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Savage P, Winter M, Parker V, Harding V, Sita-Lumsden A, Fisher RA, Harvey R, Unsworth N, Sarwar N, Short D, Aguiar X, Tidy J, Hancock B, Coleman R, Seckl MJ. Demographics, natural history and treatment outcomes of non-molar gestational choriocarcinoma: a UK population study. BJOG 2020; 127:1102-1107. [PMID: 32146729 DOI: 10.1111/1471-0528.16202] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2020] [Indexed: 12/18/2022]
Abstract
OBJECTIVE To investigate the demographics, natural history and treatment outcomes of non-molar gestational choriocarcinoma. DESIGN A retrospective national population-based study. SETTING UK 1995-2015. POPULATION A total of 234 women with a diagnosis of gestational choriocarcinoma, in the absence of a prior molar pregnancy, managed at the UKs two gestational trophoblast centres in London and Sheffield. METHODS Retrospective review of the patient's demographic and clinical data. Comparison with contemporary UK birth and pregnancy statistics. MAIN OUTCOMES Incidence statistics for non-molar choriocarcinoma across the maternal age groups. Cure rates for patients by FIGO prognostic score group. RESULTS Over the 21-year study period, there were 234 cases of non-molar gestational choriocarcinoma, giving an incidence of 1:66 775 relative to live births and 1:84 226 to viable pregnancies. For women aged under 20, the incidence relative to viable pregnancies was 1:223 494, for ages 30-34, 1:80 227, and for ages 40-45, 1:41 718. Treatment outcomes indicated an overall 94.4% cure rate. Divided by FIGO prognostic groups, the cure rates were low-risk group 100%, high-risk group 96% and ultra-high-risk group 80.5%. CONCLUSIONS Non-molar gestational choriocarcinoma is a very rare diagnosis with little prior detailed information on the demographics and natural history. The data in this study give age-related incidence data based on a large national population study. The results also demonstrated the widely varying natural history of this rare malignancy and the marked correlation of disease incidence with rising maternal age. TWEETABLE ABSTRACT National gestational choriocarcinoma database indicates a close association between increasing maternal age and incidence.
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Guo Y, Buettner K, Lane V, Wassgren C, Ketterhagen W, Hancock B, Curtis J. Computational and Experimental Studies of Flexible Fiber Flows in a Normal-Stress-Fixed Shear Cell. AIChE J 2018. [DOI: 10.1002/aic.16397] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Guo Y, Wassgren C, Ketterhagen W, Hancock B, Curtis J. Discrete element simulation studies of angles of repose and shear flow of wet, flexible fibers. SOFT MATTER 2018; 14:2923-2937. [PMID: 29611587 DOI: 10.1039/c7sm02135f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A discrete element method (DEM) model is developed to simulate the dynamics of wet, flexible fibers. The angles of repose of dry and wet fibers are simulated, and the simulation results are in good agreement with experimental results, validating the wet, flexible fiber model. To study wet fiber flow behavior, the model is used to simulate shear flows of wet fibers in a periodic domain under Lees-Edwards boundary conditions. Significant agglomeration is observed in dilute shear flows of wet fibers. The size of the largest agglomerate in the flow is found to depend on a Bond number, which is proportional to liquid surface tension and inversely proportional to the square of the shear strain rate. This Bond number reflects the relative importance of the liquid-bridge force to the particle's inertial force, with a larger Bond number leading to a larger agglomerate. As the fiber aspect ratio (AR) increases, the size of the largest agglomerate increases, while the coordination number in the largest agglomerate initially decreases and then increases when the AR is greater than four. A larger agglomerate with a larger coordination number is more likely to form for more flexible fibers with a smaller bond elastic modulus due to better connectivity between the more flexible fibers. Liquid viscous force resists pulling of liquid bridges and separation of contacting fibers, and therefore it facilitates larger agglomerate formation. The effect of liquid viscous force is more significant at larger shear strain rates. The solid-phase shear stress is increased due to the presence of liquid bridges in moderately dense flows. As the solid volume fraction increases, the effect of fiber-fiber friction coefficient increases sharply. When the solid volume fraction approaches the maximum packing density, the fiber-fiber friction coefficient can be a more dominant factor than the liquid bridge force in determining the solid-phase shear stress.
