Papers by Christos Patriotis
ABSTRACT The National Institutes of Health (NIH), National Cancer Institute's Early Detec... more ABSTRACT The National Institutes of Health (NIH), National Cancer Institute's Early Detection Research Network (EDRN) is a cross-institutional collaborative initiative seeking to accelerate the clinical application of cancer biomarker research. Over the past decade, it has been our role, as EDRN's Informatics Center (IC), to develop a comprehensive information services infrastructure as well as a set of software tools and services to support this overall initiative. We have recently developed a novel application called the Laboratory Catalog and Archive Service (LabCAS) whose focus is to extend EDRN IC data management and processing capabilities to EDRN laboratories. By leveraging the same technologies used to manage and process NASA Earth and Planetary data sets, we offer EDRN researchers an effective way of managing their laboratory data. More specifically, LabCAS enables EDRN researchers to reliably archive their experimental data, to optionally share these data in a controlled manner with other researchers, and to gain insight into these data through highly configurable data analysis pipelines tailored to the broad range of biomarker related experiments. This particular collaboration leverages expertise from NASA's Jet Propulsion Laboratory, Vanderbilt University Medical Center, and Dartmouth Medical School, as well as builds upon existing cross-governmental collaboration between NASA and the NIH.
Journal of Virology, Jul 1, 1993
Tpl-2 is a gene encoding a protein kinase which is primarily expressed in normal spleen, thymus, ... more Tpl-2 is a gene encoding a protein kinase which is primarily expressed in normal spleen, thymus, and lung tissue and is activated by provirus insertion in Moloney murine leukemia virus-induced T-cell lymphomas during the late stages of oncogenesis. Tpl-2 is composed of eight exons and spans a 35-kb genomic DNA region. The provirus integrates reproducibly in the last intron and in the same transcriptional orientation as the Tpl-2 gene. This genetic change leads to the expression of enhanced steady-state levels of a truncated Tpl-2 RNA transcript which is predicted to encode a protein with an altered C-terminal domain. Tpl-2 is transcribed from two alternating promoters, P1 and P2. The RNA transcripts originating in the two promoters harbor different 5' untranslated regions derived from the alternate noncoding exons IA and TB. Utilization of the P2 promoter, which gives rise to exon EB containing Tpl-2 RNA transcripts, was detected primarily in tumor cells. The Tpl-2 protein was expressed in COS-1 cells as an N-terminal fusion with a 12-amino-acid hemagglutinin tag. * Corresponding author. MATERIALS AND METHODS Tumors and cell lines. The MoMuLV-induced rat T-cell lymphomas and the cell lines derived from them have been described previously (17). Southern blot analysis of genomic cell DNA. DNA isolation, restriction enzyme digestion, agarose gel electrophoresis, Southern blot analysis, and hybridization were performed as previously described (1). Southern blotting was carried out with Hybond N (Amersham International) nylon membranes. The DNA was cross-linked on the membranes by UV irradiation. Labelling of DNA probes with [a-32P]dCTP was carried out with a random-prime-labelling kit (Amersham International). The filters were washed at a final stringency of 0.1x SSC (lx SSC is 0.15 M NaCl plus 0.015 M sodium citrate)-0.1% sodium dodecyl sulfate (SDS) at 65°C for at least 1 h. Northern (RNA) blot analysis of poly(A)-selected cell RNA.
Current cancer research, 2023
Springer eBooks, Nov 13, 2016
The incidence of cancer is increasing worldwide, owing to the trends toward increased lifespan an... more The incidence of cancer is increasing worldwide, owing to the trends toward increased lifespan and adaptation to western lifestyle. Although progress has been made in therapeutic and diagnostic strategies contributing to a slight reduction in mortality, cancer still remains a serious health condition and is often fatal. Many cancer deaths occur because the disease is usually diagnosed at advanced stages and has spread to distant organs with lymph node involvement, where most of the treatment options fail. It has been well demonstrated that if the disease is detected earlier the chances of 5-year cancer-free survival and reduction in mortality are better. For example, colon cancer survival rates for localized disease are 82–93 %, compared with only 5–8 % for cases with distant disease. Similarly, significant mortality reduction in cervical cancer cases is mainly due to the availability of effective screening strategies. Some cancers such as ovarian, pancreatic, and lung remain asymptomatic and are diagnosed at advanced stages with poor survival.
