Effects of Calcium and Dairy on Body Composition and Weight Loss in African-American Adults

OBJECTIVE

Our objective was to determine the effects of dairy consumption on adiposity and body composition in obese African Americans.

RESEARCH METHODS AND PROCEDURES

We performed two randomized trials in obese African-American adults. In the first (weight maintenance), 34 subjects were maintained on a low calcium (500 mg/d)/low dairy (<1 serving/d) or high dairy (1200 mg Ca/d diet including 3 servings of dairy) diet with no change in energy or macronutrient intake for 24 weeks. In the second trial (weight loss), 29 subjects were similarly randomized to the low or high dairy diets and placed on a caloric restriction regimen (-500 kcal/d).

RESULTS

In the first trial, body weight remained stable for both groups throughout the maintenance study. The high dairy diet resulted in decreases in total body fat (2.16 kg, p < 0.01), trunk fat (1.03 kg, p < 0.01), insulin (18.7 pM, p < 0.04), and blood pressure (6.8 mm Hg systolic, p < 0.01; 4.25 mm Hg diastolic, p < 0.01) and an increase in lean mass (1.08 kg, p < 0.04), whereas there were no significant changes in the low dairy group. In the second trial, although both diets produced significant weight and fat loss, weight and fat loss on the high dairy diet were approximately 2-fold higher (p < 0.01), and loss of lean body mass was markedly reduced (p < 0.001) compared with the low dairy diet.

DISCUSSION

Substitution of calcium-rich foods in isocaloric diets reduced adiposity and improved metabolic profiles in obese African Americans without energy restriction or weight loss and augmented weight and fat loss secondary to energy restriction.

LRP1B deletion in high-grade serous ovarian cancers is associated with acquired chemotherapy resistance to liposomal doxorubicin

High-grade serous cancer (HGSC), the most common subtype of ovarian cancer, often becomes resistant to chemotherapy, leading to poor patient outcomes. Intratumoral heterogeneity occurs in nearly all solid cancers, including ovarian cancer, contributing to the development of resistance mechanisms. In this study, we examined the spatial and temporal genomic variation in HGSC using high-resolution single-nucleotide polymorphism arrays. Multiple metastatic lesions from individual patients were analyzed along with 22 paired pretreatment and posttreatment samples. We documented regions of differential DNA copy number between multiple tumor biopsies that correlated with altered expression of genes involved in cell polarity and adhesion. In the paired primary and relapse cohort, we observed a greater degree of genomic change in tumors from patients that were initially sensitive to chemotherapy and had longer progression-free interval compared with tumors from patients that were resistant to primary chemotherapy. Notably, deletion or downregulation of the lipid transporter LRP1B emerged as a significant correlate of acquired resistance in our analysis. Functional studies showed that reducing LRP1B expression was sufficient to reduce the sensitivity of HGSC cell lines to liposomal doxorubicin, but not to doxorubicin, whereas LRP1B overexpression was sufficient to increase sensitivity to liposomal doxorubicin. Together, our findings underscore the large degree of variation in DNA copy number in spatially and temporally separated tumors in HGSC patients, and they define LRP1B as a potential contributor to the emergence of chemotherapy resistance in these patients.

Investigation of the relationship between transcranial impedance and intracranial pressure

Studies on piglets have shown that cranial bioimpedance (Z) measurements correlate well with invasively measured intracranial pressure (ICP). We have tested the feasibility of collecting transcranial impedance from a clinical device for measuring whole-body water content (ImpediMed SFB7). In the clinical study, 50 normal healthy volunteers had transcranial impedance measured using nine different head montages (forehead to mastoid (left/right), temporal to mastoid (left/right), forehead to temporal (left/right), forehead to occipital (left/right) and temporal to temporal). Impedance was measured 20 times over a frequency range per montage and ANOVA used to test for effects of electrode position upon recorded value. For the experimental study, five sedated and ventilated Marino sheep were instrumented for intraventricular ICP and transcranial impedance measurement. Measures of ICP were recorded while ICP was increased from baseline to greater than 50 mmHg in five steps using an intraventricular infusion of mock CSF. There is a significant effect of electrode position and gender upon transcranial impedance (p < 0.001). The temporal-mastoid electrode position had significantly lower impedance values in keeping with its shorter path length. ICP correlated with craniospinal compliance measurements and Impedance vs Freq by ICP step shows a clear ICP dependence (p = 0.007) across the sheep.

