Showing papers in "Disease Markers in 2004"
TL;DR: The present update of the database of DNA mismatch repair gene mutations of INSiGHT includes 448 mutations that primarily involve MLH1, MSH2, and MSH6 and occur in 748 families from different parts of the world.
Abstract: In 1994, the International Collaborative Group on Hereditary Nonpolyposis Colorectal Cancer (ICG-HNPCC) established an international database of mutations identified in families with Lynch (HNPCC) syndrome. The data are publicly available at http://www.nfdht.nl. The information stored in the database was systematically analyzed in 1997, and at that time, 126 different predisposing mutations were reported affecting the DNA mismatch repair genes MSH2 and MLH1 and occurring in 202 families. In 2003, the ICG-HNPCC and the Leeds Castle Polyposis Group (LCPG) merged into a new group, INSiGHT (International Society for Gastrointestinal Hereditary Tumors). The present update of the database of DNA mismatch repair gene mutations of INSiGHT includes 448 mutations that primarily involve MLH1 (50%), MSH2 (39%), and MSH6 (7%) and occur in 748 families from different parts of the world.
445 citations
TL;DR: It is demonstrated that mononucleotides are the most sensitive and specific markers for detection of tumors with defects in MMR and the new MSI Multiplex System meets the new recommendations proposed at the recent NCI workshop on HNPCC and MSI testing and overcomes problems inherent to the original five-marker panel.
Abstract: Determining whether a tumor exhibits microsatellite instability (MSI) is useful in identifying patients with hereditary non-polyposis colorectal cancer and sporadic gastrointestinal cancers with defective DNA mismatch repair (MMR). The assessment of MSI status aids in establishing a clinical prognosis and may be predictive of tumor response to chemotherapy. A reference panel of five markers was suggested for MSI analysis by a National Cancer Institute (NCI) workshop in 1997 that has helped to standardize testing. But this panel of markers has limitations resulting from the inclusion of dinucleotide markers, which are less sensitive and specific for detection of tumors with MMR deficiencies compared to other types of markers that are currently available. This study demonstrates that mononucleotides are the most sensitive and specific markers for detection of tumors with defects in MMR and identifies an optimal panel of markers for detection of MSI-H tumors. A set of 266 mono-, di-, tetra- and penta-nucleotide repeat microsatellite markers were used to screen for MSI in colorectal tumors. The best markers for detection of MSI-H tumors were selected for a MSI Multiplex System, which included five mononucleotide markers: BAT-25, BAT-26, NR-21, NR-24 and MONO-27. In addition, two pentanucleotide markers were added to identify sample mix-ups and/or contamination. We classified 153 colorectal tumors using the new MSI Multiplex System and compared the results to those obtained with a panel of 10 microsatellite markers combined with immunohistochemical (IHC) analysis. We observed 99% concordance between the two methods with nearly 100% accuracy in detection of MSI-H tumors. Approximately 5% of the MSI-H tumors had normal levels of four MMR proteins and as a result would have been misclassified based solely on IHC analysis, emphasizing the importance of performing MSI testing. The new MSI Multiplex System offers several distinct advantages over other methods of MSI testing in that it is both extremely sensitive and specific and amenable to high-throughput analysis. The MSI Multiplex System meets the new recommendations proposed at the recent 2002 NCI workshop on HNPCC and MSI testing and overcomes problems inherent to the original five-marker panel. The use of a single multiplex fluorescent MSI assay reduces the time and costs involved in MSI testing with increased reliability and accuracy and thus should facilitate widespread screening for microsatellite instability in tumors of patients with gastrointestinal cancers.
260 citations
TL;DR: Two types of ultrasound-mediated biophotonic imaging are reviewed–acousto-optical tomography and photo-acoustic tomography–both of which are based on non-ionizing optical and ultrasonic waves.
Abstract: This article reviews two types of ultrasound-mediated biophotonic imaging–acousto-optical tomography (AOT, also called ultrasound-modulated optical tomography) and photo-acoustic tomography (PAT, also called opto-acoustic or thermo-acoustic tomography)–both of which are based on non-ionizing optical and ultrasonic waves. The goal of these technologies is to combine the contrast advantage of the optical properties and the resolution advantage of ultrasound. In these two technologies, the imaging contrast is based primarily on the optical properties of biological tissues, and the imaging resolution is based primarily on the ultrasonic waves that either are provided externally or produced internally, within the biological tissues. In fact, ultrasonic mediation overcomes both the resolution disadvantage of pure optical imaging in thick tissues and the contrast and speckle disadvantages of pure ultrasonic imaging. In our discussion of AOT, the relationship between modulation depth and acoustic amplitude is clarified. Potential clinical applications of ultrasound-mediated biophotonic imaging include early cancer detection, functional imaging, and molecular imaging.
249 citations
TL;DR: This chapter provides a background on the principles and practice of AFM elastography and reviews the literature comparing cell mechanics in normal and diseased states, making a case for the use of such measurements as disease markers.