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Solzak J, Hancock B, Paul R, Radovich M. Abstract P1-10-03: Precision therapeutic combinations are synergistic against triple negative breast cancer using compensatory pathways. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p1-10-03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Triple negative breast cancer (TNBC) accounts for 15% of all breast cancer cases in the United States, and despite its lower incidence, contributes to a disproportionately higher rate of morbidity and mortality compared to other breast cancer subtypes. In an effort to treat TNBC, a cancer that has no targeted therapies, many have chosen to experiment with combinations of drugs that are chosen for their genomic expression or “hard targets”. It has been previously noted however, that single agent therapeutics can change the genomic landscape of both mice and human cells and may be responsible for resistance. Here we show that targeting a compensatory pathway after treatment with a single therapy, results in synergistic combinations and can outperform the choice of hard target therapies.
Methods: Eight TNBC cell lines were chosen based on their abundance of clinically actionable targets. The primary hard target combinations were chosen using data from TCGA and a board consisting of oncologists and researchers at Indiana University School of Medicine. Compensatory therapies were found using RNA sequencing data from untreated versus single therapeutic treated TNBC cell lines. The merged transcript RPKMs were transformed and analyzed for differential expression. Statistically significant genes were imported into Ingenuity Pathway Analysis (IPA) to identify either therapeutics or genomic targets using the Causal network analysis and Upstream regulator functions. All drug combinations were tested in their respective cell lines and cell viability was assessed via Celltiter-Fluor. Synergy of the combinations was calculated using the Chou-Talalay method.
Results: Using genomically chosen hard targets for drug combinations, all eight cell lines displayed additive or antagonistic results except low nanomolar doses for the MDA-MB-231 cell line. Dosing of MDA-MB-231s with Debrafinib and Pazopanib however, turned highly antagonistic as dosing increased. Using next-generation RNA sequencing data of TNBCs, IPA analysis identified several compensatory targets for each cell line when treated with one of the primary genomically driven drug at its IC50. Using dose escalation of the new drugs with a single hard target drug, we found that each compensatory combination displayed a striking increase in synergy across all TNBC cell lines treated when compared to their original hard target combination.
Conclusion: RNA sequencing of TNBC cells lines treated with single therapies chosen by actionable genomic landscape has revealed compensatory pathways, indicating further druggable targets. These compensatory pathways have been observed to more efficacious in treating TNBC cell lines. Using therapeutics that are either FDA approved or in clinical trials we have found that each compensatory combination shows a higher level of synergy across all cell lines. These data show that choosing a secondary therapy based on compensatory pathways may outperform hard target combinations in the clinic.
Citation Format: Solzak J, Hancock B, Paul R, Radovich M. Precision therapeutic combinations are synergistic against triple negative breast cancer using compensatory pathways [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P1-10-03.
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Solzak JP, Atale R, Hancock B, Radovich M. Abstract P6-13-09: Dual PI3K and Wnt pathway inhibition is a synergistic combination against triple negative breast cancer. Cancer Res 2016. [DOI: 10.1158/1538-7445.sabcs15-p6-13-09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Triple negative breast cancer (TNBC) accounts for 15% of all breast cancer cases in the United States, and despite its lower incidence, contributes to a disproportionately higher rate of morbidity and mortality compared to other breast cancer subtypes. Because these tumors lack expression of the estrogen, progesterone, or HER-2 receptors ("triple negative"), TNBC patients do not respond to targeted therapies that have been successfully used against tumors that over-express these proteins. Thus, there exists a critical need to improve the outcomes of TNBC patients through the implementation of novel targeted agents.
Methods: RNA-seq data from 94 TNBCs (from Indiana University and TCGA) and 20 microdissected normal breast tissues (Komen Tissue Bank) were merged and analyzed using Partek Genomics Suite. Statistically significant genes were imported into Ingenuity Pathway Analysis (IPA) to identify therapeutic targets. For in vitro studies, we tested a panel of TNBC cell lines using Buparlisib (a PI3K pathway inhibitor) and WNT974 (a WNT pathway inhibitor), individually and in combination. Cell viability was assessed via Celltiter-Fluor. Synergy between the two drugs was calculated using the Chou-Talalay method. In vivo studies were performed using the TMD-231 cell line and a patient derived xenograft (PDX) from the Jackson Laboratory. Dosing of the mice was performed using 30 mg/kg and 3 mg/kg of Buparlisib and WNT974 respectively, both in combination and individually.
