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1.
Clin Transl Radiat Oncol ; 45: 100730, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38317679

ABSTRACT

Purpose/objectives: The growing use of stereotactic body radiotherapy (SBRT) in metastatic cancer has led to its use in varying anatomic locations. The objective of this study was to review our institutional SBRT experience for axillary metastases (AM), focusing on outcomes and process. Materials/methods: Patients treated with SBRT to AM from 2014 to 2022 were reviewed. Cumulative incidence functions were used to estimate the incidence of local failure (LF), with death as competing risk. Kaplan-Meier method was used to estimate progression-free (PFS) and overall survival (OS). Univariate regression analysis examined predictors of LF. Results: We analyzed 37 patients with 39 AM who received SBRT. Patients were predominantly female (60 %) and elderly (median age: 72). Median follow-up was 14.6 months. Common primary cancers included breast (43 %), skin (19 %), and lung (14 %). Treatment indication included oligoprogression (46 %), oligometastases (35 %) and symptomatic progression (19 %). A minority had prior overlapping radiation (18 %) or surgery (11 %). Most had prior systemic therapy (70 %).Significant heterogeneity in planning technique was identified; a minority of patient received 4-D CT scans (46 %), MR-simulation (21 %), or contrast (10 %). Median dose was 40 Gy (interquartile range (IQR): 35-40) in 5 fractions, (BED10 = 72 Gy). Seventeen cases (44 %) utilized a low-dose elective volume to cover remaining axilla.At first assessment, 87 % had partial or complete response, with a single progression. Of symptomatic patients (n = 14), 57 % had complete resolution and 21 % had improvement. One and 2-year LF rate were 16 % and 20 %, respectively. Univariable analysis showed increasing BED reduced risk of LF. Median OS was 21.0 months (95 % [Confidence Interval (CI)] 17.3-not reached) and median PFS was 7.0 months (95 % [CI] 4.3-11.3). Two grade 3 events were identified, and no grade 4/5. Conclusion: Using SBRT for AM demonstrated low rates of toxicity and LF, and respectable symptom improvement. Variation in treatment delivery has prompted development of an institutional protocol to standardize technique and increase efficiency. Limited followup may limit detection of local failure and late toxicity.

2.
Med Phys ; 43(12): 6439, 2016 Dec.
Article in English | MEDLINE | ID: mdl-27908167

ABSTRACT

PURPOSE: At present, a one-size-fits-all approach is typically used for cancer therapy in patients. This is mainly because there is no current imaging-based clinical standard for the early assessment and monitoring of cancer treatment response. Here, the authors have developed, for the first time, a complete computer-aided-prognosis (CAP) system based on multiparametric quantitative ultrasound (QUS) spectroscopy methods in association with texture descriptors and advanced machine learning techniques. This system was used to noninvasively categorize and predict cell death levels in fibrosarcoma mouse tumors treated using ultrasound-stimulated microbubbles as novel endothelial-cell radiosensitizers. METHODS: Sarcoma xenograft tumor-bearing mice were treated using ultrasound-stimulated microbubbles, alone or in combination with x-ray radiation therapy, as a new antivascular treatment. Therapy effects were assessed at 2-3, 24, and 72 h after treatment using a high-frequency ultrasound. Two-dimensional spectral parametric maps were generated using the power spectra of the raw radiofrequency echo signal. Subsequently, the distances between "pretreatment" and "post-treatment" scans were computed as an indication of treatment efficacy, using a kernel-based metric on textural features extracted from 2D parametric maps. A supervised learning paradigm was used to either categorize cell death levels as low, medium, or high using a classifier, or to "continuously" predict the levels of cell death using a regressor. RESULTS: The developed CAP system performed at a high level for the classification of cell death levels. The area under curve of the receiver operating characteristic was 0.87 for the classification of cell death levels to both low/medium and medium/high levels. Moreover, the prediction of cell death levels using the proposed CAP system achieved a good correlation (r = 0.68, p < 0.001) with histological cell death levels as the ground truth. A statistical test of significance between individual treatment groups with the corresponding control group demonstrated that the predicted levels indicated the same significant changes in cell death as those indicated by the ground-truth levels. CONCLUSIONS: The technology developed in this study addresses a gap in the current standard of care by introducing a quality control step that generates potentially actionable metrics needed to enhance treatment decision-making. The study establishes a noninvasive framework for quantifying levels of cancer treatment response developed preclinically in tumors using QUS imaging in conjunction with machine learning techniques. The framework can potentially facilitate the detection of refractory responses in patients to a certain cancer treatment early on in the course of therapy to enable switching to more efficacious treatments.


