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1.
Am J Ind Med ; 65(11): 840-856, 2022 11.
Article in English | MEDLINE | ID: mdl-34775611

ABSTRACT

BACKGROUND: During 2003-2013, 1189 US oil and gas extraction (OGE) workers died while working, resulting in an average annual workplace fatality rate seven times that for all US workers. OGE work commonly involves long hours, shiftwork, irregular schedules, and long commutes, but effects of these factors on fatigue, occupational injury, and illness in OGE are largely unknown. METHODS: A scoping review of relevant OGE research during 2000-2019 was completed and supplemented by input from a NIOSH-sponsored Forum. RESULTS: Seventy-eight papers were identified; 76% reported only offshore research. Five themes for research needs emerged: build knowledge about the impacts of fatigue; explore interactions between on- and off-the-job risk factors; identify and evaluate interventions; assess effectiveness of technology; and increase the diffusion of fatigue risk management information. CONCLUSIONS: Further collaboration between researchers and OGE operators and contractors can lead to action-oriented recommendations to mitigate the effects of fatigue, inadequate sleep, and shiftwork.


Subject(s)
Occupational Injuries , Sleep , Fatigue/etiology , Humans , Sleep Deprivation , Workplace
2.
J Oncol Pharm Pract ; 24(5): 365-370, 2018 Jul.
Article in English | MEDLINE | ID: mdl-28554241

ABSTRACT

Purpose Reduction in waste of intravenous (IV) tacrolimus, an immunosuppressant used to prevent graft-versus-host disease in allogeneic hematopoietic stem cell transplantation recipients, was evaluated after standardizing the concentration. Methods A single-center, retrospective cohort study at a large academic comprehensive cancer center was performed comparing patient-specific intravenous tacrolimus doses (tacrolimus doses in 50, 100, or 250 mL of normal saline based on manufacturer's recommended concentration) to tacrolimus intravenous standard concentration (tacrolimus 1 mg in 250 mL of normal saline) continuous intravenous infusion titrated to prescribed dose. The cohort study was performed on two hematopoietic stem cell transplantation nursing units consisting of a prepilot phase during which time patient-specific intravenous tacrolimus doses were compounded and administered, followed by the pilot phase during which patients received tacrolimus intravenous standard concentration. The primary endpoint was reduction in tacrolimus intravenous bags wasted. Secondary endpoints were drug cost savings, decreased intravenous infusion line supplies, decrease in time needed to execute dose changes, reduction in infusion pump alerts, and number of patient safety events. Results Compared to the prepilot phase, there was a 64% reduction in tacrolimus intravenous bags wasted during the pilot phase ( p = 0.029), resulting in a mean monthly total cost savings of $224.31 for pilot units. Intravenous pump line use was reduced by 18% ( p = 0.067), yielding a monthly total cost savings of $84.02 for pilot units. The median time needed to execute dose changes and intravenous pump overrides was significantly reduced ( p < 0.0001, p < 0.0001, respectively). Conclusion This interdisciplinary quality improvement initiative led to increased efficiency, reduction in waste, and decreased intravenous pump alerts utilizing tacrolimus intravenous standard concentration.


Subject(s)
Graft vs Host Disease/prevention & control , Hematopoietic Stem Cell Transplantation/methods , Immunosuppressive Agents/administration & dosage , Tacrolimus/administration & dosage , Adult , Humans , Immunosuppressive Agents/therapeutic use , Infusions, Intravenous , Pilot Projects , Retrospective Studies
3.
Nature ; 471(7339): 467-72, 2011 Mar 24.
Article in English | MEDLINE | ID: mdl-21430775

ABSTRACT

Multiple myeloma is an incurable malignancy of plasma cells, and its pathogenesis is poorly understood. Here we report the massively parallel sequencing of 38 tumour genomes and their comparison to matched normal DNAs. Several new and unexpected oncogenic mechanisms were suggested by the pattern of somatic mutation across the data set. These include the mutation of genes involved in protein translation (seen in nearly half of the patients), genes involved in histone methylation, and genes involved in blood coagulation. In addition, a broader than anticipated role of NF-κB signalling was indicated by mutations in 11 members of the NF-κB pathway. Of potential immediate clinical relevance, activating mutations of the kinase BRAF were observed in 4% of patients, suggesting the evaluation of BRAF inhibitors in multiple myeloma clinical trials. These results indicate that cancer genome sequencing of large collections of samples will yield new insights into cancer not anticipated by existing knowledge.