Biochemical and Biophysical Research Communications, Jul 1, 2003
Alteration in epidermal growth factor receptor (EGFR) family signaling is among the most frequent... more Alteration in epidermal growth factor receptor (EGFR) family signaling is among the most frequently implicated effectors of human oncogenesis. Overexpression of members of this family of receptors has often been detected in many epithelial tumors and is believed to be associated with an overall poor prognosis in patients with cancer. Therefore, we hypothesized that identification of potential EGF target genes in normal cells will provide a basis for unbiased genetic analysis of this signaling pathway in cancer. We utilized Atlas Rat 1.2 nylon cDNA arrays (Clontech) to determine gene expression changes in normal rat ovarian surface epithelial (ROSE) cells following EGF treatment. The results indicate activation of genes involved in a wide variety of cellular mechanisms, including regulation of cell cycle and proliferation, apoptosis, and protein turnover. In addition, using an in vitro model of ovarian cancer, we demonstrated that malignant transformation of ROSE cells resulted in alteration of downstream effectors of the EGFR pathway, as exemplified by aberrant expression of p66Shc, c-Jun, c-Myc, c-Fos, Lot1, p21Cip/Waf, and cdc25A. These data suggest that knowledge of the downstream genetic lesions, which may result in loss of growth factor requirement of the affected cells, will be crucial for the selection of the EGFR pathway as an effective target for cancer therapy.
Journal of Virology, Apr 1, 1994
Supplemental Figure and Table Legend
BI-RADS 1 and 2 Referred for Bx (< 1 month) Screening Normals n=950 1 Benign n=85 CIS n=15 Invasi... more BI-RADS 1 and 2 Referred for Bx (< 1 month) Screening Normals n=950 1 Benign n=85 CIS n=15 Invasive n=35 Blood Draw and Questionnaire Δ Time Subsequent Cancer n=17 Blood Draw and Questionnaire Benign n=377 2 CIS n=40 Invasive n=155 Blood Draw and Questionnaire n=15 n=2 Screening Mammogram Referred for Bx n=572 1 n=176 selected for inclusion in the reference set 2 n=211 selected for inclusion in the reference 3 set n=100 selected for inclusion in the reference set BIRADS 1 and 2 n=127 3 Supplemental Figure 2
... We have consulted with the application scientists at Arcturus on how to approach this ... Mic... more ... We have consulted with the application scientists at Arcturus on how to approach this ... Microarrayimages were processed using Agilent Feature Extraction software, v9.5. RNA sample quality ... inhuman ovarian cancers [4]. The results from this collaborative study strongly suggest ...
International Journal of Gynecological Cancer, May 1, 2012
T he discovery of cancer biomarkers has been plagued by several sample-related issues, in particu... more T he discovery of cancer biomarkers has been plagued by several sample-related issues, in particular, study designs and validation processes leading to unsatisfactory progress in the translation of biomarkers to clinical use. Most often, laboratory discoveries are made using convenience samples and without due consideration of intended clinical use. A recent clinical trial conducted by Early Detection Research Network (EDRN) investigators in collaboration with Specialized Program for Research Excellence and prostate, lung, colorectal and ovarian cancer investigators failed to identify any biomarkers from among more than 70 candidates tested that can detect ovarian cancer reliably more than 6 months before the manifestation of any clinical symptoms of the disease. The single best biomarker still remains to be CA-125, which has poor diagnostic performance for premalignant or early-stage disease. Furthermore, its increased levels are found in approximately 3% of postmenopausal women, resulting in a significant number of false positives for this biomarker. The study confirmed that although the HE4 biomarker performs almost as well as CA125, it does not add value to it. This outcome emphasizes the importance of using appropriate specimens for biomarker research, from early discovery stages to clinical validation. Bias introduced by systematic differences in the case and control specimens during biomarker discovery, which can significantly inflate the performance of biomarkers, must be maximally avoided by adapting the principles of Prospectivespecimen collection, Retrospective Blinded Evaluation (PRoBE) study design. Another factor for failure is the poor understanding of the natural history of the disease and the discovery of biomarkers in advanced cancer lesions, which may not be present in the preneoplastic and early neoplastic lesions that are the precursors of aggressively growing disease. In 2000, the National Cancer Institute established a network of investigators comprising basic scientists, epidemiologists, physicians, and bioinformaticians to address some of the biomarkers developmental issues. The network (EDRN; www.cancer.gov/edrn) has emerged as the leading platform supported by the National Cancer institute to systematically discover, develop, and validate biomarkers for assessing cancer risk, early cancer detection, and diagnosis and prognosis of cancer. The EDRN has developed a 5-phase schema