Category Archives: Clinical Studies

Nanobodies: Tools for ChIP and Epigenetics targets?

Posted on September 17, 2012 by Nicole Kelesoglu

So I was exploring the wide world of epigenetics research on the internet as we often do at E3, when I came upon this paper. T. Nguyen Duc et al. Nanobody-Based Chromatin Immunoprecipitation Methods Mol Biol. 2012;911:491-505. Now this ChIP protocol isolates a transcription factor from the lysate of the hyperther- moacidophilic archaeon,  Sulfolobus solfataricus. Not as interesting for most of us as say, exploring the histone code in breast cancer cells. However what about this business of using of nanobodies rather than polyclonal antibodies for ChIP? What are nanbodies (Nab)? These are single heavy chain only antibodies, produced by llamas or camels immunized with the antigen target. Their Vhh domain is subcloned so that nanobodies can be produced cheaply, … Continue reading →

Posted in Applications, Clinical Studies, Imaging, chIP | Tagged , , | Leave a comment

Will the Long History of Breast Cancer Research Culminate with Epigenetics Based Personalized Medicine?

Posted on July 13, 2012 by Nicole Kelesoglu

In the first century A.D, Roman family Greek slaves were surgeons. Celsus wrote an encyclopedic describing their methods in latin, laying a foundation for scientific literature on medical practice and surgery. The idea of diagnosis became paramount at this time, requiring close study and record keeping of injury and disease symptoms. It was understood that some breast cancers could be extirpated with breast removal. In the 19th century, after anesthesia and antisepsis had been established, (thank heavens!) a Johns Hopkins Hospital surgeon named William Stewart Halsted introduced, perhaps, the greatest advance to breast cancer treatment. The radical mastectomy. Throughout beast cancer history, the best prognosis post treatment, seemed to be based on early stage diagnosis. (1.) Today we have exceptional … Continue reading →

Posted in Biomarkers, Breast cancer, Clinical Studies, DNA Methylation, Genomewide Methylation Profiling, History & Trends, Microarray, Personalized Medicine, Transcriptome | Tagged , , , | 1 Comment

“Divergent Epigenetic Landscapes” of AML viewed through RRBS

Posted on June 29, 2012 by Nicole Kelesoglu

Acute myeloid leukemia (AML) is most common in older adults. However, it is rarely cured by standard chemotherapy alone in older patients. According to NCI, it is critical that complete remission occurs, or there is no survival benefit. There are many clinically active therapies, including epigenetic drugs. A big translational research goal is to develop effective therapeutic strategies to demonstrate how and when oncologists should use these therapies.  A clinical combinational treatment regime could be guided in part by genome-wide methylation profiling. Genes in CpG islands and their promoters have established aberrant methylation patterns in cancers.  Perhaps also genome-wide methylation will help reveal new mechanistic details leading to new drug discoveries. Reduced representation bisulfite sequencing (RRBS) was introduced by scientists … Continue reading →

Posted in Biomarkers, Clinical Studies, DNA Methylation, Genomewide Methylation Profiling, Leukemia, Next Gen Sequencing, Oncology, Reduced representation bisulfite sequencing | Tagged , , , , , | Leave a comment

Will Epigenetics Help Overcome Cisplatin Resistance in Ovarian Cancers?

Posted on January 10, 2012 by Nicole Kelesoglu

Hello Epiexperts! There are a couple recent open access papers to point out to you this week. Both relate to ovarian cancer progression and desensitization to the chemotherapy, Cisplatin. Cisplatin resistance is the primary obstacle to surviving ovarian cancer. These cancers are rare thankfully, but the 5 year survival rate is only 15-20%. Epigentics researchers are actively engaged in confronting this challenging disease. There are several Phase II clinical trials in progress for individual and combinational therapies using DNA methylation inhibitors and histone deacetlase (HDAC) inhibitors. Until those epigenetics based therapy trial results are available, as things stand, the current outlook is bleak. Please see this piece by Donna Trussell, in the Washington Post. She writes from her personal perspective … Continue reading →

Posted in Bioinformatics, Biomarkers, Clinical Studies, DNA Methylation, Databases, Genetics, Genomewide Methylation Profiling, History & Trends, Methylated DNA Capture, Next Gen Sequencing, Oncology, Real-time PCR, Sodium Bisulfite Sequencing, Transcriptome microarray | Tagged , , , , | Leave a comment

Choose your Weapon! No Shortage of Trials for HDAC Inhibitor Drugs

Posted on September 30, 2011 by Nicole Kelesoglu

In India, Hindus call a three-pronged spear a trishul. The prongs symbolize nature, in its creative, preservative, and destructive states. Cancer research aims are akin to those natural states. Rapid cellular division is the creative state, for which chemotherapy and radiation, (or most recently synchronous chemoradiation), are used to kill the rapidly dividing cells. Angiogenesis meets a preservative requirement, bringing blood flow to tumors. Metastasis is a resulting destructive oncogenic state. Oncologist clinicians require an evolving therapy plan – a plan to wield like a specialized weapon to hit moving targets. Many clinical trials are now involving multiple drugs in synchronized or sequenced treatments. They hope to overcome obstacles like drug resistance…to promote synergistic drug actions…all to achieve improved patient … Continue reading →

Posted in Clinical Studies, Histone Modifications, Histones, History & Trends, Oncology, Pharmacology / Toxicology, Translational Research | Tagged , , | Leave a comment

Cellular Trash to Treasure – Exosomes

Posted on May 27, 2011 by Nicole Kelesoglu

Blood-Based Gene Expression Signatures in Non-Small Cell Lung Cancer.Clin Cancer Res. 2011 May 15 Thomas Zander, Andrea Hofmann, Andrea Staratschek-Jox, et al has been big in the international news recently. The authors are aiming to develop an RNA-stabilized blood test for asymptomatic lung cancer, using gene expression profiles, from what they believe to be immune effector blood cells – not cancer cells. The prognosis for lung cancer once you already have symptoms, is terrible. Their work is great news because this kind of non-invasive diagnostic test is desperately needed. However, there is another promising approach to transcriptome signature diagnostics to be aware of…Microvesicle shuttled RNA. Microvesicles, (MV), were once considered just cellular debris. We now know that blood, and many … Continue reading →

Posted in Applications, Biomarkers, Clinical Studies, Diagnostics, Flow Cytometry, Genetics, History & Trends, Next Gen Sequencing, Oncology, Pathology, Real-time PCR, Virology, microRNA, siRNA | Leave a comment

Targeting an Epigenetic Biomarker for Fragile X

Posted on March 7, 2011 by Nicole Kelesoglu

Epigenetics is bringing a needed perspective to a important public health issue. Many people with Fragile X have autism, or symptoms of autism. The condition is associated with learning, physical, social and emotional, speech and language, and sensory problems. Applied Behavioral Analysis treatment (ABA) is a set of methods which can be used to target and modify problematic symptoms and behaviors. It is effective – but also an arduous task in treating the symptoms of autism. Wouldn’t it be great if there was an epigenetic drug treatment which could be used with ABA producing an enhanced, synergistic effect? Neuroscience experts call Fragile X syndrome a disease of synaptic plasticity. Neuropychologists have already determined that early intervention produces the most effective … Continue reading →

Posted in Autism, Clinical Studies, Neuroscience, Translational Research, X-linked | Tagged , , , , , , | 1 Comment