An integrated computational and experimental study uncovers FUT9 as a metabolic driver of colorectal cancer.

Metabolic alterations play an important role in cancer and yet, few metabolic cancer driver genes are known. Here we perform a combined genomic and metabolic modeling analysis searching for metabolic drivers of colorectal cancer. Our analysis predicts FUT9, which catalyzes the biosynthesis of Ley glycolipids, as a driver of advanced-stage colon cancer. Experimental testing reveals FUT9's complex dual role; while its knockdown enhances proliferation and migration in monolayers, it suppresses colon cancer cells expansion in tumorspheres and inhibits tumor development in a mouse xenograft models. These results suggest that FUT9's inhibition may attenuate tumor-initiating cells (TICs) that are known to dominate tumorspheres and early tumor growth, but promote bulk tumor cells. In agreement, we find that FUT9 silencing decreases the expression of the colorectal cancer TIC marker CD44 and the level of the OCT4 transcription factor, which is known to support cancer stemness. Beyond its current application, this work presents a novel genomic and metabolic modeling computational approach that can facilitate the systematic discovery of metabolic driver genes in other types of cancer.

Altered expression of calcineurin, calpain, calpastatin and HMWCaMBP in cardiac cells following ischemia and reperfusion.

A rise in intracellular myocardial Ca(2+) during cardiac ischemia activates calpain (Calpn) thereby causing damage to myocardial proteins, which leads to myocyte death and consequently to loss of myocardial structure and function. Calcineurin (CaN) interacts with Calpn and causes cellular damage eventually leading to cell death. Calpastatin (Calp) and high molecular weight calmodulin-binding protein (HMWCaMBP) (homolog of Calp), inhibit Calpn activity and thus prevent cell death. CaN stimulation can also result in self-repair of damaged cardiomyocytes. The present study attempts to elucidate the expression of these proteins in cells under pre-ischemic condition (control), following ischemia induction and also reperfusion subsequent to ischemia. For the first time, flow cytometric analysis (FACS) has been used for analyzing protein expression concurrently with viability. We induced ischemia and subsequently reperfusion in 80% confluent cultures of neonatal murine cardiomyocytes (NMCC). Viability following induction was assessed with 7-AAD staining and the cells were simultaneously checked for protein expression by FACS. We observed that ischemia induction results in increased expression of CaN, Calp and Calpn. HMWCaMBP expression was reduced in live cells following ischemia which suggests that there is a poor survival outcome of cells expressing HMWCaMBP thereby making it a potential biomarker for such cells. Most live cells following ischemia expressed CaN pointing towards self-repair and favorable survival outcomes.

Regulation of N-myristoyltransferase by the calpain and caspase systems.

N-myristoyltransferase (NMT) is an essential eukaryotic enzyme which catalyzes the transfer of the myristoyl group to the terminal glycine residue of a number of proteins including those involved in signal transduction and apoptotic pathways. In higher eukaryotes, two isoforms of NMT have been identified (NMT1 and NMT2) which share about 76% amino acid sequence identity in humans. Protein-protein interactions of NMTs reveal that m-calpain interacts with NMT1 whereas caspase-3 interacts with NMT2. These findings reveal differential interactions of both isoforms of NMT with various signaling molecules. This minireview provides an overview of the regulation of N-myristoyltransferase by calpain and caspase systems.

Cardiomyocyte culture - an update on the in vitro cardiovascular model and future challenges.

The success of any work with isolated cardiomyocytes depends on the reproducibility of cell isolation, because the cells do not divide. To date, there is no suitable in vitro model to study human adult cardiac cell biology. Although embryonic stem cells and induced pluripotent stem cells are able to differentiate into cardiomyocytes in vitro, the efficiency of this process is low. Isolation and expansion of human cardiomyocyte progenitor cells from cardiac surgical waste or, alternatively, from fetal heart tissue is another option. However, to overcome various issues related to human tissue usage, especially ethical concerns, researchers use large- and small-animal models to study cardiac pathophysiology. A simple model to study the changes at the cellular level is cultures of cardiomyocytes. Although primary murine cardiomyocyte cultures have their own advantages and drawbacks, alternative strategies have been developed in the last two decades to minimise animal usage and interspecies differences. This review discusses the use of freshly isolated murine cardiomyocytes and cardiomyocyte alternatives for use in cardiac disease models and other related studies.