Abstract: The atomic force microscope (AFM) is emerging as a powerful tool in cell biology. Originally developed for high-resolution imaging purposes, the AFM also has unique capabilities as a nano-indenter to probe the dynamic viscoelastic material properties of living cells in culture. In particular, AFM elastography combines imaging and indentation modalities to map the spatial distribution of cell mechanical properties, which in turn reflect the structure and function of the underlying cytoskeleton. Such measurements have contributed to our understanding of cell mechanics and cell biology and appear to be sensitive to the presence of disease in individual cells. This chapter provides a background on the principles and practice of AFM elastography and reviews the literature comparing cell mechanics in normal and diseased states, making a case for the use of such measurements as disease markers. Emphasis is placed on the need for more comprehensive and detailed quantification of cell biomechanical properties beyond the current standard methods of analysis. A number of technical and practical hurdles have yet to be overcome before the method can be of clinical use. However, the future holds great promise for AFM elastography of living cells to provide novel biomechanical markers that will enhance the detection, diagnosis, and treatment of disease.
226 citations
TL;DR: This article compares the advantages of mono or din nucleotide repeats in determining microsatellite instability and proposes a pentaplex MSI screening test comprising 5 quasimonomorphic mononucleotide repeats.
Abstract: Microsatellite instability (MSI) analysis is becoming more and more important to detect sporadic primary tumors of the MSI phenotype as well as in helping to determine Hereditary Non-Polyposis Colorectal Cancer (HNPCC) cases. After some years of conflicting data due to the absence of consensus markers for the MSI phenotype, a meeting held in Bethesda to clarify the situation proposed a set of 5 microsatellites (2 mononucleotide repeats and 3 dinucleotide repeats) to determine MSI tumors. A second Bethesda consensus meeting was held at the end of 2002. It was discussed here that the 1998 microsatellite panel could underestimate high-level MSI tumors and overestimate low-level MSI tumors. Amongst the suggested changes was the exclusive use of mononucleotide repeats in place of dinucleotide repeats. We have already proposed a pentaplex MSI screening test comprising 5 quasimonomorphic mononucleotide repeats. This article compares the advantages of mono or dinucleotide repeats in determining microsatellite instability.
160 citations
TL;DR: There continues to be some debate as to whether a discrete MSI-L group truly exists, and future studies will need to evaluate the specific mutations in non-MSI-H tumors in an attempt to sub-classify MSI-L tumors with regard to MSS tumors so that subtle differences between these two sub-groups can be identified.
Abstract: Microsatellite instability (MSI) is a well-recognized phenomenon that is classically a feature of tumors in the hereditary non-polyposis colorectal syndrome. Ten to 15% of sporadic colorectal cancers, however, will have MSI. Microsatellite unstable tumors can be divided into two distinct MSI phenotypes: MSI-high (MSI-H) and MSI-low (MSI-L). MSI sporadic colorectal cancers with a high level of MSI (MSI-H) form a well defined group with distinct clinicopathologic features characterized by an overall better long-term prognosis. These sporadic MSI-H colorectal tumors most often arise from the epigenetic silencing of the mismatch repair gene MLH1. In contrast, MSI-L colorectal tumors have not been shown to differ in their clinicopathologic features or in most molecular features from microsatellite stable (MSS) tumors. Unlike MSI-H tumors, MSI-L tumors appear to arise through the chromosomal instability carcinogenesis pathway, similar to MSS tumors. Some groups have reported more frequent mutations in K-ras and in the methylation of methylguanine transferase in MSI-L tumors, but others have questioned these findings. Therefore, although the use of the MSI-L category is widespread, there continues to be some debate as to whether a discrete MSI-L group truly exists. Rather, it has been suggested that MSI-L tumors differ quantitatively from MSS tumors but do not differ qualitatively. Future studies will need to evaluate the specific mutations in non-MSI-H tumors in an attempt to sub-classify MSI-L tumors with regard to MSS tumors so that subtle differences between these two sub-groups can be identified.
127 citations
TL;DR: Initial results indicate the utility of protein profiling approaches for developing new diagnostic and prognostic assays for breast cancers in women with BRCA-1 breast cancers.
Abstract: Surface enhanced laser desorption/ionization (SELDI) time-of-flight mass spectrometry has emerged as a successful tool for serum based detection and differentiation of many cancer types, including breast cancers. In this study, we have applied the SELDI technology to evaluate three potential applications that could extend the effectiveness of established procedures and biomarkers used for prognostication of breast cancers. Paired serum samples obtained from women with breast cancers prior to surgery and post-surgery (6–9 mos.) were examined. In 14/16 post-treatment patients, serum protein profiles could be used to distinguish these samples from the pre-treatment cancer samples. When compared to serum samples from normal healthy women, 11 of these post-treatment samples retained global protein profiles not found in healthy women, including five low-mass proteins that remained elevated in both pre-treatment and post-treatment serum groups. In another pilot study, serum profiles were compared for a group of 30 women who were known BRCA-1 mutation carriers, half of whom subsequently developed breast cancer within three years of the sample procurement. SELDI protein profiling accurately classified 13/15 women with BRCA-1 breast cancers from the 15 non-cancer BRCA-1 carriers. Additionally, the ability of SELDI to distinguish between the serum profiles from sentinel lymph node positive and sentinel lymph node negative patients was evaluated. In sentinel lymph node positive samples, 22/27 samples were correctly classified, in comparison to the correct classification of 55/71 sentinel lymph node negative samples. These initial results indicate the utility of protein profiling approaches for developing new diagnostic and prognostic assays for breast cancers.