Subject(s)
Genome, Human/genetics , Multiple Myeloma/genetics , Mutation/genetics , Amino Acid Sequence , Blood Coagulation/genetics , CpG Islands/genetics , DNA Mutational Analysis , DNA Repair/genetics , Exons/genetics , Exosome Multienzyme Ribonuclease Complex , Genomics , Histones/metabolism , Homeodomain Proteins/genetics , Homeostasis/genetics , Humans , Methylation , Models, Molecular , Molecular Sequence Data , Multiple Myeloma/drug therapy , Multiple Myeloma/enzymology , Multiple Myeloma/metabolism , NF-kappa B/metabolism , Oncogenes/genetics , Open Reading Frames/genetics , Protein Biosynthesis/genetics , Protein Conformation , Proto-Oncogene Proteins B-raf/antagonists & inhibitors , Proto-Oncogene Proteins B-raf/genetics , Proto-Oncogene Proteins B-raf/metabolism , RNA Processing, Post-Transcriptional/genetics , Ribonucleases/chemistry , Ribonucleases/genetics , Signal Transduction/genetics , Transcription, Genetic/genetics
4.
PLoS Genet ; 10(2): e1004135, 2014 Feb.
Article in English | MEDLINE | ID: mdl-24550739

ABSTRACT

Advanced cholangiocarcinoma continues to harbor a difficult prognosis and therapeutic options have been limited. During the course of a clinical trial of whole genomic sequencing seeking druggable targets, we examined six patients with advanced cholangiocarcinoma. Integrated genome-wide and whole transcriptome sequence analyses were performed on tumors from six patients with advanced, sporadic intrahepatic cholangiocarcinoma (SIC) to identify potential therapeutically actionable events. Among the somatic events captured in our analysis, we uncovered two novel therapeutically relevant genomic contexts that when acted upon, resulted in preliminary evidence of anti-tumor activity. Genome-wide structural analysis of sequence data revealed recurrent translocation events involving the FGFR2 locus in three of six assessed patients. These observations and supporting evidence triggered the use of FGFR inhibitors in these patients. In one example, preliminary anti-tumor activity of pazopanib (in vitro FGFR2 IC50≈350 nM) was noted in a patient with an FGFR2-TACC3 fusion. After progression on pazopanib, the same patient also had stable disease on ponatinib, a pan-FGFR inhibitor (in vitro, FGFR2 IC50≈8 nM). In an independent non-FGFR2 translocation patient, exome and transcriptome analysis revealed an allele specific somatic nonsense mutation (E384X) in ERRFI1, a direct negative regulator of EGFR activation. Rapid and robust disease regression was noted in this ERRFI1 inactivated tumor when treated with erlotinib, an EGFR kinase inhibitor. FGFR2 fusions and ERRFI mutations may represent novel targets in sporadic intrahepatic cholangiocarcinoma and trials should be characterized in larger cohorts of patients with these aberrations.


Subject(s)
Bile Duct Neoplasms/drug therapy , Cholangiocarcinoma/drug therapy , ErbB Receptors/metabolism , Receptor, Fibroblast Growth Factor, Type 2/genetics , Signal Transduction/genetics , Bile Duct Neoplasms/genetics , Bile Duct Neoplasms/pathology , Bile Ducts, Intrahepatic/pathology , Cell Line, Tumor , Cholangiocarcinoma/genetics , Cholangiocarcinoma/pathology , ErbB Receptors/antagonists & inhibitors , ErbB Receptors/genetics , Erlotinib Hydrochloride , Genome, Human , Humans , Imidazoles/administration & dosage , Indazoles , Molecular Targeted Therapy , Mutation , Prognosis , Protein Kinase Inhibitors , Pyridazines/administration & dosage , Pyrimidines/administration & dosage , Quinazolines/administration & dosage , Receptor, Fibroblast Growth Factor, Type 2/antagonists & inhibitors , Receptor, Fibroblast Growth Factor, Type 2/metabolism , Sulfonamides/administration & dosage , Transcriptome
5.
Nucleic Acids Res ; 42(2): e8, 2014 Jan.
Article in English | MEDLINE | ID: mdl-24071583

ABSTRACT

As next-generation sequencing continues to have an expanding presence in the clinic, the identification of the most cost-effective and robust strategy for identifying copy number changes and translocations in tumor genomes is needed. We hypothesized that performing shallow whole genome sequencing (WGS) of 900-1000-bp inserts (long insert WGS, LI-WGS) improves our ability to detect these events, compared with shallow WGS of 300-400-bp inserts. A priori analyses show that LI-WGS requires less sequencing compared with short insert WGS to achieve a target physical coverage, and that LI-WGS requires less sequence coverage to detect a heterozygous event with a power of 0.99. We thus developed an LI-WGS library preparation protocol based off of Illumina's WGS library preparation protocol and illustrate the feasibility of performing LI-WGS. We additionally applied LI-WGS to three separate tumor/normal DNA pairs collected from patients diagnosed with different cancers to demonstrate our application of LI-WGS on actual patient samples for identification of somatic copy number alterations and translocations. With the evolution of sequencing technologies and bioinformatics analyses, we show that modifications to current approaches may improve our ability to interrogate cancer genomes.