Results: Using next-generation RNA sequencing data of TNBCs and microdissected normal breast tissue, Ingenuity Pathway Analysis identified over-expression and hyper-activation of the PI3K/AKT/mTOR pathway. When treating cell lines with the PI3K inhibitor Buparlisib, RNA sequencing revealed compensatory induction of the WNT pathway across TNBC cell lines. In particular, we observed induction of Porcupine, a Wnt maturation protein, which is the protein target of the Wnt pathway inhibitor, WNT974. When anti-tumor efficacy against these pathways was assessed, a significant reduction in cell viability using Buparlisib and WNT974 in combination was observed. Using the Chou-Talalay method, we found for MDA-MB-231 and Hs578T cell lines, a ∼50% reduction in cell viability at 100nM concentration of each drug that was highly synergistic (Combination Index = 0.33, and 0.36 respectively). In our in vivo PK study of the combination, there was no drug-drug interaction observed. Furthermore, in our PD analysis using a TMD-231 xenograft, we observed a ∼40% reduction in tumor volume after seven days. In a subsequent in vivo PDX experiment, we observed an 80% survival rate using combination therapy compared to 40% when administering the drugs individually or with vehicle control after 30 days.
Conclusion: PI3K/mTOR/AKT and Wnt pathways are strong candidates for the development of novel targeted agents for TNBC. Using two small molecule inhibitors that are currently in clinical trials as single agents (Buparlisib and WNT974) we observe significant in vitro synergy when inhibiting both pathways at low nanomolar doses. Furthermore, confirmatory in vivo xenograft studies display a similar synergy for the combination compared to single agent and vehicle controls.
Citation Format: Solzak JP, Atale R, Hancock B, Radovich M. Dual PI3K and Wnt pathway inhibition is a synergistic combination against triple negative breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-13-09.
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Hua X, Curtis J, Guo Y, Hancock B, Ketterhagen W, Wassgren C. The internal loads, moments, and stresses in rod-like particles in a low-speed, vertical axis mixer. Chem Eng Sci 2015. [DOI: 10.1016/j.ces.2015.06.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Guo Y, Wassgren C, Hancock B, Ketterhagen W, Curtis J. Validation and time step determination of discrete element modeling of flexible fibers. POWDER TECHNOL 2013. [DOI: 10.1016/j.powtec.2013.09.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Fish JA, Ettridge K, Sharplin GR, Hancock B, Knott VE. Mindfulness-based cancer stress management: impact of a mindfulness-based programme on psychological distress and quality of life. Eur J Cancer Care (Engl) 2013; 23:413-21. [PMID: 24118428 DOI: 10.1111/ecc.12136] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2013] [Indexed: 11/26/2022]
Abstract
Within the area of cancer care, mindfulness-based therapeutic interventions have been found to be efficacious in reducing psychological distress related to a cancer diagnosis; however, the impact of mindfulness-based interventions on quality of life is unclear. This study explores the impact of a Mindfulness-Based Cancer Stress Management programme on psychological distress and quality of life. Research methodology included a single-group quasi-experimental study of 26 participants experiencing distress related to a cancer diagnosis, including carers, who completed an MBCSM programme and all assessments. Participants completed the Functional Assessment of Cancer Therapy - General version 4 (FACT-G) and its associated spirituality index (FACIT-Sp-Ex), Hospital Anxiety and Depression Scale (HADS), Freiburg Mindfulness Inventory (FMI), and the Distress Thermometer at baseline, post-intervention, and three months after programme completion. Significant improvements were observed on all measures (ranges: P ≤ 0.001 to 0.008, r = -0.53 to -0.79) following the intervention, which were maintained at 3-month follow-up. Mindfulness was significantly correlated with all main outcome measures at post-intervention (range: r = -0.41 to 0.67) and 3-month follow-up (range: r = -0.49 to 0.73), providing evidence for the internal validity of the study. Our findings indicate that the MBCSM programme is effective in reducing psychological distress and improving quality of life, including spiritual well-being.