92 citations
TL;DR: This review seeks to concisely address the physics, instrumentation, advancements in tomography, and near-infrared fluorescent contrast agent development that promises selective and specific molecular targeting of diseased tissues.
Abstract: The advent of recent advances in near-infrared laser diodes and fast electro-optic detection has spawned a new research field of diagnostic spectroscopy and imaging based on targeting and reporting exogenous fluorescent agents. This review seeks to concisely address the physics, instrumentation, advancements in tomography, and near-infrared fluorescent contrast agent development that promises selective and specific molecular targeting of diseased tissues. As an example of one area of the field, recent work focusing on pharmacokinetic analysis of fluorophores targeting the epidermal growth factor receptor (EGFR) is presented in a human breast cancer xenograft mouse model to demonstrate specificity of molecularly targeted contrast agents. Finally, a critical evaluation of the limitations and the opportunities for future translation of fluorescence-enhanced optical imaging of deep tissues is presented.
89 citations
TL;DR: By correlating DOS-derived parameters with lesion pathology and specific molecular markers, it is anticipated that composite “tissue optical indices” can be developed that non-invasively characterize both tumor and normal breast-tissue function.
Abstract: Diffuse optical spectroscopy (DOS) of breast tissue provides quantitative, functional information based on optical absorption and scattering properties that cannot be obtained with other radiographic methods. DOS-measured absorption spectra are used to determine the tissue concentrations of deoxyhemoglobin (Hb-R), oxyhemoglobin (Hb-O2), lipid, and water (H2O), as well as to provide an index of tissue hemoglobin oxygen saturation (StO2). Tissue-scattering spectra provide insight into epithelial, collagen, and lipid contributions to breast density. Clinical studies of women with malignant tumors show that DOS is sensitive to processes such as increased tissue vascularization, hypoxia, and edema. In studies of healthy women, DOS detects variations in breast physiology associated with menopausal status, menstrual cycle changes, and hormone replacement. Current research involves using DOS to monitor tumor response to therapy and the co-registration of DOS with magnetic resonance imaging. By correlating DOS-derived parameters with lesion pathology and specific molecular markers, we anticipate that composite “tissue optical indices” can be developed that non-invasively characterize both tumor and normal breast-tissue function.
86 citations
TL;DR: The use of MS is reviewed in the process of cardiac biomarker discovery and validation by proteomic analysis of cardiac myocytes/tissue or serum/plasma and an example of MS in protein validation is given.
Abstract: Heart disease is the leading cause of mortality and morbidity in the world. As such, biomarkers are needed for the diagnosis, prognosis, therapeutic monitoring and risk stratification of acute injury (acute myocardial infarction (AMI)) and chronic disease (heart failure). The procedure for biomarker development involves the discovery, validation, and translation into clinical practice of a panel of candidate proteins to monitor risk of heart disease. Two types of biomarkers are possible; heart-specific and cardiovascular pulmonary system monitoring markers. Here we review the use of MS in the process of cardiac biomarker discovery and validation by proteomic analysis of cardiac myocytes/tissue or serum/plasma. An example of the use of MS in biomarker discovery is given in which the albumin binding protein sub-proteome was examined using MALDI-TOF MS/MS. Additionally, an example of MS in protein validation is given using affinity surface enhanced laser desorption ionization (SELDI) to monitor the disease-induced post-translational modification and the ternary status of myoctye-originating protein, cardiac troponin I in serum.
79 citations
TL;DR: A set of protocols for the isolation and identification of serum biomarkers for ovarian cancer that exist in the low molecular weight serum fraction is delineated and one of these contains the sequence of fibrinopeptide-A known to be elevated in many types of cancer including ovarian cancer.
Abstract: Treatment of cancer patients is greatly facilitated by detection of the cancer prior to metastasis. One of the obstacles to early cancer detection is the lack of availability of biomarkers with sufficient specificity. With modern differential proteomic techniques, the potential exists to identify high specificity cancer biomarkers. We have delineated a set of protocols for the isolation and identification of serum biomarkers for ovarian cancer that exist in the low molecular weight serum fraction. After isolation of the low molecular weight fraction by ultrafiltration, the potential biomarkers are separated by reversed phase nano liquid chromatography. Detection via TOF or FT-ICR yields a data set for each sample. We compared stage III/IV ovarian cancer serum with postmenopausal age-matched controls. Using bioinformatics tools developed at Mayo, we normalized each sample for intensity and chromatographic alignment. Normalized data sets are subsequently compared and potential biomarkers identified. Several candidate biomarkers were found. One of these contains the sequence of fibrinopeptide-A known to be elevated in many types of cancer including ovarian cancer. The protocols utilized will be examined and would be applicable to a wide variety of cancers or disease states.
