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1.  Innovative Technique of Vascular Repair in Intra-Operative IVC Rupture During Lumbar Microdiscectomy: A Case Report 
Archives of Trauma Research  2013;2(3):133-135.
Major vascular injury during a spinal surgery is a rare but most dreaded complication.
Case Presentation
A 39 years old female undergoing microscopic lumbar discectomy suddenly developed severe hypotension on table. The procedure was abandoned and the patient turned supine. It was diagnosed to be a major vessel tear and the patient was taken up for immediate successful vascular repair. To best of our knowledge such a repair procedure has not been described in literature.
Majority of such vascular injuries are dealt with primary repair of the defect by a vascular surgeon; however in our case the rent was big and placed on the undersurface making it very difficult for the vascular surgeon to approach or repair it primarily.
PMCID: PMC3950917
Microdiscectomy Complications; Vascular Injury; Inferior Vena Cava Rupture; Anastomosis; Vascular Bypass
2.  Hemolytik: a database of experimentally determined hemolytic and non-hemolytic peptides 
Nucleic Acids Research  2013;42(D1):D444-D449.
Hemolytik ( is a manually curated database of experimentally determined hemolytic and non-hemolytic peptides. Data were compiled from a large number of published research articles and various databases like Antimicrobial Peptide Database, Collection of Anti-microbial Peptides, Dragon Antimicrobial Peptide Database and Swiss-Prot. The current release of Hemolytik database contains ∼3000 entries that include ∼2000 unique peptides whose hemolytic activities were evaluated on erythrocytes isolated from as many as 17 different sources. Each entry in Hemolytik provides comprehensive information about a peptide, like its name, sequence, origin, reported function, property such as chirality, types (linear and cyclic), end modifications as well as details pertaining to its hemolytic activity. In addition, tertiary structure of each peptide has been predicted, and secondary structure states have been assigned. To facilitate the scientific community, a user-friendly interface has been developed with various tools for data searching and analysis. We hope, Hemolytik will be useful for researchers working in the field of designing therapeutic peptides.
PMCID: PMC3964980  PMID: 24174543
3.  Historical perspective of Indian neurology 
To chronicle the history of medicine and neurology in India with a focus on its establishment and evolution.
The history of neurology in India is divided into two periods: ancient and modern. The ancient period dates back to the mid-second millennium Before Christ (B.C.) during the creation of the Ayurvedic Indian system of Medicine, which detailed descriptions of neurological disorders called Vata Vyadhi. The early 20th century witnessed the birth of modern Indian medicine with the onset of formal physician training at the nation's first allopathic medical colleges located in Madras (1835), Calcutta (1835) and Mumbai (1848). Prior to India's independence from Britain in 1947, only 25 medical schools existed in the entire country. Today, there are over 355. In 1951, physicians across the field of neurology and neurosurgery united to create the Neurological Society of India (NSI). Four decades later in 1991, neurologists branched out to establish a separate organization called the Indian Academy of Neurology (IAN).
Information was gathered through literature review using PubMed, MD Consult, OVID, primary texts and research at various academic institutions in India.
Neurological disorders were first described in ancient India under Ayurveda. The transition to modern medicine occurred more recently through formal training at medical schools beginning in the 1930's. Early pioneers and founders of the NSI (1951) include Dr. Jacob Chandy, Dr. B Ramamurthi, Dr. S. T. Narasimhan and Dr. Baldev Singh. Later, Dr. J. S. Chopra, a prominent neurologist and visionary, recognized the need for primary centers of collaboration and subsequently established the IAN (1991). The future of Neurology in India is growing rapidly. Currently, there are 1100 practicing neurologists and more than 150 post-graduate trainees who join the ranks every year. As the number of neurologists rises across India, there is an increase in the amount of basic, clinical and epidemiological research being conducted across the country every day.
The history of neurology in India roots back to its rich culture and tradition. Over time, there has been great structural and organizational evolution and the future of neurology in India appears to be bright. However, the number of neurologists and research in neurology needs to experience a significant growth in the future to ensure the best patient care.
PMCID: PMC3841583  PMID: 24339562
Ayurveda; dementia; Epilepsy; history; stroke
4.  Effect of chlorine dioxide and sodium hypochlorite on the dissolution of human pulp tissue – An in vitro study 
Organic tissue dissolution is an important property of an irrigant which aids in the success of root canal treatment. Recent studies have advocated the use of Chlorine dioxide as an endodontic irrigant. The aim of this study is to compare the dissolution efficacy of chlorine dioxide and sodium hypochlorite on human pulp tissue.
