Song B.P.,Drexel University |
Jain S.,Drexel University |
Lin S.Y.,Drexel University |
Chen Q.,Drexel University |
And 4 more authors.
Journal of Molecular Diagnostics | Year: 2012
We demonstrated previously that urine contains low-molecular-weight (LMW) (<300 bp), circulation-derived DNA that can be used to detect cancer-specific mutations if a tumor is present. The goal of this study was to develop an assay to detect the colorectal cancer (CRC)associated, circulation-derived, epigenetic DNA marker hypermethylated vimentin gene (mVIM) in the urine of patients with CRC. An artificial 18-nucleotide DNA sequence was tagged at the 5′ end of the primers of the first PCR cycle to increase the amplicon size, which was then integrated into the primers of the second PCR cycle. A quantitative MethyLight PCR-based assay targeting a 39-nucleotide template was developed and used to quantify mVIM in CRC tissues and matched urine samples. mVIM was detected in 75% of LMW urine DNA samples from patients with CRC (n = 20) and in 10% of urine samples of control subjects with no known neoplasia (n = 20); 12 of 17 LMW urine DNA samples (71%) but only 2 of 17 high-molecular- weight urine DNA samples (12%) from patients with mVIM-positive tissues contained detectable mVIM, suggesting that the mVIM detected in LMW urine DNA is derived from the circulation. The detection of mVIM in urine was significantly associated with CRC compared with controls (P < 0.0001, by Fisher's exact test). A potential urine test for CRC screening using epigenetic markers is discussed. © 2012 American Society for Investigative Pathology and the Association for Molecular Pathology.
Su Y.-H.,Drexel University |
Lin S.Y.,Drexel University |
Song W.,Jbs Science, Inc. |
Song W.,Screen Inc. |
And 2 more authors.
Expert Review of Molecular Diagnostics | Year: 2014
Hepatocellular carcinoma (HCC) is the one of the leading causes of cancer mortality in the world, mainly due to the difficulty of early detection and limited therapeutic options. The implementation of HCC surveillance programs in well-defined, high-risk populations were only able to detect about 40-50% of HCC at curative stages (Barcelona Clinic Liver Cancer stages 0 & 1) due to the low sensitivities of the current screening methods. The advance of sequencing technologies has identified numerous modifications as potential candidate DNA markers for diagnosis/surveillance. Here we aim to provide an overview of the DNA alterations that result in activation of cancer pathways known to potentially drive HCC carcinogenesis and to summarize performance characteristics of each DNA marker in the periphery (blood or urine) for HCC screening. © 2014 Informa UK, Ltd.
Jbs Science, Inc. | Date: 2013-11-14
Provided herein is a method for detecting the presence or absence of a cancer in a biological sample of an individual, by determining the level of mutation and methylation of one or more genes from a group of genes comprising TP53, CTNNB1, hTERT, RASSF1A, GSTP1, p16, p15 and SFRP-1. Also provided herein is an assay to detect p53 mutations suitable for DNA isolated from biological body fluid in order to screen cancer patients. Also provided is a method for detecting the presence or absence of a liver cancer in an individual by determining the level of methylation. Also provided is a suitable method for detecting the presence or absence of a liver cancer in an individual by determining the level of methylation of the promoter of the GSTP1 gene in body fluid such as urine or blood. Also provided is a suitable method for detecting the presence or absence of a liver cancer in an individual by determining the level of methylation of the promoter of the RASSF1A gene in body fluid such as urine or blood.
