“Unmixing” Tissue Gene Expression Signatures from Tumor Biopsies

Emergent molecular measurement methods, such as DNA microarray, qRTPCR, andmany others, offer tremendous promise for the personalized treatment of cancer. Thesetechnologies measure the amount of specific proteins, RNA, DNA or other moleculartargets from tumor specimens with the goal of “fingerprinting” individual cancers. Tumorspecimens are heterogeneous; an individual specimen typically contains unknownamounts of multiple tissues types. Thus, the measured molecular concentrations resultfrom an unknown mixture of tissue types, and must be normalized to account for thecomposition of the mixture.For example, a breast tumor biopsy may contain normal, dysplastic and cancerousepithelial cells, as well as stromal components (fatty and connective tissue) and bloodand lymphatic vessels. Our diagnostic interest focuses solely on the dysplastic andcancerous epithelial cells. The remaining tissue components serve to “contaminate”the signal of interest. The proportion of each of the tissue components changes asa function of patient characteristics (e.g., age), and varies spatially across the tumorregion. Because each of the tissue components produces a different molecular signature,and the amount of each tissue type is specimen dependent, we must estimate the tissuecomposition of the specimen, and adjust the molecular signal for this composition.Using the idea of a chemical mass balance, we consider the total measured concentrationsto be a weighted sum of the individual tissue signatures, where weightsare determined by the relative amounts of the different tissue types. We develop acompositional source apportionment model to estimate the relative amounts of tissuecomponents in a tumor specimen. We then use these estimates to infer the tissuespecificconcentrations of key molecular targets for sub-typing individual tumors. Weanticipate these specific measurements will greatly improve our ability to discriminatebetween different classes of tumors, and allow more precise matching of each patient tothe appropriate treatment

A protocol describing the genetic correction of somatic human cells and subsequent generation of IPS cell

The generation of patient-specific induced pluripotent stem cells (iPSCPSCPSCs) offers unprecedented opportunities for modeling and treating human disease. In combination with gene therapy, the iPSCPSCPSC technology can be used to generate disease-free progenitor cells of potential interest for autologous cell therapy. We explain a protocol for the reproducible generation of genetically corrected iPSCPSCPSCs starting from the skin biopsies of Fanconi anemia patients using retroviral transduction with OCT4, SOX2 and KLF4. Before reprogramming, the fibroblasts and/or keratinocytes of the patients are genetically corrected with lentiviruses expressing FANCA. The same approach may be used for other diseases susceptible to gene therapy correction. Genetically corrected, characterized lines of patient-specific iPSCPSCPSCs can be obtained in 4–5 months.

Lymphocyte populations in liver biopsy specimens from patients with chronic liver disease

The characterisation of lymphocytes from liver biopsies indicates that 'activated' T lymphocytes are present in the liver in alcohol induced hepatitis, chronic active hepatitis (HBS+ve and -ve), and in primary biliary cirrhosis but not in inactive cirrhosis, chronic persistent hepatitis, extrahepatic and drug induced cholestasis. A greater percentage of lymphocytes bear Fc-receptors in chronic active hepatitis than in alcohol induced hepatitis or cholestatic liver disease. The concentration of 'activated' T cells in the peripheral blood in all groups studied was within the normal range, suggesting that the 'activated' T cells found in the liver were reacting to either native or foreign antigens within the liver. The data on Fc-receptor bearing cells are consistent with the involvement of antibody assisted K cell mediated cytotoxicity in chronic active hepatitis.