Subject(s)
DNA Copy Number Variations , High-Throughput Nucleotide Sequencing/methods , Neoplasms/genetics , Sequence Analysis, DNA/methods , Translocation, Genetic , Gene Library , Genome, Human , Genomics/methods , Humans
6.
Blood ; 121(16): 3147-52, 2013 Apr 18.
Article in English | MEDLINE | ID: mdl-23422747

ABSTRACT

Epidemiological data have suggested that African American (AA) persons are twice as likely to be diagnosed with multiple myeloma (MM) compared with European American (EA) persons. Here, we have analyzed a set of cytogenetic and genomic data derived from AA and EA MM patients. We have compared the frequency of IgH translocations in a series of data from 115 AA patients from 3 studies and 353 EA patients from the Eastern Cooperative Oncology Group (ECOG) studies E4A03 and E9487. We have also interrogated tumors from 45 AA and 196 EA MM patients for somatic copy number abnormalities associated with poor outcome. In addition, 35 AA and 178 EA patients were investigated for a transcriptional profile associated with high-risk disease. Overall, based on this cohort, genetic profiles were similar except for a significantly lower frequency of IgH translocations (40% vs 52%; P = .032) in AA patients. Frequency differences of somatic copy number aberrations were not significant after correction for multiple testing. There was also no significant difference in the frequency of high-risk disease based on gene expression profiling. Our study represents the first comprehensive comparisons of the frequency and distribution of molecular alterations in MM tumors between AA and EA patients. ECOG E4A03 is registered with ClinicalTrials.gov, number NCT00098475. ECOG E9487 is a companion validation set to the ECOG study E9486 and is registered with the National Institutes of Health, National Cancer Institute, Clinical Trials (PDQ), number EST-9486.


Subject(s)
Black or African American/genetics , Genomics/methods , Immunoglobulin Heavy Chains/genetics , Multiple Myeloma/genetics , Translocation, Genetic , Cohort Studies , Gene Expression Profiling , Humans , White People/genetics
7.
Toxicol Appl Pharmacol ; 288(1): 114-20, 2015 Oct 01.
Article in English | MEDLINE | ID: mdl-26212258

ABSTRACT

Parathion, a widely used organophosphate insecticide, is considered a high priority chemical threat. Parathion toxicity is dependent on its metabolism by the cytochrome P450 system to paraoxon (diethyl 4-nitrophenyl phosphate), a cytotoxic metabolite. As an effective inhibitor of cholinesterases, paraoxon causes the accumulation of acetylcholine in synapses and overstimulation of nicotinic and muscarinic cholinergic receptors, leading to characteristic signs of organophosphate poisoning. Inhibition of parathion metabolism to paraoxon represents a potential approach to counter parathion toxicity. Herein, we demonstrate that menadione (methyl-1,4-naphthoquinone, vitamin K3) is a potent inhibitor of cytochrome P450-mediated metabolism of parathion. Menadione is active in redox cycling, a reaction mediated by NADPH-cytochrome P450 reductase that preferentially uses electrons from NADPH at the expense of their supply to the P450s. Using human recombinant CYP 1A2, 2B6, 3A4 and human liver microsomes, menadione was found to inhibit the formation of paraoxon from parathion. Administration of menadione bisulfite (40mg/kg, ip) to rats also reduced parathion-induced inhibition of brain cholinesterase activity, as well as parathion-induced tremors and the progression of other signs and symptoms of parathion poisoning. These data suggest that redox cycling compounds, such as menadione, have the potential to effectively mitigate the toxicity of organophosphorus pesticides including parathion which require cytochrome P450-mediated activation.


