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Archive for the ‘Personalized and Precision Medicine & Genomic Research’ Category

Loss of Normal Growth Regulation

Curator: Larry H Bernstein, MD, FCAP

 

 

Reposted from Dr. Melvin Crasso

Cells from most major human solid and hematologic malignancies exhibit abnormal cellular localization of a variety of oncogenic proteins, tumor suppressor proteins, and cell cycle regulators (Cronshaw et al. 2004, Falini et al 2006). For example, certain p53 mutations lead to localization in the cytoplasm rather than in the nucleus. This results in the loss of normal growth regulation, despite intact tumor suppressor function. In other tumors, wild-type p53 is sequestered in the cytoplasm or rapidly degraded, again leading to loss of its suppressor function. Restoration of appropriate nuclear localization of functional p53 protein can normalize some properties of neoplastic cells (Cai et al. 2008; Hoshino et al. 2008; Lain et al. 1999a; Lain et al. 1999b; Smart et al. 1999), can restore sensitivity of cancer cells to DNA damaging agents (Cai et al. 2008), and can lead to regression of established tumors (Sharpless & DePinho 2007, Xue et al. 2007). Similar data have been obtained for other tumor suppressor proteins such as forkhead (Turner and Sullivan 2008) and c-Abl (Vignari and Wang 2001). In addition, abnormal localization of several tumor suppressor and growth regulatory proteins may be involved in the pathogenesis of autoimmune diseases (Davis 2007, Nakahara 2009). CRMl inhibition may provide particularly interesting utility in familial cancer syndromes (e.g. , Li-Fraumeni Syndrome due to loss of one p53 allele,

BRCA1 or 2 cancer syndromes), where specific tumor suppressor proteins (TSP) are deleted or dysfunctional and where increasing TSP levels by systemic (or local) administration of CRMl inhibitors could help restore normal tumor suppressor function. Specific proteins and R As are carried into and out of the nucleus by specialized transport molecules, which are classified as importins if they transport molecules into the nucleus, and exportins if they transport molecules out of the nucleus (Terry et al. 2007;

Sorokin et al. 2007). Proteins that are transported into or out of the nucleus contain nuclear import/localization (NLS) or export (NES) sequences that allow them to interact with the relevant transporters. Chromosomal Region Maintenance 1 (Crml or CRM1), which is also called exportin-1 or Xpol, is a major exportin.

Overexpression of Crml has been reported in several tumors, including human ovarian cancer (Noske et al. 2008), cervical cancer (van der Watt et al. 2009), pancreatic cancer (Huang et al. 2009), hepatocellular carcinoma (Pascale et al. 2005) and osteosarcoma (Yao et al. 2009) and is independently correlated with poor clinical outcomes in these tumor types.

Inhibition of Crml blocks the exodus of tumor suppressor proteins and/or growth regulators such as p53, c-Abl, p21, p27, pRB, BRCA1, IkB, ICp27, E2F4, KLF5, YAP1, ZAP, KLF5, HDAC4, HDAC5 or forkhead proteins (e.g., FOX03a) from the nucleus that are associated with gene expression, cell proliferation, angiogenesis and epigenetics. Crml inhibitors have been shown to induce apoptosis in cancer cells even in the presence of activating oncogenic or growth stimulating signals, while sparing normal (untransformed) cells. Most studies of Crml inhibition have utilized the natural product Crml inhibitor Leptomycin B (LMB). LMB itself is highly toxic to neoplastic cells, but poorly tolerated with marked gastrointestinal toxicity in animals (Roberts et al. 1986) and humans (Newlands et al. 1996). Derivatization of LMB to improve drug-like properties leads to compounds that retain antitumor activity and are better tolerated in animal tumor models (Yang et al. 2007, Yang et al. 2008, Mutka et al. 2009). Therefore, nuclear export inhibitors could have beneficial effects in neoplastic and other proliferative disorders.

In addition to tumor suppressor proteins, Crml also exports several key proteins that are involved in many inflammatory processes. These include IkB, NF-kB, Cox-2, RXRa, Commdl, HIFl, HMGBl, FOXO, FOXP and others. The nuclear factor kappa B (NF-kB/rel) family of transcriptional activators, named for the discovery that it drives immunoglobulin kappa gene expression, regulate the mRNA expression of variety of genes involved in inflammation, proliferation, immunity and cell survival. Under basal conditions, a protein inhibitor of NF-kB, called IkB, binds to NF-kB in the nucleus and the complex IkB-NF-kB renders the NF-kB transcriptional function inactive. In response to inflammatory stimuli, IkB dissociates from the IkB-NF-kB complex, which releases NF-kB and unmasks its potent transcriptional activity. Many signals that activate NF-kB do so by targeting IkB for proteolysis (phosphorylation of IkB renders it “marked” for ubiquitination and then proteolysis). The nuclear IkBa-NF-kB complex can be exported to the cytoplasm by Crml where it dissociates and NF-kB can be reactivated. Ubiquitinated IkB may also dissociate from the NF-kB complex, restoring NF-kB transcriptional activity. Inhibition of Crml induced export in human neutrophils and macrophage like cells (U937) by LMB not only results in accumulation of transcriptionally inactive, nuclear IkBa-NF-kB complex but also prevents the initial activation of NF-kB even upon cell stimulation (Ghosh 2008, Huang 2000). In a different study, treatment with LMB inhibited IL-Ιβ induced NF-kB DNA binding (the first step in NF-kB transcriptional activation), IL-8 expression and intercellular adhesion molecule expression in pulmonary microvascular endothelial cells (Walsh 2008). COMMDl is another nuclear inhibitor of both NF-kB and hypoxia-inducible factor 1 (HIFl) transcriptional activity. Blocking the nuclear export of COMMDl by inhibiting Crml results in increased inhibition of NF-kB and HIFl transcriptional activity (Muller 2009).

Crml also mediates retinoid X receptor a (RXRa) transport. RXRa is highly expressed in the liver and plays a central role in regulating bile acid, cholesterol, fatty acid, steroid and xenobiotic metabolism and homeostasis. During liver inflammation, nuclear RXRa levels are significantly reduced, mainly due to inflammation-mediated nuclear export of RXRa by Crml . LMB is able to prevent IL-Ιβ induced cytoplasmic increase in RXRa levels in human liver derived cells (Zimmerman 2006).

The role of Crml -mediated nuclear export in NF-kB, HIF-1 and RXRa signalling suggests that blocking nuclear export can be potentially beneficial in many inflammatory processes across multiple tissues and organs including the vasculature (vasculitis, arteritis, polymyalgia rheumatic, atherosclerosis), dermatologic (see below), rheumatologic

(rheumatoid and related arthritis, psoriatic arthritis, spondyloarthropathies, crystal arthropathies, systemic lupus erythematosus, mixed connective tissue disease, myositis syndromes, dermatomyositis, inclusion body myositis, undifferentiated connective tissue disease, Sjogren’s syndrome, scleroderma and overlap syndromes, etc.).

CRM1 inhibition affects gene expression by inhibiting/activating a series of transcription factors like ICp27, E2F4, KLF5, YAP1, and ZAP.

Crml inhibition has potential therapeutic effects across many dermatologic syndromes including inflammatory dermatoses (atopy, allergic dermatitis, chemical dermatitis, psoriasis), sun-damage (ultraviolet (UV) damage), and infections. CRMl inhibition, best studied with LMB, showed minimal effects on normal keratinocytes, and exerted anti-inflammatory activity on keratinocytes subjected to UV, TNFa, or other inflammatory stimuli (Kobayashi & Shinkai 2005, Kannan & Jaiswal 2006). Crml inhibition also upregulates NRF2 (nuclear factor erythroid-related factor 2) activity, which protects keratinocytes (Schafer et al. 2010, Kannan & Jaiswal 2006) and other cell types (Wang et al. 2009) from oxidative damage. LMB induces apoptosis in keratinocytes infected with oncogenic human papillomavirus (HPV) strains such as HPV 16, but not in uninfected keratinocytes (Jolly et al. 2009).

Crml also mediates the transport of key neuroprotectant proteins that may be useful in neurodegenerative diseases including Parkinson’s disease (PD), Alzheimer’s disease, and amyotrophic lateral sclerosis (ALS). For example, by (1) forcing nuclear retention of key neuroprotective regulators such as NRF2 (Wang 2009), FOXA2 (Kittappa et al. 2007), parking in neuronal cells, and/or (2) inhibiting NFKB transcriptional activity by sequestering IKB to the nucleus in glial cells, Crml inhibition could slow or prevent neuronal cell death found in these disorders. There is also evidence linking abnormal glial cell proliferation to abnormalities in CRMl levels or CRMl function (Shen 2008).

Intact nuclear export, primarily mediated through CRMl, is also required for the intact maturation of many viruses. Viruses where nuclear export, and/or CRMl itself, has been implicated in their lifecycle include human immunodeficiency virus (HIV), adenovirus, simian retrovirus type 1, Borna disease virus, influenza (usual strains as well as H1N1 and avian H5N1 strains), hepatitis B (HBV) and C (HCV) viruses, human papillomavirus (HPV), respiratory syncytial virus (RSV), Dungee, Severe Acute Respiratory Syndrome coronavirus, yellow fever virus, West Nile virus, herpes simplex virus (HSV), cytomegalovirus (CMV), and Merkel cell polyomavirus (MCV). (Bhuvanakantham 2010, Cohen 2010, Whittaker 1998). It is anticipated that additional viral infections reliant on intact nuclear export will be uncovered in the future.