High molecular weight calmodulin-binding protein: 20 years onwards-a potential therapeutic calpain inhibitor.

Apoptosis in cardiovascular diseases is considered to be a major reason for heart failure. Caspase-independent apoptosis due to calpains and other proteases occurs due to increase in intracellular Ca(2+) levels which act on a feed-forward mechanism. Calpains are Ca(2+)-activated cysteine proteases present in the cytosol as inactive proenzymes. Calpastatin is most efficient and specific calpain inhibitor present in vivo. Earlier, we had reported the expression of novel high molecular weight calmodulin-binding protein (HMWCaMBP) in human and animal cardiac tissue and in very minute quantities in brains and lungs. HMWCaMBP showed calpastatin activity and was also found to be highly homologous to calpastatin I and calpastatin II. Decreased expression of HMWCaMBP was observed during ischemia as it is susceptible to proteolysis by calpains during ischemia-reperfusion. In normal myocardium, HMWCaMBP may protect its substrate from calpains. However, during an early stage of ischemia/reperfusion due to increased Ca(2+) influx, calpain activity often exceeds HMWCaMBP activity. This leads to proteolysis of HMWCaMBP and other protein substrates, resulting in cellular damage. The role of HMWCaMBP in ischemia/reperfusion is yet to be elucidated. The present review summarizes the developments in area of HMWCaMBP from the authors' laboratory and its potential for therapy.

Detection of 16S rRNA gene for rapid identification of bacterial pathogens causing peritonitis in patients on continuous ambulatory peritoneal dialysis.

PURPOSE: Peritonitis is the most important complication with high rate of morbidity and mortality in patients on continuous ambulatory peritoneal dialysis (CAPD) despite the success and advances. Rapid and accurate identification of pathogens causing peritonitis in a CAPD patient is essential for early targeted treatment. The aim of the study was to evaluate the role of 16S rRNA gene and ITS region PCR and sequencing in detecting bacterial and fungal pathogens from the dialysate of patients undergoing CAPD. METHODS: Fifty eight peritoneal dialysate from suspected cases of peritonitis on CAPD were subjected to conventional culture as per the ISPD guidelines and automated culture system. A conventional PCR was performed to detect the 16S rRNA gene and ITS region. Sequencing and analysis were performed to identify the etiological agent from the remaining dialysate. RESULTS: Among the 58 dialysate fluid, the etiological agents were identified in 8(14%) samples by conventional culture, 28(48%) by automated culture and 47(81%) by 16S rRNA sequencing and analysis. In 8 samples there was discordance in the results of the culture and 16S rRNA PCR. BLAST search of nine sequences obtained from 16S rRNA PCR revealed that these sequences matched best with uncultured bacterial clones. In eleven samples the sequence failed. CONCLUSION: The molecular tool 16S rRNA gene and ITS region PCR and sequencing cannot be used as a standalone test as it lacks sensitivity to identify some bacterial species due to high genetic similarity in some cases and inadequate database in GenBank. However, it could be used as a supplementary test to the culture method especially in the diagnosis of culture negative peritonitis.

Scanning electron microscopy preparation protocol for differentiated stem cells.

The lack of an established protocol for scanning electron microscopy (SEM) studies on stem cells differentiating into adipogenic lineage led us to develop a protocol for the preparation of differentiated adult bone marrow-derived mesenchymal stem cells (BMSC) for SEM. This protocol describes the procedure to maintain and preserve the structural organization of cellular components following differentiation, for morphological and physical characterization. The fixation of the differentiated cells was followed by dehydration using methanol, and vacuum desiccation before microscopy. The use of longer chain alcohols as dehydrating agents was avoided in our method to reduce the dissolution of lipid deposits in cells, thus allowing the maintenance of their structural integrity. The time period for the processing of samples was reduced by avoiding the osmium tetroxide postfixation and critical point drying. Thus, this protocol helps in determining the potential, fate, and degree of stem cell differentiation. This may be useful for SEM analysis of differentiated cells, especially those grown on various scaffolds.

Voice hoarseness in a patient with underlying Eisenmenger's syndrome: a case report.