Agency: Department of Health and Human Services | Branch: National Institutes of Health | Program: SBIR | Phase: Phase I | Award Amount: 300.00K | Year: 2016
Urine DNA Kit for monitoring HCC recurrence This SBIR phase I application is to test the feasibility of developing HCC urine DNA biomarkers to address the critical unmet need for a noninvasive sensitive monitoring tool for early detection of hepatocellular carcinoma HCC recurrence HCC incidence has doubled overall in the past two decades making it one of the fastest growing malignancies in the United States and a leading cause of cancer related deaths globally There is greater than a chance of recurrence of which occurs within years in HCC patients who undergo curative therapy resection transplantation or local ablation thus limiting overall survival Currently post treatment monitoring guidelines are unclear and patients are typically monitored every months by serum AFP and imaging such as ultrasound and MRI for the first years with increasing intervals thereafter JBS Science is pioneering the development of assays detecting HCC urine DNA markers for HCC detection and management This application will apply three already developed and patented short amplicon assays TP T mRASSF A and mGSTP and develop short amplicon assays for additional known HCC hotspot mutations CTNNB and TERT promoter mutations for development of a urine DNA kit for monitoring HCC recurrence This proposal aims to test the feasibility of early detection of HCC recurrence using these five marker assays in patients treated with curative interventions Two aims are proposed Aim is for assay development and Aim is to determine the performance of the HCC urine DNA kit for detection of HCC recurrence as compared to serum AFP We will prospectively collect serial urine samples from at least HCC patients after treatment at follow up office visits from two clinical sites Johns Hopkins University and Thomas Jefferson University for monitoring recurrence Marker values will be determined for each urine sample by our urine DNA kit and analyzed for the performance of JBS urine DNA kit to screen for HCC recurrence alone or in combination with serum AFP In addition we will determine whether the urine DNA biomarker test can detect HCC earlier than current imaging MRI CT scan This proposal will lead to the development of a method that can detect HCC recurrence earlier than the current methods by either replacing or combining AFP with a simple and non invasive urine DNA test This will bring more patients to sophisticated imaging diagnosis such as MRI or CT in a quick and accurate manner in locating the tumor for treatment PUBLIC HEALTH RELEVANCE Liver cancer is leading cause of cancer related deaths globally and one of the most fatal cancers worldwide mainly due to late detection and a high recurrence rate andgt Current post treatment monitoring guidelines are not clear and there is a need to develop an effective method for noninvasive and sensitive monitoring for liver cancer recurrence The goal of this Phase I project is to develop a urine DNA test that can detect liver cancer recurrence earlier than the current methods by analyzing liver cancer associated genetic alterations
Agency: Department of Health and Human Services | Branch: National Institutes of Health | Program: SBIR | Phase: Phase II | Award Amount: 1.90M | Year: 2013
DESCRIPTION provided by applicant Development of a urine test for the early detection of liver cancer The need to develop an effective method of detecting hepatocellular carcinoma HCC is urgent HCC is the third leading cause of cancer deaths and has a year survival rate of less than If HCC is identified early the survival rate can be as high as The survival rate drops significantly however to as low as if the cancer has spread to other organs The goal of this project is to develop a noninvasive urine based diagnostic test that would allow for early detection of liver cancer Such a test if applied to high risk populations o surveyed patients could significantly increase survival rates and could contribute to improved quality and duration of life Conventional diagnostic methods such as ultrasound imaging and the AFP blood test are either expensive ultrasound or relatively insensitive AFP blood test sensitivity to early stage I II HCC We propose a new diagnostic method based on our phase I marker urine test for detecting small fractions of HCC derived genetically and epigenetically modified DNA present in the urine of patients with liver cancer JBS Science Inc has successfully accomplished the phase I study that demonstrates feasibility in several key areas of this proposal Encouragingly the JBS phase I HCC urine test had a sensitivity of and a specificity of and was able to detect of AFP negative HCC which represents of HCC in a well controlled open labeled study using archived urine DNA samples The goal of this phase II study is to further develop the urine test to detect at least of the urin samples from patients with early stage stages I II HCC in a blinded pre validation study and obtain sufficient information to prepare for a large multicenter validation study PUBLIC HEALTH RELEVANCE The need is urgent to have an effective method for noninvasive detection of early stage liver cancer which is the third leading cause of cancer death worldwide and has one of the highest recurrence rates The current standard methods for screening rely on the serum level of alpha fetoprotein which has only sensitivity The goal of this project is to develop a urine DNA test to detect early stages of liver cancer by analyzing liver cancer associated genetic and epigenetic modifications