The HIV-1 Rev protein, which traffics through nucleolus and shuttles between the nucleus and cytoplasm, facilitates export of unspliced and singly spliced HIV transcripts containing Rev Response Elements (RRE) RNA by the CRMl export pathway. Inhibition of Rev-mediated RNA transport using CRMl inhibitors such as LMBor PKF050-638 can arrest the HIV-1 transcriptional process, inhibit the production of new HIV-1 virions, and thereby reduce HIV-1 levels (Pollard 1998, Daelemans 2002). Dengue virus (DENV) is the causative agent of the common arthropod-borne viral disease, Dengue fever (DF), and its more severe and potentially deadly Dengue hemorrhagic fever (DHF). DHF appears to be the result of an over exuberant inflammatory response to DENV. NS5 is the largest and most conserved protein of DENV. CRMl regulates the transport of NS5 from the nucleus to the cytoplasm, where most of the NS5 functions are mediated. Inhibition of CRMl -mediated export of NS5 results in altered kinetics of virus production and reduces induction of the inflammatory chemokine interleukin-8 (IL-8), presenting a new avenue for the treatment of diseases caused by DENV and other medically important flaviviruses including hepatitis C virus (Rawlinson 2009).

Other virus-encoded RNA-binding proteins that use CRMl to exit the nucleus include the HSV type 1 tegument protein (VP 13/14, or hUL47), human CMV protein pp65, the SARS Coronavirus ORF 3b Protein, and the RSV matrix (M) protein (Williams 2008, Sanchez 2007, Freundt 2009, Ghildyal 2009).

Interestingly, many of these viruses are associated with specific types of human cancer including hepatocellular carcinoma (HCC) due to chronic HBV or HCV infection, cervical cancer due to HPV, and Merkel cell carcinoma associated with MCV. CRMl inhibitors could therefore have beneficial effects on both the viral infectious process as well as on the process of neoplastic transformation due to these viruses.

CRMl controls the nuclear localization and therefore activity of multiple DNA metabolizing enzymes including histone deacetylases (HDAC), histone acetyltransferases (HAT), and histone methyltransferases (HMT). Suppression of cardiomyocyte hypertrophy with irreversible CRMl inhibitors has been demonstrated and is believed to be linked to nuclear retention (and activation) of HDAC 5, an enzyme known to suppress a hypertrophic genetic program (Monovich et al. 2009). Thus, CRMl inhibition may have beneficial effects in hypertrophic syndromes, including certain forms of congestive heart failure and hypertrophic cardiomyopathies.

 

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Larry H Bernstein, MD, FCAP, Curator

http://pharmaceuticalintelligence.com/6/7/2014/Health benefit of anthocyanins from apples and berries noted for men

After significant studies have been completed, particularly on a relationship between anthocyanins consumption and decreasd risk of Parkinson’s Disease in men, it is unclear why a comparable effect is not seen in women.  This would lead one to ask questions about predominant time course of development in relationship to androgen activity.  Pre- and postmenopausal status would seem to make no difference. It is reported that the anthocyanins cross the blood brain barrier.  There are other questions that need to be raised.  There is a decline in the production of transthyretin by the choroid plexus in the elderly – not sex related – with an elevation of homocysteine that is reciprocal to decline in transthyretin-RBP complex, that is related to AD.  This is mediated by cystathionine-beta synthase, and involves matrix metalloproteinases.  A mechanism for Parkinson’s Disease has been postulated to be related to Parkin gene expression, but how does this work, and why do we see the sex assymetry?

Eating flavonoids protects men against Parkinson’s disease

General DietMissed – Medical Breakthroughs • Tags: AnthocyaninFlavonoidHarvard University,HealthNeurologyParkinsonParkinson DiseaseUniversity of East Anglia

http://healthresearchreport.me/       07 Apr 2012

Men who eat flavonoid-rich foods such as berries, tea, apples and red wine significantly reduce their risk of developing Parkinson’s disease, according to new research by Harvard University and the University of East Anglia (UEA).

Published today in the journal Neurology ®, the findings add to the growing body of evidence that regular consumption of some flavonoids can have a marked effect on human health. Recent studies have shown that these compounds can offer protection against a wide range of diseases including heart disease, hypertension, some cancers and dementia.

This latest study is the first study in humans to show that flavonoids can protect neurons against diseases of the brain such as Parkinson’s.

Around 130,000 men and women took part in the research. More than 800 had developed Parkinson’s disease within 20 years of follow-up. After a detailed analysis of their diets and adjusting for age and lifestyle, male participants who ate the most flavonoids were shown to be 40 per cent less likely to develop the disease than those who ate the least. No similar link was found for total flavonoid intake in women.

The research was led by Dr Xiang Gao of Harvard School of Public Health in collaboration with Prof Aedin Cassidy of the Department of Nutrition, Norwich Medical School at UEA.

“These exciting findings provide further confirmation that regular consumption of flavonoids can have potential health benefits,” said Prof Cassidy.

“This is the first study in humans to look at the associations between the range of flavonoids in the diet and the risk of developing Parkinson’s disease and our findings suggest that a sub-class of flavonoids called anthocyanins may have neuroprotective effects.”

Prof Gao said: “Interestingly, anthocyanins and berry fruits, which are rich in anthocyanins, seem to be associated with a lower risk of Parkinson’s disease in pooled analyses. Participants who consumed one or more portions of berry fruits each week were around 25 per cent less likely to develop Parkinson’s disease, relative to those who did not eat berry fruits. Given the other potential health effects of berry fruits, such as lowering risk of hypertension as reported in our previous studies, it is good to regularly add these fruits to your diet.”

Flavonoids are a group of naturally occurring, bioactive compunds found in many plant-based foods and drinks. In this study the main protective effect was from higher intake of anthocyanins, which are present in berries and other fruits and vegetables including aubergines, blackcurrants and blackberries. Those who consumed the most anthocyanins had a 24 per cent reduction in risk of developing Parkinson’s disease and strawberries and blueberries were the top two sources in the US diet.

The findings must now be confirmed by other large epidemiological studies and clinical trials.

Parkinson’s disease is a progresssive neurological condition affecting one in 500 people, which equates to 127,000 people in the UK. There are few effective drug therapies available.  Dr Kieran Breen, director of research at Parkinson’s UK said: “This study raises lots of interesting questions about how diet may influence our risk of Parkinson’s…   there are still a lot of questions to answer and much more research to do before we really know how important diet might be for people with Parkinson’s.”

 

Eating berries may lower risk of Parkinson’s

Missed – Medical Breakthroughs • Tags: BerryDoctor of PhilosophyFlavonoidParkinson,Parkinson DiseaseXiang Gao

http://healthresearchreport.me/    Public release date: 13-Feb-2011

ST. PAUL, Minn. –New research shows men and women who regularly eat berries may have a lower risk of developing Parkinson’s disease, while men may also further lower their risk by regularly eating apples, oranges and other sources rich in dietary components called flavonoids. The study was released today and will be presented at the American Academy of Neurology’s 63rd Annual Meeting in Honolulu April 9 to April 16, 2011.

Flavonoids are found in plants and fruits and are also known collectively as vitamin P and citrin. They can also be found in berry fruits, chocolate, and citrus fruits such as grapefruit.

The study involved 49,281 men and 80,336 women. Researchers gave participants questionnaires and used a database to calculate intake amount of flavonoids. They then analyzed the association between flavonoid intakes and risk of developing Parkinson’s disease. They also analyzed consumption of five major sources of foods rich in flavonoids: tea, berries, apples, red wine and oranges or orange juice. The participants were followed for 20 to 22 years.

During that time, 805 people developed Parkinson’s disease. In men, the top 20 percent who consumed the most flavonoids were about 40 percent less likely to develop Parkinson’s disease than the bottom 20 percent of male participants who consumed the least amount of flavonoids. In women, there was no relationship between overall flavonoid consumption and developing Parkinson’s disease. However, when sub-classes of flavonoids were examined, regular consumption of anthocyanins, which are mainly obtained from berries, were found to be associated with a lower risk of Parkinson’s disease in both men and women.

“This is the first study in humans to examine the association between flavonoids and risk of developing Parkinson’s disease,” said study author Xiang Gao, MD, PhD, with the Harvard School of Public Health in Boston. “Our findings suggest that flavonoids, specifically a group called anthocyanins, may have neuroprotective effects. If confirmed, flavonoids may be a natural and healthy way to reduce your risk of developing Parkinson’s disease.”
May 10, 2013

Could eating peppers prevent Parkinson’s?

Missed – Medical Breakthroughs • Tags: American Neurological AssociationAnnals of Neurology,Group Health CooperativeNicotineParkinsonParkinson’s diseaseSolanaceaeUniversity of Washington

Contact: Dawn Peters sciencenewsroom@wiley.com 781-388-8408 Wiley

Dietary nicotine may hold protective key

New research reveals that Solanaceae—a flowering plant family with some species producing foods that are edible sources of nicotine—may provide a protective effect against Parkinson’s disease. The study appearing today inAnnals of Neurology, a journal of the American Neurological Association and Child Neurology Society, suggests that eating foods that contain even a small amount of nicotine, such as peppers and tomatoes, may reduce risk of developing Parkinson’s.

Parkinson’s disease is a movement disorder caused by a loss of brain cells that produce dopamine. Symptoms include facial, hand, arm, and leg tremors, stiffness in the limbs, loss of balance, and slower overall movement. Nearly one million Americans have Parkinson’s, with 60,000 new cases diagnosed in the U.S. each year, and up to ten million individuals worldwide live with this disease according to the Parkinson’s Disease Foundation. Currently, there is no cure for Parkinson’s, but symptoms are treated with medications and procedures such as deep brain stimulation.

Previous studies have found that cigarette smoking and other forms of tobacco, also a Solanaceae plant, reduced relative risk of Parkinson’s disease. However, experts have not confirmed if nicotine or other components in tobacco provide a protective effect, or if people who develop Parkinson’s disease are simply less apt to use tobacco because of differences in the brain that occur early in the disease process, long before diagnosis.