Thoracic myelopathy due to an intramedullary herniated nucleus pulposus: first case report and review of the literature

BACKGROUND AND IMPORTANCE

Herniation of intervertebral discs is relatively common. Migration usually occurs in the ventral epidural space; very rarely discs migrate in the subdural space. No cases of intradural intramedullary disc have been reported in humans.

CLINICAL PRESENTATION

A case of a herniated intervertebral disc directly into the spinal cord parenchyma is presented. The patient presented with 2 weeks of progressive bilateral lower extremity numbness and weakness, saddle hypoesthesia, urinary dysfunction and gait disturbance. Spine magnetic resonance imaging (MRI) with gadolinium revealed a solitary well-defined intramedullary lesion (T7-T8 level) with ring enhancement and focal cord expansion with significant surrounding edema. Metastatic workup and neural axis imaging was negative. A thoracic laminectomy and myelotomy was performed; the lesion was pearlescent and well circumscribed. It was densely adherent to the ventral pia and gross totally removed. Pathology was consistent with nucleus pulposus.

CONCLUSION

Intradural intramedullary migration of a herniated intervertebral disc is extremely rare but should be considered in the differential. It may present in a variety of clinical scenarios, including thoracic myelopathy, and mimic intramedullary spinal cord tumor.

Abstract 3967: The Cancer Genome Project high throughput analysis pipeline

The Cancer Genome Project (CGP) was set up in 2000 to use systematic mutation screening methods to increase our understanding of human cancer. With the advent of next generation sequencing, and the large volumes of data that it generates, a new suite of software was required to rapidly and accurately screen these data for somatic changes. We have built an analysis pipeline to track and analyse large numbers of tumour samples, using in-house and externally available tools. The analysis pipeline is built around a ∼2,000 node compute farm and Lustre filesystem which outputs into our archive and data storage system, FileTrk. FileTrk holds the raw data files (BAM, CEL etc), the results of the analysis and any versioning information about the software used to generate these results. Sample lanes are aligned back to the genome using Burrows-Wheeler Aligner (BWA) and lane-to-lane comparisons are made to ensure data integrity. Lanes from each sample are merged into a single sample BAM file and once 30 - 40x coverage is reached and the lanes have been quality assessed the sample is locked and ready for analysis. Mutation callers detect point mutations (Caveman, in-house software), small insertions/deletions (Pindel), breakpoints (BRASS, in-house software) and copy number changes (ASCAT & PICNIC, in-house software). The resulting mutations are post-processed to remove false positives, annotated to the RNA and protein level using standard nomenclature (Vagrent, in-house software) and uploaded to a database. Interfaces have been developed to enable the selection of random sets of mutations for validation, the outcome of the validations is recorded so specificity can be calculated for each sample in the system. IT systems are being developed to automatically export lists of somatic changes to COSMIC, the ICGC data portal and raw data to the European Genome-Phenome Archive (EGA).

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3967. doi:1538-7445.AM2012-3967

Circulating DNA and next-generation sequencing

Personalising cancer medicine depends upon the implementation of personalised diagnostics and therapeutics. Detailed genomic screening is likely to play a central role in this. As the range of drugs and other therapies for cancer continues to increase, there is an increasingly urgent need for sensitive and specific measures of disease burden to guide treatment regimens. The ability to quantify disease burden with high accuracy and sensitivity in patients with cancer would open many potential routes to personalising therapeutic choices. For example, the intensity of therapy could be guided by the amount of disease at diagnosis; monitoring the response of patients to drugs could allow extension of the period of treatment in responders or early changeover of therapy in nonresponders; and early prediction of recurrence could allow salvage therapy to be instituted before complications of relapse develop. The detection of tumour-specific rearrangements in DNA free in the serum or plasma may provide a substantial advance in the accuracy of monitoring disease burden in patients with solid tumours.