and go/ no-go criteria for selecting biomarkers that are useful. In the 5-phase schema, phase 1 includes the exploratory discovery stage to identify potentially useful biomarkers. In phase 2, biomarkers are studied to determine their capacity for distinguishing between cases with cancer and those without. Phase 2 is called the validation phase. Repositories of longitudinally collected preclinical specimens from research cohorts are used in phase 3 to determine the capacity of a biomarker to detect preclinical disease. Phase 4 consists of the use of prospective screening studies. Finally, large-scale population studies that evaluate not just the role of the biomarker for the detection of cancer but the overall impact of screening on the population comprise phase 5. The criteria have been further expanded, especially for phases 2 and 3, which include the following (1) prospective collection of samples from the target population, (2) retrospective random sampling of cases and controls after the outcome status is ascertained. Specimens assayed for biomarkers are blinded to the case-control status. This design is also known as the PRoBE study design. The PRoBE design has been the basis of EDRN’s efforts to collect reference samples for quickly and cheaply evaluating biomarkers. The speaker will describe how EDRN is addressing some challenges associated with the discovery, development, and validation of biomarkers and will propose an international alliance of cohort consortia, which are engaged in screendetected and clinically detected ovarian and other cancers. It is hoped that one such collaboration will help us measure the extent of and potential ways to address overdiagnosis and to develop biomarkers of progression. SUPPLEMENT ARTICLE
John Wiley & Sons, Ltd eBooks, Jun 9, 2017
European journal of biochemistry, Sep 1, 1989
This study describes tightly bound DNA-protein complexes in DNA of matrices isolated from Friend ... more This study describes tightly bound DNA-protein complexes in DNA of matrices isolated from Friend erythroleukemia cells. When after radio-iodination of the associated proteins, such DNA is electrophoresed on agarose and the gel is subsequently subjected to autoradiography, the protein components of three or four complexes are visualized. Their two-dimentional electrophoretic analysis revealed that each possesses a simple but specific polypeptide composition, including a set of five non-histone proteins, characteristic for the matrix, and the core histones H3 and H4.
Cancer Cell, Dec 1, 2020
Cancer biomarker research has become a data-intensive discipline requiring innovative approaches ... more Cancer biomarker research has become a data-intensive discipline requiring innovative approaches for data analysis that can combine traditional and data-driven methods. Significant leveraging can be done transferring methodologies and capabilities across scientific disciplines, such as planetary science and astronomy, each of which are grappling with and developing similar solutions for the analysis of massive scientific data.
Nucleic Acids Research, 1993
Protein synthesis in cytosolic and rough endoplasmic reticulum associated ribosomes is directed b... more Protein synthesis in cytosolic and rough endoplasmic reticulum associated ribosomes is directed by factors, many of which have been well characterized. Although these factors have been the subject of intense study, most of the corresponding factors regulating protein synthesis in the mitochondrial ribosomes remain unknown. In this report we present the cloning and initial characterization of the gene encoding the rat mitochondrial elongation factor-G (rEF-G.J. The rat gene encoding EF-Gmt (rMefg) maps to rat chromosome 2 and it is expressed In all tissues with highest levels in liver, thymus and brain. Its DNA sequence predicts a 752 amino acid protein exhibiting 72% homology to the yeast Saccharomyces cerevisiae mitochondrial elongation factor-G (YMEF-G), 62% and 61 % homology to the Thermus thermophilus and E.coli elongation factor-G (EF-G) respectively and 52% homology to the rat elongation factor-2 (EF-2). The deduced amino acid sequence of EF-G contains characteristic motifs shared by all GTP binding proteins. Therefore, similarly to other elongation factors, the enzymatic function of EF-Gmt is predicted to depend on GTP binding and hydrolysis. EF-Gmt differs from its cytoplasmic homolog, EF-2, in that it contains an aspartic acid residue at amino acid position 621 which corresponds to the EF-2 histidine residue at position 715. Since this histidine residue, following posttranslational modification into diphthamide, appears to be the sole cellular target of diphtheria toxin and Pseudomonas aeruginosa endotoxin A, we conclude that EF-Gmt will not be inactivated by these toxins. The severe effects of these toxins on protein elongation in tissues expressing EF-G,mt suggest that EF-Gmt and EF-2 exhibit nonoverlapping functions. The cloning and characterization of the mammalian mitochondrial elongation factor G will permit us to address its role in the regulation of normal GenBank accession nos L14683, L14684 mitochondrial function and in disease states attributed to mitochondrial dysfunction.