For the present population-based study Dr. Susan Searles Nielsen and colleagues from the University of Washington in Seattle recruited 490 patients newly diagnosed with Parkinson’s disease at the university’s Neurology Clinic or a regional health maintenance organization, Group Health Cooperative. Another 644 unrelated individuals without neurological conditions were used as controls. Questionnaires were used to assess participants’ lifetime diets and tobacco use, which researchers defined as ever smoking more than 100 cigarettes or regularly using cigars, pipes or smokeless tobacco.

Vegetable consumption in general did not affect Parkinson’s disease risk, but as consumption of edible Solanaceae increased, Parkinson’s disease risk decreased, with peppers displaying the strongest association. Researchers noted that the apparent protection from Parkinson’s occurred mainly in men and women with little or no prior use of tobacco, which contains much more nicotine than the foods studied.

“Our study is the first to investigate dietary nicotine and risk of developing Parkinson’s disease,” said Dr. Searles Nielsen. “Similar to the many studies that indicate tobacco use might reduce risk of Parkinson’s, our findings also suggest a protective effect from nicotine, or perhaps a similar but less toxic chemical in peppers and tobacco.” The authors recommend further studies to confirm and extend their findings, which could lead to possible interventions that prevent Parkinson’s disease.

###

This study is published in Annals of Neurology. Media wishing to receive a PDF of this article may contact sciencenewsroom@wiley.com.

Full citation: “Nicotine from Edible Solanaceae and Risk of Parkinson Disease.” Susan Searles Nielsen, Gary M. Franklin, W.T. Longstreth Jr, Phillip D. Swanson and Harvey Checkoway. Annals of Neurology; Published May 9, 2013 (DOI:10.1002/ana.23884).

URL Upon Publication: http://doi.wiley.com/10.1002/ana.23884

Author Contact: To arrange an interview with Dr. Susan Searles Nielsen, please contact Leila Gray with the University of Washington Health Sciences News Office at +1 206-685-0381 or at leilag@uw.edu.

About the Journal

Annals of Neurology, the official journal of the American Neurological Association and the Child Neurology Society, publishes articles of broad interest with potential for high impact in understanding the mechanisms and treatment of diseases of the human nervous system. All areas of clinical and basic neuroscience, including new technologies, cellular and molecular neurobiology, population sciences, and studies of behavior, addiction, and psychiatric diseases are of interest to the journal. The journal is published by Wiley on behalf of the
American Neurological Association and Child Neurology Society. For more information, please visit http://onlinelibrary.wiley.com/journal/10.1002/ana.

Flavonoids from berries shown to protect men against Parkinson’s disease

December 19, 2013 · by MrT

by: John Phillip, John is a Certified Nutritional Consultant and Health Researcher

(NaturalNews) Past research bodies have confirmed the health-protective effect of a natural diet rich in flavonoids to protect against a wide range of diseases including heart disease, hypertension, some cancers, and dementia. Researchers from Harvard University and the University of East Anglia have published the result of a study in the journalNeurology that demonstrates how these plant-based phytonutrients can significantly lower the risk of developing Parkinson’s disease, especially in men.

Flavonoids from healthy foods such as berries, tea, apples, and red wine cross the delicate blood-brain barrier to protect neurons against neurologic diseases such as Parkinson’s. This large scale study included more than 130,000 men and women participants that were followed for a period of twenty years. During this time, more than 800 individuals developed Parkinson’s disease.

A diet high in flavonoids from berries lowers Parkinson’s disease risk by forty percent

After a detailed analysis of their diets and adjusting for age and lifestyle, male participants who ate the most flavonoids were shown to be forty percent  less likely to develop the disease than those who ate the least. No similar link was found for total flavonoid intake in women.

This was the first study to examine the connection between flavonoid consumption and the development of Parkinson’s disease. The findings suggest that a sub-class of flavonoids called anthocyanins may exhibit neuroprotective effects. Participants consuming one or more portions of berry fruits each week were around twenty-five percent less likely to develop Parkinson’s disease, relative to those who did not eat berry fruits.

Flavonoids are the bioactive, naturally occurring chemical compounds found in many plant-based foods and drinks.

This study demonstrated the main protective effect was from the consumption of anthocyanins, which are present in berries and other fruits and vegetables including aubergines, blackcurrants, and blackberries. Strawberries and blueberries are the two most common sources of flavonoids in the US diet, contributing to a twenty-four percent lowered risk in this research.

Parkinson’s disease is among a group of chronic diseases presently affecting one in 500 people, with new cases on the rise. Drug therapies are ineffective and bear significant side effects.

Nutrition experts recommend adding a minimum of three to five servings of flavonoids to your diet each week. Include all varieties of berries, apples, and green tea to guard against Parkinson’s disease and other neurodegenerative illnesses.

 

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Good and Bad News Reported for Ovarian Cancer Therapy

Reporter, Curator: Stephen J. Williams, Ph.D.

 

In a recent Fierce Biotech report

FDA review red-flags AstraZeneca’s case for ovarian cancer drug olaparib”,

John Carroll reports on a disappointing ruling by the FDA on AstraZeneca’s PARP1 inhibitor olaparib for maintenance therapy in women with cisplatin refractory ovarian cancer with BRCA mutation.   Early clinical investigations had pointed to efficacy of PARP inhibitors in ovarian tumors carrying the BRCA mutation. The scientific rationale for using PARP1 inhibitors in BRCA1/2 deficiency was quite clear:

  1. DNA damage can result in

1. double strand breaks (DSB)

  1.  DSB can be repaired by efficient homologous recombination (HR) or less efficient non-homologous end joining (NHEJ)

b. BRCA1 involved in RAD51 dependent HR at DSB sites

  1. In BRCA1 deficiency DSB repaired by less efficient NHEJ

 

 

2. single strand breaks, damage (SSB)

  1. PARP1 is activated by DNA damage and poly-ADP ribosylates histones and other proteins marking DNA for SSB repair
  2. SSB repair usually base excision (BER) or sometimes nucleotide excision repair (NER)

B. if PARP inhibited then SSB gets converted to DSB

C. in BRCA1/2 deficient background repair is forced to less efficient NHEJ thereby perpetuating some DNA damage pon exposure to DNA damaging agent

 

A good review explaining the pharmacology behind the rationale of PARP inhibitors in BRCA deficient breast and ovarian cancer is given by Drs. Christina Annunziata and Susan E. Bates in PARP inhibitors in BRCA1/BRCA2 germline mutation carriers with ovarian and breast cancer

(http://f1000.com/prime/reports/b/2/10/) and below a nice figure from their paper:

 

parpbrcadnadamage

 

 

 

 

 

 

 

(from Christina M Annunziata and Susan E Bates. PARP inhibitors in BRCA1/BRCA2 germline mutation carriers with ovarian and breast cancer.  F1000 Biol Reports, 2010; 2:10.)  Creative Commons

Dr. Sudipta Saha’s post BRCA1 a tumour suppressor in breast and ovarian cancer – functions in transcription, ubiquitination and DNA repair discusses how BRCA1 affects the double strand DNA repair process, augments histone modification, as well as affecting expression of DNA repair genes.

Dana Farber’s Dr. Ralph Scully, Ph.D., in Exploiting DNA Repair Targets in Breast Cancer (http://www.dfhcc.harvard.edu/news/news/article/5402/), explains his research investigating why multiple DNA repair pathways may have to be targeted with PARP therapy concurrent with BRCA1 deficiency.

 

However FDA investigators voiced their skepticism of AstraZeneca’s clinical results, namely

  • Small number of patients enrolled
  • BRCA1/2 cohort were identified retrospectively
  • results skewed by false benefit from “underperforming” control arm
  • possible inadvertent selection bias
  • hazard ratio suggesting improvement in progression free survival but higher risk/benefit

The FDA investigators released their report two days before an expert panel would be releasing their own report (reported in the link below from FierceBiotech)

UPDATED: FDA experts spurn AstraZeneca’s pitch for ovarian cancer drug olaparib

in which the expert panel reiterated the findings of the FDA investigators.   The expert panel’s job was to find if there was any clinical benefit for continuing consideration of olaparib, basically stating

“This trial has problems,” noted FDA cancer chief Richard Pazdur during the panel discussion. If investigators had “pristine evidence of a 7-month advantage in PFS, we wouldn’t be here.”

The expert panel was concerned for the above reasons as well as the reported handful of lethal cases of myelodysplastic syndrome and acute myeloid leukemia in the study, although the panel noted these patients had advanced disease before entering the trial, raising the possibility that prior drugs may have triggered their deaths.

 

This was certainly a disappointment as ….

it was at last year’s ASCO (2013) that investigators at Perelman School of Medicine at the University of Pennsylvania and Sheba Medical Center in Tel Hashomer, Israel presented data showing that in 193 cisplatin-refractory ovarian cancer patients carrying a BRCA1/2 mutation, 31% had a partial or complete tumor regression. In addition the study also showed good response in pancreatic and prostate cancer with tolerable side effects.

 

See here for study details: http://www.uphs.upenn.edu/news/News_Releases/2013/05/domchek/

 

As John Carrol from FierceBiotech notes, the decision may spark renewed interest by Pfizer of a bid for AstraZeneca as the potential FDA rejection would certainly dampen AstraZeneca’s future growth and profit plans. Last month AstraZeneca’s CEO made the case to shareholders to reject the Pfizer offer by pointing to AstraZeneca’s potential beefed-up pipeline. AstraZeneca had projected olaparib as a potential $2 billion-a-year seller, although some industry analysts see sales at less than half that amount.

A company spokeswoman said the monotherapy use of olaparib for ovarian cancer assessed by the U.S. expert panel this week was only one element of a broad development program.

 

 

Please see a table of current oncology clinical trials with PARP1 inhibitors

at end of this post

 

However, on the same day, FierceBiotechreports some great news (at least in Europe) on the ovarian cancer front:

 

EU backs Roche’s Avastin for hard-to-treat ovarian cancer

As Arlene Weintraub   of FierceBiotech reports:

EU Committee for Medicinal Products for Human Use (CHMP) handed down a positive ruling on Avastin, recommending that the European Commission approve the drug for use in women with ovarian cancer that’s resistant to platinum-based chemotherapy. It’s the first biologic to receive a positive opinion from the CHMP for this hard-to-treat form of the disease.