BACKGROUND: The natural history of patients diagnosed with Eisenmenger's Syndrome typically revolve around the pediatric population. Medical advances have allowed these patients to live longer and present with a different subset of symptoms as a result of the progression of their disease process. CASE PRESENTATION: In this case report, we discuss a 77-year-old Caucasian female with Eisenmenger's Syndrome presenting with hoarseness. Clinical and imaging studies reveal a left vocal cord paralysis secondary to a progressively enlarging patent ductus arteriosus (PDA) and dilation of pulmonary arteries causing mass effect on the left recurrent laryngeal nerve. CONCLUSION: From a clinical perspective, this case highlights the need for otolaryngologists to be aware of the pathophysiology of Eisenmenger's Syndrome as it progresses with age.

A Road Map to Personalizing Targeted Cancer Therapies Using Synthetic Lethality.

Targeted therapies rely on the genetic and epigenetic status of the tumor cells and are seen as the most promising approach to treat cancer today. However, current targeted therapies focus on directly inhibiting those molecules that are altered in tumor cells. Unfortunately, targeting these molecules, even with specific inhibitors, is challenging as tumor cells rewire their genetic circuitry to eliminate genetic dependency on these targets. Here, we describe how synthetic lethality approaches can be used to identify genetic dependencies and develop personalized targeted therapies. We also discuss strategies to specifically target these genetic dependencies, using small molecule and biologic drugs.

Molecular characterization of an MLL1 fusion and its role in chromosomal instability.

Chromosomal rearrangements involving the mixed-lineage leukemia (MLL1) gene are common in a unique group of acute leukemias, with more than 100 fusion partners in this malignancy alone. However, do these fusions occur or have a role in solid tumors? We performed extensive network analyses of MLL1-fusion partners in patient datasets, revealing that multiple MLL1-fusion partners exhibited significant interactions with the androgen-receptor signaling pathway. Further exploration of tumor sequence data from TCGA predicts the presence of MLL1 fusions with truncated SET domain in prostate tumors. To investigate the physiological relevance of MLL1 fusions in solid tumors, we engineered a truncated version of MLL1 by fusing it with one of its known fusion partners, ZC3H13, to use as a model system. Functional characterization with cell-based assays revealed that MLL1-ZC3H13 fusion induced chromosomal instability, affected mitotic progression, and enhanced tumorsphere formation. The MLL1-ZC3H13 chimera consistently increased the expression of a cancer stem cell marker (CD44); in addition, we detected potential collateral lethality between DOT1L and MLL1 fusions. Our work reveals that MLL1 fusions are likely prevalent in solid tumors and exhibit a potential pro-tumorigenic role.

Calmodulin-binding proteins: A journey of 40 years.

The proteins which bind to calmodulin in a Ca2+-dependent and reversible manner are known as calmodulin-binding proteins. These proteins are involved in a multitude of processes in which Ca2+ and calmodulin play crucial roles. Our group elucidated the mechanism and importance of these proteins in normal and diseased conditions. Various calmodulin-binding proteins were discovered and purified from bovine tissue including a heat stable calmodulin-binding protein 70, calmodulin-dependent protein kinase VI and a high molecular weight calmodulin-binding protein (HMWCaMBP). We observed a complex interplay occurs between these and other Ca2+ and calmodulin-binding proteins during cardiac ischemia and reperfusion. Purified cardiac HMWCaMBP is a homolog form of calpastatin and an inhibitor of the Ca2+-activated cysteine proteases, calpains and therefore can have cardioprotective role in ischemic conditions. Calcineurin is a Ca2+ and calmodulin-dependent serine/threonine protein phosphatase showed increased phosphatase activity in ischemic heart through its direct interaction with Hsp70 and expression of calcineurin following ischemia suggests self-repair and favorable survival outcomes. Calcineurin was also found to be present in other tissues including the eye; where its expression and calcineurin phosphatase activity varied. In neurons, calcineurin may play a key role in initiating apoptosis-related pathways especially in epilepsy. In colorectal cancer we demonstrated high calcineurin phosphatase activity and simultaneous overexpression of calcineurin. The impact of calcineurin signaling on neuronal apoptosis in epilepsy and its use as a diagnostic marker for colorectal cancer requires in-depth study.

Expression-based analyses indicate a central role for hypoxia in driving tumor plasticity through microenvironment remodeling and chromosomal instability.