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Raassen TJIP, Hancock B. Factors influencing choice of surgical route of repair of genitourinary fistula, and the influence of route of repair on surgical outcomes: findings from a prospective cohort study. BJOG 2013; 120:1441. [DOI: 10.1111/1471-0528.12230] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2013] [Indexed: 11/28/2022]
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Hua X, Curtis J, Hancock B, Ketterhagen W, Wassgren C. The kinematics of non-cohesive, sphero-cylindrical particles in a low-speed, vertical axis mixer. Chem Eng Sci 2013. [DOI: 10.1016/j.ces.2013.05.063] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Nehring RB, Hancock B, Catanese M, Stinson MET, Winkelman D, Wood J, Epp J. Reduced Myxobolus cerebralis actinospore production in a Colorado reservoir may be linked to changes in Tubifex tubifex population structure. JOURNAL OF AQUATIC ANIMAL HEALTH 2013; 25:205-220. [PMID: 23944286 DOI: 10.1080/08997659.2013.788581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Elucidating the dynamics of a parasitic infection requiring two hosts in a natural ecosystem can be a daunting task. Myxobolus cerebralis (Mc), the myxozoan parasite that causes whirling disease in some salmonids, was detected in the Colorado River upstream of Windy Gap Reservoir (WGR) in 1988. Subsequently, whirling disease was implicated in the decline of wild Rainbow Trout Oncorhynchus mykiss in the river when WGR was identified as a point source of Mc triactinomyxons (TAMs). Between 1997 and 2004, numerous investigations began to elucidate the etiology of Mc in WGR. During this period, Mc TAM production in WGR declined more than 90%. Explanations for the decline have included differences in stream discharge between years, changes in the thermal regime of the lake, severe drought, changes in the fish population structure in WGR, and reductions in the prevalence and severity of Mc infection in salmonids in the Colorado and Fraser rivers upstream of WGR. All of these have been discredited as explanations for the reduced TAM production. In 2005, a new study was conducted to replicate the studies completed in 1998. In this paper, the results of a new real-time polymerase chain reaction assay utilized to quantify the mitochondrial 16S rDNA specific to each of four lineages of Tubifex tubifex in pooled samples of 50 oligochaetes are presented. These results suggest that compared with 1998, the densities of aquatic oligochaetes and T. tubifex have increased, TAM production has been greatly reduced, and the decline is congruent with the dominance of lineages I, V, and VI of T. tubifex-three lineages that are refractory or highly resistant to Mc infection-in the oligochaete population. While it is possible that the resistant lineages function as biofilters that deactivate Mc myxospores, the reason for the decline in TAM production in WGR remains an enigma.
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Guo Y, Wassgren C, Ketterhagen W, Hancock B, Curtis J. Some computational considerations associated with discrete element modeling of cylindrical particles. POWDER TECHNOL 2012. [DOI: 10.1016/j.powtec.2012.05.015] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Lin PC, Irrechukwu O, Roque R, Hancock B, Fishbein KW, Spencer RG. Multivariate analysis of cartilage degradation using the support vector machine algorithm. Magn Reson Med 2011; 67:1815-26. [PMID: 22179972 DOI: 10.1002/mrm.23189] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Accepted: 07/28/2011] [Indexed: 01/05/2023]
Abstract
An important limitation in MRI studies of early osteoarthritis is that measured MRI parameters exhibit substantial overlap between different degrees of cartilage degradation. We investigated whether multivariate support vector machine analysis would permit improved tissue characterization. Bovine nasal cartilage samples were subjected to pathomimetic degradation and their T(1), T(2), magnetization transfer rate (k(m) ), and apparent diffusion coefficient (ADC) were measured. Support vector machine analysis performed using certain parameter combinations exhibited particularly favorable classification properties. The areas under the receiver operating characteristic (ROC) curve for detection of extensive and mild degradation were 1.00 and 0.94, respectively, using the set (T(1), k(m), ADC), compared with 0.97 and 0.60 using T(1), the best univariate classifier. Furthermore, a degradation probability for each sample, derived from the support vector machine formalism using the parameter set (T(1), k(m), ADC), demonstrated much stronger correlations (r(2) = 0.79-0.88) with direct measurements of tissue biochemical components than did even the best-performing individual MRI parameter, T(1) (r(2) = 0.53-0.64). These results, combined with our previous investigation of Gaussian cluster-based tissue discrimination, indicate that the combinations (T(1), k(m)) and (T(1), k(m), ADC) may emerge as particularly useful for characterization of early cartilage degradation.
