‘Domino’ systems biology and the ‘A’ of ATP

AbstractWe develop a strategic ‘domino’ approach that starts with one key feature of cell function and the main process providing for it, and then adds additional processes and components only as necessary to explain provoked experimental observations. The approach is here applied to the energy metabolism of yeast in a glucose limited chemostat, subjected to a sudden increase in glucose. The puzzles addressed include (i) the lack of increase in Adenosine triphosphate (ATP) upon glucose addition, (ii) the lack of increase in Adenosine diphosphate (ADP) when ATP is hydrolyzed, and (iii) the rapid disappearance of the ‘A’ (adenine) moiety of ATP. Neither the incorporation of nucleotides into new biomass, nor steady de novo synthesis of Adenosine monophosphate (AMP) explains. Cycling of the ‘A’ moiety accelerates when the cell's energy state is endangered, another essential domino among the seven required for understanding of the experimental observations. This new domino analysis shows how strategic experimental design and observations in tandem with theory and modeling may identify and resolve important paradoxes. It also highlights the hitherto unexpected role of the ‘A’ component of ATP

miR-145-5p and miR-203a-5p overcome imatinib resistance in myelogenous leukemic cells through metabolic reprogramming

Imatinib is the most effective therapy for chronic myeloid leukemia (CML), but many patients eventually develop resistance to it after an initial satisfactory response. This study investigated the potential of three miRNAs (miR-106b-5p, miR-145-5p, miR-203a-5p) in overcoming imatinib resistance in leukemic cells. The imatinib-resistant K562 (IR-K562) cells were developed and transfected with one of the three miRNAs to evaluate their potency in overcoming imatinib resistance. The changes in the metabolic profile were studied using flux balance analysis (FBA) and the data was validated using qRT-PCR.Among the three miRNAs, the ectopic expression of either miR-145-5p or miR-203a-5p was able to sensitize the IR-K562 cells to imatinib. The concentration of key oncometabolites; glucose, lactate, and glutamine, in the culture media of the miR-transfected IR-K562 cells, reverted to the same levels as seen in imatinib-sensitive K562 cells. In addition, the FBA analysis revealed that the metabolism of lipid, fatty acids, and electron transport chain were significantly altered in resistant cells. The FBA data was also validated at the molecular level. Interestingly, the imatinib treatment coupled with the transfection of miR-145-5p or miR-203a-5p cells could reverse the metabolic flux of IR-K562 to the levels seen in imatinib-sensitive K562 cells. This study highlights the key metabolic changes that occur during development of imatinib resistance. It also identifies the specific miRNAs which can be targeted to overcome imatinib resistance in CML

How can immunotherapy be used to target Amyloid Beta for treating Alzheimer Disease?

Neurodegenerative diseases including Alzheimer's disease are characterized by the build-up amyloid beta plaques resulting in non-regenerative nerve cell death. The nerve cell death causes limited brain activity, that triggers damage to cognitive and memory. Currently, no therapy for Alzheimer's disease is available and patients are treated for alleviating the symptoms. One of the suitable options could be antibody immunotherapy.The aim of this review to discuss antibody immunotherapy for the removal of amyloid beta plaques. The monoclonal antibodies bind amyloid beta plaques. This interaction leads to the activation of microglia in the nerve tissue and cleaning of deposits. The process of cleaning of amyloid deposits halts the brain damage, declines death of nerve tissue to maintain synaptic integrity of the brain. Immunotherapy leads a promising approach as a treatment option for Alzheimer’s disease because it targets the key mechanism by which nerve damage is being caused. However, with the limitation of monoclonal antibodies in order to cross the blood-brain barrier, the immunotherapy remains the key factor in making a viable treatment for patients with Alzheimer's disease. Although, there are methods been tested to increasethe absorption of monoclonal antibodies through the blood-brain barrier

Antileukemic Activity of hsa-miR-203a-5p by Limiting Glutathione Metabolism in Imatinib-Resistant K562 Cells

Imatinib has been the first and most successful tyrosine kinase inhibitor (TKI) for chronic myeloid leukemia (CML), but many patients develop resistance to it after a satisfactory response. Glutathione (GSH) metabolism is thought to be one of the factors causing the emergence of imatinib resistance. Since hsa-miR-203a-5p was found to downregulate Bcr-Abl1 oncogene and also a link between this oncogene and GSH metabolism is reported, the present study aimed to investigate whether hsa-miR-203a-5p could overcome imatinib resistance by targeting GSH metabolism in imatinib-resistant CML cells. After the development of imatinib-resistant K562 (IR-K562) cells by gradually exposing K562 (C) cells to increasing doses of imatinib, resistant cells were transfected with hsa-miR-203a-5p (R+203). Thereafter, cell lysates from various K562 cell sets (imatinib-sensitive, imatinib-resistant, and miR-transfected imatinib-resistant K562 cells) were used for GC-MS-based metabolic profiling. L-alanine, 5-oxoproline (also known as pyroglutamic acid), L-glutamic acid, glycine, and phosphoric acid (Pi)—five metabolites from our data, matched with the enumerated 28 metabolites of the MetaboAnalyst 5.0 for the GSH metabolism. All of these metabolites were present in higher concentrations in IR-K562 cells, but intriguingly, they were all reduced in R+203 and equated to imatinib-sensitive K562 cells (C). Concludingly, the identified metabolites associated with GSH metabolism could be used as diagnostic markers