Can transcriptomic alterations drive the evolution of tumors? We asked if changes in gene expression found in all patients arise earlier in tumor development and can be relevant to tumor progression. Our analyses of non-mutated genes from the non-amplified regions of the genome of 158 triple-negative breast cancer (TNBC) cases identified 219 exclusively expression-altered (EEA) genes that may play important role in TNBC. Phylogenetic analyses of these genes predict a "punctuated burst" of multiple gene upregulation events occurring at early stages of tumor development, followed by minimal subsequent changes later in tumor progression. Remarkably, this punctuated burst of expressional changes is instigated by hypoxia-related molecular events, predominantly in two groups of genes that control chromosomal instability (CIN) and those that remodel tumor microenvironment (TME). We conclude that alterations in the transcriptome are not stochastic and that early-stage hypoxia induces CIN and TME remodeling to permit further tumor evolution.

Insulin Cannot Induce Adipogenic Differentiation in Primary Cardiac Cultures.

Cardiac tissue contains a heterogeneous population of cardiomyocytes and nonmyocyte population especially fibroblasts. Fibroblast differentiation into adipogenic lineage is important for fat accumulation around the heart which is important in cardiac pathology. The differentiation in fibroblast has been observed both spontaneously and due to increased insulin stimulation. The present study aims to observe the effect of insulin in adipogenic differentiation of cardiac cells present in primary murine cardiomyocyte cultures. Oil Red O (ORO) staining has been used for observing the lipid accumulations formed due to adipogenic differentiation in murine cardiomyocyte cultures. The accumulated lipids were quantified by ORO assay and normalized using protein estimation. The lipid accumulation in cardiac cultures did not increase in presence of insulin. However, addition of other growth factors like insulin-like growth factor 1 and epidermal growth factor promoted adipogenic differentiation even in the presence of insulin and other inhibitory molecules such as vitamins. Lipid accumulation also increased in cells grown in media without insulin after an initial exposure to insulin-containing growth media. The current study adds to the existing knowledge that the insulin by itself cannot induce adipogenic induction in the cardiac cultures. The data have significance in the understanding of cardiovascular health especially in diabetic patients.

Therapeutic relevance of the protein phosphatase 2A in cancer.

Chromosomal Instability (CIN) is regarded as a unifying feature of heterogeneous tumor populations, driving intratumoral heterogeneity. Polo-Like Kinase 1 (PLK1), a serine-threonine kinase that is often overexpressed across multiple tumor types, is one of the key regulators of CIN and is considered as a potential therapeutic target. However, targeting PLK1 has remained a challenge due to the off-target effects caused by the inhibition of other members of the polo-like family. Here we use synthetic dosage lethality (SDL), where the overexpression of PLK1 is lethal only when another, normally non-lethal, mutation or deletion is present. Rather than directly inhibiting PLK1, we found that inhibition of PP2A causes selective lethality to PLK1-overexpressing breast, pancreatic, ovarian, glioblastoma, and prostate cancer cells. As PP2A is widely regarded as a tumor suppressor, we resorted to gene expression datasets from cancer patients to functionally dissect its therapeutic relevance. We identified two major classes of PP2A subunits that negatively correlated with each other. Interestingly, most mitotic regulators, including PLK1, exhibited SDL interactions with only one class of PP2A subunits (PPP2R1A, PPP2R2D, PPP2R3B, PPP2R5B and PPP2R5D). Validation studies and other functional cell-based assays showed that inhibition of PPP2R5D affects both levels of phospho-Rb as well as sister chromatid cohesion in PLK1-overexpressing cells. Finally, analysis of clinical data revealed that patients with high expression of mitotic regulators and low expression of Class I subunits of PP2A improved survival. Overall, these observations point to a context-dependent role of PP2A that warrants further exploration for therapeutic benefits.

Expression of calcineurin, calpastatin and heat shock proteins during ischemia and reperfusion.