Minor salivary gland tumors: a clinicopathological study of 18 cases

Introduction: Minor salivary gland tumors (MSGTs) are infrequent, representing 10-15% of all salivary neoplasms. Despite this low frequency, MSGTs conform a heterogeneous group of neoplasms characterized by a broad range of histological types. Patients and method: We identified cases of MSGT in a retrospective study of the biopsies made in the period 1997-2007 in the Service of Oral Surgery (Dental Clinic of the University of Barcelona, Spain). The data collected comprised patient age and sex, the clinical characteristics and location of the tumor, the duration of the lesion, its size, the treatment provided, and the histopathological findings. Results: Of the 18 cases of MSGT studied, 12 corresponded to women (66.7%) and 6 to men (33.3%). The great majority (94.4%) were benign tumors. The preferential location was the posterior third of the hard palate (33.2%), followed by the soft palate (16.7%) and the mucosa of the upper lip (16.7%). The histopathological diagnoses of our MSGTs comprised 10 pleomorphic adenomas (55.3%), 2 cystadenomas (11.1%), 1 myoepithelioma (5.6%), 1 sialadenoma papilliferum (5.6%), 1 basal cell adenoma (5.6%), 1 Warthin"s tumor (5.6%), 1 canalicular adenoma (5.6%), and 1 low-grade polymorphic adenocarcinoma (5.6%). Discussion and conclusions: Coinciding with our own results, the literature describes a high recurrence rate for MSGTs (5-30%) when surgical removal is incomplete. Six percent of all benign minor salivary gland tumors are considered to relapse, versus 65% of all malignant lesions. Periodic clinical controls are required, since the possibility of malignant transformation must be taken into account

Endorectal Magnetic Resonance Imaging and Spectroscopy Are Useful for Selecting Candidates for Biopsy among Patients with Persistently Elevated Prostate Specific Antigen

To evaluate the efficacy of endorectal Magnetic Resonance Imaging (MRI) and Magnetic Resonance Spetroscopic Imaging (MRSI) combined with total prostate-specific antigen (tPSA) and free prostate-specific antigen (fPSA) in selecting candidates for biopsy. Subjects and Methods: 246 patients with elevated tPSA (median: 7.81 ng/ml) underwent endorectal MRI and MRSI before Transrectal Ultrasound (TRUS) biopsy (10 peripheral + 2 central cores); patients with positive biopsies were treated with radical intention; those with negative biopsies were followed up and underwent MRSI before each additional biopsy if tPSA rose persistently. Mean follow-up: 27.6 months. We compared MRI, MRSI, tPSA, and fPSA with histopathology by sextant and determined the association between the Gleason score and MRI and MRSI. We determined the most accurate combination to detect prostate cancer (PCa) using receiver operating curves; we estimated the odds ratios (OR) and calculated sensitivity, specificity, and positive and negative predictive values. Results: No difference in tPSA was found between patients with and without PCa (p = 0.551). In the peripheral zone, the risk of PCa increased with MRSI grade; patients with high-grade MRSI had the greatest risk of PCa over time (OR = 328.6); the model including MRI, MRSI, tPSA, and fPSA was more accurate (Area under Curve: AUC = 95.7%) than MRI alone (AUC = 85.1%) or fPSA alone (AUC = 78.1%), but not than MRSI alone (94.5%). In the transitional zone, the model was less accurate (AUC = 84.4%). The association (p = 0.005) between MRSI and Gleason score was significant in both zones. Conclusions: MRSI is useful in patients with elevated tPSA. High-grade MRSI lesions call for repeated biopsies. Men with negative MRSI may forgo further biopsies because a significantly high Gleason lesion is very unlikely

Benign fibro-osseous lesions of the maxillas: analysis of 11 cases

Introduction: A study is made of the principal characteristics of the oral lesions biopsied in our Service of Oral Surgery and histologically diagnosed as corresponding to fibro-osseous lesions of the maxillas. Patients and methods: A retrospective review was made of all the biopsies made in a Service of Oral Surgery between 1996 and 2003. The reason for consultation was analyzed, along with patient age, sex, clinical and radiological characteristics, tentative diagnosis, histological diagnosis and treatment provided. Results: A total of 1238 biopsies were performed during the study period. Of these, only 11 corresponded to benign fibro-osseous lesions (7 women and 4 men). The mean patient age was 44 years (range 19-72 years). The most frequent location was the mandible (8 of the cases). In 7 patients the lesions constituted casual radiological findings; 4 presented bulging of the vestibular cortical bone, though only one of them reported pain. The histological diagnoses comprised 7 cemento-ossifying fibromas and 4 fibrous dysplasias. In 9 cases surgical resection was carried out, while in one case an incisional biopsy was performed, and in the remaining case curettage was decided. Discussion: These lesions are more frequent in women than in men, and the age at presentation is variable. In terms of lesion location, fibrous dysplasia is more common in the upper maxilla, while cemento-ossifying fibroma is more frequently found in the mandible. The diagnosis of such lesions is established upon contrasting the data obtained from the anamnesis, physical examination, the radiological characteristics, the intraoperative findings and the histological study, since both disorders have similar clinical and histological features- despite the fact that they constitute distinct disease conditions.