In this study, 2% Sodium hypochlorite, 5% Chlorine dioxide and isotonic saline solution (control) were used. Thirty human pulp tissue specimens were exposed to three test solutions (n = 10) for 30 min following which the loss of weight was compared from the original weight by using a digital analytical balance.
Sodium hypochlorite was more efficient in dissolving human pulp tissue when compared to Chlorine dioxide. Isotonic saline solution failed to dissolve any of the specimens.
5% Chlorine dioxide is capable of dissolving human pulp tissue but sodium hypochlorite was more effective.
PMCID: PMC3862608  PMID: 24532904
Sodium hypochlorite; Chlorine dioxide; Pulp tissue dissolution
7.  Neuroprotective Role of a Novel Copper Chelator against Aβ42 Induced Neurotoxicity 
Alzheimer's disease (AD) is a progressive neurodegenerative disease and associated with the extracellular deposits of amyloid-β peptide in hippocampus region. Metal ions like Cu, Fe and Zn are known to associate with the amyloid beta (Aβ) at high concentration and interaction of these ions with soluble and aggregated forms of Aβ peptide help in development of AD. Here we showed Cu mediated neurotoxicity in the eye tissues of transgenic Drosophila expressing human amyloid β and its rescue through a novel Cu chelator. In this context, we have synthesised and characterized the compound L 2,6-Pyridinedicarboxylic acid, 2,6-bis[2-[(4-carboxyphenyl) methylene] hydrazide] by Mass spectra (MS) and Elemental analysis (EA). The Cu chelation potential of the compound L is tested in vivo in Drosophila. Oral administration of Copper to the transgenic larvae resulted in severe degeneration in eye tissues, which was rescued by the supplementation of compound L. The levels of anti-oxidant markers like SOD and MDA were measured in compound L treated flies and found a significant rescue (P < 0.001). Further rescue of the eye degeneration phenotypes as revealed by SEM affirm the role of copper in Aβ toxicity. Hence, use of compound L, an amidoamine derivative, could be a possible therapeutic measure for Aβ induced neurotoxicity.
PMCID: PMC3789492  PMID: 24159420
8.  An Evaluation of Mass Drug Administration Compliance Against Filariasis of Tikamgarh District of Madhya Pradesh-A Household-Based Community Study 
Mass drug administration (MDA) means once-in-a-year administration of diethyl carbamazine (DEC) tablet to all people (excluding children under 2 years, pregnant women and severely ill persons) in identified endemic areas. It aims at cessation of transmission of lymphatic filariasis.
To study the coverage and compliance of MDA in Tikamgarh district during the campaign in April 2010.
Materials and Methods:
The activities under MDA involved administration of DEC tablets to eligible population from endemic area by health staff and Integrated Child Development Scheme (ICDS) functionaries referred as drug distributors (DD) make house-to-house visits on select dates in 2010. DEC was administered to all people (excluding children under 2 years, pregnant women and severely ill persons) with the instruction to ingest the tablet preferably on the spot.
Study Design:
Cross-sectional population based house-to-house visit.
Urban and rural areas in Tikamgarh district identified as endemic for filariasis where MDA 2010 was undertaken.
Study Variables:
Exploratory - Rural and urban clusters of Tikamgarh district; Outcome - coverage, compliance, actual coverage, side effects.
Percentage and proportions.
Four clusters, each comprising 30 households from Tikamgarh endemic district, yielded an eligible population of 641. The coverage rate was 607 (94.6% of eligible) with variation across different areas. The compliance with drug ingestion was 89.9% with a gap of 10.1% to be targeted by intensive IEC. The effective coverage (85.2%) was just above the target (85%). Side effects of DEC were minimum, transient and drug-specific. Overall coverage was marginally better in rural areas. The causes of poor coverage and compliance have been discussed and relevant suggestions have been made.
PMCID: PMC3894026  PMID: 24479075
Diethyl carbamazine; lymphatic filariasis; Mass drug administration
9.  βArrestin-1 and Mcl-1 Modulate Self-Renewal Growth of Cancer Stem-Like Side-Population Cells in Non-Small Cell Lung Cancer 
PLoS ONE  2013;8(2):e55982.