OBJECTIVE: Calcineurin (CaN) interacts with calpains (Calpn) and causes cellular damage eventually leading to cell death. Calpastatin (Calp) is a specific Calpn inhibitor, along with CaN stimulation has been implicated in reduced cell death and self-repair. Molecular chaperones, heat shock proteins (Hsp70 and Hsp90) acts as regulators in Calpn signaling. This study aims to elucidate the role of CaN, Calp and Hsps during induced ischemia and reperfusion in primary cardiomyocyte cultures (murine). METHODS AND RESULTS: Protein expression was analyzed concurrently with viability using flow cytometry (FACS) in ischemia- and reperfusion-induced murine cardiomyocyte cultures. The expression of Hsp70 and Hsp90, both being molecular chaperones, increased during ischemia with a concurrent increase in death of cells expressing these proteins. The relative expression of Hsp70 and Hsp90 during ischemia with respect to CaN was enhanced in comparison to Calp. Reperfusion slightly decreased the number of cells expressing these chaperones. There was no increase in death of cells co-expressing Hsp70 and Hsp90 along with CaN and Calp. CaN expression peaked during ischemia and subsequent reperfusion reduced its expression and cell death. Calp expression increased both during ischemia and subsequent reperfusion but cell death decreased during reperfusion. CONCLUSION: The present study adds to the existing knowledge that Hsp70, Hsp90, CaN and Calp interact with each other and play significant role in cardio protection.

Novel myristoylation of the sperm-specific hexokinase 1 isoform regulates its atypical localization.

The hexokinase 1 variant in mammalian spermatozoa (HK1S) has a unique N-terminus and this isoform atypically localizes to the plasma membrane. However, the mechanism of this process currently remains ambiguous. In this report, we show that fatty acylation underlies the specific sorting of HK1S. Employing chimeric reporter constructs, we first established that compartmentalization of HK1S does not function exclusively in sperm cells and that this feature is swappable to somatic HEK293 cells. Although the N-terminus lacks the classical consensus signature for myristoylation and the sequence-based predictions fail to predict myristoylation of HK1S, complementary experimental approaches confirmed that HK1S is myristoylated. Using live-cell confocal microscopy, we show that the mutation of a single amino acid, the myristoyl recipient Gly(2), impedes the prominent feature of plasma membrane association and relocates the enzyme to the cytosol but not the nucleus. Additionally, substitutions of the putatively palmitoylated Cys(5) is also reflected in a similar loss of compartmentalization of the protein. Taken together, our findings conclusively demonstrate that the N-terminal 'MGQICQ' motif in the unique GCS domain of HK1S acquires hydrophobicity by dual lipidic modifications, N-myristoylation and palmitoylation, to serve the requirements for membranous associations and thus its compartmentalization.

Enrichment of cardiomyocytes in primary cultures of murine neonatal hearts.

In vitro culture of neonatal murine cardiomyocytes is vital for understanding the functions of the heart. Cardiomyocyte cultures are difficult to maintain because they do not proliferate after birth. The maintenance of primary cultures of viable and functional cardiomyocytes is considerably affected by the yield from initial steps of isolation procedures. This protocol describes an efficient and rapid method for isolation and maintenance of long-term cultures of neonatal murine cardiomyocytes by effectively shortening the trypsin enzyme digestion period and the cardiomyocyte enrichment step.

Enhanced protective immunity derived from dendritic cells with phagocytosis of CD40 ligand transgene-engineered apoptotic tumor cells via increased dendritic cell maturation.

AIMS AND BACKGROUND: Dendritic cells (DCs) play a pivotal role in regulating CD8+ cytotoxic T-lymphocyte (CTL) responses. Currently, DC vaccines have been used in experimental animal models and clinical trials for evaluation of antitumor immunity. However, their efficacy is limited, warranting the improvement of DC-based cancer vaccines. CD40 ligand (CD40L) stimulates DC activation and maturation via CD40-CD40L interaction. We demonstrated that DCs that had phagocytized apoptotic tumor cells induced antitumor immunity. METHODS: We generated CD40L-expressing (EG7-CD40L) and the control (EG7-Null) EG7 tumor cells by transfection of EG7 tumor cells with CD40L-expressing adenoviral vector AdVCD40L and the control vector AdV(pLpA), respectively. We also generated DC vaccines (DC-EG7/CD40L and the control DC-EG7/Null) using DCs with phagocytosis of irradiated EG7-CD40L and EG7-Null tumor cells, and assessed their phenotype and immunogenicity by flow cytometry and animal studies in C57BL/6 mice. RESULTS: We demonstrate that an irradiation of 9000-rad induced Annexin V-expressing cell apoptosis in most (~75%) tumor cells, and provide evidence for phagocytosis of apoptotic tumor cells by flow cytometry and confocal microscopy. The DC-EG7/CD40L cells showed higher expression of DC maturation markers (Ia(b), CD40, CD80, and CD86) and peptide/major histocompatibility complex I than the control DC-EG7/Null cells. In addition, DC-EG7/CD40L vaccine stimulates more efficient (0.97%) tumor-specific CTL responses than DC-EG7/Null cells (0.31%). Furthermore, 80% (4/5) of mice immunized with DC-EG7/CD40L vaccine become tumor-free after EG7 tumor cell challenge, whereas DC-EG7/Null vaccine only delays immunized mouse death. CONCLUSIONS: Dendritic cells that have phagocytized CD40L-expressing apoptotic tumor cells appear to offer new strategies in DC cancer vaccines.