Please see here for official press release: CHMP recommends EU approval of Roche’s Avastin for platinum-resistant recurrent ovarian cancer

 

EU had been getting pressure from British doctors to approve Avastin based on clinical trial results although it may be important to note that the EU zone seems to have an ability to recruit more numbers for clinical trials than in US. For instance an EU women’s breast cancer prevention trial had heavy recruitment in what would be considered a short time frame compared to recruitment times for the US.

 

Below is a table on PARP1 inhibitors in current clinical trials (obtained from NewMedicine’s Oncology KnowledgeBase™). nm|OK is a relational knowledgeBASE covering all major aspects of product development in oncolology. The database comprises 6 modules each dedicated in a specific sector within the oncology field.

 

PARP1 Inhibitors Currently in Clinical Trials for Ovarian Cancer

 

Developer and

Drug Name

Development Status & Location
– Indications
AbbVie

Current as of: March 27, 2014

PARP inhibitor: ABT-767

Phase I (begin 5/11, ongoing 2/14) Europe (Netherlands) – solid tumors with BRCA1 or BRCA2 mutations, locally advanced or metastatic • ovarian cancer, advanced or metastatic • fallopian tube cancer, advanced or metastatic • peritoneal cancer, advanced or metastatic
AstraZeneca
Affiliate(s):
· Myriad GeneticsCurrent as of: June 26, 2014Generic Name: Olaparib
Brand Name: Lynparza
Other Designation: AZD2281, KU59436, KU-0059436, NSC 747856
Phase I (begin 7/05, closed 9/08) Europe (Netherlands, UK, Poland); phase II (begin 6/07, closed 2/08, completed 5/09) USA, Australia, Europe (Germany, Spain, Sweden, UK), phase II (begin 7/08, closed 2/09) USA, Australia, Europe (Belgium, Germany, Poland, Spain, UK), Israel, phase II (begin 8/08, closed 12/09, completed 3/13) USA, Australia, Canada, Europe (Belgium, France, Germany, Poland, Romania, Spain, Ukraine, UK), Israel, Russia; phase II (begin 2/10, closed 7/10) USA, Australia, Canada, Europe (Belgium, Czech Republic, Germany, Italy, Netherlands, Spain, UK), Japan, Panama, Peru (combination); MAA (accepted 9/13) EU, NDA (filed 2/14) USA – ovarian cancer, advanced or metastatic, BRCA positive • ovarian cancer, recurrent, platinum sensitive • ovarian cancer, advanced, refractory, BRCA1 or BRCA2-associatedPhase I (begin 5/08, ongoing 5/12) USA; phase II (begin 7/08, closed 10/09) Canada – breast cancer, locally advanced, BRCA1/BRCA2-associated or hereditary metastatic or inoperable • ovarian cancer, locally advanced, BRCA1/BRCA2-associated or hereditary metastatic or inoperable • breast cancer, triple-negative, BRCA-positive • ovarian cancer, high-grade serous and/or undifferentiated, BRCA-positive

Phase I (begin 10/10, ongoing 1/13) USA (combination) – ovarian cancer, inoperable or metastatic, refractory • breast cancer, inoperable or metastatic, refractory

Phase III (begin 8/13) USA, Australia, Brazil, Canada, Europe (France, Italy, Netherlands, Poland, Russia, Spain, UK), Israel, South Korea, phase III (begin 9/13) USA, Australia, Brazil, Canada, Europe (France, Germany, Italy, Netherlands, Poland, Russia, Spain, UK), Israel – ovarian cancer, serous, high grade, BRCA mutated, platinum-sensitive, relapsed, third line, maintenance • ovarian cancer, serous or endometrioid, high grade, BRCA mutated, platinum responsive (PR or CR), maintenance, first line • primary peritoneal cancer, high grade, BRCA mutated, platinum responsive (PR or CR), maintenance • fallopian tube cancer, high grade, BRCA mutated, platinum responsive (PR or

BioMarin Pharmaceutical

Current as of: June 14, 2014

PARP inhibitor:

BMN-673, BMN673, LT-673

Phase I/II (begin 1/11, ongoing 3/14) USA – solid tumors, advanced, recurrent

Phase I (begin 2/13, closed 4/13, completed 5/14) USA – healthy volunteers

Phase I/II (begin 11/13) USA – solid tumors, relapsed or refractory, BRCA mutated, second line

BiPar Sciences

Current as of: April 16, 2009

Parp inhibitor:

BSI-401

Preclin (ongoing 4/09) – solid tumors
Clovis Oncology
Affiliate(s):
· University of Newcastle Upon Tyne
· Cancer Research Campaign Technology
· PfizerCurrent as of: June 21, 2014Generic Name: Rucaparib
Brand Name: Rucapanc
Other Designation: AG140699, AG014699, AG-14,699, AG-14669, AG14699, AG140361, AG-14361, AG-014699, CO-338, PF-01367338
Phase I (begin 03, completed 05) Europe (UK) (combination), phase I (begin 2/10, closed 11/13) Europe (France, UK) (combination) – solid tumors, advanced

Phase II (begin 12/07, closed 10/13) Europe (UK) – breast cancer, advanced or metastatic, in patients carrying BRCA1 or BRCA2 mutations • ovarian cancer, advanced or metastatic, in patients carrying BRCA1 or BRCA2 mutations

Phase I/II (begin 11/11, ongoing 6/14) USA, Europe (UK) – solid tumors, metastatic, with mutated BRCA • breast cancer, metastatic, HEr2 negative, with mutated BRCA

Sanofi

Current as of: June 03, 2013

Generic Name: Iniparib
Brand Name: Tivolza
Other Designation: BSI-201, NSC 746045, SAR240550

Phase I/Ib (begin 3/06, closed 3/10) USA (combination), phase I (begin 7/10, closed 11/10) USA, phase I (begin 9/10, ongoing 2/11) Japan (combination); phase Ib (begin 1/07, ongoing 1/11) USA (combination) – solid tumors, advanced, refractory
Phase II (begin 5/08, closed 1/09) USA – ovarian cancer, advanced, refractory, BRCA-1 or BRCA-2 associated • fallopian tube cancer, advanced, refractory, BRCA-1 or BRCA-2 associated • peritoneal cancer, advanced, refractory, BRCA-1 or BRCA-2 associated
Tesaro
Affiliate(s):
· MerckCurrent as of: May 18, 2014Generic Name: Niraparib
Other Designation: MK-4827, MK4827
Phase I (begin 9/08, closed 2/11) USA, Europe (UK) – solid tumors, locally advanced or metastatic • ovarian cancer, locally advanced or metastatic, BRCA mutant • chronic lymphocytic leukemia (CLL), relapsed or refractory • prolymphocytic leukemia, T cell, relapsed or refractory
Phase Ib (begin 11/10, closed 3/11, terminated 10/12) USA (combination) – solid tumors, locally advanced or metastatic • ovarian cancer, serous, high grade, platinum resistant or refractoryPhase III (begin 5/13, ongoing 5/14) USA – ovarian cancer, platinum-sensitive, high grade serous or BRCA mutant, chemotherapy responsive • fallopian tube cancer • primary peritoneal cancer
Teva Pharmaceutical Industries

Current as of: May 04, 2013

Designation:

CEP-9722

Phase I (begin 5/11, closed 11/12, terminated 10/13) USA, phase I (begin 6/09, closed 7/12, completed 1/12) Europe (France and UK) (combination) – solid tumors, advanced, third line
Phase I (begin 5/11, completed 1/13) Europe (France) (combination) – solid tumors, advanced • mantle cell lymphoma (MCL), advanced

 

 

Summary of Combination Ovarian Cancer Trials with Avastin (current and closed)

 