TL;DR: This work has shown clear trends in women’s ob-Gyn morbidity and mortality during the first trimester of pregnancy and these trends are continuing into the second half of the decade.
Abstract: Kathryn L. Terrya, Patrick M. Slussb, Steven J. Skatesc,d, Samuel C. Mokd, Bin Yed, Allison F. Vitonisa and Daniel W. Cramera Ob-Gyn Center Epidemiology Center, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women’s Hospital, Boston, MA, USA Reproductive Endocrinology Unit Laboratory, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA Biostatistics Center, Massachusetts General Hospital, Boston, MA, USA Laboratory of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women’s Hospital, Boston, MA, USA
University of Alabama at Birmingham1, Eastern Virginia Medical School2, University of Pittsburgh3, Science Applications International Corporation4, University of Texas Health Science Center at San Antonio5, Fred Hutchinson Cancer Research Center6, National Institutes of Health7, Uniformed Services University of the Health Sciences8, Johns Hopkins University9
TL;DR: This manuscript describes a detailed design of a three-phase study to validate the clinical usefulness of SELDI-TOF-MS in the identification of patients with prostatic adenocarcinoma (PCA).
Abstract: Multiple studies have reported that analysis of serum and other bodily fluids using surface enhanced laser desorption/ionization time of flight mass spectroscopy (SELDI-TOF-MS) can identify a “fingerprint” or “signature” of spectral peaks that can separate patients with a specific disease from normal control patients. Ultimately, classification by SELDI-TOF-MS relies on spectral differences in position and amplitude of resolved peaks. Since the reproducibility of quantitation, resolution and mass accuracy of the SELDI-TOF-MS, or any high throughput mass spectrometric technique, has never been determined this method has come under some skepticism as to its clinical usefulness. This manuscript describes a detailed design of a three-phase study to validate the clinical usefulness of SELDI-TOF-MS in the identification of patients with prostatic adenocarcinoma (PCA). At the end of this validation study, the usefulness of the general SELDI-TOF-MS approach to identifying patients with PCA will be demonstrated and how it compares with PCA diagnosis by measuring prostate specific antigen.
TL;DR: Issues related to performance and validation of biomarkers with a focus on “doing no harm” are reviewed, and bearing in mind that it is the ultimate goal of early detection to save lives.
Abstract: Approximately 1 man in 6 will be diagnosed with prostate cancer during his life lifetime, and over 200,000 men in the U.S. are diagnosed with prostate cancer annually. Since the widespread adoption of PSA testing, about 60-70% of men at risk in the U.S. have had a blood test for prostate cancer. With this, prostate cancer death rates have decreased, yet only slightly. Thirty thousand men still die each year from this disease. PSA testing fails to identify a small but significant proportion of aggressive cancers, and only about 30% of men with a "positive" PSA have a positive biopsy. Additionally, of men who are treated for prostate cancer, about 25% require additional treatment, presumably due to disease recurrence. Also of concern is the growing evidence that there are some prostate cancers for which treatment may not be necessary. Very long-term studies from the U.S. and Europe, following men with prostate cancer have found that some tumors do not progress over time. In these individuals, prostate cancer treatment is unnecessary and harmful as these men do not benefit from treatment but will be at risk of treatment-related side effects and complications. They suggest a fundamental problem with prostate cancer: it is not possible, at this time, to predict the natural history of the disease. It is for these reasons that the most important challenge in prostate cancer today is the inability to predict the behavior of an individual tumor in an individual patient. Here we review issues related to performance and validation of biomarkers with a focus on "doing no harm", and bearing in mind that it is the ultimate goal of early detection to save lives. Improved diagnostic and prognostic biomarkers are needed for prostate cancer, and the use of these markers should ultimately translate into increased life span and quality of life. The ultimate goal would be to not only have accurate biomarkers suitable for early diagnosis, but also biomarkers that identify men at greatest risk of developing aggressive disease. Technology has been brought to bear on this problem, and the major approaches are genomics, expression analysis, and proteomics. Proteomics and DNA methylation assays may soon be used in sensitive and specific diagnostic testing of serum and tissues for cancer. Expression arrays may be used to establish both a more specific diagnosis and prognosis for a particular tumor. The proteome is only beginning to be understood, and alternative splicing and post-translational modifications of proteins such as glycosylation and phosphorylation are challenging areas of study. Finally, risk assessment and prognosis are being pursued through analysis of genomic polymorphisms (single nucleotide polymorphisms, SNPs). This huge task is only beginning, and requires the combined expertise of molecular epidemiologists, oncologists, surgeons, pathologists, and basic scientists.
TL;DR: Estimates of the hereditary burden of CRC may be conservative when considering the existence of low-penetrant genes such as the Ashkenazi I1307K mutation, the recently described autosomal recessive form of familial adenomatous polyposis (FAP)-like families, and the hereditary breast and colon cancer (HBCC) syndrome.