Subject(s)
Cholinesterase Inhibitors/toxicity , Cytochrome P-450 Enzyme Inhibitors/pharmacology , Cytochrome P-450 Enzyme System/metabolism , Insecticides/toxicity , Liver/drug effects , Organophosphate Poisoning/prevention & control , Parathion/toxicity , Vitamin K 3/pharmacology , Acetylcholinesterase/metabolism , Activation, Metabolic , Animals , Cholinesterase Inhibitors/metabolism , Cytochrome P-450 Enzyme Inhibitors/metabolism , Cytoprotection , Disease Models, Animal , Dose-Response Relationship, Drug , Female , GPI-Linked Proteins/metabolism , Humans , Insecticides/metabolism , Liver/enzymology , Microsomes, Liver/drug effects , Microsomes, Liver/enzymology , NADP/metabolism , Organophosphate Poisoning/enzymology , Organophosphate Poisoning/etiology , Oxidation-Reduction , Paraoxon/metabolism , Paraoxon/toxicity , Parathion/metabolism , Rats, Long-Evans , Recombinant Proteins/metabolism , Time Factors , Vitamin K 3/metabolism
8.
Clin Sci (Lond) ; 128(12): 895-904, 2015 Jun.
Article in English | MEDLINE | ID: mdl-25626417

ABSTRACT

Complex I (CI) is the largest of the five multi-subunit complexes constituting the human oxidative phosphorylation (OXPHOS) system. Seven of its catalytic core subunits are encoded by mitochondrial DNA (ND (NADH dehydrogenase)1-6, ND4L (NADH dehydrogenase subunit 4L)), with mutations in all seven having been reported in association with isolated CI deficiency. We investigated two unrelated adult patients presenting with marked exercise intolerance, persistent lactic acidaemia and severe muscle-restricted isolated CI deficiency associated with sub-sarcolemmal mitochondrial accumulation. Screening of the mitochondrial genome detected novel mutations in the MTND1 (NADH dehydrogenase subunit 1) gene, encoding subunit of CI [Patient 1, m.3365T>C predicting p.(Leu20Pro); Patient 2, m.4175G>A predicting p.(Trp290*)] at high levels of mitochondrial DNA heteroplasmy in skeletal muscle. We evaluated the effect of these novel MTND1 mutations on complex assembly showing that CI assembly, although markedly reduced, was viable in the absence of detectable ND1 signal. Real-time PCR and Western blotting showed overexpression of different CI assembly factor transcripts and proteins in patient tissue. Together, our data indicate that the mechanism underlying the expression of the biochemical defect may involve a compensatory response to the novel MTND1 gene mutations, promoting assembly factor up-regulation and stabilization of respiratory chain super-complexes, resulting in partial rescue of the clinical phenotype.


Subject(s)
Electron Transport Complex I/deficiency , Exercise Tolerance/genetics , Mitochondrial Myopathies/genetics , Mutation , NADH Dehydrogenase/genetics , Adolescent , DNA, Mitochondrial/genetics , Exercise Test/methods , Female , Humans , Mitochondrial Myopathies/enzymology , Muscle, Skeletal/enzymology , Pedigree , Young Adult
9.
Cancer Cell ; 12(2): 131-44, 2007 Aug.
Article in English | MEDLINE | ID: mdl-17692805

ABSTRACT

Activation of NF-kappaB has been noted in many tumor types, however only rarely has this been linked to an underlying genetic mutation. An integrated analysis of high-density oligonucleotide array CGH and gene expression profiling data from 155 multiple myeloma samples identified a promiscuous array of abnormalities contributing to the dysregulation of NF-kappaB in approximately 20% of patients. We report mutations in ten genes causing the inactivation of TRAF2, TRAF3, CYLD, cIAP1/cIAP2 and activation of NFKB1, NFKB2, CD40, LTBR, TACI, and NIK that result primarily in constitutive activation of the noncanonical NF-kappaB pathway, with the single most common abnormality being inactivation of TRAF3. These results highlight the critical importance of the NF-kappaB pathway in the pathogenesis of multiple myeloma.


Subject(s)
Gene Expression Regulation, Neoplastic , Multiple Myeloma/genetics , Mutation/genetics , NF-kappa B/genetics , Neoplasm Proteins/metabolism , Adenoviridae , Baculoviral IAP Repeat-Containing 3 Protein , CD40 Antigens/genetics , CD40 Antigens/metabolism , Cells, Cultured , Deubiquitinating Enzyme CYLD , Enzyme Activation , Fluorescent Antibody Technique , Gene Deletion , Gene Expression Profiling , Humans , Immunoblotting , Immunoenzyme Techniques , In Situ Hybridization, Fluorescence , Inhibitor of Apoptosis Proteins/genetics , Inhibitor of Apoptosis Proteins/metabolism , Lymphotoxin beta Receptor/genetics , Lymphotoxin beta Receptor/metabolism , Multiple Myeloma/metabolism , Multiple Myeloma/pathology , NF-kappa B/metabolism , NF-kappa B p50 Subunit/genetics , NF-kappa B p50 Subunit/metabolism , NF-kappa B p52 Subunit/genetics , NF-kappa B p52 Subunit/metabolism , Neoplasm Proteins/genetics , Nucleic Acid Hybridization , Plasmids , Polymerase Chain Reaction , Protein Serine-Threonine Kinases/genetics , Protein Serine-Threonine Kinases/metabolism , Signal Transduction , TNF Receptor-Associated Factor 2/genetics , TNF Receptor-Associated Factor 2/metabolism , TNF Receptor-Associated Factor 3/genetics , TNF Receptor-Associated Factor 3/metabolism , Transfection , Transmembrane Activator and CAML Interactor Protein/genetics , Transmembrane Activator and CAML Interactor Protein/metabolism , Tumor Suppressor Proteins/genetics , Tumor Suppressor Proteins/metabolism , Ubiquitin-Protein Ligases , NF-kappaB-Inducing Kinase
10.
J Biochem Mol Toxicol ; 29(12): 545-51, 2015 Dec.
Article in English | MEDLINE | ID: mdl-26179144