Agency: Department of Health and Human Services | Branch: National Institutes of Health | Program: SBIR | Phase: Phase I | Award Amount: 225.00K | Year: 2015
DESCRIPTION provided by applicant This SBIR phase I application is being submitted in response to the Program Announcement PAR entitled andquot Methods of Development for Obtaining Comprehensive Genomic Information from Human Specimens that are Easy to collect and store andquot This proposal specifically addresses the request for sensitive and cost effective technologies for obtaining high quality and comprehensive genomic data from urine which is both an easy to collect and easy to handle form of human specimen We have already developed the standard operating procedures SOP to collect urine for genetic studies which can be used for research purposes that have been implemented in the NCI EDRN funded validation study protocol ID We have also developed a patented fractionation method that enables us to separate the DNA into two distinct species based on fragment sizes DNA larger than kb is designated as high molecular weight HMW DNA which is mostly derived from the cell debris of the urinary tract Conversely the DNA ranging from to bp is designated as low molecular weight LMW DNA which is derived mostly from the circulation We have shown that LMW DNA can be used for the detection of circulation derived genetic markers of cancer if the tumor is present In phase I Aim of this application is to demonstrate that HMW urine DNA can replace whole blood as a DNA source for obtaining comprehensive and high quality genomic information We will also demonstrate that LMW urine DNA can be a source for cell free apoptotic DNA for detecting somatic acquired genetic variants from the entire body similar to plasma DNA Aim We propose to use TP codon mutations as a somatic mutation marker to compare the LMW urine DNA and plasma DNA for the sensitivity of detecting circulation derived mutations In phase II we propose to develop the urine DNA collection kit JBS Hi Lo urine DNA kit to optimize the use of urine which is both easy to collect and easy to handle including sample transportation and storage for clinical use It is anticipated that this proposal will lead to the development of a kit that will provide a complete end to end solution that addresses all the steps from sample collection and nucleic acid extraction to sequencing for obtaining complete genomic information with various applications in both clinic and research PUBLIC HEALTH RELEVANCE With advancing genomic technologies and simultaneous falling costs of whole genome sequencing and analysis there is an opportunity to enhance clinical and public health value of genetic tests by expanding them to deliver comprehensive genomic data from human specimens that are easy to collect and handle We propose our method of using urine DNA which is absolutely non invasive and is of particular value in remote and under sourced environments The goal of this project is to develop the JBS Hi Lo urine DNA kit that will provide a complete end to end solution to address all the steps from sample collection and nucleic acid extraction to next generation sequencing NGS for obtaining complete genomic information for various applications in clinic and research
Jbs Science, Inc. | Date: 2015-06-16
This application relates to a DNA marker for HBV-HCC detection and the methods, kits for quantitatively measuring the amount of HBV DNA and bisulfite treated HBV DNA, and methylated HBV DNA, and the aberrant methylation of the HBV genome for the used in the chronic HBV infected populations. Detection of the presence or absence of HCC, with elevated methylation levels in the one or more regions of DNA of the mammals as compared to the level of methylation in the one or more regions of DNA in the one or more control body fluids or tissues indicating the presence of the cancer, and the absence of elevated methylation levels indicating the absence of HCC.
PubMed | Jbs Science, Inc.
Type: | Journal: The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society | Year: 2016
Recently, we demonstrated that treatment with all-trans-retinoic acid (tRA) induced a paradoxical effect on immune activation during the development of autoimmune lupus. Here, we further describe its negative effects on mediating neuroinflammation and neurodegeneration. Female MRL/lpr mice were orally administered tRA or VARA (retinol mixed with 10% tRA) from 6 to 14 weeks of age. Both treatments had a significant effect on brain weight, which correlated with histopathological evidence of focal astrogliosis, meningitis, and ventriculitis. Infiltration of CD138- and Iba1-positve immune cells was observed in the third ventricle and meninges of treated mice that co-labeled with ICAM-1, indicating their inflammatory nature. Increased numbers of circulating plasma cells, autoantibodies, and total IgG were also apparent. IgG and C3 complement deposition in these brain regions were also prominent as was focal astrogliosis surrounding the ventricular lining and meninges. Using Fluoro-Jade staining, we further demonstrate that neuroinflammation was accompanied by neurodegeneration in the cortex of treated mice compared with vehicle controls. These findings indicate that vitamin A exposure exacerbates the immunogenic environment of the brain during the onset of systemic autoimmune disease. Vitamin A may therefore compromise the immuno-privileged nature of the central nervous system under a predisposed immunogenic environment.