Abstract: The annual worldwide incidence of colorectal cancer (CRC) is 944,717 with a mortality of 492,411 [1]. Approximately 5% to 10% of this total CRC burden is due to primary Mendelian inheritance factors, making hereditary CRC a major public health problem throughout the world. These estimates of the hereditary burden of CRC may be conservative when considering the existence of low-penetrant genes such as the Ashkenazi I1307K mutation [2], the recently described autosomal recessive form of familial adenomatous polyposis (FAP)-like families due to the MYH mutation [3, 4], and the hereditary breast and colon cancer (HBCC) syndrome [5,6]. Understanding the role of genetics in the etiology of CRC has increased rapidly during the past decade, due to the prodigious advances in molecular genetics [7]. Indeed, this information has evolved so rapidly that it has outpaced the ability of physicians to keep abreast of these fast-breaking events.
TL;DR: The studies showed that MSI and IHC analysis of colorectal and endometrial cancer, are reliable cost-effective tools that can be used to identify patients with HNPCC.
Abstract: Hereditary nonpolyposis colorectal cancer (HNPCC, Lynch syndrome) is a dominantly inherited syndrome characterized by the development of colorectal cancer, endometrial cancer and other cancers and the presence of microsatellite instability (MSI) in tumors. The Bethesda guidelines have been proposed for the identification of families suspected of HNPCC that require further molecular analysis. We have evaluated the yield of MSI-analysis in a large series of Dutch families suspected of HNPCC. We also analysed whether the loss of mismatch repair (MMR) protein detected by immunohistochemistry (IHC) of colorectal cancer (CRC) and endometrial cancer correlated with the presence of MSI and/or a MMR gene mutation. The results showed that the Bethesda criteria with a few modifications are appropriate to identify families eligible for genetic testing. In addition, we found that MSI and IHC-analysis of CRC using antibodies against MLH1, MSH2, MSH6 and PMS2 proteins are equally effective for identifying carriers of the known MMR gene defects. However, as long as the role of other putative MMR genes in hereditary CRC has not been elucidated, IHC-analysis cannot completely replace MSI. For this reason, we prefer MSI-analysis as first step in families suspected of HNPCC. On the other hand, in families fulfilling the revised Amsterdam criteria in which the probability of detecting a mutation is relatively high, we would recommend IHC as first diagnostic step because the result might predict the specific underlying MMR gene mutation. MSI or IHC-analysis of endometrial cancer alone was found to be less sensitive compared with these tests performed in colorectal cancer. Therefore, probably the best approach in the analysis of this cancer is to perform both techniques. The identification of HNPCC is important as it makes it possible to target effective preventative measures. Our studies showed that MSI and IHC analysis of colorectal and endometrial cancer, are reliable cost-effective tools that can be used to identify patients with HNPCC.
TL;DR: Two-dimensional gel based Western blots, protein antigen microarrays, and multiplex ELISA reactions have been applied by this group to antigen based biomarker detection and validation, resulting in the identification of numerous cancer biomarker candidates.
Abstract: The identification of autoantibodies to tumor cell proteins by proteomics approaches has great potential impact on cancer biomarker discovery. The humoral immune response represents a form of biological amplification of signals that are otherwise weak due to very low concentrations of antigen, especially in the early stages of cancers. In addition, proteomics can detect immunoreactivity directed against protein post-translational modifications. Two-dimensional gel based Western blots, protein antigen microarrays, and multiplex ELISA reactions have been applied by our group to antigen based biomarker detection and validation. The latter two are based on liquid-phase separations that are suitable for automation. This work has resulted in the identification of numerous cancer biomarker candidates. Large clinical studies are currently planned to establish their value in early cancer diagnosis.
TL;DR: The Human Proteome Organization has mounted a Pilot Phase focussed on key problems essential for standardization of specimen collection, specimen handling, choice of fractionation and analysis technologies, and search engines and databases for protein identifications.
Abstract: The Human Proteome Organization (HUPO) Plasma Proteome Project has mounted a Pilot Phase focussed on key problems essential for standardization of specimen collection, specimen handling, choice of fractionation and analysis technologies, and search engines and databases for protein identifications. This international collaboration will lay the groundwork for many large-scale clinical and epidemiological studies of health and disease.
TL;DR: A methodology for the clinical evaluation ofPutative prognostic and predictive markers in cancer, with considerations of pitfalls in the early evaluation, rationale for development and optimization of assay methodology, and examples of possible clinical trials for assessing the clinical utility of putative markers are presented.
Abstract: The elucidation of the human genome and advances in knowledge about molecular abnormalities, signaling pathways, influence of the local tissue milieu and the relevance of genetic polymorphisms offer hope of designing more effective, individualized cancer treatment plans. Although the scientific and medical literature is replete with reports of putative prognostic or predictive markers for cancer, few new diagnostics have been incorporated into routine clinical practice. Criteria are needed to a) identify markers that have the promise to be clinically useful; b) assess the best methodology for clinical evaluation of the markers in question and c) confirm or validate that using the marker adds useful information compared to using standard prognostic factors alone. This review presents a methodology for the clinical evaluation of putative prognostic and predictive markers in cancer, with considerations of pitfalls in the early evaluation, rationale for development and optimization of assay methodology, and examples of possible clinical trials for assessing the clinical utility of putative markers.