Indication in Development ovarian cancer, advanced, recurrent, persistent • ovarian cancer, progressive, platinum resistant, second line • fallopian tube cancer, progressive, platinum resistant, second line • primary peritoneal cancer, progressive, platinum resistant, second line
Latest Status Phase II (begin 4/02, closed 8/04) USA, phase II (begin 11/04, closed 10/05) USA; phase III (begin 10/09) Europe (Belgium, Bosnia and Herzegovina, Denmark, Finland, France, Germany, Greece, Italy, Netherlands, Norway, Portugal, Spain, Sweden), Turkey
Clinical History Refer to the Combination Trial Module for trials of Avastin in combination with various chemotherapeutic regimens.According to results from the AURELIA clinical trial (protocol ID: MO22224; 2009-011400-33; NCT00976911), the median PFS in women with progressive platinum resistant ovarian, fallopian tube or primary peritoneal cancer treated with Avastin in combination with chemotherapy, was 6.7 months compared to 3.4 months in those treated with chemotherapy alone for an HR of 0.48 (range =0.38–0.60).. In addition, the objective response rate was 30.9% in women treated with Avastin compared to 12.6% in those on chemotherapy (p=0.001). Certain AE (Grade 2 to 5) that occurred more often in the Avastin arm compared to the chemotherapy alone arm were high blood pressure (20% versus 7%) and an excess of protein in the urine (11% versus 1%). Gastrointestinal perforations and fistulas occurred in 2% of women in the Avastin arm compared to no events in the chemotherapy arm (Pujade-Lauraine E, etal, ASCO12, Abs. LBA5002).A multicenter (n=124), randomized, open label, 2-arm, phase III clinical trial (protocol ID: MO22224; 2009-011400-33; NCT00976911; http://clinicaltrials.gov/ct2/results?term=NCT00976911 ), dubbed AURELIA, was initiated in October 2009, in Europe (Belgium, Bosnia and Herzegovina, Denmark, Finland, France, Germany, Greece, Italy, Netherlands, Norway, Portugal, Spain, and Sweden), and Turkey, to evaluate the efficacy and safety of Avastin added to chemotherapy versus chemotherapy alone in patients with epithelial ovarian, fallopian tube or primary peritoneal cancer with disease progression within 6 months of platinum therapy in the first line setting. The trials primary outcome measure is PFS. Secondary outcome measures include objective response rate, biological PFS interval, OS, QoL, and safety and tolerability. According to the protocol, all patients are treated with standard chemotherapy with IV paclitaxel (80 mg/m²) on days 1, 8, 15 and 22 of each 4-week cycle; or IV topotecan at a dose of 4 mg/m² on days 1, 8 and 15 of each 4-week cycle, or 1.25 mg/kg on days 1-5 of each 3-week cycle; or IV liposomal doxorubicin (40 mg/m²) every 4 weeks. Patients (n=179) randomized to arm 2 of the trial are treated with IV Avastin at a dose of 10 mg/kg twice weekly or 15 mg/kg thrice weekly concomitantly with the chemotherapy choice. Treatment continues until disease progression. Subsequently, patients are treated with the standard of care. Patients in arm 1 (n=182), on chemotherapy only may opt to be treated with IV Avastin (15 mg/kg) three times weekly. The trial was set up in cooperation with the Group d’Investigateurs Nationaux pour l’Etude des Cancers Ovariens (GINECO) and was conducted by the international network of the Gynecologic Cancer Intergroup (GCIG) and the pan-European Network of Gynaecological Oncological Trial Groups (ENGOT), under PI Eric Pujade-Lauraine, MD, Hopitaux Universitaires, Paris Centre, Hôpital Hôtel-Dieu (Paris, France). The trial enrolled 361 patients and was closed as of May 2012..Results were presented from a phase II clinical trial (protocol ID: CDR0000068839; GOG-0170D; NCT00022659) of bevacizumab in patients with persistent or recurrent epithelial ovarian cancer or primary peritoneal cancer that was performed by the Gynecologic Oncology Group to determine the ORR, PFS, and toxicity for this treatment. Patients must have been administered 1-2 prior cytotoxic regimens. Treatment consisted of bevacizumab (15 mg/kg) IV every 3 weeks until disease progression or prohibitive toxicity. Between April 2002 and August 2004, 64 patients were enrolled, of which 2 were excluded for wrong primary and borderline histology and 62 were evaluable (1 previous regimen=23, 2 previous regimens=39). The median disease free interval from completion of primary cytotoxic chemotherapy to first recurrence was 6.5 months. Early results demonstrated that some patients had confirmed objective responses and PFS in some was at least 6 months. Observed Grade 3 or 4 toxicities included allergy (Grade 3=1), cardiovascular (Grade 3=4; Grade 4=1), gastrointestinal (Grade 3=3), hepatic (Grade 3=1), pain (Grade 3=2), and pulmonary (Grade 4=1). As of 11/04, 36 patients were removed from the trial, including 29 for disease progression and 1 for toxicity in 33 cases reported. Preliminary evidence exists for objective responses to bevacizumab (Burger R, et al, ASCO05, Abs. 5009).An open label, single arm, 2-stage, phase II clinical trial (protocol ID: AVF2949g, NCT00097019) of bevacizumab in patients with platinum resistant, advanced (Stage III or IV), ovarian cancer or primary peritoneal cancer for whom subsequent doxorubicin or topotecan therapy also has failed was initiated in November 2004 at multiple locations in the USA to determine the safety and efficacy for this treatment.A multicenter phase II clinical trial was initiated in April 2002 to determine the 6-month PFS of patients with persistent or recurrent ovarian epithelial or primary peritoneal cancer treated with bevacizumab (protocol ID: GOG-0170D, CDR0000068839, NCT00022659). IV bevacizumab is administered over 30-90 minutes on day 1. Treatment is repeated every 21 days in the absence of disease progression or unacceptable toxicity. Patients are followed every 3 months for 2 years, every 6 months for 3 years, and then annually thereafter. A total of 22-60 patients will be accrued within 12-30 months. Robert A. Burger, MD, of Chao Family Comprehensive Cancer Center is Trial Chair.This trial was closed in August 2004.

 

 

Sources

http://www.fiercebiotech.com/story/fda-review-red-flags-astrazenecas-case-ovarian-cancer-drug-olaparib/2014-06-23

 

http://www.fiercebiotech.com/story/fda-experts-spurn-astrazenecas-pitch-ovarian-cancer-drug-olaparib/2014-06-25

 

http://www.fiercepharma.com/story/eu-backs-roches-avastin-hard-treat-ovarian-cancer/2014-06-27

 

In a followup to this original posting A Report From the Institute of Medicine of the National Academies of Sciences, Engineering, and Medicine entitled

Evolving Approaches in Research and Care for Ovarian Cancers

was generated in a ViewPoint piece in JAMA which discussed their Congressional mandated report on the State of the Science in Ovarian Cancer Research, titled

Ovarian Cancers: Evolving Paradigms in Research and Care 

highlights some of the research gaps felt by the committee in the current state of ovarian cancer research including:

  • consideration in research protocols of the multitude of histologic and morphologic subtypes of ovarian cancer, including the feeling of the committee that high grade serous OVCA originates from the distal end of the fallopian tube (espoused by Dr. Doubeau and Dr. Christopher Crum) versus originating from the ovarian surface epithelium
  • a call for expanded screening and prevention research with mutimodal screening including CA125 with secondary transvaginal screen
  • better patient education of the risk/benefit of genetic testing including BRCA1/2 as well as in consideration for PARP inhibitor therapy
  • treatments should be standardized and disseminated including more research in health outcomes and decision support for personalized therapy

This Perspective article can be found here: jvp160038

Some other posts relating to OVARIAN CANCER on this site include

Efficacy of Ovariectomy in Presence of BRCA1 vs BRCA2 and the Risk for Ovarian Cancer

Testing for Multiple Genetic Mutations via NGS for Patients: Very Strong Family History of Breast & Ovarian Cancer, Diagnosed at Young Ages, & Negative on BRCA Test

Ultrasound-based Screening for Ovarian Cancer

Dasatinib in Combination With Other Drugs for Advanced, Recurrent Ovarian Cancer

BRCA1 a tumour suppressor in breast and ovarian cancer – functions in transcription, ubiquitination and DNA repair

 

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Michael Snyder @Stanford University sequenced the lymphoblastoid transcriptomes and developed an allele-specific full-length transcriptome

 

Reporter: Aviva Lev-Ari, PhD, RN

 

Allelic Expression of Deleterious Protein-Coding Variants across Human Tissues

http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004304

  • Kimberly R. Kukurba,
  • Rui Zhang,
  • Xin Li,
  • Kevin S. Smith,
  • David A. Knowles,
  • Meng How Tan,
  • Robert Piskol,
  • Monkol Lek,
  • Michael Snyder,
  • Daniel G. MacArthur,
  • Jin Billy Li mail,
  • Stephen B. Montgomery mail

Conceived and designed the experiments: SBM KRK JBL. Performed the experiments: RZ KSS MHT RP ML. Analyzed the data: KRK RZ XL DAK DGM SBM. Contributed reagents/materials/analysis tools: MS DGM JBL SBM. Wrote the paper: KRK DGM MS JBL SBM.

Abstract

Personal exome and genome sequencing provides access to loss-of-function and rare deleterious alleles whose interpretation is expected to provide insight into individual disease burden. However, for each allele, accurate interpretation of its effect will depend on both its penetrance and the trait’s expressivity. In this regard, an important factor that can modify the effect of a pathogenic coding allele is its level of expression; a factor which itself characteristically changes across tissues. To better inform the degree to which pathogenic alleles can be modified by expression level across multiple tissues, we have conducted exome, RNA and deep, targeted allele-specific expression (ASE) sequencing in ten tissues obtained from a single individual. By combining such data, we report the impact of rare and common loss-of-function variants on allelic expression exposing stronger allelic bias for rare stop-gain variants and informing the extent to which rare deleterious coding alleles are consistently expressed across tissues. This study demonstrates the potential importance of transcriptome data to the interpretation of pathogenic protein-coding variants.

Author Summary

Gene expression is a fundamental cellular process that contributes to phenotypic diversity. Gene expression can vary between alleles of an individual through differences in genomic imprinting or cis-acting regulatory variation. Distinguishing allelic activity is important for informing the abundance of altered mRNA and protein products. Advances in sequencing technologies allow us to quantify patterns of allele-specific expression (ASE) in different individuals and cell-types. Previous studies have identified patterns of ASE across human populations for single cell-types; however the degree of tissue-specificity of ASE has not been deeply characterized. In this study, we compare patterns of ASE across multiple tissues from a single individual using whole transcriptome sequencing (RNA-Seq) and a targeted, high-resolution assay (mmPCR-Seq). We detect patterns of ASE for rare deleterious and loss-of-function protein-coding variants, informing the frequency at which allelic expression could modify the functional impact of personal deleterious protein-coding across tissues. We demonstrate that these interactions occur for one third of such variants however large direction flips in allelic expression are infrequent.

SOURCE

 

 

Researchers Report Generating Personal Transcriptome Using Long Reads

June 23, 2014

 

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb) – Using a long-read-based approach, Stanford University researchers reported generating a personal transcriptome in the Proceedings of the National Academy of Sciences.

Senior author Michael Snyder and his colleagues sequenced the lymphoblastoid transcriptomes of three family members using the Pacific Biosciences system, reads from which they compared to shorter reads from the Illumina platform. From those transcriptomes, they developed an allele-specific full-length transcriptome for one of the family members. They were able to distinguish the two alleles even for complicated genes such as HLA genes.

“Here, we generate the deepest and longest single-molecule long-read dataset to date, to our [knowledge], for a trio of human cell lines,” Snyder and his colleagues wrote in their paper. They further “show[ed] that we can determine SNVs de novo and that using a [principal components] approach, molecules from genes with multiple heterozygous SNVs can be attributed to the two alleles.”