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Zekri J, Cheah NL, Evans L, Hancock B. Serum potassium, calcium and magnesium in patients receiving ESHAP chemotherapy for relapsed lymphomas. J R Coll Physicians Edinb 2010; 39:301-6. [PMID: 21152465 DOI: 10.4997/jrcpe.2009.403] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
UNLABELLED Etoposide, methylprednisolone, cytarabine and cisplatin (ESHAP) is one of the mostly widely used chemotherapy regimens for patients with relapsed lymphomas. Cisplatin administration is commonly associated with electrolyte imbalance. Careful monitoring of renal function and serum electrolytes is therefore essential in this setting. AIMS To review the practice of electrolyte monitoring - potassium (K), calcium (Ca) and magnesium (Mg) - in patients receiving ESHAP and the frequency and severity of abnormalities and their management. METHODS Twenty-one consecutive patients received ESHAP. The medical records of 16 patients were retrievable and reviewed retrospectively. Results of serum K, Ca and Mg were collected prior to and after cycles 1, 2 and 3 of ESHAP, if measured. RESULTS Serum K levels prior to every cycle did not show any noticeable change. The means were 4.42, 4.34 and 4.43 mmol/l before cycles 1, 2 and 3, respectively. In one patient hypokalaemia was severe, refractory and symptomatic when preceded by hypomagnesaemia. Serum-adjusted calcium levels showed only minimal reduction. The means were 2.46, 2.40 and 2.38 mmol/l before cycles 1, 2 and 3 respectively. Mean serum Mg levels prior to every cycle showed progressive reduction; 0.84, 0.75 and 0.67 mmol/l before cycles 1, 2 and 3, respectively. This was associated with a progressive increase in the amount of required Mg supplementation. Serum K, Ca and Mg was measured prior to 100%, 67% and 35% of administered cycles, respectively. CONCLUSION In patients receiving ESHAP, hypokalaemia can occasionally be seen, especially if preceded by hypomagnesaemia. Mild cumulative hypocalcaemia is recognised. Hypomagnesaemia is a progressive complication and physicians need be aware of its importance. alcaemia is recognised. Hypomagnesaemia is a progressive complication and physicians need be aware of its importance.
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Ubayasiri K, Hancock B, Duncan T. A case of primary choriocarcinoma of the fallopian tube. J OBSTET GYNAECOL 2010; 30:881-3. [PMID: 21126145 DOI: 10.3109/01443615.2010.511729] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Zhang Z, Hancock B, Leen S, Ramaswamy S, Sollott SJ, Boheler KR, Juhaszova M, Lakatta EG, Spencer RG, Fishbein KW. Compatibility of superparamagnetic iron oxide nanoparticle labeling for ¹H MRI cell tracking with ³¹P MRS for bioenergetic measurements. NMR IN BIOMEDICINE 2010; 23:1166-72. [PMID: 20853523 PMCID: PMC3161830 DOI: 10.1002/nbm.1545] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Revised: 03/01/2010] [Accepted: 03/12/2010] [Indexed: 05/04/2023]
Abstract
Labeling of cells with superparamagnetic iron oxide nanoparticles permits cell tracking by (1)H MRI while (31)P MRS allows non-invasive evaluation of cellular bioenergetics. We evaluated the compatibility of these two techniques by obtaining (31)P NMR spectra of iron-labeled and unlabeled immobilized C2C12 myoblast cells in vitro. Broadened but usable (31)P spectra were obtained and peak area ratios of resonances corresponding to intracellular metabolites showed no significant differences between labeled and unlabeled cell populations. We conclude that (31)P NMR spectra can be obtained from cells labeled with sufficient iron to permit visualization by (1)H imaging protocols and that these spectra have sufficient quality to be used to assess metabolic status. This result introduces the possibility of using localized (31)P MRS to evaluate the viability of iron-labeled therapeutic cells as well as surrounding host tissue in vivo.