TL;DR: The MRSI techniques as molecular imaging methods to detect and quantify metabolic changes in various tumor tissue types, especially in extracranial tumor tissues that contain high concentrations of fat are reviewed.
Abstract: Cancer cells display heterogeneous genetic characteristics, depending on the tumor dynamic microenvironment. Abnormal tumor vasculature and poor tissue oxygenation generate a fraction of hypoxic tumor cells that have selective advantages in metastasis and invasion and often resist chemo- and radiation therapies. The genetic alterations acquired by tumors modify their biochemical pathways, which results in abnormal tumor metabolism. An elevation in glycolysis known as the “Warburg effect” and changes in lipid synthesis and oxidation occur. Magnetic resonance spectroscopy (MRS) has been used to study tumor metabolism in preclinical animal models and in clinical research on human breast, brain, and prostate cancers. This technique can identify specific genetic and metabolic changes that occur in malignant tumors. Therefore, the metabolic markers, detectable by MRS, not only provide information on biochemical changes but also define different metabolic tumor phenotypes. When combined with the contrast-enhanced Magnetic Resonance Imaging (MRI), which has a high sensitivity for cancer diagnosis, in vivo magnetic resonance spectroscopic imaging (MRSI) improves the diagnostic specificity of malignant human cancers and is becoming an important clinical tool for cancer management and care. This article reviews the MRSI techniques as molecular imaging methods to detect and quantify metabolic changes in various tumor tissue types, especially in extracranial tumor tissues that contain high concentrations of fat. MRI/MRSI methods have been used to characterize tumor microenvironments in terms of blood volume and vessel permeability. Measurements of tissue oxygenation and glycolytic rates by MRS also are described to illustrate the capability of the MR technology in probing molecular information non-invasively in tumor tissues and its important potential for studying molecular mechanisms of human cancers in physiological conditions.
TL;DR: The biological significance and underlying genetic abnormalities in cancers with the MSI-L phenotype are debated and remain to be fully characterised.
Abstract: A departure from the concept of simple adenoma to carcinoma sequence is the realization that colorectal cancer (CRC) develops through at least two major molecular pathogenic pathways, namely chromosomal instability (CIN) and microsatellite instability (MSI) [1,2]. The mechanisms underlying CIN might have been the first to be deciphered but they are just being understood in detail. It is proposed that CIN may be associated with defects in mitotic spindle apparatus hence tumors arising through this pathway are usually characterized by widespread chromosomal deletions, translocations and loss of heterozygosity at the molecular level. On the other hand, MSI pathway is responsible for up to 15% of all CRCs that also include a number of familial syndromes [3,4]. Hereditary non-polyposis colorectal cancer (HNPCC also known as Lynch syndrome) is the prototype for the tumors characterized by MSI. Tumors developing through this pathway have alterations in the length of short, repeated (usully mononucleotide or dinucleotide) sequences of DNA, i.e., microsatellites [5–10]. This phenomenon reflects the underlying defect in the DNA mismatch repair (MMR) system which is a multi-protein complex responsible for correction of errors arising during normal cell division [5,7,11,12]. In 1997, the National Cancer Institute Workshop on Hereditary Non-polyposis Colorectal Cancer Syndrome proposed specific markers for MSI assessment which included BAT25, BAT26, D5S346, D2S123 and D17S250, known as Bethesda panel [13]. If no alterations are found the tumor is classified as microsatellite stable (MSS) and if two or more loci are abnormal the tumor is classified as showing a high level of microsatellite instability (MSI-H). In cases showing abnormalities at one locus, testing of an additional five loci is recommended. If abnormal loci constitute less than 40% of the tested markers, the tumor is classified as showing a low level of microsatellite instability (MSIL). MSS cancers account for up to 85% of all CRCs and occur in sporadic and hereditary settings such as familial adenomatous polyposis (FAP) and attenuated FAP. The biological significance and underlying genetic abnormalities in cancers with the MSI-L phenotype are debated and remain to be fully characterised. It has been reported that on morphological grounds, MSS and MSI-L cancers are indistinguishable. MSI-H cancers constitute up to 15% of all CRCs. MSI-H cancers (sporadic and in hereditary non-polyposis colorectal cancer (HNPCC) patients) have characteristic anatomical and histological features. Proximal colon incidence is seen in the majority of cases. Most of the tumors are polypoid masses and some may display a mucinous cut surface [14,15]. Stricture formation due to a diffuse growth pattern is uncommon; however, extensive necrosis is often observed. The tumors usually have a well-defined margin. A significant fraction of tumors are also classified as poorly differentiated. A characteristic feature of diagnostic importance is the presence of tumor infiltrating lymphocytes (TIL), most of which are cytotoxic T cells. B lymphocytes’ aggregates are
TL;DR: This work has developed and contrasted the use of both proteomic and metabonomic patterns in urine for the detection of interstitial cystitis and applied a novel pattern recognition tool that employs an unsupervised system as a fitness test for a supervised system (a genetic algorithm).