Such personal transcriptomes, Snyder and his colleagues added, are expected to become important in the understanding of individual biology and disease.

He and his colleagues used the PacBio platform to sequence some 711,000 circular consensus read molecules from the GM12878 cell line. They generated longer sub-reads for this study — an average 1,188 basepairs — than they did for the human organ panel dataset — an average 999.9 basepairs — that they presented last year in Nature Biotechnology.

They additionally noted that though both datasets equally represented shorter molecules between 0.8 kilobases and 1.3 kilobases in length, the present dataset better represented molecules longer than 1.7 kilobases.

The Stanford team also sequenced 100 million 101-basepair pair-end reads on the Illumina platform that they then analyzed using Cufflinks.

Both technologies, they reported, uncovered some 99,000 annotated exon-exon junctions, and Illumina reads covered an additional 92,000 or so annotated junctions while the PacBio reads covered a further 992 junctions. Additionally, of the 22,600 spliced genes classified by Gencode as either protein-coding genes or lincRNAs, long-read single molecule sequencing and 101-basepair paired-end sequencing identified 9,200 of them. Forty genes were found solely through long reads, 6,400 genes by 101-basepair paired-end sequencing, and 7,000 genes weren’t found using either approach.

The researchers had hypothesized that since circular consensus read generation needs read lengths to be at least twice as long as the cDNA length that consensus split-mapped molecules (CSMM) wouldn’t include a large number of longer genes.

However, they found that genes with and without a CSMM had similar lengths, though genes with a CSMM were less likely to be smaller than one kilobase, which the researchers said was likely due to the magnetic beads in the loading procedure preferring longer fragments.

Both expression and mature gene length, Snyder and his colleagues added, are important factors in whether or not a gene received a full-length consensus split-mapped molecule.

Such long reads, the researchers said, could include a number of novel exon-intron structures. To eliminate potential artifacts, the researchers focused on 12,000 full-length novel isoforms that could be attributed to a known gene and for which the exon-intron junction was annotated or otherwise supported by short-read sequencing.

Of these, 55 percent were novel combinations of known splice sites; 34 percent had a single novel donor or acceptor; and 11 percent had two or more novel splice sites.

Again comparing this work to their previous human organ panel dataset, Snyder and his colleagues found that some 2,100 genes had a novel isoform in the HOP sample, 4,300 in the current sample, and 600 were in both.

A goal of transcriptomic research, the researchers said, is to be able to assign RNA molecules to the allele from which they are expressed. And long-read sequencing is supposed to be able, they added, to determine each SNV affecting single RNA molecules.

To trace the origin of these alleles found in the GM12878 daughter cell line, they folded in data from the parental GM12891 and GM12892 lines, and examined that parental data for the presence or absence of SNVs present in the daughter.

Through a principal components analysis, they could separate out the two alleles based on the eigenvectors. For 166 genes with at least two annotated heterozygous SNVs, the researchers found that 158 of them had two or more SNVs, two genes had one SNV, and six genes did not appear to be heterozygous.

A few genes — particularly HLA genes — contained a number of SNVs, and for these, too, the researchers were mostly able to determine phasing.

“Even for complicated genes (e.g., HLA genes, whose sequences may differ considerably from the reference sequence) the two alleles are usually clearly distinguishable,” Snyder and his colleagues wrote.

They noted, though, that deeper sequencing would be necessary to determine whether one allele behaves different than another for different genes.

 

Related Stories

Team Finds Medically Relevant Info Using Personalized ‘Omics Profiling on Stanford’s SnyderMarch 15, 2012 / GenomeWeb Daily News

Team Taps PacBio SMRT Sequencing to Track Outcomes at Sites Targeted for Genome EditingApril 15, 2014 / In Sequence

Tumor Type Targeted Sequencing Method Picks Up Personalized Circulating Tumor DNA MarkersApril 8, 2014 / In Sequence

Long-read Sequencing Offers Phasing Data for HIV Drug Resistance MutationsMarch 24, 2014 / GenomeWeb Daily News

Genomics in the JournalsJanuary 30, 2014 / GenomeWeb Daily News

SOURCE

http://www.genomeweb.com//node/1407251?utm_source=SilverpopMailing&utm_medium=email&utm_campaign=PerkinElmer,%20Enzo%20Settle%20IP%20Fight;%20Long-Read-based%20Transcriptome;%20Cancer%20Research%20Grants;%20More%20%20-%2006/23/2014%2004:05:00%20PM

 

 

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Larry H Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/6-19-2014/larryhbern/Gene Switch Takes Blood Cells to Leukemia and Back Again

Kevin Mayer

 

Summary

Loss-of-function mutations in a gene called Pax5 have been known to drive normal blood cells to turn into leukemia cells. Such mutations are permanent, so it remained unclear whether an initial, temporary loss of function would instigate an irreversible cascade of events leading to an accumulation of undifferentiated lymphoblasts, or whether an ongoing loss of function would be needed to maintain the disease state.

 

With the publication of a new study, the question has become more than academic. The study, by researchers at Melbourne’s Walter and Eliza Hall Institute, has not only shown that switching off Pax5 causes cancer in a murine model of B-progenitor acute lymphoblastic leukemia (B-ALL), it has also demonstrated that switching on Pax5 essentially cures the disease.

The results of the study appeared June 15 in the journal Genes & Development, in an article entitled “Pax5 loss imposes a reversible differentiation block in B-progenitor acute lymphoblastic leukemia.” The article described how the researchers used transgenic RNAi to reversibly suppress endogenous Pax5 expression in the hematopoietic compartment of mice, which cooperates with activated signal transducer and activator of transcription 5 (STAT5) to induce B-ALL.

“In this model, restoring endogenous Pax5 expression in established B-ALL triggers immunophenotypic maturation and durable disease remission by engaging a transcriptional program reminiscent of normal B-cell differentiation,” wrote the authors. “Notably, even brief Pax5 restoration in B-ALL cells causes rapid cell cycle exit and disables their leukemia-initiating capacity.”

Institute researcher Grace Liu noted that Pax5, which is frequently “lost” in childhood B-ALL, is essential for normal development of B cells. “When Pax5 function is compromised, developing B cells can get trapped in an immature state and become cancerous,” she said. “We have shown that restoring Pax5 function, even in cells that have already become cancerous, removes this ‘block,’ and enables the cells to develop into normal white blood cells.”

Simply restoring Pax5 sufficed to normalize cancer cells. That is, re-engaging the stalled differentiation program in immature white blood cells restored normal development “despite the presence of additional oncogenic lesions.”

Institute researcher Ross Dickins, Ph.D., said that forcing B-ALL cells to resume their normal development could provide a new strategy for treating leukemia: “While B-ALL has a relatively good prognosis compared with other cancers, current treatments can last years and have major side effects. By understanding how specific genetic changes drive B-ALL, it may be possible to develop more specific treatments that act faster with fewer side effects.”

“It is very difficult to develop drugs that restore the function of genes that are lost during cancer development,” Dr. Dickins added. “However, by understanding the mechanisms by which Pax5 loss causes leukemia, we can begin to look at ways of developing drugs that could have the same effect as restoring Pax5 function.”

Pax5 is just one of about 100 genes known to suppress human tumors. Now that Pax5 has been scrutinized with genetic switch technology, the researchers speculate that similar technology could be used to characterize other tumor suppressor genes.

 

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Second Annual Single-Cell Sequencing of Cancer Rountable August 20,21, 2014 Washington DC

Reporter:  Stephen J. Williams, PhDSingle-Cell Sequencing | August 20-21, 2014

CSHL, UCLA & Einstein to Lead Roundtable Discussions on Single-Cell Sequencing

Interactive discussions on three of the key questions researchers are facing when considering single-cell analysis will be held on the second day of the Single-Cell Sequencing Conference at Next Generation Dx Summit, taking place August 20-21, 2014 in Washington, DC. For full program details and to register, please visit NextGenerationDx.com/Single-Cell-Sequencing.Making Single-Cell Analysis Cost Effective for Clinical Use

Moderator: James Hicks, Ph.D., Research Professor, Cancer Genomics, Cold Spring Harbor Laboratory

  • Methods for capture: What are the tradeoffs?
  • Combining RNA, DNA and protein analysis
  • What genomic assays are most informative?
  • Can assays be certifiable?

Finding a Needle in a Haystack: Towards Diagnosing Rare Soft Tissue Cancer Stem Cells (CSCs)
Moderator: Michael Masterman-Smith, Ph.D., Entrepreneurial Scientist, UCLA California NanoSystems Institute

  • Rethinking companion diagnostics for cancer to incorporate analysis of CSCs
  • Current direct methodologies of CSC detection/isolation
  • Current proxy methodologies of CSC detection/isolation
  • The hope and promise of single-cell assay tools and technologies

Why Single-Cell Sequencing?
Moderator: Jan Vijg, Ph.D., Professor and Chairman, Genetics, Albert Einstein College of Medicine
Sample limitations, e.g., prenatal diagnostics and CTCs

  • Sample limitations, e.g., prenatal diagnostics and CTCs
  • To study cell-to-cell variation, e.g., in tumors as well as normal tissues
  • To overcome technological constraints, e.g., detecting somatic mutations
  • Cell-to-cell fluctuations in gene expression can easily impair function, yet can be undetectable by measuring averages
  • How many different cell types are there?
View Brochure    |   Register (Advance Registration Ends July 18)  |   NextGenerationDx.com/Single-Cell-Sequencing


About the Conference

Sequencing data from bulk DNA or RNA from multiple cells provide global information on average states of cell populations. But with whole-genome amplification and NGS, researchers can detect variation in individual cancer cells and dissect tumor evolution. Such cancer genome sequencing will improve oncology by detecting rare tumor cells early, measuring intra-/intertumor heterogeneity, guiding chemotherapy and controlling drug resistance. The Single-Cell Sequencing conference explores the latest strategies, data analyses and clinical considerations that influence and aid cancer diagnosis, prognosis and prediction and will lead to individualized cancer therapy.