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Radovich M, Clare S, Clare S, Pardo I, Hancock B, Sledge G, Rufenbarger C, Rufenbarger C, Storniolo A, Storniolo A, Mathieson T, Mathieson T, Sun J, Sun J, Henry J, Henry J, Hilligoss E, Elliott J, Richt R, Hickenbotham M, Glasscock J, Liu Y, Schneider B. Next-Generation Whole Transcriptome Sequencing of Triple-Negative Breast Tumors and Normal Tissues. Cancer Res 2009. [DOI: 10.1158/0008-5472.sabcs-09-6134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Triple-negative breast cancer predominately affects pre-menopausal women and women of African-American descent and has been plagued by the absence of targeted therapies leading to poor survival. Using a new cutting edge technology, next-generation sequencing, we embarked on a study to analyze the whole transcriptomes of triple-negative tumors and normal tissues from pre-menopausal women in order to comprehensively identify new targets by analyzing all full length transcripts expressed in these tissues. This approach is independent of pre-determined gene selection as is common with microarrays, and allows for the analysis of RNA species that have not been previously profiled in breast cancer.Methods: cDNA libraries were created from RNA isolated from 8 triple-negative tumors and 2 normal breast tissues. Triple negative tumors were procured from Origene Technologies and normal breast tissues were procured from the Susan G. Komen for the Cure tissue bank at Indiana University. Normal samples were from healthy pre-menopausal volunteers with no history of disease. In order to eliminate bias from stromal tissue, normal samples were laser capture microdissected for ductal cells and RNA extracted from the excised tissue. cDNA libraries were prepared and subsequently sequenced on an Applied Biosystems (ABI) SOLiD3 sequencer using a 50bp fragment run. Mapping of whole reads to the human genome was performed using the SOLiD Analysis Pipeline Tool software (ABI) followed by a split-read alignment in order to map reads crossing exon-exon junctions. Gene expression profiles for each sample were then created and statistically compared to identify the most differentially expressed genes. In order to analyze for fusion genes, a split-read alignment of non-mapping reads to a composite transcriptome formed from previously mapped reads (clusters) was performed.Results: Sequencing of the 10 samples produced 513 million filtered reads equaling 25.66GB of data. Mapping of the reads to the genome revealed 1.14 million transcribed regions (exons). A preliminary analysis of gene expression shows 55.2% of the transcribed loci to have significant differential expression between tumor and normal. In a further analysis for gene fusions, several candidate fusions were bioinformatically detected. These are currently being reviewed and validated.Discussion: Herein we present a preliminary analysis of the transcriptomes of triple-negative breast cancers in comparison to normal tissues. A multitude of analyses are ongoing, including but not limited to: gene fusions, differentially expressed novel genes, novel transcripts, alternative splicing, intrinsic subtyping, and presence of viral genes. In addition 2 more triple-negative tumors and 8 normal samples will also be sequenced. In the current analysis, differentially expressed non-coding RNAs was highly pervasive among the samples indicating a major role of this RNA species in tumorigenesis. In addition, triple-negative breast cancers may contain fusion genes that could be “drivers” of this malignancy. Further validation of these differentially expressed RNAs and fusion genes in a larger set of samples with subsequent functional studies is planned.
Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 6134.
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Hancock B, Radovich M, Kassem N, Mi D, Skaar T, Schneider B. Resequencing of the Vascular Endothelial Growth Factor Promoter Reveals Haplotype Structure and Functional Diversity. Cancer Res 2009. [DOI: 10.1158/0008-5472.sabcs-09-2122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Our group has previously reported that SNPs in the VEGF promoter are strongly associated with efficacy and toxicity to the anti-VEGF antibody bevacizumab in metastatic breast cancer. In order to better understand the biologic mechanism for our previously reported biomarkers, we embarked on a comprehensive evaluation of the genetic variation in the VEGF promoter coupled with a study of its intrinsic function. By resequencing 96 DNA samples (48 Caucasians, 48 African-Americans) for the VEGF promoter, we elucidated its complete haplotype structure and identified SNPs that were not previously reported in prior resequencing efforts. SNPs that were identified included twenty previously reported SNPs/insertions/deletions, one novel SNP, and one novel deletion. Among these variants, we identified five SNPs (VEGF-3818G/T, -2305G/T, -1210C/A, -1154G/A, & -7C/T) that tag six haplotypes capturing 74% of the genetic variation of the VEGF promoter. Subsequently, we cloned the six major haplotypes into reporter constructs in order to determine the effect of genetic variation on function. The reporter assays were performed in 5 breast cancer cell lines representing all ER and HER-2 statuses along with an inflammatory breast cancer cell line. We demonstrate that there is significant variation in promoter-induced expression among the haplotypes. More importantly, we show that the haplotypes containing the SNPs previously reported to be associated with increased survival with the use of bevacizumab are high-expressing haplotypes, thus lending putative functional evidence to the prior clinical finding. Further, we also report the presence of a low-expressing haplotype predominantly in African-Americans. Altogether, these results set the foundation for future studies elucidating the role of VEGF genetic variation with response to anti-angiogenic therapy and associations with angiogenesis-related diseases.
Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 2122.
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Karavidas K, Zhang L, Zenk J, Iro H, Shehata E, Hancock B, Renehan A, McGurk M. Multicenter experience in extracapsular dissection of benign parotid neoplasms—1064 cases. Int J Oral Maxillofac Surg 2009. [DOI: 10.1016/j.ijom.2009.03.243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Pettengell R, Donatti C, Hoskin P, Poynton C, Kettle PJ, Hancock B, Johnson S, Dyer MJS, Rule S, Walker M, Wild D. The impact of follicular lymphoma on health-related quality of life. Ann Oncol 2007; 19:570-6. [PMID: 18056649 DOI: 10.1093/annonc/mdm543] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The purpose of this study was to determine whether there was a relationship between disease activity and health functioning, as measured by a range of patient-reported outcome (PRO) measures in patients with follicular lymphoma (FL). PATIENTS AND METHODS A total of 222 patients with FL were recruited from eight sites across the UK and they completed a number of PRO measures. The participants were analyzed across five disease states: 'active disease-newly diagnosed', 'active disease-relapsed', 'partial response', 'complete response' and 'disease free'. The relationship between these disease states and their level of health functioning was assessed as well as the relationship between being 'on' or 'off' chemotherapy and disease state. RESULTS In terms of health-related quality of life (HRQoL), participants in the relapsed category had the lowest mean physical well-being, emotional well-being, functional well-being and social well-being score. In a regression analysis, the 'active disease-relapsed' group acted as a significant predictor for each PRO variable. In addition, the remission group acted as a significant predictor of high anxiety scores as measured by the Hospital Anxiety and Depression Scale. CONCLUSION The results of this study demonstrate that various aspects of patient-reported health outcomes differ according to disease state in patients with FL. For those patients who have relapsed, they are more likely to experience worse HRQoL and other patient-reported health outcomes than patients newly diagnosed, in partial or complete remission or when completely disease free.
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Monteiro M, McGurk M, Hancock B, Renehan A, Zenk J, Iro H. Multi centre experience of extracapsular dissection of benign parotid neoplasms. Br J Oral Maxillofac Surg 2007. [DOI: 10.1016/j.bjoms.2007.07.078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Wheatley K, Ives N, Eggermont A, Kirkwood J, Cascinelli N, Markovic SN, Hancock B, Lee S, Suciu S. Interferon-α as adjuvant therapy for melanoma: An individual patient data meta-analysis of randomised trials. J Clin Oncol 2007. [DOI: 10.1200/jco.2007.25.18_suppl.8526] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
8526 Background: Many randomised trials have evaluated the role of adjuvant interferon-a (IFN) in high-risk melanoma, some suggesting benefit and others not. To assess the totality of current evidence, an individual patient data (IPD) meta-analysis of all available trials was performed. Methods: Standard IPD meta-analysis methods were used to assess event-free (EFS) and overall survival (OS), with odds ratios (OR) and 95% confidence intervals (CI) calculated. Trials were divided by dose of IFN - high (20 MU/m2), intermediate (5–10 MU), low (3 MU) and very low (1 MU). Subgroup analyses by patient age, gender and disease characteristics were also performed. Results: IPD was provided for 10 of 13 reported trials of IFN vs. no IFN (for the other 3 trials published data were used). 6067 patients (IPD available for 85%) were included in the analysis, with over 3,700 and 3,000 events for EFS and OS. There was statistically significant benefit for IFN for both EFS (OR=0.87, CI=0.81–0.93, p=0.00006) and OS (0.9, 0.84–0.97, p=0.008). There was no evidence of differences according to dose (Table 1; trend p>0.1) or duration of IFN. This proportional survival advantage translates into an absolute benefit of about 3% (CI 1%-5%) at 5 years. The effect of IFN did not differ with age, gender, tumor site, Breslow thickness, clinical nodes or disease stage. Only for ulceration was there some evidence of an interaction (p=0.03); patients with ulcerated tumors had greater benefit from IFN (EFS: OR=0.76, OS: OR=0.77) than those with no ulceration (EFS: OR=0.94, OS: OR=0.98). Conclusions: This meta-analysis provides evidence that adjuvant IFN significantly reduces the risk of relapse and improves overall survival, although the absolute survival benefit is relatively small. This analysis does not however, clarify the optimal (high, intermediate or low) dose of IFN. Given the large number of subgroup analyses performed, the apparent increased benefit in patients with ulceration requires confirmation. No significant financial relationships to disclose.