Side population (SP) cells have been reported to have properties of cancer stem-like cells (CSCs) in non-small cell lung carcinoma (NSCLC), yet their molecular features have not been fully elucidated. Here we show that, NSCLC-SP cells were enriched in G0/G­1 phase of cell cycle, had higher aldehyde dehydrogenase activity as well as higher clonogenic and self-renewing ability compared to main population (MP) cells. Interestingly, SP cells were also able to trans-differentiate into angiogenic tubules in vitro and were highly tumorigenic as compared to MP cells. SP-derived tumors demonstrated the intratumoral heterogeneity comprising of both SP and MP cells, suggesting the self-renewal and differentiation ability of SP cells are manifested in vivo as well. βArrestin-1 (βArr1) is involved in the progression of various cancers including NSCLCs and we find that depletion of βArr1 significantly blocked the SP phenotype; whereas depletion of βArr2 had relatively minor effects. Ectopic expression of βArr1 resulted in increased SP frequency and ABCG2 expression while abrogation of βArr1 expression suppressed the self-renewal growth and expansion of A549 cells. Anti-apoptotic protein Mcl-1 is known to be one of the key regulators of self-renewal of tissue stem cells and is thought to contribute to survival of NSCLC cells. Our experiments show that higher levels of Mcl-1 were expressed in SP cells compared to MP cells at both transcriptional and translational levels. In addition, Obatoclax, a pharmacological inhibitor of Mcl-1, could effectively prevent the self-renewal of both EGFR-inhibitor sensitive and resistant NSCLC cells. In conclusion, our findings suggest that βArr1 and Mcl-1 are involved in the self-renewal and expansion of NSCLC-CSCs and are potential targets for anti-cancer therapy.
PMCID: PMC3572139  PMID: 23418490
10.  Nicotine-mediated induction of E-selectin in aortic endothelial cells requires Src kinase and E2F1 transcriptional activity 
Smoking is highly correlated with enhanced likelihood of atherosclerosis by inducing endothelial dysfunction. In endothelial cells, various cell-adhesion molecules including E-selectin, are shown to be upregulated upon exposure to nicotine, the addictive component of tobacco smoke; however, the molecular mechanisms underlying this induction are poorly understood. Here we demonstrate that nicotine induced E-selectin transcription in human aortic endothelial cells (HAECs) could be significantly blocked by α7-nAChR subunit inhibitor, α-BT, Src-kinase inhibitor, PP2, or siRNAs against Src or β-Arrestin-1 (β-Arr1). Further, chromatin immunoprecipitations show that E-selectin is an E2F1 responsive gene and nicotine stimulation results in increased recruitment of E2F1 on E-selectin promoter. Inhibiting E2F1 activity using RRD-251, a disruptor of the Rb-Raf-1 kinase interaction, could significantly inhibit the nicotine induced recruitment of E2F1 to the E-selectin promoter as well as E-selectin expression. Interestingly, stimulation of HAECs with nicotine results in increased adhesion of U937 monocytic cells to HAECs and could be inhibited by pre-treatment with RRD-251. Similarly, depletion of E2F1 or Src using RNAi blocked the increased adhesion of monocytes to nicotine stimulated HAECs. These results suggest that nicotine stimulated adhesion of monocytes to endothelial cells is dependent on the activation of α7-nAChRs, β-Arr1 and cSrc regulated increase in E2F1-mediated transcription of E-selectin gene. Therefore, agents such as RRD-251 that can target activity of E2F1 may have potential therapeutic benefit against cigarette-smoke induced atherosclerosis.
PMCID: PMC3273677  PMID: 22240023
E-selectin; atherosclerosis; monocyte adhesion; RRD-251; β-arrestin-1; Src; Rb
11.  Comparative evaluation of 15% ethylenediamine tetra-acetic acid plus cetavlon and 5% chlorine dioxide in removal of smear layer: A scanning electron microscope study 
The purpose of this study was to compare the efficacy of smear layer removal by 5% chlorine dioxide and 15% Ethylenediamine Tetra-Acetic Acid plus Cetavlon (EDTAC) from the human root canal dentin.
Materials and Methods
Fifty single rooted human mandibular anterior teeth were divided into two groups of 20 teeth each and control group of 10 teeth. The root canals were prepared till F3 protaper and initially irrigated with 2% Sodium hypochlorite followed by 1 min irrigation with 15% EDTAC or 5% Chlorine dioxide respectively. The control group was irrigated with saline. The teeth were longitudinally split and observed under Scanning electron microscope SEM (×2000).
Statistical Analysis Used:
The statistical analysis was done using General Linear Mixed Model.
At the coronal thirds, no statistically significant difference was found between 15% EDTAC and 5% Chlorine dioxide in removing smear layer. In the middle and apical third region 15% EDTAC showed better smear layer removal ability than 5% Chlorine dioxide.
Final irrigation with 15% EDTAC is superior to 5% chlorine dioxide in removing smear layer in the middle and apical third of radicular dentin.
