A case study of normalization, missing data and variable selection methods in lipidomics.

Lipidomics is an emerging field of science that holds the potential to provide a readout of biomarkers for an early detection of a disease. Our objective was to identify an efficient statistical methodology for lipidomics-especially in finding interpretable and predictive biomarkers useful for clinical practice. In two case studies, we address the need for data preprocessing for regression modeling of a binary response. These are based on a normalization step, in order to remove experimental variability, and on a multiple imputation step, to make the full use of the incompletely observed data with potentially informative missingness. Finally, by cross-validation, we compare stepwise variable selection to penalized regression models on stacked multiple imputed data sets and propose the use of a permutation test as a global test of association. Our results show that, depending on the design of the study, these data preprocessing methods modestly improve the precision of classification, and no clear winner among the variable selection methods is found. Lipidomics profiles are found to be highly important predictors in both of the two case studies.

Use of force sensors to detect and analyse lameness in dairy cows.

Force sensors were used to detect lameness in dairy cows in two trials. In the first trial, leg weights were recorded during approximately 12,000 milkings with balances built into the floor of the milking robot. Cows that put less weight on one leg or kicked frequently during milking were checked first with a locomotion scoring system and then with a clinical inspection. A locomotion score of more than 2 was considered lame, and these cows' hooves were examined at hoof trimming to determine the cause and to identify any hoof lesions. In the second trial 315 locomotion scores were recorded and compared with force sensor data. The force sensors proved to be a good method for recognising lameness. Computer curves drawn from force sensor data helped to find differences between leg weights, thus indicating lameness and its duration. Sole ulcers and white line disease were identified more quickly by force sensors than by locomotion scoring, but joint problems were more easily detected by locomotion scoring.

A probabilistic neural network model for lameness detection.

A 4-balance system for measuring the leg-load distribution of dairy cows during milking to detect lameness was developed. Leg weights of 73 cows were successfully recorded during almost 10,000 robotic milkings over a period of 5 mo. Cows were scored weekly for locomotion, and lame cows were inspected clinically for hoof lesions. Unsuccessful measurements, caused by cows standing outside the balances, were removed from the data with a special algorithm, and the mean leg loads and number of kicks during milking were calculated. To develop an expert system to automatically detect lameness cases, a model was needed, and a classifying probabilistic neural network model was chosen for the task. The data were divided into 2 parts and 5,074 measurements from 37 cows were used to train a classifying probabilistic neural network model. The operation of the model was evaluated for its ability to detect lameness in the validating data set, which had 4,868 measurements from 36 cows. The model was able to classify 96.2% of the measurements correctly as sound or lame cows, and 100% of the lameness cases in the validation data were identified. The number of measurements (equal to the number of milkings) causing false alarms was 1.1%. The model developed has the potential to be used as an on-farm decision aid and can be used in a real-time lameness monitoring system.

Expression of SLC26A3, CFTR and NHE3 in the human male reproductive tract: role in male subfertility caused by congenital chloride diarrhoea.

Congenital chloride diarrhoea (CLD) is a rare inherited disease caused by mutations in the solute carrier family 26 member 3 (SLC26A3) gene. Disruption of intestinal Cl(-)/HCO(3)(-) exchange causes watery Cl(-) rich diarrhoea from birth, and recently male subfertility was observed as a novel manifestation. Expression of SLC26A3, together with interacting proteins cystic fibrosis transmembrane conductance regulator (CFTR) and Na(+)/H(+) exchanger 3 (NHE3), was studied using immunohistochemistry in the testis (n = 2) and efferent ducts (ED) (n = 1) of patients with CLD (V317del genotype) and in the testis and epididymis (n = 11), seminal vesicle (n = 9) and prostate (n = 4) of the controls. SLC26A3 was immunolocalized in the head of the elongating spermatids (stages III-VI) and CFTR in the elongating spermatids (stages III and IV) and pachytene (stages III-V) and diplotene spermatocytes. In the non-ciliated cells of the ED, apical expression of all three proteins was observed, but only SLC26A3 and CFTR were detected on the luminal border of the apical mitochondria-rich cells (AMRC) of the ductus epididymis and in the epithelium of the seminal vesicle. Only CFTR was present in the epithelium of the prostatic duct. In the patient with CLD, the expression of both SLC26A3 and CFTR was absent in the ED, but testicular expression was identical to that of the controls. These results suggest a primary role for SLC26A3 in male reproduction. Tissue-specific co-expression with CFTR and NHE3 supports diverse functions of SLC26A3 and may have an impact on pathophysiology of male subfertility both in CLD and in cystic fibrosis (CF), as well as spermatoceles.