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Burton C, Linch D, Hoskin P, Milligan D, Dyer MJS, Hancock B, Mouncey P, Smith P, Qian W, MacLennan K, Jack A, Webb A, Cunningham D. A phase III trial comparing CHOP to PMitCEBO with or without G-CSF in patients aged 60 plus with aggressive non-Hodgkin's lymphoma. Br J Cancer 2006; 94:806-13. [PMID: 16508640 PMCID: PMC3216418 DOI: 10.1038/sj.bjc.6602975] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The management of older patients with aggressive non-Hodgkin's lymphoma presents a challenge to the physician. Age is a poor prognostic indicator, due to reduced ability to tolerate and maintain dose-intensive chemotherapy. Generally, older patients demonstrate a lower response rate, reduced survival and increased toxicity, although the majority of large randomised trials exclude older patients. This randomised trial was conducted in patients 60 years or over to compare CHOP (cyclophosphamide 750 mg m−2, doxorubicin 50 mg m−2, vincristine 1.4 mg m−2, prednisolone 100 mg) with PMitCEBO (mitoxantrone 7 mg m−2, cyclophosphamide 300 mg m−2, etoposide 150 mg m−2, vincristine 1.4 mg m−2, bleomycin 10 mg m−2 and prednisolone 50 mg). Due to the myelosuppressive nature of these regimens, patients were also randomised to the addition of G-CSF. The formal results of this trial with long-term follow-up are now reported. Data were analysed to assess efficacy and toxicity. Overall response rate was 84% in the CHOP arm and 83% in the PMitCEBO arm, with overall response rates of 83% for the use of G-CSF and 84% for no G-CSF. At median 44 months follow-up, there was no significant difference in failure-free, progression-free or overall survival between the CHOP and PMitCEBO arms. At 3 years, the actuarial failure-free survival was 44% in CHOP recipients and 42% in PMitCEBO recipients and the 3-year actuarial overall survival was 46% and 45% respectively. There was no significant difference in the failure-free, progression-free or overall survival with the addition of G-CSF.
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Burton C, Smith P, Vaughan-Hudson G, Qian W, Hoskin P, Cunningham D, Hancock B, Linch D. Comparison of CHOP versus CIOP in good prognosis younger patients with histologically aggressive non-Hodgkin lymphoma. Br J Haematol 2005; 130:536-41. [PMID: 16098067 DOI: 10.1111/j.1365-2141.2005.05640.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
CHOP (cyclophosphamide, doxorubicin, vincristine and prednisolone) has been the standard chemotherapy regimen used for diffuse large cell lymphomas for over 30 years. Idarubicin is a 4-demethoxy-anthracycline analogue of daunorubicin that has proven activity in non-Hodgkin lymphoma, and has been reported to cause less cardiotoxicity. We therefore initiated a randomised trial of standard dose CHOP versus CIOP (cyclophosphamide, idarubicin, vincristine and prednisolone), in which doxorubicin 50 mg/m2 was substituted by idarubicin 10 mg/m2, a dose thought to have equivalent anti-lymphoma activity. This trial was closed prematurely after 211 patients had completed therapy when a lower complete remission (CR) rate was noted in the CIOP arm. The formal results with long-term follow up are now reported. Overall response rate was 84% in the CHOP arm and 78% in the CIOP arm, CR rates were 70% and 52% respectively in all patients (P=0.013) and 73% and 52% respectively for the eligible patients (P=0.0084). At a median of 8 years follow-up, 4-year progression-free survival for all patients was 56% in the CHOP arm and 40% in the CIOP arm (P=0.0096). Overall survival for all patients was 65% in the CHOP arm and 56% in the CIOP arm (P=0.14). Results for eligible patients were comparable. CIOP containing idarubicin at a dose of 10 mg/m2 is clearly inferior to standard CHOP.
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Brown JE, Lester J, Ellis S, Gutcher S, Turner L, Purohit OP, Hancock B, Coleman R. Can an annual infusion of zoledronic acid protect against cancer-treatment induced bone loss (CTIBL)? J Clin Oncol 2005. [DOI: 10.1200/jco.2005.23.16_suppl.8023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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