PMCID: PMC3703697  PMID: 23853455
Chlorine dioxide; ethylenediamine tetra-acetic acid plus cetavlon; smear layer removal
12.  Percutaneous Transvenous Angioplasty of Left Innominate Vein Stenosis Following Right Side Permanent Pacemaker Implantation- A Left Femoral Vein to Left Axillary Vein Approach 
Central venous stenosis after the insertion of a permanent pacemaker is a well recognized complication. This late complication is encountered when there is a need to change the pacemaker lead or extract it. We describe a young male who had such a complication after many years after right side pacemaker implantation. The lesion was managed percutaneously leading to placement of a new lead from the left side.
PMCID: PMC3513405  PMID: 23233760
Percutaneous Transvenous Angioplasty; Innominate Vein Stenosis; Permanent Pacemaker Implantation
13.  Lupus Nephritis. A Retrospective Analysis of Clinical Presentation and Outcomes from a single center 
Background and Objectives
Lupus nephritis (LN) is an ominous complication of Systemic lupus erythematosus (SLE) and the risk factors for the disease progression are not very well characterized.
Design, Setting, Participants and measurements
In a retrospective study, we evaluated the mode of presentation and outcomes of 163 consecutive patients with biopsy proven LN, who presented to our center between January 1999 and September 2008. Using stepwise logistic regression analysis we assessed risk factors independently associated with response to treatment as well as to progression to end stage renal disease (ESRD) in proliferative LN (PLN).
Ninety percent of our patients belonged to minority population. Among 122 patients with class III and IV LN (PLN), 76 patients received intravenous cyclophosphamide (IVC) and 38 mycophenolate for induction while 34 patients received IVC, and 63 mycophenolate for maintenance. Thirty six (30%) patients with PLN progressed to ESRD and 3 patients died over a mean follow-up of 37.5 months. On multivariate analysis, chronicity index (CI) (p=0.0007) and hypertension (p=0.042) positively correlated with progression to ESRD and death and CI was associated with increased probability of non-response to treatment (p=0.001). Additionally, mycophenolate as maintenance agent was associated with increased likelihood of sustained complete remission and partial remission [p=0.045].
In patients with LN, Hypertension and a high CI are independent risk factors for progression to ESRD or death. Furthermore, a high CI is associated with poor response and mycophenolate as a maintenance agent may improve the response to treatment.
PMCID: PMC3176993  PMID: 21681076
lupus nephritis; outcomes; lupus; SLE; LN
14.  Nicotine Induces Inhibitor of Differentiation-1 in a Src-dependent Pathway Promoting Metastasis and Chemoresistance in Pancreatic Adenocarcinoma1 
Neoplasia (New York, N.Y.)  2012;14(12):1102-1114.
Smoking is a significant risk factor for pancreatic cancer, but the molecular mechanisms by which tobacco smoke components promote the growth and progression of these cancers are not fully understood. While nicotine, the addictive component of tobacco smoke, is not a carcinogen, it has been shown to promote the growth of non-small cell lung and pancreatic cancers in a receptor-dependent fashion. Here, we show that stimulation of pancreatic cancer cells with nicotine concentrations that are within the range of human exposure results in activation of Src kinase, which facilitated the induction of the inhibitor of differentiation-1 (Id1) transcription factor. Depletion of Id1 prevented nicotine-mediated induction of proliferation and invasion of pancreatic cancer cells, indicating that it is a major mediator of nicotine function. Nicotine could promote the growth and metastasis of pancreatic cancers orthotopically implanted into SCID mice; in addition, cells stably expressing a short hairpin RNA for Id1 did not grow or metastasize in response to nicotine. Nicotine could also confer resistance to apoptosis induced by gemcitabine in pancreatic cancer cells in vitro and depletion of Src or Id1 rendered the cells sensitive to gemcitabine. Further, nicotine could effectively inhibit the chemotherapeutic effects of gemcitabine on pancreatic tumors xenografted into mice. Clinical analyses of resected pancreatic cancer specimens demonstrated a statistically significant correlation between Id1 expression and phospho-Src, tumor grade/differentiation, and worsening overall patient survival. These results demonstrate that exposure to tobacco smoke components might promote pancreatic cancer progression, metastasis, and chemoresistance and highlight the role of Id1 in these processes.
PMCID: PMC3540937  PMID: 23308043
15.  Role of PheE15 Gate in Ligand Entry and Nitric Oxide Detoxification Function of Mycobacterium tuberculosis Truncated Hemoglobin N 
PLoS ONE  2012;7(11):e49291.
