Aug
12
Mon
2013
Invited Talk: Epigenetic Changes due to DNA Methylation in Human Epithelial Tumors @ Acharya Hall
Aug 12 @ 12:18 pm – 12:39 pm

sathyaK. Satyamoorthy, Ph.D.
Director, Life Sciences Centre, Manipal University, India


Epigenetic Changes due to DNA Methylation in Human Epithelial Tumors

Extensive global hypomethylation in the genome and hypermthylation of selective tumor specific suppressor genes appears to be a hallmark of human cancers.  Data suggests that hypermethylation of promoter region in genes is more closely related to subsequent gene expression; contrary to gene-body DNA methylation.  The intricate balance between these two may contribute to the progressive process of development, differentiation and carcinogenesis.  Epigenetic changes encompass, apart from DNA methylation, chromatin modifications through post-translational changes in histones and control by miRNAs.  At the genome level, effects from these are compounded by copy number variations (CNVs) which may ultimately influence protein functions.    From clinical perspective, changes in DNA methylation occur very early which are reversible and are influenced by environmental factors.  Therefore, these can be potential resource for identifying therapeutic targets as well as biomarkers for early screening of cancer.  Our current efforts in profiling genome wide DNA methylation changes in oral, cervical and breast cancers through DNA methylation microarray analysis has revealed number of alterations critical for survival, progression and metastatic behavior of tumors.  Bioinformatics and functional analysis revealed several key regulatory molecules controlled by DNA methylation and suggests that DNA methylation changes in several CpG islands appear to co-segregate in the regions of miRNAs as well as in the CNVs.  We have validated the signatures for methylation of CpG islands through bisufite sequencing for essential genes in clinical samples and have undertaken transcriptional and functional analysis in tumor cell lines.    These results will be presented.

Aug
13
Tue
2013
Invited Talk: Regulation of the MHC complex and HLA solubilisation by the Flavivirus, Japanese Encephalitis Virus @ Acharya Hall
Aug 13 @ 12:13 pm – 12:40 pm

ManjunathR. Manjunath, Ph.D.
Associate Professor, Dept of Biochemistry, Indian Institute of Science, Bengaluru, India


REGULATION OF THE MHC COMPLEX AND HLA SOLUBILISATION BY THE FLAVIVIRUS, JAPANESE ENCEPHALITIS VIRUS

Viral encephalitis caused by Japanese encephalitis virus (JEV) and West Nile Virus (WNV) is a mosquito-borne disease that is prevalent in different parts of India and other parts of South East Asia. JEV is a positive single stranded RNA virus that belongs to the Flavivirus genus of the family Flaviviridae. The genome of JEV is about 11 kb long and codes for a polyprotein which is cleaved by both host and viral encoded proteases to form 3 structural and 7 non-structural proteins. It is a neurotropic virus which infects the central nervous system (CNS) and causes death predominantly in newborn children and young adults. JEV follows a zoonotic life-cycle involving mosquitoes and vertebrate, chiefly pigs and ardeid birds, as amplifying hosts. Humans are infected when bitten by an infected mosquito and are dead end hosts. Its structural, pathological, immunological and epidemiological aspects have been well studied. After entry into the host following a mosquito bite, JEV infection leads to acute peripheral neutrophil leucocytosis in the brain and leads to elevated levels of type I interferon, macrophage-derived chemotactic factor, RANTES,TNF-α and IL-8 in the serum and cerebrospinal fluid.

Major Histocompatibility Complex (MHC) molecules play a very important role in adaptive immune responses. Along with various classical MHC class I molecules, other non-classical MHC class I molecules play an important role in modulating innate immune responses. Our lab has shown the activation of cytotoxic T-cells (CTLs) during JEV infection and CTLs recognize non-self peptides presented on MHC molecules and provide protection by eliminating infected cells. However, along with proinflammatory cytokines such as TNFα, they may also cause immunopathology within the JEV infected brain. Both JEV and WNV, another related flavivirus have been shown to increase MHC class I expression. Infection of human foreskin fibroblast cells (HFF) by WNV results in upregulation of HLA expression. Data from our lab has also shown that JEV infection upregulates classical as well as nonclassical (class Ib) MHC antigen expression on the surface of primary mouse brain astrocytes and mouse embryonic fibroblasts.