NADPH oxidase NOX4 mediates stellate cell activation and hepatocyte cell death during liver fibrosis development.

A role for the NADPH oxidases NOX1 and NOX2 in liver fibrosis has been proposed, but the implication of NOX4 is poorly understood yet. The aim of this work was to study the functional role of NOX4 in different cell populations implicated in liver fibrosis: hepatic stellate cells (HSC), myofibroblats (MFBs) and hepatocytes. Two different mice models that develop spontaneous fibrosis (Mdr2−/−/p19ARF−/−, Stat3Δhc/Mdr2−/−) and a model of experimental induced fibrosis (CCl4) were used. In addition, gene expression in biopsies from chronic hepatitis C virus (HCV) patients or non-fibrotic liver samples was analyzed. Results have indicated that NOX4 expression was increased in the livers of all animal models, concomitantly with fibrosis development and TGF-β pathway activation. In vitro TGF-β-treated HSC increased NOX4 expression correlating with transdifferentiation to MFBs. Knockdown experiments revealed that NOX4 downstream TGF-β is necessary for HSC activation as well as for the maintenance of the MFB phenotype. NOX4 was not necessary for TGF-β-induced epithelial-mesenchymal transition (EMT), but was required for TGF-β-induced apoptosis in hepatocytes. Finally, NOX4 expression was elevated in patients with hepatitis C virus (HCV)-derived fibrosis, increasing along the fibrosis degree. In summary, fibrosis progression both in vitro and in vivo (animal models and patients) is accompanied by increased NOX4 expression, which mediates acquisition and maintenance of the MFB phenotype, as well as TGF-β-induced death of hepatocytes.

Central odontogenic fibroma: retrospective study of 8 clinical cases

Introduction and Objectives: The central odontogenic fibroma (COF) is a benign odontogenic tumour derived from the dental mesenchymal tissues. It is a rare tumour and only 70 cases of it have been published. Bearing in mind the rareness of the tumour, 8 new cases of central odontogenic fibroma have been found by analyzing the clinical, radiological and histopathological characteristics of COF. Patients and Method: A retrospective study was carried out on 3011 biopsies in the Service of Oral and Maxillofacial Surgery of the Dental Clinic of Barcelona University between January 1995 and March 2008. 85 odontogenic tumours were diagnosed of which 8 were central odontogenic fibroma. The radiological study was based on orthopantomographs, periapical and occlusal radiographies and computerised tomographics. The variables collected were: sex, age, clinical characteristics of the lesion, treatment received and possible reappearances of the tumour. Results: The central odontogenic fibroma represents 9.4% of all odontogenic tumours. Of the 8 cases, 5 were diagnosed in men and 3 in women. The average age was 19.9 years with an age range of 11 to 38 years. The most common location of the tumour was in the mandible. All cases were associated with unerupted teeth. Of the 8 tumours, 3 provoked rhizolysis of the adjacent teeth and 4 cases caused cortical bone expansion. 50% of the patients complained of pain associated to the lesion. No case of recurrence was recorded up to 2 years after the treatment. Conclusions: Central odontogenic fibromas usually evolve asymptomatically although they can manifest very aggressively provoking dental displacement and rhizolysis. Radiologically, COF manifest as a uni or multilocular radiotransparent image although they can be indistinguishable from other radiotransparent lesions making diagnosis more difficult. COF treatment involves conservative surgery as well as follow-up patient checks.

Effects of exercise on mitochondrial DNA content in skeletal muscle of patients with COPD