The truncated hemoglobin N, HbN, of Mycobacterium tuberculosis is endowed with a potent nitric oxide dioxygenase (NOD) activity that allows it to relieve nitrosative stress and enhance in vivo survival of its host. Despite its small size, the protein matrix of HbN hosts a two-branched tunnel, consisting of orthogonal short and long channels, that connects the heme active site to the protein surface. A novel dual-path mechanism has been suggested to drive migration of O2 and NO to the distal heme cavity. While oxygen migrates mainly by the short path, a ligand-induced conformational change regulates opening of the long tunnel branch for NO, via a phenylalanine (PheE15) residue that acts as a gate. Site-directed mutagenesis and molecular simulations have been used to examine the gating role played by PheE15 in modulating the NOD function of HbN. Mutants carrying replacement of PheE15 with alanine, isoleucine, tyrosine and tryptophan have similar O2/CO association kinetics, but display significant reduction in their NOD function. Molecular simulations substantiated that mutation at the PheE15 gate confers significant changes in the long tunnel, and therefore may affect the migration of ligands. These results support the pivotal role of PheE15 gate in modulating the diffusion of NO via the long tunnel branch in the oxygenated protein, and hence the NOD function of HbN.
PMCID: PMC3493545  PMID: 23145144
16.  Is serum retinol binding protein-4: A predictor for diabetes in genetically high risk population? 
Retinol binding protein-4 (BP-4) a new adipocytokine, specifically binds to retinol, through experimental studies, reported its link between obesity and insulin resistance (IR). But till date no studies are available on influence of genetic predisposition of diabetes on RBP-4 expression. Hence, we aimed to study the influence of genetic predisposition of diabetes on the serum RBP-4 and its role in development of IR and diabetes in genetically high risk population.
Materials and Methods:
Healthy non diabetic individuals (age 18 to 22) were grouped into Group I: Control (n = 81), whose parents are non diabetic, non hypertensive and does not have any family history of coronary heart diseases. Group II: (n = 157) with one of their parents diabetic and Group III: (n = 47) with both parents diabetic. In all the participants, we estimated fasting serum RBP-4, insulin and glucose. Homeostasis model for assessment-insulin resistance (HOMA-IR) and homeostasis model for assessment-beta cell dysfunction (HOMA-B) were calculated from fasting serum insulin and glucose levels.
In this study, we observed significantly higher RBP-4 levels 12.71 ± 2.3 in Group-II and 13.25 ± 2 in Group-III, respectively when compared to Group-I 11.4 ± 1.8 (P < 0.01). RBP-4 showed a significantly strong positive correlation with plasma insulin, glucose and HOMA-IR in genetically high risk population (group II and III) P < 0.01. Linear regression analysis revealed a strong positive association of RBP-4 with parental diabetes even after adjusting for BMI, age and sex (OR 1.53, 95% CI 1.089-1.40).
Higher serum RBP-4 and its positive correlation with Insulin, glucose, and HOMA-IR in healthy non diabetic participants of genetically high risk population, indicating its role as predictor for the onset of diabetes in coming future.
PMCID: PMC3702081  PMID: 23833574
Adipocytokines; diabetes; insulin resistance; retinol binding protein-4
17.  EGFR/Src/Akt signaling modulates Sox2 expression and self-renewal of stem-like side-population cells in non-small cell lung cancer 
Molecular Cancer  2012;11:73.
Cancer stem cells are thought to be responsible for the initiation and progression of cancers. In non-small cell lung cancers (NSCLCs), Hoechst 33342 dye effluxing side population (SP) cells are shown to have stem cell like properties. The oncogenic capacity of cancer stem-like cells is in part due to their ability to self-renew; however the mechanistic correlation between oncogenic pathways and self-renewal of cancer stem-like cells has remained elusive. Here we characterized the SP cells at the molecular level and evaluated its ability to generate tumors at the orthotopic site in the lung microenvironment. Further, we investigated if the self-renewal of SP cells is dependent on EGFR mediated signaling.
SP cells were detected and isolated from multiple NSCLC cell lines (H1650, H1975, A549), as well as primary human tumor explants grown in nude mice. SP cells demonstrated stem-like properties including ability to self-renew and grow as spheres; they were able to generate primary and metastatic tumors upon orthotopic implantation into the lung of SCID mice. In vitro study revealed elevated expression of stem cell associated markers like Oct4, Sox2 and Nanog as well as demonstrated intrinsic epithelial to mesenchymal transition features in SP cells. Further, we show that abrogation of EGFR, Src and Akt signaling through pharmacological or genetic inhibitors suppresses the self-renewal growth and expansion of SP-cells and resulted in specific downregulation of Sox2 protein expression. siRNA mediated depletion of Sox2 significantly blocked the SP phenotype as well as its self-renewal capacity; whereas other transcription factors like Oct4 and Nanog played a relatively lesser role in regulating self-renewal. Interestingly, Sox2 was elevated in metastatic foci of human NSCLC samples.