There are no reports that have discussed the expression of these molecules on other cells like endothelial and astrocyte that play an important role in viral invasion in humans. We have studied the expression of human classical class I molecules HLA-A, -B, -C and the non-classical HLA molecules, HLA-E as well as HLA-F in immortalized human brain microvascular endothelial cells (HBMEC), human endothelial cell line (ECV304), human glioblastoma cell line (U87MG) and human foreskin fibroblast cells (HFF). Nonclassical MHC molecules such as mouse Qa-1b and its human homologue, HLA-E have been shown to be the ligand for the inhibitory NK receptor, NKG2A/CD94 and may bridge innate and adaptive immune responses. We show that JEV infection of HBMEC and ECV 304 cells upregulates the expression of HLA-A, and –B antigens as well as HLA-E and HLA-F. Increased expression of total HLA-E upon JEV infection was also observed in other human cell lines as well like, human amniotic epithelial cells, AV-3, FL and WISH cells. Further, we show for the first time that soluble HLA-E (sHLA-E) was released from infected ECV and HBMECs. In contrast, HFF cells showed only upregulation of cell-surface HLA-E expression while U87MG, a human glioblastoma cell line neither showed any cell-surface induction nor its solubilization. This shedding of sHLA-E was found to be dependent on matrix metalloproteinase (MMP) and an important MMP, MMP-9 was upregulated during JEV infection. Treatment with IFNγ resulted in the shedding of sHLA-E from ECV as well as U87MG but not from HFF cells. Also, sHLA-E was shed upon treatment with IFNβ and both IFNβ and TNFα, when present together caused an additive increase in the shedding of sHLA-E. HLA-E is an inhibitory ligand for CD94/NKG2A receptor of Natural Killer cells. Thus, MMP mediated solubilization of HLA-E from infected endothelial cells may have important implications in JEV pathogenesis including its ability to compromise the blood brain barrier.

Manjunath (2)

Invited Talk: The system of PAS proteins (HIF and AhR) as an interface between environment and skin homeostasis @ Acharya Hall
Aug 13 @ 2:33 pm – 2:50 pm

andreyAndrey Panteleyev, Ph.D.
Vice Chair, Division of Molecular Biology, NBICS Centre-Kurchatov Institute, Moscow, Russia


The system of PAS proteins (HIF and AhR) as an interface between environment and skin homeostasis

Regulation of normal skin functions as well as etiology of many skin diseases are both tightly linked to the environmental impact. Nevertheless, molecular aspects of skin-environment communication and mechanisms coordinating skin response to a plurality of environmental stressors remain poorly understood.

Our studies along with the work of other groups have identified the family of PAS dimeric transcription factors as an essential sensory and regulatory component of communication between skin and the environment. This protein family comprises a number of hypoxia-induced factors (HIF-alpha proteins), aryl hydrocarbon receptor (AhR), AhR nuclear translocator (ARNT), and several proteins implicated in control of rhythmic processes (Clock, Period, and Bmal proteins). Together, various PAS proteins (and first of all ARNT – as the central dimerization partner in the family) control such pivotal aspects of cell physiology as drug/xenobiotic metabolism, hypoxic and UV light response, ROS activity, pathogen defense, overall energy balance and breathing pathways.

In his presentation Dr. Panteleyev will focus on the role of ARNT activity and local hypoxia in control of keratinocyte differentiation and cornification. His recent work revealed that ARNT negatively regulates expression of late differentiation genes through modulation of amphiregulin expression and downstream alterations in activity of EGFR pathway. All these effects are highly dependent on epigenetic mechanisms such as histone deacetylation. Characterisation of hypoxia as a key microenvironmental factor in the skin and the role of HIF pathway in control of dermal vasculature and epidermal functions is another major focus of Dr. Panteleyev’s presentation.

In general, the studies of Dr. Panteleyev’s laboratory provide an insight into the PAS-dependent maintenance of skin homeostasis and point to the potential role of these proteins in pathogenesis of environmentally-modulated skin diseases such as barrier defects, desquamation abnormalities, psoriasis, etc.