Abstract: The advent of systems biology approaches that have stemmed from the sequencing of the human genome has led to the search for new methods to diagnose diseases. While much effort has been focused on the identification of disease-specific biomarkers, recent efforts are underway toward the use of proteomic and metabonomic patterns to indicate disease. We have developed and contrasted the use of both proteomic and metabonomic patterns in urine for the detection of interstitial cystitis (IC). The methodology relies on advanced bioinformatics to scrutinize information contained within mass spectrometry (MS) and high-resolution proton nuclear magnetic resonance (1H-NMR) spectral patterns to distinguish IC-affected from non-affected individuals as well as those suffering from bacterial cystitis (BC). We have applied a novel pattern recognition tool that employs an unsupervised system (self-organizing-type cluster mapping) as a fitness test for a supervised system (a genetic algorithm). With this approach, a training set comprised of mass spectra and 1H-NMR spectra from urine derived from either unaffected individuals or patients with IC is employed so that the most fit combination of relative, normalized intensity features defined at precise m/z or chemical shift values plotted in n-space can reliably distinguish the cohorts used in training. Using this bioinformatic approach, we were able to discriminate spectral patterns associated with IC-affected, BC-affected, and unaffected patients with a success rate of approximately 84%.
TL;DR: This research presents a novel and scalable approach called “Cellulare Respiratoria-guided Thrombosis Assisted Hemostasis Research” (CASR) that aims to provide real-time information about the “building blocks” of the immune system and its role in blood clotting.
Abstract: Alessandro Celia,c, Roberto Lorenzetb, Barbara C. Furiec and Bruce Furiec,∗ Laboratorio di Biologia Cellulare Respiratoria, Dipartimento Cardiotoracico dell’Universit a di Pisa, Pisa, Italy Antonio Taticchi Unit for Atherosclerosis and Thrombosis, Istituto Ricerche Farmacologiche Mario Negri, Consorzio Mario Negri Sud, S. Maria Imbaro, Italy Center for Hemostasis and Thrombosis Research, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
TL;DR: How the pathologist may suspect a diagnosis of hereditary non-polyposis colorectal cancer (HNPCC) on the basis of histological criteria and patient age alone is indicated.
Abstract: The aim of this paper is to indicate how the pathologist may suspect a diagnosis of hereditary non-polyposis colorectal cancer (HNPCC) on the basis of histological criteria and patient age alone. A single morphological feature, namely the presence of intra-epithelial lymphocytes (tumor infiltrating lymphocytes), identifies the majority of colorectal cancers (CRC) with the DNA microsatellite instability-high phenotype. A number of pathological criteria can help to distinguish HNPCC from sporadic MSI-H CRC, though age below 60 years is an important pointer towards HNPCC. Immunohistochemistry to demonstrate loss of expression of DNA mismatch repair genes serves as a highly reliable test of mismatch repair deficiency if antibodies to hMLH1, hMSH2, hMSH6 and hPMS2 are employed.
TL;DR: The frequency and the distribution of HLA-B27 subtypes in spondylarthropathy (SpA) patients and controls were investigated in a sample Turkish population, and B∗2705 was the predominant allele among patients with SpA.
Abstract: The frequency and the distribution of HLA-B27 subtypes in spondylarthropathy (SpA) patients and controls were investigated in a sample Turkish population. B27 subtyping was performed by PCR-SSP method in two groups: 49 unrelated HLA-B27 positive Turkish patients with the diagnosis of SpA according to the European Spondyloarthropathy Study Group Criteria, and 55 HLA-B27 positive healthy controls. The frequency of HLA-B∗27 was 2.6% in the Turkish population, and B∗2705 was the predominant allele among patients with SpA. The difference was mainly between male patients and male controls The proportion of B∗2705 among B27-positive patients and controls was significantly different (P = 0.02). Our study supports other reports from different populations which showed that B∗2705 and B∗2702 were more frequent in Caucasian patients with SpA.
TL;DR: The value of 31P-MRS as an imaging technique to determine in vivo markers of disease and in the diagnosis, prognosis, and follow-up of human diseases is demonstrated.
Abstract: Phosphorus Magnetic Resonance Spectroscopy (31P-MRS) has been utilized to study energy, carbohydrate, and phospholipid metabolism in vitro and in vivo in live tissues non-invasively. Despite its lack of sensitivity, its application has extended to in situ human tissues and organs since proper signal localization was devised. Follow-up of phosphocreatine in neuromuscular diseases and schizophrenia and follow-up of phospholipid-related molecules in tumors are described here to demonstrate the value of 31P-MRS as an imaging technique to determine in vivo markers of disease and in the diagnosis, prognosis, and follow-up of human diseases.
TL;DR: A metrological analysis may enhance case-control studies by guiding optimization of the measurements underlying the biomarker by using functional principal components analysis (PCA) as the basis for assessing measurement reproducibility.