Ollier disease and Maffucci syndrome are caused by somatic mosaic mutations of IDH1 and IDH2

Ollier disease and Maffucci syndrome are characterized by multiple central cartilaginous tumors that are accompanied by soft tissue hemangiomas in Maffucci syndrome. We show that in 37 of 40 individuals with these syndromes, at least one tumor has a mutation in isocitrate dehydrogenase 1 (IDH1) or in IDH2, 65% of which result in a R132C substitution in the protein. In 18 of 19 individuals with more than one tumor analyzed, all tumors from a given individual shared the same IDH1 mutation affecting Arg132. In 2 of 12 subjects, a low level of mutated DNA was identified in non-neoplastic tissue. The levels of the metabolite 2HG were measured in a series of central cartilaginous and vascular tumors, including samples from syndromic and nonsyndromic subjects, and these levels correlated strongly with the presence of IDH1 mutations. The findings are compatible with a model in which IDH1 or IDH2 mutations represent early post-zygotic occurrences in individuals with these syndromes.

Abstract 4836: In vitro drug sensitivity testing along with full genome and transcriptome sequencing and phosphoproteomics: Comprehensive “next-generation” molecular oncology portrait of a sarcoma for facilitating treatment decisions

We describe here comprehensive multi-layered genomic, molecular, functional and drug-sensitivity profiles of cancer specimens for clinical diagnostic and therapeutic use. A clinically and histologically atypical metastatic bone tumor was studied with the intent to inform clinicians in real time, should actionable findings emerge. This represents a pilot for future individualized molecular oncology.

Methods: We describe integration of the following profiling data: 1) Full genomic sequencing and bioinformatic analysis with 31x coverage of the tumor and 36x of germline DNA 2) aCGH analysis of the tumor and comparison with tumor derived primary cell line 3) Full transcriptome sequencing and microarray analysis 4) Bioinformatic analysis linking gene expression profiles from the patient's tumor with published data on 47 normal and 57 cancer types 5) Phosphoprotein analysis with antibody microarrays and MS covering most therapeutically relevant pathways 6) IHC profiles with multiple antibodies 7) Establishment and molecular representativity of an in vitro cell culture model and mouse xenograft 8) development of personalized plasma-DNA based monitoring of tumor load 9) High-throughput drug sensitivity testing of the patient-derived cell line against a panel of 1500 compounds, including most clinically actionable cancerdrugs and their combinations.

Selected key results: The tumor resembled malignant fibrocytic histiocytoma, was pleiomorphic with high mitotic counts. Clinical presentation was atypical with multiple metastatic bone lesions but no primary tumor. Genome sequencing revealed 12 genomic rerrangements and 34 putative missense mutations, including an oncogenic p53 mutation. Array-CGH revealed p16 deletion, and amplification of PDGFRA, KIT and VEGFR2 at 4q, but no clear overexpression. In vitro drug sensitivity testing revealed little impact of targeted drugs and kinase inhibitors like sunitinib, but strong inhibition by eg. bortezomib, daunorubicin, taxanes and zolendronic acid, which helped clinicial treatment decisions. The bone cancer initially responded to the treatment, but later progressed in soft tissues.

Conclusions: This deep individualized molecular oncology study highlights the advantages and challenges of translating molecular oncology data on individual patients. Transcriptome and protein expression of the primary tumors and drug sensitivity testing with representative in vitro cell lines may be informative even when diagnostic or therapeutically “actionable” gene mutations are not found.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4836. doi:10.1158/1538-7445.AM2011-4836

Abstract 46: COSMIC: Enhancing the analysis of whole somatic mutant tumor genomes

COSMIC, the Catalogue Of Somatic Mutations In Cancer (http://www.sanger.ac.uk/cosmic), is a comprehensive web resource for the investigation of somatic mutations in human cancer with data curated and centrally combined from a variety of sources. Currently, point mutation data have been manually curated from the scientific literature on 89 genes, together with full mutation details on a further 57 fusion gene pairs (Release v50, Nov 2010), defined as known cancer genes in the Cancer Gene Census (http://www.sanger.ac.uk/genetics/CGP/Census). Further, in collaboration with the IARC TP53 database, COSMIC now contains the somatic mutation data for the key p53 tumor suppressor gene. Details of many large candidate gene screens, together spanning almost 20,000 genes have also been curated from three sources, the scientific literature, the Cancer Genome Project labs at the Sanger Institute, UK (CGP), and The Cancer Genome Atlas (TCGA) web portal. Finally, COSMIC now presents the results of 48 whole-genome screens, detailing 2689 genomic rearrangements, 1661 coding mutations and 55,440 non-coding mutations.

