds with TDZ significantly enhanced the frequency of multiple shoot regeneration from the explants. Ontogeny of the shoots clearly indicated the organogenetic pathway of shoot regeneration and no callus induction. Multiple shoots were elongated on a medium fortified with BAP and gibberellic acid (GA3) and grafted on root stocks prepared from the same cultivar of chickpea.

Twist1 is a basic helix-loop-helix transcription factor and is known to play a role in tumor progression through regulation of genes involved in epithelial-mesenchymal transition. Twist1 is a known transcriptional target of signal transducer and activator of transcription-3 (Stat3). In previous studies, Stat3 was shown to play a role in skin tumor progression in the two-stage skin carcinogenesis model, at least in part, by regulating the levels of Twist1. Recent studies using keratinocyte-specific knockout (KO) of Twist1 indicate that Twist1 regulates keratinocyte proliferation during skin tumor promotion. Western blot analysis of lysates from both Twist1 deficient mouse primary keratinocytes and from epidermis isolated from BK5.Cre x Twist1flox/flox mice indicated that Twist1 KO leads to reduced levels of the cell cycle proteins Cyclin E1, E2F1, and Cdk2 and increased expression of p21 following treatment with 12-O-tetradecanoylphorbol-13-acetate (TPA). ChIP analysis of epidermal lysates from BK5.Cre x Twist1flox/flox mice revealed that Twist1 bound to the promoter regions of Cyclin E1, E2F1, and c-Myc, indicating direct transcriptional regulation of these cell cycle regulators. Moreover, Twist1 KO in keratinocytes impeded cell cycle progression by reducing the number of cells that advanced to S-phase. Further analyses have demonstrated that deletion of Twist1 either in primary keratinocytes or in vivo leads to an upregulation of p53, which is responsible for the increased expression of p21 observed in these cells. Keratinocyte specific deletion of Twist1 in vivo suppressed epidermal proliferation induced by TPA treatment compared to that observed in wild-type (WT) mice. To further characterize the potential role of Twist1 during epithelial carcinogenesis, we analyzed the impact of Twist1 deletion in vivo on bulge region keratinocyte stem cells (KSCs). Keratinocyte specific deletion of Twist1 in vivo led to a significant reduction in the number of label-retaining cells as well as the number of α6-integrin+/CD34+ cells in the hair follicles of untreated mice. An ongoing two-stage skin carcinogenesis experiment shows that BK5.Cre x Twist1flox/flox mice have significantly reduced tumor development as observed by decreased tumor multiplicity and delayed latency compared WT mice. Furthermore, tumors that developed in BK5.Cre x Twist1flox/flox mice have significantly reduced size compared to tumors on WT mice. Collectively, these findings suggest that Twist1 has a novel role in epithelial carcinogenesis by regulating proliferation and migration of keratinocytes and KSCs. Research supported by RP140108, CA76520, and T32 ES007247. Citation Format: Jaya Srivastava, Okkyung Rho, John DiGiovanni. Twist1 regulates keratinocyte stem cell proliferation and migration and is required for skin tumor formation. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2106. doi:10.1158/1538-7445.AM2015-2106

A number of studies have established the role of receptor tyrosine kinases (RTKs) and their downstream signaling targets, including PI3K/Akt/mTOR and Stat3, as important regulatory factors of epidermal proliferative capacity during both chemical (two-stage) and UV skin carcinogenesis. We have previously shown that total protein levels of Twist1 can be regulated by Stat3 in the two-stage skin carcinogenesis model and that nuclear localization of Twist1 was restricted to the proliferative compartment. Twist1, a protein commonly associated with the induction of EMT, has previously been shown to associate with cell cycle effectors, such as p53 and p21, as well as impact cell cycle progression. The cell cycle regulatory functions of Twist1 have been linked to p53 via phosphorylation of Twist1 at Ser42 by Akt. To investigate the role of Twist1 in cellular proliferation, primary keratinocytes were infected with lentiviral particles to create Twist1 knockdown or overexpressing cells, and were used, together with wild-type primary keratinocytes, to analyze the role of Twist1 during cell cycle progression. Western blot analysis of lysates from primary keratinocytes indicated that the expression of cell cycle regulatory proteins Cyclin E1, NF-κB, and c-Myc, coincided with the decrease or increase of Twist1. Protein levels of p21 exhibited an inverse correlation to Twist1 expression. Additionally, ChIP analysis identified Cyclin D1, Cyclin E1, c-Myc, and NF-κB as novel transcriptional targets of Twist1. To further investigate the role of Twist1, we have established transgenic mice with deletion of Twist1 in the basal compartment of the epidermis using BK5.Cre (i.e. BK5.Cre x Twistflox/flox mice). BK5.Cre x Twistflox/flox mice exhibited a significant reduction in epidermal thickness and labeling index (LI) compared to wild-type mice following treatment with TPA. In comparison to wild-type mice, acetone treated Bk5.Cre x Twistflox/flox mice also displayed a significant reduction of epidermal LI. Western blot analysis of epidermal lysates collected from BK5.Cre x Twistflox/flox mice treated with TPA demonstrated a reduction of Cyclin E1 and reduced phosphorylation of Rb at Ser795 compared to wild-type mice, further implicating the regulatory capacity of Twist1 during keratinocyte proliferation. Twist1 Ser42 phosphorylation also correlated with expression of the aforementioned cell cycle proteins. Collectively, these results, combined with other data to be presented, suggest that Twist1 plays a key role in keratinocyte proliferation during skin tumor promotion. Research supported by CA76520 and T32 ES007247. Citation Format: Jaya Srivastava, Everardo Macias, Kaoru Kiguchi, John DiGiovanni. Twist1 regulates the cell cycle and proliferative capacity of keratinocytes during tumor promotion. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5355. doi:10.1158/1538-7445.AM2014-5355

