Deleterious variants in TRAK1 disrupt mitochondrial movement and cause fatal encephalopathy

This is the author accepted manuscript. The final version is available from Oxford University Press via the DOI in this record.The corrigendum to this article is in ORE: http://hdl.handle.net/10871/33588Cellular distribution and dynamics of mitochondria are regulated by several motor proteins and a microtubule network. In neurons, mitochondrial trafficking is crucial because of high energy needs and calcium ion buffering along axons to synapses during neurotransmission. The trafficking kinesin proteins (TRAKs) are well characterized for their role in lysosomal and mitochondrial trafficking in cells, especially neurons. Using whole exome sequencing, we identified homozygous truncating variants in TRAK1 (NM_001042646:c.287-2A > C), in six lethal encephalopathic patients from three unrelated families. The pathogenic variant results in aberrant splicing and significantly reduced gene expression at the RNA and protein levels. In comparison with normal cells, TRAK1-deficient fibroblasts showed irregular mitochondrial distribution, altered mitochondrial motility, reduced mitochondrial membrane potential, and diminished mitochondrial respiration. This study confirms the role of TRAK1 in mitochondrial dynamics and constitutes the first report of this gene in association with a severe neurodevelopmental disorder.D.M.E. and J.K. are supported by the Office of Naval Research (ONR) Grant N000141410538. M.S. is supported by the BBSRC (BB/K006231/1), a Wellcome Trust Institutional Strategic Support Award (WT097835MF, WT105618MA), and a Marie Curie Initial Training Network (ITN) action PerFuMe (316723). M.C.V.M., J.S., H.P., C.F., T.V. and W.A.G. are supported by the NGHRI Intramural Research Program. G.R. is supported by the Kahn Family Foundation and the Israeli Centers of Excellence (I-CORE) Program (ISF grant no. 41/11)

Spectral morphometric characterization of breast carcinoma cells

The spectral morphometric characteristics of standard haematoxylin and eosin breast carcinoma specimens were evaluated by light microscopy combined with a spectral imaging system. Light intensity at each wavelength in the range of 450–800 nm was recorded for 104 pixels from each field and represented as transmitted light spectra. A library of six characteristic spectra served to scan the cells and reconstruct new images depicting the nuclear area occupied by each spectrum. Fifteen cases of infiltrating ductal carcinoma and six cases of lobular carcinoma were examined; nine of the infiltrating ductal carcinoma and three of the lobular carcinoma showed an in situ component. The spectral morphometric analysis revealed a correlation between specific patterns of spectra and different groups of breast carcinoma cells. The most consistent result was that lobular carcinoma cells of in situ and infiltrating components from all patients showed a similar spectral pattern, whereas ductal carcinoma cells displayed spectral variety. Comparison of the in situ and the infiltrating ductal solid, cribriform and comedo carcinoma cells from the same patient revealed a strong similarity of the spectral elements and their relative distribution in the nucleus. The spectrum designated as number 5 in the library incorporated more than 40% of the nuclear area in 74.08% of the infiltrating lobular cells and in 13.64% of the infiltrating ductal carcinoma cells (P < 0.001). Spectrum number 2 appeared in all infiltrating ductal cells examined and in none of the lobular cells. These results indicate that spectrum number 5 is related to infiltrating lobular carcinoma, whereas spectrum number 2 is characteristic for infiltrating ductal carcinoma cells. Spectral similarity mapping of central necrotic regions of comedo type in situ carcinoma revealed nuclear fragmentation into defined segments composed of highly condensed chromatin. We conclude that the spectral morphometric features found for lobular and ductal cell populations may serve future automated histological diagnostics. © 1999 Cancer Research Campaig

MicroRNA profiles discriminate among colon cancer metastasis

MicroRNAs are being exploited for diagnosis, prognosis and monitoring of cancer and other diseases. Their high tissue specificity and critical role in oncogenesis provide new biomarkers for the diagnosis and classification of cancer as well as predicting patients' outcomes. MicroRNAs signatures have been identified for many human tumors, including colorectal cancer (CRC). In most cases, metastatic disease is difficult to predict and to prevent with adequate therapies. The aim of our study was to identify a microRNA signature for metastatic CRC that could predict and differentiate metastatic target organ localization. Normal and cancer tissues of three different groups of CRC patients were analyzed. RNA microarray and TaqMan Array analysis were performed on 66 Italian patients with or without lymph nodes and/or liver recurrences. Data obtained with the two assays were analyzed separately and then intersected to identify a primary CRC metastatic signature. Five differentially expressed microRNAs (hsa-miR-21, -103, -93, -31 and -566) were validated by qRT-PCR on a second group of 16 American metastatic patients. In situ hybridization was performed on the 16 American patients as well as on three distinct commercial tissues microarray (TMA) containing normal adjacent colon, the primary adenocarcinoma, normal and metastatic lymph nodes and liver. Hsa-miRNA-21, -93, and -103 upregulation together with hsa-miR-566 downregulation defined the CRC metastatic signature, while in situ hybridization data identified a lymphonodal invasion profile. We provided the first microRNAs signature that could discriminate between colorectal recurrences to lymph nodes and liver and between colorectal liver metastasis and primary hepatic tumor