Subject(s)
Diagnosis, Computer-Assisted/methods , Image Processing, Computer-Assisted/methods , Machine Learning , Ultrasonography , Animals , Cell Death , Cell Line, Tumor , Cell Transformation, Neoplastic , Fibrosarcoma/diagnostic imaging , Fibrosarcoma/pathology , Mice
3.
Technol Cancer Res Treat ; 13(5): 435-44, 2014 Oct.
Article in English | MEDLINE | ID: mdl-24000993

ABSTRACT

Modulation of the tumour microvasculature has been demonstrated to affect the effectiveness of radiation, stimulating the search for anti-angiogenic and vascular-disrupting treatment modalities. Microbubbles stimulated by ultrasound have recently been demonstrated as a radiation enhancer when used with different cancer models including PC3. Here, photoacoustics imaging technique was used to assess this treatment's effects on haemoglobin levels and oxygen saturation. Correlations between this modality and power doppler assessments of blood flow, and histology measurements of vascular integrity and cell death were also investigated. Xenograft prostate tumours in SCID mice were treated with 0, 2, or 8 Gy radiation combined with microbubbles exposed to 500 kHz ultrasound at a peak negative pressure of 0, 570, and 750 kPa. Tumours were assessed and levels of total haemoglobin, oxygen saturation were measured using photoacoustics before and 24 hours after treatment along with power doppler measured blood flow. Mice were then sacrificed and tumours were assessed for cell death and vascular composition using immunohistochemistry. Treatments using 8 Gy and microbubbles resulted in oxygen saturation decreasing by 28 ± 10% at 570 kPa and 25 ± 29% at 750 kPa, which corresponded to 44 ± 9% and 40 ± 14% respective decreases in blood flow as measured with power doppler. Corresponding histology indicated 31 ± 5% at 570 kPa and 37 ± 5% at 750 kPa in terms of cell death. There were drops in intact vasculature of 15 ± 2% and 20 ± 2%, for treatments at 570 kPa and 750 kPa. In summary, photoacoustic measures of total haemoglobin and oxygen saturation paralleled changes in power doppler indicators of blood flow. Destruction of tumour microvasculature with microbubble-enhanced radiation also led to decreases in blood flow and was associated with increases in cell death and decreases in intact vasculature as detected with CD31 labeling.


Subject(s)
Microbubbles/therapeutic use , Prostatic Neoplasms/pathology , Animals , Cell Line, Tumor , Diagnostic Imaging , Humans , Male , Mice, SCID , Photoacoustic Techniques , Prostatic Neoplasms/radiotherapy , Radiation Tolerance/radiation effects , Sonication , Sound , Tumor Burden , Xenograft Model Antitumor Assays
4.
Technol Cancer Res Treat ; 12(1): 53-60, 2013 Feb.
Article in English | MEDLINE | ID: mdl-22905807

ABSTRACT

Blood vessels within tumours represent a key component for cancer cell survival. Disruption of these vessels can be achieved by inducing vascular endothelial-cell apoptosis. Moreover, endothelial cell apoptosis has been proven to be enhanced by ceramide-increasing drugs. Herein, we introduce a novel therapeutic approach which uses ultrasound-stimulated microbubbles used in combination with radiation to cause a rapid accumulation of ceramide in endothelial cells in-vitro. We also test this modality directly with other cell types as a general method of killing cancer cells. Human umbilical vein endothelial cells (HUVEC), acute myeloid leukemia cells (AML), murine fibrosarcoma cells (KHT-C), prostate cancer cells (PC3), breast cancer cells (MDA-MB-231) and astrocytes were used to evaluate this mechanism of inducing cell death. Survival was measured by clonogenic assays, and ceramide content was detected using immunohistochemistry. Exposure of cell types to ultrasound-stimulated bubbles alone resulted in increases in ceramide for all cell types and survivals of 12 ±â€…2%, 65 ±â€…5%, 83 ±â€…2%, 58 ± 4%, 58 ±â€…3%, 18 ±â€…7% for HUVEC, AML, PC3, MDA, KHT-C and astrocyte cells, respectively. Results from selected cell types involving radiation treatments indicated additive treatment enhancements and increases in intracellular ceramide content one hour after exposure to ultrasound-activated microbubbles and radiation. Endothelial cell survival decreased from 8 ±â€…1% after 2 Gy of radiation treatment alone and from 12 ±â€…2% after ultrasound and microbubbles alone, to 1 ±â€…1% with combined treatment. In Asmase +/+ astrocytes, survival decreased from 56 ±â€…2% after 2 Gy radiation alone and from 17 ±â€…7% after ultrasound and microbubbles alone, to 5 ±â€…2% when combined. Using ASMase deficient astrocytes (Asmase -/- ) and Sphingosine-1-phosphate (S1P), we also demonstrate that ultrasound-activated microbubbles stimulate ASMase activity and ceramide production. These findings suggest that ultrasound-stimulated microbubbles could be used as a new biomechanical method to enhance the effects of radiation.