ABSTRACT

Nuclear receptors and transcription factors regulate the mRNA expression of many drug metabolizing enzymes, including the carboxylesterases (Ces). However, there are few data regarding whether these changes in mRNA expression result in alteration of protein levels or activity. In the present study, we sought to determine the isoform-specific regulation of hepatic Ces mRNA expression and activity following the administration of pharmacological activators of the constitutive androstane receptor (CAR), pregnane X receptor (PXR), and nuclear factor E2-related protein (Nrf2) to mice. The CAR activator 1,4-bis-[2-(3,5-dichloropyridyloxy)] benzene (TCPOBOP) and PXR ligand pregnenolone-16a-carbonitrile (PCN) increased Ces mRNA expression of various Ces2 isoforms, whereas the Nrf2 activator butylated hydroxyanisole primarily reduced Ces3a mRNA expression and induced Ces1g mRNA. TCPOBOP and PCN increased Ces2 hydrolytic activity in an isoform-specific manner. Taken together, these data demonstrate that activation of CAR, PXR, and Nrf2 regulates not only Ces mRNA expression, but also isoform-specific activity.


Subject(s)
Carboxylesterase/genetics , Gene Expression Regulation, Enzymologic/drug effects , Isoenzymes/genetics , Trans-Activators/pharmacology , Animals , Male , Mice , Mice, Inbred C57BL , Pregnenolone Carbonitrile/pharmacology , Pyridines/pharmacology , RNA, Messenger/genetics
11.
Therapie ; 70(1): 95-109, 2015.
Article in English, French | MEDLINE | ID: mdl-25747841

ABSTRACT

The initiation of Horizon 2020--the European Union's 8th Framework Programme for Research and Innovation, allotted a budget of 79 billion euros--provides an opportunity to review France's participation in previous Framework Programmes. Indeed, French participation does not match either its scientific importance or its financial investment. While France contributed 16.5 to 17% of the EU's 7th Framework Programme research budget, its return through the funding of coordinated projects in which French teams are participating stands at around 12.5 to 13%, a shortfall of 600 million euros. Although the situation depends on the type of activity, French participation in clinical research appears to be smaller than that of its neighbours, with fewer responses to European calls for proposals. While France has many assets, which include the assured funding of clinical research, structured thematic networks and the initiation of major national programmes, it suffers from the dilution of resources due to France's regional development policy, the lack of multidisciplinarity and the ignorance of both the medical and scientific community and the institutions to which they belong as to how Horizon 2020 actually works. We propose three types of strategy to encourage proposals for coordinated clinical research projects or projects involving French teams, and to help in the drawing up of applications: Broaden the vision of our children, students and colleagues, helping them to adapt to the globalisation of knowledge throughout their educational and professional lives. Recognise the value of European actions to influence the European landscape and change mentalities. Help and support project initiators by pooling skills within a limited number of expert centres designed to assist them in their funding application. • Broaden the vision of our children, students and colleagues, helping them to adapt to the globalisation of knowledge throughout their educational and professional lives. • Recognise the value of European actions to influence the European landscape and change mentalities. • Help and support project initiators by pooling skills within a limited number of expert centres designed to assist them in their funding application.