The haem detoxification pathway of the malaria parasite Plasmodiumfalciparum is a potential biochemical target for drug development. Free haem, released after haemoglobin degradation, is polymerized by the parasite to form haemozoin pigment. Plasmodiumfalciparum histidine-rich protein-2 (Pfhrp-2) has been implicated as the catalytic scaffold for detoxification of haem in the malaria parasite. Previously we have shown that a hexapeptide repeat sequence (Ala-His-His-Ala-Ala-Asp), which appears 33 times in Pfhrp-2, may be the major haem binding site in this protein. The haem binding studies carried out by ourselves indicate that up to 18 equivalents of haem could be bound by this protein with an observed Kd of 0.94µM. Absorbance spectroscopy provides evidence that chloroquine is capable of extracting haem bound to Pfhrp-2. This was supported by the Kd value, of 37nM, observed for the haem-chloroquine complex. The native PAGE studies reveal that the formation of the haem-Pfhrp-2 complex is disrupted by chloroquine. These results indicate that chloroquine may be acting by inhibiting haem detoxification/binding to Pfhrp-2. Moreover, the higher affinity of chloroquine for haem than Pfhrp-2 suggests a possible mechanism of action for chloroquine; it may remove the haem bound to Pfhrp-2 and form a complex that is toxic to the parasite.

The nutrient removal-capacity of four chosen aquatic macrophytes was tested in both natural and laboratory conditions. Laboratory experiments were performed under controlled conditions using ‘microcosm’ methods wherein the plants were grown in three different nutrient concentrations. For field experiments, three ponds were selected that had different levels of plant nutrient concentrations and accordingly were treated as polluted, moderately polluted, and relatively unpolluted, respectively, the object being to study the nutrient removal-capacity of chosen aquatic macrophytes living in ‘natural’ conditions. For the present investigation, four common and widespread aquatic plants growing in all three ponds were chosen: Water-hyacinth (Eichhornia crassipes [Mart.] Solms), Water-lettuce (Pistia stratiotes L.), Round-leafed Water-fern (Salvinia rotundifolia Willd.), and Lesser Duckweed (Lemna minor L.). These plants were selected also because of their frequent presence in aquatic bodies in the region and their high reproductive capacity.From the results it is revealed that, during the summer and rainy seasons, the highest content of nitrogen was removed by the Eichhornia, followed by the Pistia > Lemna > Salvinia, while during winter the highest content of nitrogen was removed by the Eichhornia followed by the Lemna > Pistia > Salvinia. Higher phosphorus removal was found in summer than in the rainy or the winter season. Phosphorus removal by the macrophytes was in the order of the Eichhornia > Pistia > Lemna > Salvinia, during the summer and rainy seasons, whereas the highest content of phosphorus was removed by Lemna in the winter months.The nutrient removal-capacity was rated to be highest by the Water-hyacinth, followed by the Pistia, then the Lemna, and lowest by the Salvinia. It was also evident that the nutrient removal increased with increasing nutrient concentration in the wastewater. The removal of nitrate by the selected macrophytes ranged from 42.0% to 96.2%, while phosphate removal ranged from 36.3% to 70.2%. A positive and significant correlation was obtained between the concentration of nitrate and phosphate in the waters and plant tissues that were studied, and it is thought that a useful strategy to employ might be to grow the Eichhornia and the Lemna together at least where winter temperatures were likely to be low enough to favour the Lemna at that season, though at other times it is apt to be a nuisance.