Sessions include presentations spanning the opportunities of clinical single-cell analysis from:

  • Sunney Xie, Ph.D., Mallinckrodt Professor. Chemistry and Chemical Biology, Harvard University
  • Maximilian Diehn, M.D., Ph.D., Assistant Professor, Radiation Oncology, Stanford Cancer Institute, Institute for Stem Cell Biology & Regenerative Medicine, Stanford University
  • Denis Smirnov, Associate Scientific Director, US Biomarker Oncology, Janssen R&D US
  • James Hicks, Ph.D., Research Professor, Cancer Genomics, Cold Spring Harbor Laboratory
  • Jan Vijg, Ph.D., Professor and Chairman, Genetics, Albert Einstein College of Medicine
  • John F. Zhong, Ph.D., Associate Professor, Pathology, University of Southern California School of Medicine
  • Mark Hills, Ph.D., Research Scientist, Peter M. Lansdorp Laboratory, BC Cancer Research Centre
  • Michael Masterman-Smith, Ph.D., Entrepreneurial Scientist, UCLA California NanoSystems Institute
  • Parveen Kumar, Research Scientist, Thierry Voet Laboratory, Human Genetics, University of Leuven
  • Peter Nemes, Ph.D., Assistant Professor, Chemistry, George Washington University
  • Theresa Zhang, Ph.D., Vice President, Research Services, Personal Genome Diagnostics
  • Yong Wang, Ph.D., Senior Postdoctoral Fellow, Nicholas E. Navin Laboratory, Genetics, Bioinformatics, MD Anderson Cancer Center
  • Zivana Tezak, Ph.D., Associate Director, Science and Technology, Personalized Medicine, Office of In Vitro Diagnostic Device Evaluation and Safety (OIVD), Center for Devices and Radiological Health (CDRH), FDA

 


Recommended Pre-Conference Courses

NGS Data Analysis – Determining Clinical Utility of Genome Variants
Monday, August 18 | 9:00am – 12:00pm
This course will explore the strategies of genomic data analysis and interpretation, an emergent discipline that seeks to deliver better answers from NGS data so that patients and their physicians can determine informed healthcare decisions. View Details

NGS as a Diagnostics Platform
Monday, August 18 | 2:00pm – 5:00pm
The focus of this short course will be on understanding the use of NGS in clinical diagnosis, practical implementation of NGS in clinical laboratories and analysis of large data sets by using bioinformatics tools to parse and interpret data in relation to the clinical phenotype. The concluding presentation will be dedicated to quality and standardization of NGS assays. View Details

Register   |   View Agenda   | NextGenerationDx.com

LinkedIn YouTube Twitter #NGDx14

Next Generation Dx Summit 2014
Cambridge Healthtech Institute, 250 First Avenue, Suite 300, Needham, MA 02494
www.healthtech.com

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Preventive Care: Anticipated Changes caused by Genomics in the Clinic and Personalised Medicine

Reporter: Aviva Lev-Ari, PhD, RN

23andMe CEO on Her Mission to Shake Up Preventive Care

, Anne E. Wojcicki

June 02, 2014

Editor’s Note: In this segment of Medscape One-on-One, Editor-in-Chief Eric J. Topol, MD, talks with Anne E. Wojcicki, co-founder and CEO of 23andMe, about her desire to shake up the practice of medicine by using patients’ genetic data to enhance preventive care and disease treatment. Although the US Food and Drug Administration (FDA) ordered 23andMe to stop marketing its $99 genetic screening tests to consumers last November, Ms. Wojcicki, a Yale-educated biologist, says her company is pressing on with its mission, having already genetically screened some 650,000 people, including Dr. Topol.

Taking Biology to Wall Street

Eric J. Topol, MD: Hello. I’m Eric Topol, and this is Medscape One-on-One. As we continue our series on some of the most interesting people in the world of medicine, I am thrilled to speak with Anne Wojcicki from 23andMe, who has done a lot to try to shake up the world of medicine and healthcare. It’s great to have you with us. Let’s start with some of your background. You went to college at Yale. After that you went into Wall Street?

Anne E. Wojcicki: I grew up on the Stanford campus [Editor’s note: Ms. Wojcicki’s father, Stanley Wojcicki, is a physicist and professor emeritus at Stanford University] and went to Yale for undergraduate education. I was a biology major, and very haphazardly I got an introduction to a Wall Street firm. I was investing in healthcare companies for 10 years.

Dr. Topol: What was the big lesson out of that decade for you?

Ms. Wojcicki: In the beginning, I loved it because there was all this innovation. My first investment, ironically, was Affymetrix, a genome company. There was this amazing spirit of innovation. Then the bubble burst in 2000 and a lot of innovation dried up. I started to understand more about how the healthcare system worked and to realize that there are all of these great people in the system, but the system was encouraging a type of healthcare that I didn’t want.

Primarily, if I think of what I really want, I want to be healthy at 100 and I don’t want to take any medications. But you are part of a healthcare system where, if you are diabetic, many people can make money, and if you never become diabetic, no one makes money. I just felt that the system wasn’t getting to the issues that I wanted, which were prevention and wellness.

Dr. Topol: You got to that sense with a lot of experience from another perspective — not from the inside but from the outside. How did you go from that to the idea of starting a consumer genomics company?

Involving the Consumer

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Ms. Wojcicki: Every year I would see these glossy brochures that talked about personalized medicine. Everyone had these great quotes about how personalized medicine is coming and the genome project was done, but it wasn’t actually happening. More and more I realized that the consumer — you, the individual — can never make choices; everyone is making choices for you. I was doing research on, ironically, Affymetrix and Illumina, so I started and ended my career with that. I remember talking to Steven McCarroll at the Broad Institute, and he was like a kid in a candy store, saying, “It’s the most exciting time. We are finally getting whole genetic data and it’s inexpensive and reliable. It’s going to change the world.” I kept thinking, if you are going to change the world and usher in personalized medicine, and understand the risks and what you are at risk for, and what you are not at risk for, you have to get the consumer involved.

After those discussions I started to realize that there was the potential for marrying inexpensive genetics with the Livestrong/Susan G. Komen kind of enthusiasm and what was happening on YouTube and Facebook. So I put together this community to help people access their genetic data and make it really fun for them. We wanted to do research that involved everyone, [allowing them to contribute their own] information.

Dr. Topol: This was back in 2006, when you founded the company?

Ms. Wojcicki: Correct.

 WATCH VIDEO

 

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An alternative approach to overcoming the apoptotic resistance of pancreatic cancer

Reporter: Aviva Lev-Ari, PhD, RN

Use of herbal medicines and natural products: An alternative approach to overcoming the apoptotic resistance of pancreatic cancer


Abstract

Pancreatic cancer has a poor prognosis with a 5-year survival rate of <5%. It does not respond well to either chemotherapy or radiotherapy, due partly to cancer cell apoptotic resistance (AR). AR has been attributed to certain genetic abnormalities or defects in apoptotic signaling pathways. In pancreatic cancer, significant mutations of K-ras and p53, constitutive activation of NFκB, over-expression of heat shock proteins (Hsp90, Hsp70), histone deacetylase (HDACs) and the activities of other proteins (COX-2, Nrf2 and bcl-2 family members) are closely linked with resistance to apoptosis and invasion. AR has also been associated with aberrant signaling of MAPK, PI3K–AKT, JAK/STAT, SHH, Notch, and Wnt/β-catenin pathways. Strategies targeting these signaling molecules and pathways provide an alternative for overcoming pancreatic cancer AR. The use of herbal medicines or natural products (HM/NPs) alone or in combination with conventional anti-cancer agents has been shown to produce beneficial effects through actions upon multiple molecular pathways involved in AR. The current standard first-line chemotherapeutic agents for pancreatic cancer are gemcitabine (Gem) or Gem-containing combinations; however, the efficacy is dissatisfied and this limitation is largely attributed to resistance to apoptosis. Meanwhile, emerging data have pointed to a combination of HM/NPs that may augment the sensitivity of pancreatic cancer cells to Gem. Greater understanding of how these compounds affect the molecular mechanisms of apoptosis may propel development of HM/NPs as anti-cancer agents and/or adjuvant therapies forward.

In this review, we give a critical appraisal of the use of HM/NPs alone and in combination with anti-cancer drugs. We also discuss the potential regulatory mechanisms whereby AR is involved in these protective pathways.