Agency: Department of Health and Human Services | Branch: | Program: SBIR | Phase: Phase I | Award Amount: 247.25K | Year: 2012
DESCRIPTION (provided by applicant): The need to develop an effective method of detecting primary and recurrent hepatocellular carcinoma (HCC) is urgent. HCC is the third leading cause of cancer deaths and has a 5-year survival rate of less than 10%. If HCC is identified early, the survival rate can be as high as 40%. The survival rate drops significantly, however, to as low as 2% if the cancer has spread to other organs. HCC is also characterized by a high recurrence rate (60%-70%). Consequently, patientswith HCC must undergo imaging studies and a blood test to determine alpha- fetoprotein (AFP) levels every 6 months. The goal of this project is to explore the feasibility of a noninvasive, urine-based diagnostic test that would allow early detection of newonset and recurrent liver cancer and that would provide an effective tool for cancer management. Such a test, if applied to high-risk populations or surveyed patients, could significantly increase survival rates and could contribute to improved quality and duration of life Conventional diagnostic methods, such as ultrasound imaging and the AFP blood test, are either expensive (ultrasound) or relatively insensitive (AFP blood test). We propose a new diagnostic method, based on our progress in detecting theHCC-specific p53 mutation in the urine of patients with HCC that will enable detection of small fractions of HCC-derived genetic and epigenetically modified DNA present in the urine of patients with liver cancer. JBS Science Inc. has performed preliminaryexperiments that demonstrate feasibility in several key areas of this proposal. The aim will be to detect mutations in the p53 codon 249 (which is specific for HCC), and aberrant hypermethylation of the APC and GSTP-1 genes in at least 90% of the urine samples from patients whose HCC tissues are marker-positive. In phase II, we will further develop and evaluate the urine DNA test using clinical samples for the early detection of liver cancer based on the results from phase I. PUBLIC HEALTH RELEVANCE: There is a need to develop an effective method for noninvasive detection of early-stage liver cancer, which is the third leading cause of cancer deaths worldwide and has one of the highest recurrence rates. The current standard methods for screening rely on the serum level of alpha-fetoprotein, which has only 60% sensitivity. The goal of this phase I project is to explore the ability of a urine DNA test to detect early stages o liver cancer by analyzing liver cancer-associated genetic and epigenetic modifications.
Agency: Department of Health and Human Services | Branch: | Program: SBIR | Phase: Phase I | Award Amount: 300.00K | Year: 2012
DESCRIPTION (provided by applicant): Our overall goal is to develop a urine DNA-based screening test for the early detection of colorectal cancer (CRC) that is noninvasive, patient-friendly, and more sensitive than existing noninvasive screening tests. Despite the availability of colonoscopy, the current standard of care for CRC screening, CRC remains the nation's second leading cause of cancer mortality because of the low compliance (lt 40%) due to inconvenience, fear of discomfort, and the risk involvedin the invasive screening test. The 5-year survival rate for CRC is 93% if it is diagnosed at stage I but only 8% if diagnosed at stage IV [1, 2]. Thus, the need is urgent to increase CRC screening for more than 70 million people in the United States age50 and older. Current available noninvasive CRC screening tests include the fecal occult blood test (FOBT), fecal immunochemical test (FIT), the stool DNA test (PreGenPlus, Exact Sciences, Maynard, MA), next generation stool DNA test, and the Septin 9 plasma test. Unfortunately, the high cost, the inconvenience of sample collection, or the low sensitivities of these tests result in an overall less than satisfactory compliance rate (~60%) for CRC screening. Therefore, a less unpleasant, noninvasive, low cost, and highly sensitive screening test is needed to enhance the compliance rate and to increase the rate of early detection of advanced adenoma and CRC to improve the prognosis of the disease. Urine contains nucleic acids that can be used for the early detection of diseases and cancers that occur at non-urinary tract sites. We have successfully detected mVIM in urine of patients with CRC with a sensitivity of 75% in a small pilot study. Based on these data, our mVIM urine test has been included in the EDRN 6000-subject phase II validation study (Protocol ID 320). JBS Science Inc. has performed preliminary experiments and proposes to develop a JBS CRC urine test detecting three markers, mVIM and mutated K-ras and BRAF DNA, to ensure that at least 70% sensitivity to detect CRC can be obtained in a blinded prevalidation study. JBS Science Inc has demonstrated the feasibility of several key areas of this proposal. The goal of this application will be to develop robust assays for K-ras and BRAF mutations combined with a developed mVIM assay for the JBS CRC urine test (Aim 1) and to train this test in an open-label training set and then validate this test in a blinded test set of urine samples (Aim 2) in the phase I study In phase II, we will further develop and evaluate the urine DNA test in a large validation study. PUBLIC HEALTH RELEVANCE: There is an urgent need to develop a sensitive, patient-friendly, noninvasive screening test to identify individuals who have high likelihood of having CRC and bring them to colonoscopy for confirmation and treatment, so CRC can be detected earlier and the prognosis of the disease can be improved. The goal of this phase I project is to explore the ability of a urine DNA test to detect early stages of colon cancer by analyzing colon cancer-associated genetic and epigenetic modifications.