Subject(s)
Inventions , Research/organization & administration , Academies and Institutes/economics , Academies and Institutes/organization & administration , Biomedical Research/economics , Biomedical Research/statistics & numerical data , Biomedical Research/trends , Budgets , European Union , Financing, Government , France , Goals , International Cooperation , Internationality , Inventions/economics , Public Policy , Public-Private Sector Partnerships , Research/economics , Research/legislation & jurisprudence , Research/trends , Research Support as Topic , Resource Allocation
12.
Genome Res ; 21(1): 47-55, 2011 Jan.
Article in English | MEDLINE | ID: mdl-21147910

ABSTRACT

Advanced prostate cancer can progress to systemic metastatic tumors, which are generally androgen insensitive and ultimately lethal. Here, we report a comprehensive genomic survey for somatic events in systemic metastatic prostate tumors using both high-resolution copy number analysis and targeted mutational survey of 3508 exons from 577 cancer-related genes using next generation sequencing. Focal homozygous deletions were detected at 8p22, 10q23.31, 13q13.1, 13q14.11, and 13q14.12. Key genes mapping within these deleted regions include PTEN, BRCA2, C13ORF15, and SIAH3. Focal high-level amplifications were detected at 5p13.2-p12, 14q21.1, 7q22.1, and Xq12. Key amplified genes mapping within these regions include SKP2, FOXA1, and AR. Furthermore, targeted mutational analysis of normal-tumor pairs has identified somatic mutations in genes known to be associated with prostate cancer including AR and TP53, but has also revealed novel somatic point mutations in genes including MTOR, BRCA2, ARHGEF12, and CHD5. Finally, in one patient where multiple independent metastatic tumors were available, we show common and divergent somatic alterations that occur at both the copy number and point mutation level, supporting a model for a common clonal progenitor with metastatic tumor-specific divergence. Our study represents a deep genomic analysis of advanced metastatic prostate tumors and has revealed candidate somatic alterations, possibly contributing to lethal prostate cancer.


Subject(s)
DNA Mutational Analysis , Gene Dosage/genetics , Genes, Neoplasm/genetics , Neoplasm Metastasis/genetics , Prostatic Neoplasms/genetics , Comparative Genomic Hybridization , DNA, Neoplasm/analysis , Exons/genetics , Genes, Tumor Suppressor , Humans , Male , Neoplasm Metastasis/pathology , Oligonucleotide Array Sequence Analysis , Oncogenes/genetics , Point Mutation/genetics , Prostatic Neoplasms/pathology , Sequence Analysis, DNA
13.
Blood ; 120(5): 1067-76, 2012 Aug 02.
Article in English | MEDLINE | ID: mdl-22498740

ABSTRACT

Emerging evidence indicates that tumors can follow several evolutionary paths over a patient's disease course. With the use of serial genomic analysis of samples collected at different points during the disease course of 28 patients with multiple myeloma, we found that the genomes of standard-risk patients show few changes over time, whereas those of cytogenetically high-risk patients show significantly more changes over time. The results indicate the existence of 3 temporal tumor types, which can either be genetically stable, linearly evolving, or heterogeneous clonal mixtures with shifting predominant clones. A detailed analysis of one high-risk patient sampled at 7 time points over the entire disease course identified 2 competing subclones that alternate in a back and forth manner for dominance with therapy until one clone underwent a dramatic linear evolution. With the use of the Vk*MYC genetically engineered mouse model of myeloma we modeled this competition between subclones for predominance occurring spontaneously and with therapeutic selection.


Subject(s)
Clonal Evolution/genetics , DNA Copy Number Variations , Genes, Dominant/physiology , Multiple Myeloma/genetics , Multiple Myeloma/pathology , Animals , Cells, Cultured , Clonal Evolution/immunology , Clonal Evolution/physiology , Cluster Analysis , DNA Copy Number Variations/genetics , Disease Progression , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Humans , Mice , Mice, Inbred C57BL , Mice, Transgenic , Microarray Analysis , Models, Biological , Multiple Myeloma/immunology , Recurrence
15.
Int J Gynecol Cancer ; 24(2): 329-38, 2014 Feb.
Article in English | MEDLINE | ID: mdl-24418928

ABSTRACT

OBJECTIVE: Integration of carcinogenic human papillomaviruses (HPVs) into the host genome is a significant tumorigenic factor in specific cancers including cervical carcinoma. Although major strides have been made with respect to HPV diagnosis and prevention, identification and development of efficacious treatments for cervical cancer patients remains a goal and thus requires additional detailed characterization of both somatic events and HPV integration. Given this need, the goal of this study was to use the next generation sequencing to simultaneously evaluate somatic alterations and expression changes in a patient's cervical squamous carcinoma lesion metastatic to the lung and to detect and analyze HPV infection in the same sample. MATERIALS AND METHODS: We performed tumor and normal exome, tumor and normal shallow whole-genome sequencing, and RNA sequencing of the patient's lung metastasis. RESULTS: We generated over 1.2 billion mapped reads and identified 130 somatic point mutations and indels, 21 genic translocations, 16 coding regions demonstrating copy number changes, and over 36 genes demonstrating altered expression in the tumor (corrected P < 0.05). Sequencing also revealed the HPV type 18 (HPV-18) integration in the metastasis. Using both DNA and RNA reads, we pinpointed 3 major events indicating HPV-18 integration into an intronic region of chromosome 6p25.1 in the patient's tumor and validated these events with Sanger sequencing. This integration site has not been reported for HPV-18. CONCLUSIONS: We demonstrate that DNA and RNA sequencing can be used to concurrently characterize somatic alterations and expression changes in a biopsy and delineate HPV integration at base resolution in cervical cancer. Further sequencing will allow us to better understand the molecular basis of cervical cancer pathogenesis.