Our findings suggest that Sox2 is a novel target of EGFR-Src-Akt signaling in NSCLCs that modulates self-renewal and expansion of stem-like cells from NSCLC. Therefore, the outcome of the EGFR-Src-Akt targeted therapy may rely upon the expression and function of Sox2 within the NSCLC-CSCs.
PMCID: PMC3497614  PMID: 23009336
Cancer stem-like cells; Side-population cells; Self-renewal; EGFR; Sox2
18.  Regulation of GAD65 expression by SMAR1 and p53 upon Streptozotocin treatment 
BMC Molecular Biology  2012;13:28.
GAD65 (Glutamic acid decarboxylase 65 KDa isoform) is one of the most important auto-antigens involved in Type 1 diabetes induction. Although it serves as one of the first injury markers of β-islets, the mechanisms governing GAD65 expression remain poorly understood. Since the regulation of GAD65 is crucial for the proper functioning of insulin secreting cells, we investigated the stress induced regulation of GAD65 transcription.
The present study shows that SMAR1 regulates GAD65 expression at the transcription level. Using a novel protein-DNA pull-down assay, we show that SMAR1 binding is very specific to GAD65 promoter but not to the other isoform, GAD67. We show that Streptozotocin (STZ) mediated DNA damage leads to upregulation of SMAR1 and p53 expression, resulting in elevated levels of GAD65, in both cell lines as well as mouse β-islets. SMAR1 and p53 act synergistically to up-regulate GAD65 expression upon STZ treatment.
We propose a novel mechanism of GAD65 regulation by synergistic activities of SMAR1 and p53.
PMCID: PMC3459802  PMID: 22978699
SMAR1; Diabetes; GAD65; p53; Streptozotocin
19.  A Novel Five Gene Signature Derived from Stem-Like Side Population Cells Predicts Overall and Recurrence-Free Survival in NSCLC 
PLoS ONE  2012;7(8):e43589.
Gene expression profiling has been used to characterize prognosis in various cancers. Earlier studies had shown that side population cells isolated from Non-Small Cell Lung Cancer (NSCLC) cell lines exhibit cancer stem cell properties. In this study we apply a systems biology approach to gene expression profiling data from cancer stem like cells isolated from lung cancer cell lines to identify novel gene signatures that could predict prognosis. Microarray data from side population (SP) and main population (MP) cells isolated from 4 NSCLC lines (A549, H1650, H460, H1975) were used to examine gene expression profiles associated with stem like properties. Differentially expressed genes that were over or under-expressed at least two fold commonly in all 4 cell lines were identified. We found 354 were upregulated and 126 were downregulated in SP cells compared to MP cells; of these, 89 up and 62 downregulated genes (average 2 fold changes) were used for Principle Component Analysis (PCA) and MetaCore™ pathway analysis. The pathway analysis demonstrated representation of 4 up regulated genes (TOP2A, AURKB, BRRN1, CDK1) in chromosome condensation pathway and 1 down regulated gene FUS in chromosomal translocation. Microarray data was validated using qRT-PCR on the 5 selected genes and all showed robust correlation between microarray and qRT-PCR. Further, we analyzed two independent gene expression datasets that included 360 lung adenocarcinoma patients from NCI Director's Challenge Set for overall survival and 63 samples from Sungkyunkwan University (SKKU) for recurrence free survival. Kaplan-Meier and log-rank test analysis predicted poor survival of patients in both data sets. Our results suggest that genes involved in chromosome condensation are likely related with stem-like properties and might predict survival in lung adenocarcinoma. Our findings highlight a gene signature for effective identification of lung adenocarcinoma patients with poor prognosis and designing more aggressive therapies for such patients.
PMCID: PMC3430700  PMID: 22952714
20.  Nuclear Factor I isoforms regulate gene expression during the differentiation of human neural progenitors to astrocytes 
Stem cells (Dayton, Ohio)  2009;27(5):1173-1181.