The COSMIC website is designed to allow easy and intuitive browsing of this data, in isolation or various combinations. As the amount and variability of data has increased, the methods of acquiring and interacting with the data have been enhanced. The COSMIC website now provides mining capabilities, with numerous specialization filters, graphically presenting selected data. A more extensive mining tool is the COSMIC Biomart, allowing selection of data using any definitions found in the COSMIC system.

With the increasing significance of genomic data in cancer, COSMIC has integrated with the two largest genome browsers, the Ensembl system and the UCSC cancer genomics browser; links are available from and to Ensembl, whilst per-tissue summaries are provided graphically in the UCSC browser. In addition, COSMIC has integrated its own genome browser, a version of ‘Gbrowse’, which provides custom genomic views of the majority of COSMIC data, together with CONAN copy number graphs, within the context of full genome annotations. Looking to the future, much novel global cancer genomics data will soon be made available via the ICGC data coordination centre. COSMIC is well placed to utilize this as a major new source of mutation information, maintaining COSMIC's position as a central resource in human cancer genetics.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 46. doi:10.1158/1538-7445.AM2011-46

Management of liver trauma

BACKGROUND

Blunt and penetrating liver trauma is common and often presents major diagnostic and management problems.

METHODS

A literature review was undertaken to determine the current consensus on investigation and management strategies.

RESULTS

The liver is the most frequently injured organ following abdominal trauma. Immediate assessment with ultrasound has replaced diagnostic peritoneal lavage in the resuscitation room, but computerised tomography remains the gold standard investigation. Nonoperative management is preferred in stable patients but laparotomy is indicated in unstable patients. Damage control techniques such as perihepatic packing, hepatotomy plus direct suture, and resectional debridement are recommended. Major complex surgical procedures such as anatomical resection or atriocaval shunting are now thought to be redundant in the emergency setting. Packing is also recommended for the inexperienced surgeon to allow control and stabilisation prior to transfer to a tertiary centre. Interventional radiological techniques are becoming more widely used, particularly in patients who are being managed nonoperatively or have been stabilised by perihepatic packing.

CONCLUSIONS

Management of liver injuries has evolved significantly throughout the last two decades. In the absence of other abdominal injuries, operative management can usually be avoided. Patients with more complex injuries or subsequent complications should be transferred to a specialist centre to optimise final outcome.

Management of liver trauma

BACKGROUND

Blunt and penetrating liver trauma is common and often presents major diagnostic and management problems.

METHODS

A literature review was undertaken to determine the current consensus on investigation and management strategies.

RESULTS

The liver is the most frequently injured organ following abdominal trauma. Immediate assessment with ultrasound has replaced diagnostic peritoneal lavage in the resuscitation room, but computerised tomography remains the gold standard investigation. Nonoperative management is preferred in stable patients but laparotomy is indicated in unstable patients. Damage control techniques such as perihepatic packing, hepatotomy plus direct suture, and resectional debridement are recommended. Major complex surgical procedures such as anatomical resection or atriocaval shunting are now thought to be redundant in the emergency setting. Packing is also recommended for the inexperienced surgeon to allow control and stabilisation prior to transfer to a tertiary centre. Interventional radiological techniques are becoming more widely used, particularly in patients who are being managed nonoperatively or have been stabilised by perihepatic packing.

CONCLUSIONS

Management of liver injuries has evolved significantly throughout the last two decades. In the absence of other abdominal injuries, operative management can usually be avoided. Patients with more complex injuries or subsequent complications should be transferred to a specialist centre to optimise final outcome.