Therapeutic approaches to enhance the BCR-ABL tyrosine kinase inhibitors efficacy in chronic myeloid leukemia

Chronic Myeloid Leukemia (CML) is a well-known myeloproliferative disease characterized by the presence of the Philadelphia chromosome and its oncogenic product, BCR-ABL, a constitutively expressed tyrosine kinase that is present in the majority of the patients. The treatment of CML was transformed by the introduction of imatinib mesylate commercially known as Gleevec; a BCR-ABL tyrosine kinase inhibitor (TKI) which dramatically increased the survival rate and quality life of the patients. Despite having high efficacy majority of the patients have developed resistance to imatinib. To overcome this problem, new treatment options are required to treat CML patients. In this regard, the fragment-based drug discovery is a novel and generic methodology which uses the combination of targeted chemotherapeutic drugs with the suitable fragments from the screened library. These ligandefficient individual fragments examine the chemical space of the target transporter protein, covering a relatively large area due to their small sizes, may provide a way to future medicine to treat CML patients

miRNA: An Alternative Therapy for Chronic Myeloid Leukemia

Chronic myeloid leukemia is a myeloproliferative neoplasm that results due to the expression of BCR/ABL P210 oncoprotein in hematopoietic stem cells. This oncoprotein causes constitutive expression of tyrosine kinase and disrupts normal signaling pathways of cell cycle progression and differentiation. The use of targeted therapy, tyrosine kinase inhibitors (TKIs), although proved to be useful, poor drug response, drug resistance, adverse side effects, high cost has posed a severe threat to CML patients. This has shifted the attention of the scientific community to search for a more viable alternative that can tackle not only TKI related problems but also modulate the leukemogenic signaling pathways by silencing Bcr/Abl expression at the transcript level. MicroRNAs provide a beautiful avenue of therapeutic research in haematological malignancies including CML. They are promising prognostic as well diagnostic molecules, and with rapid advancement in miRNA based research and underlying signaling network in CML, the use of miRNA as prognostic, diagnostic biomarker or as a therapeutic agent alone, or in combination with TKIs is sure to see the light of the day. This paper is an endeavour to synthesize our present knowledge about CML, the signaling pathways involved in the disease and importance of microRNA in CML emphasizing on why microRNA is a better alternative than the currently available TKIs

Downregulation of Bcr-Abl oncogene in Chronic Myeloid Leukemia by microRNAs

The well-known myeloproliferative malignancy, chronic myeloid leukemia (CML), causes due to the formation of short and modified Philadelphia chromosome having the Bcr-Abl oncogene. Many therapeutic approaches have been made for the treatment of CML, the best one was the development of Tyrosine Kinase Inhibitors (TKIs), mainly Imatinib. But after the development of mutation against Imatinib, researchers moved towards RNA interference (RNAi) of BCR-ABL mRNA via microRNAs. In this review, we identified 105 miRNAs by Target Scan, miRbase and miRNAMap, which target the proteins of CML signaling pathway. These are selected on the basis of their constitutive activation in the Bcr-Abl positive cell lines. Targeting these proteins by miRNAs might effectively enhance chemotherapy-induced cytotoxicity in CML cells. Out of these 105 miRNAs, 21 were found to commonly effective against those proteins. These 21 microRNAs may or may not have been studied in CML cases, but have been studied in other solid or myeloid tumors. This review might be helpful in extending the studies regarding regulation of CML signaling proteins by miRNAs

Biological significance of autoregulation through steady state analysis of genetic networks

Biological significance of autoregulation through steady state analysis of genetic network

A steady-state modeling approach to validate an in vivo mechanism of the GAL regulatory network in Saccharomyces cerevisiae

Cellular regulation is a result of complex interactions arising from DNA–protein and protein–protein binding, autoregulation, and compartmentalization and shuttling of regulatory proteins. Experiments in molecular biology have identified these mechanisms recruited by a regulatory network. Mathematical models may be used to complement the knowledge-base provided by in vitro experimental methods. Interactions identified by in vitro experiments can lead to the hypothesis of multiple candidate models explaining the in vivo mechanism. The equilibrium dissociation constants for the various interactions and the total component concentration constitute constraints on the candidate models. In this work, we identify the most plausible in vivo network by comparing the output response to the experimental data. We demonstrate the methodology using the GAL system of Saccharomyces cerevisiae for which the steady-state analysis reveals that Gal3p neither dimerizes nor shuttles between the cytoplasm and the nucleus