Background Exhausting exercise reduces the mitochondrial DNA (mtDNA) content in the skeletal muscle of healthy subjects due to oxidative damage. Since patients with chronic obstructive pulmonary disease (COPD) suffer enhanced oxidative stress during exercise, it was hypothesised that the mtDNA content will be further reduced. Objective To investigate the effects of exercise above and below the lactate threshold (LT) on the mtDNA content of skeletal muscle of patients with COPD. Methods Eleven patients with COPD (676 8 years; forced expiratory volume in 1s (FEV1)456 8%ref) and 10 healthy controls (666 4 years; FEV1 906 7% ref) cycled 45 min above LT (65% peak oxygen uptake (V9O2 peak)and another 7 patients (656 6 years; FEV1 506 4%ref)and 7 controls (566 9 years;FEV1 926 6%ref) cycled 45 min below their LT (50% V9O2 peak). Biopsies from the vastus lateralis muscle were obtained before exercise, immediately after and 1 h, 1 day and 1 week later to determine by PCR the mtDNA/nuclear DNA (nDNA) ratio (a marker of mtDNA content) and the expression of the peroxisome proliferator-activated receptor- g coactivator-1 a (PGC-1a)mRNA and the amount of reactive oxygen species produced during exercise was estimated from total V9O2. Results Skeletal muscle mtDNA/nDNA fell significantly after exercise above the LT both in controls and in patients with COPD, but the changes were greater in those with COPD. These changes correlated with production of reactive oxygen species, increases in manganese superoxide dismutase and PGC-1 a mRNA and returned to baseline values 1 week later. This pattern of response wa was also observed, albeit minimised, in patients exercising below the LT. Conclusions In patients with COPD, exercise enhances the decrease in mtDNA content of skeletal muscle and the expression of PGC-1 a mRNA seen in healthy subjects probably due to oxidative stress.

Tissue distribution of retinoids in common dolphins (Delphinus delphis).

Exposure to organochlorines induces retinoid deficiency in mammals; hence, retinoids are potential biomarkers of the impact of these pollutants. Appropriate target tissues to monitor retinoids in cetaceans have not been properly identified because of a lack of information on the contribution of each tissue to total body retinoids. Therefore, we have addressed this issue by studying the contribution of the main body tissues to retinoids in 21 common dolphins obtained from incidental catches and in apparent good health and nutritive condition. Although concentrations in the liver were highest, those in blubber were also high and accounted for 43% of the total retinoid load of the compartments examined. As blubber can be obtained using non-invasive biopsy techniques, this tissue is proposed as a reliable indicator of retinoid status in cetaceans. However, blubber topographical variation in structure and composition requires standardization of sampling sites. Retinoid concentrations did not differ significantly between sexes or with body size for any of the tissues, but the lipid content of blubber strongly influenced these concentrations. Biopsies from healthy, free-ranging individuals are preferred to samples from stranded animals. Further research on the influence of factors (age, sex, reproductive condition, diet) that potentially affect retinoid levels is required to implement the use of retinoids as biomarkers of pollutant exposure in cetaceans.

Expression of Glycogen Phosphorylase Isoforms in Cultured Muscle from Patients with McArdle´s Disease Carrying the p.R771PfsX33 PYGM Mutation

Mutations in the PYGM gene encoding skeletal muscle glycogen phosphorylase (GP) cause a metabolic disorder known as McArdle's disease. Previous studies in muscle biopsies and cultured muscle cells from McArdle patients have shown that PYGM mutations abolish GP activity in skeletal muscle, but that the enzyme activity reappears when muscle cells are in culture. The identification of the GP isoenzyme that accounts for this activity remains controversial.

Microcalcification evaluation in computer assisted diagnosis for digital mammography

In order to develop applications for z;isual interpretation of medical images, the early detection and evaluation of microcalcifications in digital mammograms is verg important since their presence is oftenassociated with a high incidence of breast cancers. Accurate classification into benign and malignant groups would help improve diagnostic sensitivity as well as reduce the number of unnecessa y biopsies. The challenge here is the selection of the useful features to distinguish benign from malignant micro calcifications. Our purpose in this work is to analyse a microcalcification evaluation method based on a set of shapebased features extracted from the digitised mammography. The segmentation of the microcalcificationsis performed using a fixed-tolerance region growing method to extract boundaries of calcifications with manually selected seed pixels. Taking into account that shapes and sizes of clustered microcalcificationshave been associated with a high risk of carcinoma based on digerent subjective measures, such as whether or not the calcifications are irregular, linear, vermiform, branched, rounded or ring like, our efforts were addressed to obtain a feature set related to the shape. The identification of the pammeters concerning the malignant character of the microcalcifications was performed on a set of 146 mammograms with their real diagnosis known in advance from biopsies. This allowed identifying the following shape-based parameters as the relevant ones: Number of clusters, Number of holes, Area, Feret elongation, Roughness, and Elongation. Further experiments on a set of 70 new mammogmms showed that the performance of the classification scheme is close to the mean performance of three expert radiologists, which allows to consider the proposed method for assisting the diagnosis and encourages to continue the investigation in the senseof adding new features not only related to the shape