Abstract: Biomarker discovery and development requires measurement reproducibility studies in addition to case-control studies. Parallel pursuit of reproducibility studies is especially important for emerging technologies such as protein biomarkers based on time-of-flight mass spectrometry, the case considered in this paper. For parallel studies, a way to improve reproducibility prior to identification of protein species is necessary. One approach is use of functional principal components analysis (PCA) as the basis for assessing measurement reproducibility. Reproducibility studies involve repeated measurement of a reference material such as a human serum standard. Measurement in our example is by SELDI-TOF (surface-enhanced laser desorption and ionization time-of-flight) mass spectrometry. Reproducibility is defined in reference to a source of variation, which in our example is associated with a type of commercially available protein biochip. We obtained spectra for 8 spots on each 11 chips. Two spectra are generally more alike when obtained from the same chip rather than different chips. Thus, our experiment indicates potential improvements from reducing variation in chip manufacture and chip handling during measurement. Our analysis involves careful registration of the spectra and characterization of the spectral differences. As shown by our example, a metrological analysis may enhance case-control studies by guiding optimization of the measurements underlying the biomarker.
TL;DR: A strategy for identifying markers of breast cancer in NAF is proposed that utilizes mass spectrometry (MS) to simultaneously screen hundreds or thousands of proteins in each sample and the best potential markers identified by the MS analysis can then be extensively characterized using an ELISA microarray assay.
Abstract: Identifying useful markers of cancer can be problematic due to limited amounts of sample. Some samples such as nipple aspirate fluid (NAF) or early-stage tumors are inherently small. Other samples such as serum are collected in larger volumes but archives of these samples are very valuable and only small amounts of each sample may be available for a single study. Also, given the diverse nature of cancer and the inherent variability in individual protein levels, it seems likely that the best approach to screen for cancer will be to determine the profile of a battery of proteins. As a result, a major challenge in identifying protein markers of disease is the ability to screen many proteins using very small amounts of sample. In this review, we outline some technological advances in proteomics that greatly advance this capability. Specifically, we propose a strategy for identifying markers of breast cancer in NAF that utilizes mass spectrometry (MS) to simultaneously screen hundreds or thousands of proteins in each sample. The best potential markers identified by the MS analysis can then be extensively characterized using an ELISA microarray assay. Because the microarray analysis is quantitative and large numbers of samples can be efficiently analyzed, this approach offers the ability to rapidly assess a battery of selected proteins in a manner that is directly relevant to traditional clinical assays.
TL;DR: High levels of plasma fibrinogen, a2A- antiplasmin with low plasma protein C activity could lead to a prothrombotic tendency in insulin dependent diabetic patients, and in non-insulin dependent diabetic Patients, the above mentioned parameters together with high levels of ADP-induced platelet aggregation and plasminogen activator inhibitor may increase the risk of thrombosis complications.
Abstract: Diabetes mellitus is associated with disturbances in haemostasis that could contribute to the development of thrombotic complications.The present study was undertaken to determine the behavior of coagulation variables and fibrinolytic system in diabetes mellitus. Forty five diabetic patients and forty five matched controls were evaluated by doing the following haemostatic parameter, prothrombin time, partial thromboplastin time, thrombin time, coagulation factors assay II, VII, IX, & plasma fibrinogen, ADP-induced platelet aggregation, protein C, a2- antiplasmin, PAI and FDPs. Generally diabetic patients have high levels of fibrinogen, a2- antiplasmin, & PAI and lower level of protein C. Other haemostatic parameters did not show statistically significant difference between diabetic patients and control group. Significantally elevated levels of PAI, a2- antiplasmin together with low protein C level in diabetic patients may result in the disturbance of haemostatic balance favoring thrombotic events. Conclusion: High levels of plasma fibrinogen, a2A- antiplasmin with low plasma protein C activity could lead to a prothrombotic tendency in insulin dependent diabetic patients. Moreover, in non-insulin dependent diabetic patients, the above mentioned parameters together with high levels of ADP-induced platelet aggregation and plasminogen activator inhibitor may increase the risk of thrombotic complications. Obesity can be considered as an additional risk factor for development of thrombosis in diabetic patients.
TL;DR: The highest mutation rate was observed with 5 mutations at D8S1179 locus at different alleles, and the event was always single repeat related.
Abstract: Paternity tests are carried out by the analysis of hypervariable short tandem repeat DNA loci. These microsatellite sequences mutate at a higher rate than that of bulk DNA. The occurrence of germline mutations at STR loci posses problems in interpretation of resulting genetic profiles. We recently analyzed 59–159 parent/child allele transfers at 13 microsatellite loci. We identified 12 mutations in 7 microsatellite loci. No mutations were occurred in other 6 loci. The highest mutation rate was observed with 5 mutations at D8S1179 locus at different alleles. The event was always single repeat related. The mutation rate was between 0 and 1.5 x 10-2 per locus per gamete per generation. The mutation event is very crucial for forensic DNA testing and accumulation of STR mutation data is extremely important for genetic profile interpretation.