DNA and Cell Biology, Sep 1, 1994
DNA of the attachment sites of Friend erythroleukemia cells, isolated according to the convention... more DNA of the attachment sites of Friend erythroleukemia cells, isolated according to the conventional procedure, represents short, nuclease-resistant fragments with sizes below 400 bp, belonging to the class of mouse satellite. A number of experiments have indicated that their unusual resistance is due to complexing with RNA. By various approaches, it was confirmed that similar fragments might be recovered from total DNA following extensive digestion with DNase I. In situ hybridizations revealed further that at mitosis the sequences of the attachment sites are located at the centromeric/telomeric regions of the chromosomes, while at interphase they are redistributed into 9-13 well-defined clusters spread throughout the entire nuclear area. Parallel biochemical and electronmicroscopic studies have clarified, moreover, that the all three compartments of the matrix harbor such sequences. Thus, it appears that the attachment sites described function only at interphase, anchoring the both ends of each interphase chromosome to the matrix structures.
Journal of Virology, Mar 1, 1993
Tumor progression locus 2 (Tpl-2) encodes a novel serine-threonine protein kinase which is activa... more Tumor progression locus 2 (Tpl-2) encodes a novel serine-threonine protein kinase which is activated by provirus integration in the late stages of oncogenesis in Moloney leukemia virus (MoMuLV) induced rat T-cell lymphomas. In this report, we present evidence that the provirus integrated in the Tpl-2 locus in 1 of 10 T-cell lymphomas harboring a Tpl-2 rearrangement (2779) is a recombinant between MoMuLV and virus-like 30 (VL3O) sequences (Mo-VL30). Recombination between MoMuLV and VL30 may contribute to the transduction ofras, as suggested by the finding that VL3O flanks the ras oncogene in all of the ras transducing viruses isolated from rats to date. The Mo-VL3O recombinant described here represents evidence that recombination between MoMuLV and VL30 can be uncoupled from the transduction of ras, and it may precede the transduction. Sequence comparison between clones of Mo-VL30, Harvey sarcoma virus (Ha-MSV), and genomic c-Ha-ras revealed that all three share a 124-bp region of 87.3% homology. This region was detected at nucleotide positions-1845 to-1720 of c-Ha-ras and 20 bp 5' of the recombination breakpoint between VL30 and ras in Ha-MSV. On the basis of the sequence comparison between VL30, Ha-MSV, and c-Ha-ras, we are proposing a model which explains how V13O may have facilitated the transduction of c-Ha-ras and perhaps the other ras proto-oncogenes. According to this model, the sequence homology between V130 and c-Ha-ras targets this gene for transduction by promoting the integration of the provirus in this locus through homologous recombination.
Journal of Virology, May 1, 1990
Moloney murine leukemia virus-induced rat T-cell lymphomas harbor proviruses integrated near c-my... more Moloney murine leukemia virus-induced rat T-cell lymphomas harbor proviruses integrated near c-myc and near Mlvi-l/Mis-llPvt-1, another locus of common integration which maps 270 kilobases 3' of c-myc. In this report, we present the characterization of a new locus of common integration in Moloney murine leukemia virus-induced T-cell lymphomas (Mlvi4) which maps 30 kilobases 3' of c-myc, between c-myc and Mlvi-1. The Mlvi4 locus, whose chromosomal map location is conserved in rats, mice, and humans, is also the target of chromosomal rearrangements in a variety of animal and human tumors. Evidence presented elsewhere shows * Corresponding author. presented elsewhere showed that provirus integration in Mlvi4 also activates c-myc (1Sa) and Mlvi-1 (31, 32) by cis-acting mechanisms operating over long distances of genomic DNA. Provirus insertion in this locus, therefore, affects the expression of at least three genes, c-myc, Mlvi-1, and Mlvi4, the first two of which are located at a significant distance from the site of integration.
Nature Reviews Cancer, Sep 6, 2021
Detection of cancer at an early stage when it is still localized improves patient response to med... more Detection of cancer at an early stage when it is still localized improves patient response to medical interventions for most cancer types. The success of screening tools such as cervical cytology to reduce mortality has spurred significant interest in new methods for early detection (for example, using non-invasive blood-based or biofluid-based biomarkers). Yet biomarkers shed from early lesions are limited by fundamental biological and mass transport barriers-such as short circulation times and blood dilution-that limit early detection. To address this issue, synthetic biomarkers are being developed. These represent an emerging class of diagnostics that deploy bioengineered sensors inside the body to query early-stage tumours and amplify disease signals to levels that could potentially exceed those of shed biomarkers. These strategies leverage design principles and advances from chemistry, synthetic biology and cell engineering. In this Review, we discuss the rationale for development of biofluid-based synthetic biomarkers. We examine how these strategies harness dysregulated features of tumours to amplify detection signals, use tumour-selective activation to increase specificity and leverage natural processing of bodily fluids (for example, blood, urine and proximal fluids) for easy detection. Finally, we highlight the challenges that exist for preclinical development and clinical translation of synthetic biomarker diagnostics.
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Papers by Christos Patriotis