Abbreviations

  • 5-FU5-fluorouracil;
  • ARapoptotic resistance;
  • ASK1apoptosis signal-regulating kinase 1;
  • BDbrucine D;
  • COX-2cyclooxygenase-2;
  • EGCGepigallocatechin-3-gallate;
  • EGFRepidermal growth factor receptor;
  • EriBeriocalyxin B;
  • ERKextracellular signal-regulated kinase;
  • Gemgemcitabine;
  • GnsRh2ginsenoside Rh2;
  • GSK3βglycogen synthase kinase 3β;
  • HDACshistone deacetylase;
  • HDACIshistone deacetylase inhibitors;
  • HM/NPsherbal medicines and natural products;
  • Hspheat shock proteins;
  • ILinterleukin;
  • JAK,Janus-activated kinases;
  • JNKJun N-terminal kinase;
  • KeapKelch-like ECH-associated protein;
  • MAPKs,mitogen-activated protein kinases;
  • MMP-9matrix metalloproteinase 9;
  • Nrf2nuclear factor erythroid 2-related factor 2;
  • PI3Kphosphatidylinositol 3-kinase;
  • ROSreactive oxygen species;
  • SHHSonic hedgehog;
  • STATsignal transducers and activators of transcription;
  • TRAILtumor necrosis factor-related-apoptosis-inducing-ligand;
  • VEGFvascular endothelial growth factor

Keywords

  • Brucein D;
  • Chinese medicine;
  • Eriocalyxin B;
  • Gemcitabine;
  • Reactive oxygen species
 
Corresponding author at: School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Room 609A, Lo Kwee-Seong Integrated Biomedical Sciences Building, Shatin, New Territories, Hong Kong. Tel.: +852 3943 6879; fax: +852 2603 5123.
 Corresponding author contact informationSOURCE

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Cancer Labs at School of Medicine @ Technion: Janet and David Polak Cancer and Vascular Biology Research Center

Cancer Labs at School of Medicine @ Technion

Reporter: Aviva Lev-Ari, PhD, RN

Article ID #139: Cancer Labs at School of Medicine @ Technion: Janet and David Polak Cancer and Vascular Biology Research Center. Published on 5/28/2014

WordCloud Image Produced by Adam Tubman

Janet and David Polak Cancer and Vascular Biology Research CenterThe Rappaport Faculty of Medicine Research Institute and Faculty of Medicine, Technion – Israel Institute of Technology, Haifa, Israel

The center was established in 2003 to promote an in-depth interdisciplinary basic and clinical research on the control of cellular and molecular processes that are involved in cancer initiation and progression. We strongly believe that the understanding of basic biological processes that underlie normal development and their deregulation in cancer, is crucial for our ability to identify molecular targets for early detection, intervention, and cure of the disease. We are interested in a broad view of cancer – from the single malignantly transformed cell and its microenvironment, through the entire tumor in the animal. We focus on targeted ubiquitin-mediated degradation of key regulatory proteins that are involved in malignant transformation [Prof. Aaron Ciechanover (Nobel Prize in Chemistry 2004)], angiogenesis and cancer progression (Prof. Gera Neufeld), metastasis and tumor microenvironment (Prof. Israel Vlodavsky), as well as genetic and genomic dissection of embryonic and cancer transcriptional networks (Dr. Amir Orian). Towards these objectives, we combine molecular, biochemical, cell biological with Drosophila genetic and genomics experimental approaches, as well as employing advanced models of angiogenesis and metastasis.

We believe that scientific excellence and collegiality go together. Therefore, the center has an open and friendly atmosphere, creating a highly stimulating environment. The center is located in the 11th Floor of the Rappaport Faculty of Medicine building. It currently trains 45 graduate students, post-doctoral fellows, clinicians and researchers that are at the heart of our research. Formal and informal collaborations between individuals and laboratories are on-going and encouraged. We are running a series of joint seminars to which we invite researchers from Israel and abroad. The Center has advanced state-of-the-art microscopic and image analysis equipment, as well as other shared pieces of infrastructural equipment . The center is an integral part of the Faculty of Medicine and the Rappaport Research Institute which are home for excellent research groups, and enjoys their advanced Interdepartmental Equipment Unit. It is also adjacent to the Rambam Medical Center – the major hospital in the north of Israel – which provides us with access to rich clinical material and collaboration with clinicians. Many of them spend active research periods in our laboratories and bring the bench closer to the patient bed and vice versa. The Center is in an active phase of growth, and offers excellent research opportunities, space and facilities for students, post-doctoral fellows, and physicians.

Research Groups

The Ubiquitin System and Cellular Protein Turnover and Interactions

Immunity and Host Defense

Cardiovascular Biology

The Central Nervous System in Health and Disease

Developmental Biology and Cancer Research

Genetics

SOURCE 

http://www.rappaport.org.il/Rappaport/Templates/ShowPage.asp?DBID=1&TMID=842&FID=76

The cancer and vascular biology research center was established in 2003 to promote an in-depth interdisciplinary basic and clinical research on the control of cellular and molecular processes that are involved in cancer development and progression. Our goal is to advance knowledge in fundamental biological questions that are highly relevant for cancer.

The cancer and vascular biology research center was established in 2003 to promote an in-depth interdisciplinary basic and clinical research on the control of cellular and molecular processes that are involved in cancer development and progression. Our goal is to advance knowledge in fundamental biological questions that are highly relevant for cancer.

SOURCE

http://www.technioncancer.co.il/index.php

Home  >>  Research Groups

Aaron Ciechanover
Protein Turnover

Intracellular protein degradation and mechanisms of cancer
Israel Vlodavsky
Cancer Biology

Impact of heparanase and the tumor microenvironment on cancer progression: Basic aspects and clinical implications
Gera Neufeld
Tumor Progression & Angiogenesis

Blood vessels and tumor progression: The neuropilin connection
Amir Orian
Genetic Networks

Genetic networks in development and cancer
Home
About the Cancer Centers
Research Groups
Administration / Contact
Join – Us
Seminars and Events
Links
Beyond Science
Friends and supporters

Ms. Sigal Alfasi – Izrael, Center’s coordinator
e-mail: gsigal@tx.technion.ac.il
Tel: +972-4-829-5424
Fax: +972-4-852-3947

SOURCE

http://www.technioncancer.co.il/ResearchGroups.php

Yuval Shaked, PhD

Assistant Professor of Molecular Pharmacology

PhD, 2004 – Hebrew University, Israel

Understanding host – tumor interactions during cancer therapy

Personalized medicine holds promise of better cures with fewer side effects for many diseases. Individualized cancer therapy is sometimes utilized after multiple attempts of standard therapies and is based on several considerations, such as tumor type, acquired resistance to a specific therapy, previous treatment protocols, and other tumor-related factors. We have recently demonstrated that many cancer therapies can induce pro-tumorigenic or metastatic effects that derive not only from the tumor cells themselves, but also from host cells within the tumor microenvironment. The focus of research in my laboratory is to identify, characterize, and seek ways to block such pro-tumorigenic host effects observed after anti-cancer therapy, and thus potentially improve the outcome of current cancer therapies. Our findings may foster a paradigm shift in cancer therapy by minimizing the gap between preclinical findings and the clinical setting, laying the foundation for development of entirely new strategies for improving cancer therapy.

SOURCE

http://www.rappaport.org.il/Rappaport/Templates/ShowPage.asp?DBID=1&TMID=610&FID=77&PID=0&IID=1268

 

Other Related articled published on this Open Access Online Scientific Journal included the following:

D&D NT’s Solution: Galectin Proteins for Therapy and Diagnosis of Autoimmune Inflammatory and Cancer Diseases, Dr. Itshak Golan, CEO

http://pharmaceuticalintelligence.com/2014/05/28/dd-nts-solution-galectin-proteins-for-therapy-and-diagnosis-of-autoimmune-inflammatory-and-cancer-diseases-dr-itshak-golan-ceo/

MaimoniDex RA:  Monoclonal Antibodies for Therapy and Diagnosis of Cancer and Autoimmune Inflammatory Diseases – Dr. Itshak Golan, CEO

http://pharmaceuticalintelligence.com/2014/05/28/maimonidex-ra-monoclonal-antibodies-for-therapy-and-diagnosis-of-cancer-and-autoimmune-inflammatory-diseases-dr-itshak-golan-ceo/

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Levels of Tumor-associated Gene Expression & Cancer Biomarkers: OncoCyte’s PanC-Dx Diagnostic Tests of Cornell Medical College Blood Samples derived from Healthy and Lung Cancer Patients

Reporter: Aviva Lev-Ari, PhD, RN

OncoCyte, Cornell Collaborate on Lung Cancer Dx

NEW YORK (GenomeWeb) – BioTime subsidiary OncoCyte has entered into a deal with Cornell University to collaborate on developing a lung cancer diagnostic test, the parties announced today.

As part of the deal, Weill Cornell Medical College will provide blood samples derived from healthy patients and lung cancer patients. OncoCyte researchers will then use the firm’s PanC-Dx diagnostic tests to analyze the samples to determine levels of tumor-associated gene expression, including levels of the company’s proprietary PanC-Dx cancer biomarkers.

A data set from more than 700 patients will be produced that combines the results of the analyses with results from a clinical study being conducted by OncoCyte’s collaborators at the Wistar Institute. Those two entities announced a collaboration in the fall to develop a lung cancer diagnostic test.

Using the data, OncoCyte will evaluate potential cancer markers in order to develop a multimarker test for detecting lung cancer. OncoCyte retains all rights to develop and market its proprietary lung cancer diagnostic products under the terms of the deal, the partners said. Further financial and other terms were not disclosed.

PanC-Dx is a class of non-invasive diagnostic tests based on a set of cancer markers characterized by gene expression patterns in several cancer types. How the marker panel performs in determining disease progression in various categories of patients “will determine the specific nature of the test to be developed and the approval pathway that OncoCyte will pursue,” the partners said.

They noted that the US Preventative Services Task Force recently recommended that certain high-risk patients undergo annual screenings for lung cancer. The task force suggested screening using low-dose computed tomography, a technology that while sensitive in detecting early stage lung cancer in large clinical studies also has a high false-positive rate of about 25 percent.

OncoCyte CEO Joseph Wagner said in a statement that the high number of false-positive results could result in more than $1 billion annually in unnecessary healthcare costs in the US. “Physicians, payers, and patients would therefore welcome a simple to use, low-cost, blood-based test that can help guide patient management decisions by non-invasively ruling out the presence of cancer,” he said.

 

 

 

SOURCE

<a href="http://www.genomeweb.com//node/1394021?utm_source=SilverpopMailing&utm_medium=email&utm_campaign=Lab21,%20Novacyt%20Merger;%20Agilent%20SISCAPA%20Workflows;%20OncoCyte,%20Cornell%20Lung%20Cancer%20Dx%20Deal;%20More%20-%2005/27/2014%2004:00:00%20PM[/embed]">http://www.genomeweb.com//node/1394021?utm_source=SilverpopMailing&utm_medium=email&utm_campaign=Lab21,%20Novacyt%20Merger;%20Agilent%20SISCAPA%20Workflows;%20OncoCyte,%20Cornell%20Lung%20Cancer%20Dx%20Deal;%20More%20-%2005/27/2014%2004:00:00%20PM

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