Subject(s)
Carcinoma, Squamous Cell/virology , Human papillomavirus 18/physiology , Lung Neoplasms/virology , Uterine Cervical Neoplasms/virology , Virus Integration , Biopsy , Carcinoma, Squamous Cell/secondary , Exome , Female , Gene Expression Profiling , Genes, Viral , Genome, Human , Human papillomavirus 18/isolation & purification , Humans , Lung Neoplasms/secondary , Sequence Analysis, DNA , Sequence Analysis, RNA , Uterine Cervical Neoplasms/pathology
16.
Paediatr Anaesth ; 24(8): 845-50, 2014 Aug.
Article in English | MEDLINE | ID: mdl-24915995

ABSTRACT

OBJECTIVES: To determine the limits of performance of the Farman Entrainer used with the t-piece for pediatric anesthesia in areas with limited oxygen supplies. METHODS: Bench tests were conducted with different system configurations, normal and 'emergency situation' ventilation patterns were replicated to reproduce a range of circumstances the anesthetist may encounter. RESULTS: We found that Fi0(2) rises and flow decreases with increasing CPAP, but probably within safe limits. A one way valve is essential to avoid high concentration of volatile agent. Very high ventilation rates reduce flow significantly. Increasing oxygen input from an oxygen concentrator increases the flow output but does not increase Fi0(2). CONCLUSION: The basic characteristics of the system are within normally accepted parameters for t-piece anesthesia, safety in practice requires to be demonstrated by a clinical study.


Subject(s)
Respiration, Artificial/instrumentation , Equipment Design
17.
Haematologica ; 98(10): 1586-92, 2013 Oct.
Article in English | MEDLINE | ID: mdl-23716545

ABSTRACT

Multiple myeloma can be categorized into hyperdiploid or non-hyperdiploid myeloma based on the number of chromosomes found in the tumor clone. Among the non-hyperdiploid myelomas, the hypodiploid subtype has the most aggressive clinical phenotype, but the genetic differences between groups are not completely defined. In order to understand the genetic background of hypodiploid multiple myeloma better, we compared the genomic (array-based comparative genomic hybridization) and transcriptomic (gene expression profiling) background of 49 patients with hypodiploid myeloma with 50 other non-hyperdiploid and 125 hyperdiploid myeloma patients. There were significant chromosomal and gene expression differences between hyperdiploid patients and non-hyperdiploid and hypodiploid patients. Non-hyperdiploid and hypodiploid patients shared most of the chromosomal abnormalities; nevertheless a subset of these abnormalities, such as monosomies 13, 14 and 22, was markedly increased in hypodiploid patients. Furthermore, deletions of 1p, 12p, 16q and 17p, all associated with poor outcome or progression in multiple myeloma, were significantly enriched in hypodiploid patients. Molecular risk-stratification indices reinforce the worse prognosis associated with hypodiploid multiple myeloma compared with non-hyperdiploid multiple myeloma. Gene expression profiling clustered hypodiploid and non-hyperdiploid subgroups closer than hyperdiploid myeloma but also highlighted the up-regulation of CCND2, WHSC1/MMSET and FGFR3 in the hypodiploid subtype. In summary, hypodiploid multiple myeloma is genetically similar to non-hyperdiploid multiple myeloma but characterized by a higher prevalence of genetic alterations associated with poor outcome and disease progression. It is provocative to hypothesize that hypodiploid multiple myeloma is an advanced stage of non-hyperdiploid multiple myeloma.


Subject(s)
Biomarkers, Tumor/genetics , Diploidy , Leukemia, Plasma Cell/diagnosis , Leukemia, Plasma Cell/genetics , Cohort Studies , Humans , Multiple Myeloma/diagnosis , Multiple Myeloma/genetics
18.
J Biochem Mol Toxicol ; 27(2): 165-71, 2013 Feb.
Article in English | MEDLINE | ID: mdl-23401056

