Mitochondrial genomics in the cancer cell line encyclopedia and a scoring method to effectively pair cell lines for cytoplasmic hybridization.

Mitochondrial sequence variants have been associated with many human diseases, including cancer. A well-established experimental strategy to assess the impact of mitochondrial sequence variants is to generate cytoplasmic hybrids (cybrids). Cybridization facilitates the study of mitochondrial DNA (mtDNA) mutations under a controlled nuclear genetic background. However, in generating cybrids, it is important to select most suitable mtDNA donor and recipient cells so that any change in recipient's cellular phenotype may be attributed to the introduction, through the donor, of mutations in the gene of interest. Here we catalog mitochondrial sequence variants, gene expression, and haplogroups across 937 publicly available cancer cell lines curated by the Cancer Cell Line Encyclopedia (CCLE). We then present DoReMi (Donor, Recipient Mitochondrial DNA matching) as a method to score candidate donor and recipient cell lines based on their mtDNA mutational profiles, including their heteroplasmy levels. DoReMi will allow researchers to design successful cybrid experiments for querying the role of mutations in their mitochondrial-encoded gene of interest. Researchers may also apply DoReMi to study their own cell lines. DoReMi and the other resources provided by this study help optimize cybridization experiments. This software is available for use at http://mendel.gene.cwru.edu/laframboiselab/software.php.

Selected mitochondrial DNA landscapes activate the SIRT3 axis of the UPRmt to promote metastasis.

By causing mitochondrial DNA (mtDNA) mutations and oxidation of mitochondrial proteins, reactive oxygen species (ROS) leads to perturbations in mitochondrial proteostasis. Several studies have linked mtDNA mutations to metastasis of cancer cells but the nature of the mtDNA species involved remains unclear. Our data suggests that no common mtDNA mutation identifies metastatic cells; rather the metastatic potential of several ROS-generating mutations is largely determined by their mtDNA genomic landscapes, which can act either as an enhancer or repressor of metastasis. However, mtDNA landscapes of all metastatic cells are characterized by activation of the SIRT/FOXO/SOD2 axis of the mitochondrial unfolded protein response (UPRmt). The UPRmt promotes a complex transcription program ultimately increasing mitochondrial integrity and fitness in response to oxidative proteotoxic stress. Using SOD2 as a surrogate marker of the UPRmt, we found that in primary breast cancers, SOD2 is significantly increased in metastatic lesions. We propose that the ability of selected mtDNA species to activate the UPRmt is a process that is exploited by cancer cells to maintain mitochondrial fitness and facilitate metastasis.

Automated routing of DICOM CT, MR, and CR images: solving the pitfalls of vendor-specific DICOM implementations.

This paper details our experience in developing and implementing an automated DICOM Image Router. This workstation serves as a gateway between image acquisition devices and image display and storage devices. Images are checked for demographic input errors and data format inconsistencies between the source and destination devices. Based on the configured rules, and image may be held for manual correction and/or distributed to multiple locations. Distribution is based on easily configured environmental variables and rules files which may be changed as needed. For example, CT images are typically sent to the archive and to a radiologist's display workstation. If the patient came from the Emergency Department, a copy of the images are sent to a clinician display workstation located in the Emergency Department. If the patient has suffered trauma to the head, a copy of the images are sent to a display workstation in the Neurosurgery Department for possible consultation. The software was developed on a UNIX-based platform and utilizes a Fast Ethernet network. To date, images from a variety of devices have been acquired: General Electric HiSpeed CT/I scanner, General Electric Signa MRI scanner, Philips Thoravision Digital Chest unit, and Fuji AC-3CS Computed Radiography (CR) unit. Each device has presented new challenges in providing a uniform look to patient demographics in the PACS archive. The workstation also provides a buffer in the event of network outages, storing images for later transmission when the network and/or a workstation recover.

PACS and CR implementation in a level I trauma center emergency department.

Implementation of a picture archive and communication system (PACS) at a large teaching hospital is an expensive and daunting endeavor. The approach taken at the University of Alabama Hospitals has been to assemble an institution-wide system through focused integration of smaller mini-PACS. Recently a mini-PACS using Computed Radiography (CR) has been placed in the Emergency Department (ED) of a Level I Trauma Center completely replacing conventional screen-film radiography. This area of the hospital produces approximately 250 images per day and provided many challenging requirements: the need for rapid radiography; providing good image quality for difficult examinations with potentially uncooperative patients; reproduction of lost films to maintain availability of images to multiple consulting teams; and frequently unknown patient demographics. The PACS includes both vendor-supplied and in-house developed devices for image storage, distribution, and display. Digital images are produced using two photo-stimulable phosphor CR systems. Currently, all radiographic examinations are acquired digitally with production of a hard copy film as well as electronic distribution via the PACS. Interpretation of images is done primarily via hard copy with a goal of transition to soft copy interpretation. This paper discusses the functional requirements of the PACS and solutions to workflow issues arising in the ED.