 

Delegate Talk: Inflammation Induced Epigenetic Changes in Endothelial Cells: Role in Vascular Insulin Resistance @ Acharya Hall
Aug 13 @ 6:39 pm – 6:49 pm
Delegate Talk: Inflammation Induced Epigenetic Changes in Endothelial Cells: Role in Vascular Insulin Resistance @ Acharya Hall | Vallikavu | Kerala | India

Aswath Balakrishnan, Kapaettu Satyamoorthy and Manjunath B Joshi


Introduction
Insulin resistance is a hall mark of metabolic disorders such as diabetes. Reduced insulin response in vasculature leads to disruption of IR/Akt/eNOS signaling pathway resulting in vasoconstriction and subsequently to cardiovascular diseases. Recent studies have demonstrated that inflammatory regulator interleukin-6 (IL-6), as one of the potential mediators that can link chronic inflammation with insulin resistance. Accumulating evidences suggest a significant role of epigenetic mechanisms such as DNA methylation in progression of metabolic disorders. Hence the present study aimed to understand the role of epigenetic mechanisms involved during IL-6 induced vascular insulin resistance and its consequences in cardiovascular diseases.

Materials and Methods
Human umbilical vein endothelial cells (HUVEC) and Human dermal microvascular endothelial cells (HDMEC) were used for this study. Endothelial cells were treated in presence or absence of IL-6 (20ng/ml) for 36 hours and followed by insulin (100nM) stimulation for 15 minutes. Using immunoblotting, cell lysates were stained for phosphor- and total Akt levels to measure insulin resistance. To investigate changes in DNA methylation, cells were treated with or without neutrophil conditioned medium (NCM) as a physiological source of inflammation or IL-6 (at various concentrations) for 36 hours. Genomic DNA was processed for HPLC analysis for methyl cytosine content and cell lysates were analyzed for DNMT1 (DNA (cytosine-5)-methyltransferase 1) and DNMT3A (DNA (cytosine-5)-methyltransferase 3A) levels using immunoblotting.

Results
Endothelial cells stimulated with insulin exhibited an increase in phosphorylation of Aktser 473 in serum free conditions but such insulin response was not observed in cells treated with IL-6, suggesting chronic exposure of endothelial cells to IL-6 leads to insulin resistance. HPLC analysis for global DNA methylation resulted in decreased levels of 5-methyl cytosine in cells treated with pro-inflammatory molecules (both by NCM and IL-6) as compared to untreated controls. Subsequently, analysis in cells treated with IL-6 showed a significant decrease in DNMT1 levels but not in DNMT3A. Other pro-inflammatory marker such as TNF-α did not exhibit such changes.

Conclusion
Our study suggests: a) Chronic treatment of endothelial cells with IL-6 results in insulin resistance b) Neutrophil conditioned medium and IL-6 decreases methyl cytosine levels c) DNMT1 but not DNMT3a levels are reduced in cells treated with IL-6.

Aug
14
Wed
2013
Invited Talk: A draft map of the human proteome @ Amriteshwari Hall
Aug 14 @ 10:42 am – 11:30 am

akhileshAkhilesh Pandey, Ph.D.
Professor, Johns Hopkins University School of Medicine, Baltimore, USA


A draft map of the human proteome

We have generated a draft map of the human proteome through a systematic and comprehensive analysis of normal human adult tissues, fetal tissues and hematopoietic cells as an India-US initiative. This unique dataset was generated from 30 histologically normal adult tissues, fetal tissues and purified primary hematopoietic cells that were analyzed at high resolution in the MS mode and by HCD fragmentation in the MS/MS mode on LTQ-Orbitrap Velos/Elite mass spectrometers. This dataset was searched against a 6-frame translation of the human genome and RNA-Seq transcripts in addition to standard protein databases. In addition to confirming a large majority (>16,000) of the annotated protein-coding genes in humans, we obtained novel information at multiple levels: novel protein-coding genes, unannotated exons, novel splice sites, proof of translation of pseudogenes (i.e. genes incorrectly annotated as pseudogenes), fused genes, SNPs encoded in proteins and novel N-termini to name a few. Many proteins identified in this study were identified by proteomic methods for the first time (e.g. hypothetical proteins or proteins annotated based solely on their chromosomal location). We have generated a catalog of proteins that show a more tissue-restricted pattern of expression, which should serve as the basis for pursuing biomarkers for diseases pertaining to specific organs. This study also provides one of the largest sets of proteotypic peptides for use in developing MRM assays for human proteins. Identification of several novel protein-coding regions in the human genome underscores the importance of systematic characterization of the human proteome and accurate annotation of protein-coding genes. This comprehensive dataset will complement other global HUPO initiatives using antibody-based as well as MRM mass spectrometry-based strategies. Finally, we believe that this dataset will become a reference set for use as a spectral library as well as for interesting interrogations pertaining to biomedical as well as bioinformatics questions.

Akhilesh (2)