Ischemia and reperfusion induce differential expression of calpastatin and its homologue high molecular weight calmodulin-binding protein in murine cardiomyocytes.

In the heart, calpastatin (Calp) and its homologue high molecular weight calmodulin-binding protein (HMWCaMBP) regulate calpains (Calpn) by inhibition. A rise in intracellular myocardial Ca2+ during cardiac ischemia activates Calpn thereby causing damage to myocardial proteins, which leads to myocyte death and consequently to loss of myocardial structure and function. The present study aims to elucidate expression of Calp and HMWCaMBP with respect to Calpn during induced ischemia and reperfusion in primary murine cardiomyocyte cultures. Ischemia and subsequently reperfusion was induced in ∼ 80% confluent cultures of neonatal murine cardiomyocytes (NMCC). Flow cytometric analysis (FACS) has been used for analyzing protein expression concurrently with viability. Confocal fluorescent microscopy was used to observe protein localization. We observed that ischemia induces increased expression of Calp, HMWCaMBP and Calpn. Calpn expressing NMCC on co-expressing Calp survived ischemic induction compared to NMCC co-expressing HMWCaMBP. Similarly, living cells expressed Calp in contrast to dead cells which expressed HMWCaMBP following reperfusion. A significant difference in the expression of Calp and its homologue HMWCaMBP was observed in localization studies during ischemia. The current study adds to the existing knowledge that HMWCaMBP could be a putative isoform of Calp. NMCC on co-expressing Calp and Calpn-1 survived ischemic and reperfusion inductions compared to NMCC co-expressing HMWCaMBP and Calpn-1. A significant difference in expression of Calp and HMWCaMBP was observed in localization studies during ischemia.

Proton-gated ion channels in mouse bone marrow stromal cells.

A variety of ion channels like acid sensing ion channels (ASICs) and several members of the transient receptor potential (TRP) cation channel family are known to be activated by protons. The present study describes proton-gated current in mouse bone marrow stromal cells (BMSCs), by using whole cell patch clamp. Rapid application of extracellular solution of pH ≤ 6.5, evoked slow inactivating current with mean peak value of 328 ± 31pA, (n = 25) at pH 5.0. The reversal potential was close to the theoretical Na(+) equilibrium potential, indicating that majority of the current is mediated by Na(+) and partially carried by Ca(2+) as revealed by ion substitution experiments and Ca(2+) imaging. ASICs blocker amiloride (1mM) and nonselective cation channel blocker flufenamic acid (0.3mM) reduced the current amplitudes by 36 ± 5% (n = 10) and 39 ± 7% (n = 14) respectively. Co-application of flufenamic acid and amiloride further decreased the current by 70 ± 7% (n = 7). However, capsazepine, SKF 96365 and ruthenium red had no effect. 10mM of Ca(2+) and 2mM of La(3+) inhibited the current by 39 ± 6% (n = 5) and 46 ± 6% (n = 4) respectively. Zn(2+) (300 µM) and Gd(3+) (500 µM) had no effect on the current amplitude. Low pH mediated cell death was completely inhibited by co-application of La(3+) and amiloride. Reverse Transcriptase-PCR detected expression of mRNAs of ASICs and TRP family. In summary, our results demonstrate the functional expression of low pH-activated ion channels in mouse BMSCs.