ABSTRACT

Deltamethrin, a type II pyrethroid, is a widely used insecticide. The purpose of this study was to determine whether perinatal deltamethrin exposure altered the expression of adipogenic and lipogenic genes in white adipose tissue (WAT) in adult pups. C57BL/6 pregnant mice were administered 0, 1, or 3 mg/kg of deltamethrin orally every 3 days throughout gestation and lactation. Offspring were weaned on postnatal day 25, and WAT was collected from 5-month-old male mice. Perinatal deltamethrin exposure decreased the mRNA expression of adipogenesis-related transcription factors Pparγ, Cebpα, and lipogenic genes Srebp1c, Acc-1, Cd36, Lpl, Scd-1; along with Nrf2 and target genes Nqo1 and Gclc at the 1 mg/kg treatment. Cytokine expression of Fas/Tnf-R and Cd209e at the 1 mg/kg treatment was significantly decreased, and expression of Tnf, Cd11c, and Fas/Tnf-R was decreased at the 3 mg/kg treatment. Developmental deltamethrin exposure did not overtly affect body weight or adipose weight, but decreased mRNA expression of specific genes that may potentially disrupt normal adipogenesis and lipid and glucose metabolism if the offspring are challenged by changes in diet or environment.


Subject(s)
Adipose Tissue, White/metabolism , Gene Expression Regulation/drug effects , Insecticides/toxicity , Nitriles/toxicity , Prenatal Exposure Delayed Effects/metabolism , Pyrethrins/toxicity , Adipogenesis/drug effects , Adipose Tissue, White/pathology , Animals , Female , Glucose/metabolism , Lipid Metabolism/drug effects , Male , Mice , Pregnancy , Prenatal Exposure Delayed Effects/pathology
19.
BMJ Open ; 13(7): e070159, 2023 07 05.
Article in English | MEDLINE | ID: mdl-37407039

ABSTRACT

INTRODUCTION: The Australian population presenting with surgical pathology is becoming older, frailer and more comorbid. Shared decision-making is rapidly becoming the gold standard of care for patients considering high-risk surgery to ensure that appropriate, value-based healthcare decisions are made. Positive benefits around patient perception of decision-making in the immediacy of the decision are described in the literature. However, short-term and long-term holistic patient-centred outcomes and cost implications for the health service require further examination to better understand the full impact of shared decision-making in this population. METHODS: We propose a novel multidisciplinary shared decision-making model of care in the perioperative period for patients considering high-risk surgery in the fields of general, vascular and head and neck surgery. We assess it in a two arm prospective randomised controlled trial. Patients are randomised to either 'standard' perioperative care, or to a multidisciplinary (surgeon, anaesthetist and end-of-life care nurse practitioner or social worker) shared decision-making consultation. The primary outcome is decisional conflict prior to any surgical procedure occurring. Secondary outcomes include the patient's treatment choice, how decisional conflict changes longitudinally over the subsequent year, patient-centred outcomes including life impact and quality of life metrics, as well as morbidity and mortality. Additionally, we will report on healthcare resource use including subsequent admissions or representations to a healthcare facility up to 1 year. ETHICS AND DISSEMINATION: This study has been approved by the Hunter New England Human Research Ethics Committee (2019/ETH13349). Study findings will be presented at local and national conferences and within scientific research journals. TRIAL REGISTRATION NUMBER: ACTRN12619001543178.


Subject(s)
Quality of Life , Surgeons , Humans , Aged , Prospective Studies , Australia , Decision Making, Shared , Randomized Controlled Trials as Topic
20.
Proc (Bayl Univ Med Cent) ; 36(1): 1-7, 2023.
Article in English | MEDLINE | ID: mdl-36578607

ABSTRACT

A detailed understanding of the molecular and immunological changes that occur longitudinally across tumors exposed to immune checkpoint inhibitors is a significant knowledge gap in oncology. To address this unmet need, we created a statewide biospecimen collection and clinical informatics system to enable longitudinal tumor and immune profiling and to enhance translational research. The Texas Immuno-Oncology Biorepository (TIOB) consents patients to collect, process, store, and analyze serial biospecimens of tissue, blood, urine, and stool from a diverse population of over 100,000 cancer patients treated each year across the Baylor Scott & White Health system. Here we sought to demonstrate that these samples were fit for purpose with regard to downstream multi-omic assays. Plasma, urine, peripheral blood mononuclear cells, and stool samples from 11 enrolled patients were collected from various cancer types. RNA isolated from extracellular vesicles derived from plasma and urine was sufficient for transcriptomics. Peripheral blood mononuclear cells demonstrated excellent yield and viability. Ten of 11 stool samples produced RNA quality to enable microbiome characterization. Sample acquisition and processing methods are known to impact sample quality and performance. We demonstrate that consistent acquisition methodology, sample preparation, and sample storage employed by the TIOB can produce high-quality specimens, suited for employment in a wide array of multi-omic platforms, enabling comprehensive immune and molecular profiling.

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