Potential use of spectral image analysis for the quantitative evaluation of estrogen receptors in breast cancer

Evaluation of estrogen receptor (ER) content is an important factor in the choice of therapy and prognosis of breast cancer patients. In this study, we demonstrate a new spectral image analysis technique for objective and quantitative evaluations of stained specimens. The SpectraCubeTM system was used to analyze nuclear antigens in thirteen cases of breast cancer stained by the immunoperoxidase method with hematoxylin counterstain. Spectral imaging segregated the spectrum of diaminobenzidine (DAB) from the background color of hematoxylin and a spectral index was calculated. The spectral index essentially agreed with the pathologist's index (on a scale of 0 to 3) in seven out of the thirteen cases. A substantial number of ER positive pixels was detected in the two cases scored as 0 by the pathologist's index. In a test case scored as 1 by the pathologist's index we detected a significant number of pixels, representing 47% of the nuclei, with DAB-intensity values higher than the cut-off value of 1.2. These data suggest that spectral image analysis is a sensitive method providing intensive information with high reproducibility. Our spectral imaging method is highly flexible, enabling the user to define the spatial resolution of the analyzed specimen by choosing the number of pixels per one nucleus

The loss of calretinin expression indicates aganglionosis in Hirschsprung’s disease

Background: Hirschsprung’s disease (HD) is a congenital disorder characterised by the absence of ganglion cells in the large bowel, leading to functional obstruction and colonic dilatation proximal to the affected segment. A subclass of nerve cell bodies in both submucosa and myenteric ganglia of the human gastrointestinal tract were found to show immunopositivity for calretinin, a calcium binding protein, which plays an important role in the organisation and functioning of the central nervous system. Aim: To investigate calretinin immunostaining in ganglionic and aganglionic HD colon specimens, and compare it with staining for S100, neurone specific enolase, and c-kit. Methods: Ten large bowel, full thickness specimens from patients with classic rectosigmoid HD were selected from the pathology repository. In total, 54 paraffin wax blocks—24 from the ganglionic zone, 17 from the aganglionic zone, and 13 from the transitional zone—were processed. Results: Calretinin was not expressed in aganglionic segments of HD and associated nerve fibres, whereas in ganglionic HD segments and in normal colon both ganglion cells and nerve fibres were immunopositive. In addition, c-kit showed an altered distribution in the interstitial cells of Cajal. The transitional zone showed a broad spectrum of histomorphological and immunohistochemical patterns of both calretinin and c-kit expression. Conclusion: The absence of calretinin expression may serve as a diagnostic aid in identifying aganglionic segments in HD

Potential use of spectral image analysis for the quantitative evaluation of estrogen receptors in breast cancer

Evaluation of estrogen receptor (ER) content is an important factor in the choice of therapy and prognosis of breast cancer patients. In this study, we demonstrate a new spectral image analysis technique for objective and quantitative evaluations of stained specimens. The SpectraCubeTM system was used to analyze nuclear antigens in thirteen cases of breast cancer stained by the immunoperoxidase method with hematoxylin counterstain. Spectral imaging segregated the spectrum of diaminobenzidine (DAB) from the background color of hematoxylin and a spectral index was calculated. The spectral index essentially agreed with the pathologist's index (on a scale of 0 to 3) in seven out of the thirteen cases. A substantial number of ER positive pixels was detected in the two cases scored as 0 by the pathologist's index. In a test case scored as 1 by the pathologist's index we detected a significant number of pixels, representing 47% of the nuclei, with DAB-intensity values higher than the cut-off value of 1.2. These data suggest that spectral image analysis is a sensitive method providing intensive information with high reproducibility. Our spectral imaging method is highly flexible, enabling the user to define the spatial resolution of the analyzed specimen by choosing the number of pixels per one nucleus