Even though astrocytes are critical for both normal brain functions and the development and progression of neuropathological states, including neuroinflammation associated with neurodegenerative diseases, the mechanisms controlling gene expression during astrocyte differentiation are poorly understood. Thus far, several signaling pathways were shown to regulate astrocyte differentiation, including JAK-STAT, BMP-2/Smads, and Notch. More recently, a family of Nuclear Factor-1 (NFI-A, -B, -C, and -X) was implicated in the regulation of vertebral neocortex development, with NFI-A and -B controlling the onset of gliogenesis. Here, we developed an in vitro model of differentiation of stem cells towards neural progenitors and subsequently astrocytes. The transition from stem cells to progenitors was accompanied by an expected change in the expression profile of markers, including Sox-2, Musashi-1, and Oct4. Subsequently, generated astrocytes were characterized by proper morphology, increased glutamate uptake, and marker gene expression. We used this in vitro differentiation model to study the expression and functions of NFIs. Interestingly, stem cells expressed only background levels of NFIs, while differentiation to neural progenitors activated the expression of NFI-A. More importantly, NFI-X expression was induced during the later stages of differentiation towards astrocytes. In addition, NFI-X and -C were required for the expression of GFAP and SPARCL1, which are the markers of astrocytes at the later stages of differentiation. We conclude that an expression program of NFIs is executed during the differentiation of astrocytes, with NFI-X and -C controlling the expression of astrocytic markers at late stages of differentiation.
PMCID: PMC3417285  PMID: 19418463
neural progenitors; astrocytes; differentiation; NFI; GFAP; SPARCL1
21.  Urine VCAM-1 as a marker of renal pathology activity index in lupus nephritis 
Arthritis Research & Therapy  2012;14(4):R164.
Although renal pathology is highly predictive of the disease course in lupus nephritis, it cannot be performed serially because of its invasive nature and associated morbidity. The goal of this study is to investigate whether urinary levels of CXC ligand 16 (CXCL16), monocyte chemotactic protein-1 (MCP-1) or vascular cell adhesion molecule-1 (VCAM-1) in patients with lupus nephritis are predictive of particular features of renal pathology in renal biopsies obtained on the day of urine procurement.
CXCL16, MCP-1, and VCAM-1 levels were measured in urine samples from 74 lupus nephritis patients and 13 healthy volunteers. Of the patients enrolled, 24 patients had a concomitant kidney biopsy performed at the time of urine collection. In addition, patients with other renal diatheses were also included as controls.
All three molecules were elevated in the urine of systemic lupus erythematosus patients, although VCAM-1 (area under curve = 0.92) and MCP-1 (area under curve = 0.87) were best at distinguishing the systemic lupus erythematosus samples from the healthy controls, and were also most strongly associated with clinical disease severity and active renal disease. For patients in whom concurrent renal biopsies had also been performed, urine VCAM-1 exhibited the strongest association with the renal pathology activity index and glomerulonephritis class IV, although it correlated negatively with the chronicity index. Interestingly, urinary VCAM-1 was also elevated in anti-neutrophil cytoplasmic antibodies-associated glomerulonephritis, focal segmental glomerulosclerosis and membranous nephropathy but not in minimal-change disease.
Urinary VCAM-1 emerges as a reliable indicator of the activity:chronicity ratios that mark the underlying renal pathology in lupus nephritis. Since VCAM-1 is involved in the acute phase of inflammation when leukocytic infiltration is ongoing, longitudinal studies are warranted to establish whether tracking urine VCAM-1 levels may help monitor clinical and pathological disease activity over time.
PMCID: PMC3580557  PMID: 22788914
22.  The use of specific anti-growth factor antibodies to abrogate the oncological consequences of transfusion in head & neck squamous cell carcinoma: an in vitro study 
Head & Neck Oncology  2012;4:22.
Perioperative blood transfusion is associated with reduced prognosis in a number of solid malignancies. We investigate its role in a head & neck squamous cell cancer (HNSCC) cell lines. Growth of these cell lines was analogous to endothelial growth. Direct exposure to transfusion products exaggerated this effect. It was logical therefore to assess the effects of anti-endothelial antibodies on this interaction.
Materials and methods
Control (HUVEC) and tumour cell lines were exposed to transfusion products. The pre-incubation of the transfusion product with anti-endothelial growth factors was assessed by a growth assay. Where appropriate cells were pre-incubated for 1 hour with 10 μl of a mixture of 100 μl of each and anti-ligand antibodies, the corresponding blood product supplement was incubated with 10 μl of a mixture of 100 μl each of anti-ligand antibodies 1 hour before supplementation to the appropriate cell line. All results are representative of at least two independent experiments carried out in triplicate.
The antibody did not directly reduce growth in the tumour cell line, however there was a significant reduction (p < 0.001) in tumour cell line vascular mimicry caused by transfusion products pre-incubation with anti-endothelial growth factor antibody. This was found in several other tumours.
Perioperative blood transfusion is associated with reduced prognosis in a number of solid malignancies including HNSCC. However this phenomenon is abrogated by the use of anti-endothelial growth factor antibodies. This suggests that the original effect was mediated by the endothelial growth factor family.
PMCID: PMC3448501  PMID: 22591514
23.  Identification of miRNAs in C. roseus and their potential targets 
Bioinformation  2012;8(2):75-80.