Inherited forms of renal cell carcinoma.

It is estimated that up to 2% of renal cell cancer (RCC) clusters in families. Several forms of hereditary RCC have been characterized with specific clinical, histopathological, and genetic features. The most common of these is von Hippel-Lindau (VHL) disease caused by mutations in the VHL gene and predisposing to clear cell RCC. Predisposition to papillary RCC is present in hereditary leiomyomatosis and renal cell cancer (HLRCC) and hereditary papillary renal cell carcinoma (HPRC). Identification of the genetic defects causing these diseases has enlightened the molecular pathogenesis of RCC, and moreover, provided means to improve patient management. Genetic testing enables early diagnosis of the disease, after which individuals at-risk can be guided to regular surveillance. Screening facilitates detection of presymptomatic early tumors broadening treatment options and potentially improving prognosis. Thus, identification of individuals with inherited cancer susceptibility is important as special management of these patients improves disease outcome. The purpose of this review is to provide clues for identification and management of hereditary renal cancer patients in clinical practice.

Exclusion of large deletions and other rearrangements in BRCA1 and BRCA2 in Finnish breast and ovarian cancer families.

In the Finnish population, identified mutations in BRCA1 and BRCA2 account for a less than expected proportion of hereditary breast and ovarian cancer. All previous studies performed in our country have concentrated on finding germ-line mutations in the coding and splice-site regions of these two genes. Therefore, we wanted to use a different methodological approach and search for large genomic rearrangements, to exclude the possibility of biased BRCA1 and BRCA2 mutation spectra due to known limitations of the previously used PCR-based detection methods. Our results support earlier notions that other genes than BRCA1 and BRCA2 will explain a majority of the still unexplained cases of hereditary susceptibility to breast and ovarian cancer.

Mapping of five new putative anion transporter genes in human and characterization of SLC26A6, a candidate gene for pancreatic anion exchanger.

A second distinct family of anion transporters, in addition to the classical SLC4 (or AE) family, has recently been delineated. Members of the SLC26 family are structurally well conserved and can mediate the electroneutral exchange of Cl(-) for HCO(-)(3) across the plasma membrane of mammalian cells like members of the SLC4 family. Three human transporter proteins have been functionally characterized: SLC26A2 (DTDST), SLC26A3 (CLD or DRA), and SLC26A4 (PDS) can transport with different specificities the chloride, iodine, bicarbonate, oxalate, and hydroxyl anions, whereas SLC26A5 (prestin) was suggested to act as the motor protein of the cochlear outer hair cell. We report the expansion of the SLC26 family with five new members in chromosomes 3, 6, 8, 12, and 17 and mapping of SLC26A1 to 4p16.3. We have characterized one of them, SLC26A6, in more detail. It maps to chromosome 3p21.3, encodes a predicted 738-amino-acid transmembrane protein, and is most abundantly expressed in the kidney and pancreas. Pancreatic ductal cell lines Capan-1 and Capan-2 express SLC26A6, and immunohistochemistry localizes SLC26A6 protein to the apical surface of pancreatic ductal cells, suggesting it as a candidate for a luminal anion exchanger. The functional characterization of the novel members of this tissue-specific gene family may provide new insights into anion transport physiology in different parts of the body.

Expression of growth factors and growth factor receptors in capillary hemangioblastoma.

To elucidate the mechanisms underlying the regulation of growth and differentiation of capillary hemangioblastoma we studied the expression of selected growth factors and growth factor receptors by immunocytochemistry. As stromal cells of capillary hemangioblastoma express high levels of vascular endothelial growth factor (VEGF) and placental growth factor (P1GF) mRNA, we studied the distribution of the corresponding VEGF and P1GF proteins. We also studied the expression of epidermal growth factor receptor (EGFR) and platelet-derived growth factor receptors (PDGFR) because their ligands have been reported to promote angiogenesis. The stromal cells expressed abundant EGFR and, in addition, some stromal cells expressed PDGFR-alpha but not PDGFR-beta. In contrast, the endothelial cells co-expressed PDGFR-alpha and PDGFR-beta. VEGF and P1GF were expressed by scattered stromal cells; however, more intense staining was observed in the endothelial cells of the intratumoral blood vessels, possibly indicating the secreted growth factors bound to their target receptors. We conclude that capillary hemangioblastomas express a variety of growth factor receptors and ligands, potentially involved in both autocrine and paracrine loops. The uniformly high EGFR expression is unique among brain tumors and may be associated with the typical morphology of capillary hemangioblastoma. The expression of highly angiogenic growth factors and their receptors may contribute to the rich vascularity of this enigmatic tumor.