MicroRNAs are small (20-22 nucleotides) none coding, regulatory RNAs, whose pivotal role in gene expression has been associated in number of diseases, therefore prediction of miRNA is an essential yet challenging field. In this study miRNAs of C. roseus are predicted along with their possible target genes. A total of 19,899 ESTs were downloaded from dbEST database and processed and trimmed through SeqClean. Nine sequences were trashed and 31 sequences were trimmed by the program and the resulting sequences were submitted to Repeatmasker and TGICL for clustering and assembly. This contig database was now used to find the putative miRNAs by performing a local BLAST with the miRNAs of B. rapa retrieved from miRBase. The targets were scanned by hybridizing screened ESTs with the UTRs of human using miRanda software. Finally, 7 putative miRNAs were found to hybridize with the various targets of signal transduction and apoptosis that may play significant role in preventing diseases like Leukemia, Arthritis and Alzheimer.
PMCID: PMC3282260  PMID: 22359439
24.  Rb-Raf-1 interaction disruptor RRD-251 induces apoptosis in metastatic melanoma cells and synergizes with dacarbazine 
Molecular cancer therapeutics  2010;9(12):3330-3341.
Metastatic melanoma is an aggressive cancer with very low response rate against conventional chemotherapeutic agents such as dacarbazine (DTIC). Inhibitor of Rb-Raf-1 interaction (RRD-251) was tested against the melanoma cell lines SK-MEL-28, SK-MEL-5 and SK-MEL-2. RRD-251 was found to be a potent inhibitor of melanoma cell proliferation, irrespective of V600E B-Raf mutation status of the cell lines. In a SK-MEL-28 xenograft experiment, RRD-251 exerted a significant suppression of tumor growth compared to vehicle (p=0.003). Similar to in vitro effects, tumors from RRD-251 treated animals showed decreased Rb-Raf-1 interaction in vivo. Growth suppressive effects of RRD-251 were associated with induction of apoptosis as well as a G1 arrest, with an accompanying decrease in S-phase cells. RRD-251 inhibited Rb phosphorylation, and downregulated E2F1 protein levels in these cells. Real-time PCR analysis showed that RRD-251 caused downregulation of cell cycle regulatory genes thymidylate synthase (TS) and cdc6 as well as anti-apoptotic gene Mcl-1. Combinatorial treatment of RRD-251 and DTIC resulted in a significantly higher apoptosis in DTIC resistant cell lines SK-MEL-28 and SK-MEL-5, as revealed by increased Caspase-3 activity and PARP cleavage. Since aberrant Rb/E2F pathway is associated with melanoma progression and resistance to apoptosis, these results suggest that the Rb-Raf-1 inhibitor could be an effective agent for melanoma treatment, either alone or in combination with DTIC.
PMCID: PMC3058238  PMID: 21139044
Rb-E2F pathway; Melanoma; Apoptosis; Cell cycle; Dacarbazine
25.  Small molecule regulators of Rb-E2F pathway as modulators of transcription 
Biochimica et biophysica acta  2010;1799(10-12):788-794.
The retinoblastoma tumor suppressor protein, Rb, plays a major role in the regulation of mammalian cell cycle progression. It has been shown that Rb function is essential for the proper modulation of G1/S transition and inactivation of Rb contributes to deregulated cell proliferation. Rb exerts its cell cycle regulatory functions mainly by targeting the E2F family of transcription factors and Rb has been shown to physically interact with E2Fs1, 2 and 3, repressing their transcriptional activity. Multiple genes involved in DNA synthesis and cell cycle progression are regulated by E2Fs, and Rb prevents their expression by inhibiting E2F activity, inducing growth arrest. It has been established that inactivation of Rb by phosphorylation, mutation, or by the interaction of viral oncoproteins lead to a release of the repression of E2F activity, facilitating cell cycle progression. Rb-mediated repression of E2F activity involves the recruitment of a variety of transcriptional co-repressors and chromatin remodeling proteins, including histone deacetylases, DNA methyl transferases and Brg1/Brm chromatin remodeling proteins. Inactivation of Rb by sequential phosphorylation events during cell cycle progression leads to a dissociation of these co-repressors from Rb, facilitating transcription. It has been found that small molecules that prevent the phosphorylation of Rb prevents the dissociation of certain co-repressors from Rb, especially Brg1, leading to the maintenance of Rb mediated transcriptional repression and cell cycle arrest. Such small molecules have anti-cancer activities and will also act as valuable probes to study chromatin remodeling and transcriptional regulation.
PMCID: PMC2997897  PMID: 20637913
Raf-1; cyclin-dependent kinases; RRD-251; cell cycle arrest; transcriptional repression

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