Subject(s)
Neoplasms/therapy , Ultrasonic Therapy , Animals , Cell Line , Cell Survival/radiation effects , Ceramides/metabolism , Humans , Mice , Microbubbles
5.
Br J Cancer ; 107(3): 469-76, 2012 Jul 24.
Article in English | MEDLINE | ID: mdl-22790798

ABSTRACT

BACKGROUND: Tumour vasculature is an important component of tumour growth and survival. Recent evidence indicates tumour vasculature also has an important role in tumour radiation response. In this study, we investigated ultrasound and microbubbles to enhance the effects of radiation. METHODS: Human bladder cancer HT-1376 xenografts in severe combined immuno-deficient mice were used. Treatments consisted of no, low and high concentrations of microbubbles and radiation doses of 0, 2 and 8 Gy in short-term and longitudinal studies. Acute response was assessed 24 h after treatment and longitudinal studies monitored tumour response weekly up to 28 days using power Doppler ultrasound imaging for a total of 9 conditions (n=90 animals). RESULTS: Quantitative analysis of ultrasound data revealed reduced blood flow with ultrasound-microbubble treatments alone and further when combined with radiation. Tumours treated with microbubbles and radiation revealed enhanced cell death, vascular normalisation and areas of fibrosis. Longitudinal data demonstrated a reduced normalised vascular index and increased tumour cell death in both low and high microbubble concentrations with radiation. CONCLUSION: Our study demonstrated that ultrasound-mediated microbubble exposure can enhance radiation effects in tumours, and can lead to enhanced tumour cell death.


Subject(s)
Contrast Media/therapeutic use , Microbubbles , Radiation-Sensitizing Agents/pharmacology , Urinary Bladder Neoplasms/radiotherapy , Animals , Cell Death/radiation effects , Cell Line, Tumor , Endothelial Cells/radiation effects , Humans , Longitudinal Studies , Male , Mice , Mice, SCID , Neovascularization, Pathologic/radiotherapy , Radiation Dosage , Regional Blood Flow/radiation effects , Ultrasonics , Ultrasonography , Urinary Bladder Neoplasms/blood supply , Urinary Bladder Neoplasms/diagnostic imaging , Urinary Bladder Neoplasms/pathology , Xenograft Model Antitumor Assays
6.
Curr Oncol ; 19(3): e177-83, 2012 Jun.
Article in English | MEDLINE | ID: mdl-22670107

ABSTRACT

We present a patient with lymphoepithelioma-like carcinoma (LELC) of the breast whose diagnosis is illustrative of the pathology nuances that must be taken into account to successfully reach correct identification of the disease. We also present an overview of our patient's proposed treatment in the context of 16 other reported LELC cases. Although LELC cases are rare, a sufficient number have been reported to discern the natural history of this pathologic entity and to undertake a review of those cases and of the application of oncologic first principles in their management. Given the potential for locoregional spread and distant metastases in LELC, adjuvant therapy has a role in the treatment of this entity.

7.
Curr Oncol ; 19(3): e211-5, 2012 Jun.
Article in English | MEDLINE | ID: mdl-22670111

ABSTRACT

To reduce local recurrence, adjuvant locoregional radiotherapy is given routinely for post-mastectomy breast patients with 4 or more positive lymph nodes. Most institutions adopt a 3- or 4-field radiotherapy technique, in which the field and shielding placements are informed by bony anatomic landmarks viewed on digitally reconstructed radiographs.Here, we report on a 40-year-old woman who underwent a lumpectomy with axillary node dissection, followed by chemotherapy, completion mastectomy, and adjuvant locoregional radiotherapy (50 Gy in 25 fractions) for a multicentric pT1cN2aM0 invasive ductal carcinoma of the right breast. At 9 months after radiotherapy, she presented with a palpable brachial lymph node, a major draining node of the upper extremity, in the axilla, abutting the previous anterior supraclavicular and axillary radiation fields. This occurrence highlights the potential superolateral border of the level i axillary nodal chain and its relationship to the upper extremity lymphatics via the brachial ("sentry") node. Adapting the delineated nodal target volume in locoregional radiotherapy of the breast for disease with extensive nodal involvement or other high-risk pathologic indications may be warranted in certain situations. Careful imaging and an informed discussion with the patient is needed before deciding to treat the sentry node and including the acromial-clavicular joints, balanced with the potential increased risk of lymphedema.

8.
Curr Oncol ; 15(5): 229-33, 2008 Oct.
Article in English | MEDLINE | ID: mdl-19008997

ABSTRACT

Patients with chronic lymphocytic leukemia (CLL) are at a significantly increased risk of developing cutaneous squamous cell carcinoma (SCC), in part because of their impaired immunosurveillance. Here, we report the cases of 4 patients with CLL who had locally aggressive cutaneous scc managed with radiotherapy for local recurrence following surgical excision. All tumours were located in the head-and-neck region. All patients initially achieved complete regression of disease; however, 2 had local recurrence a mean of 8 months after treatment completion. One patient died from progressive SCC. Our findings agree with the high rates reported in literature of multiple tumours, local recurrence, metastases, and mortality from scc in patients with cll. Radiotherapy plays an important role in patient management, and it is the recommended treatment modality when complete surgical excision of disease would result in anatomic and functional defects. Radiotherapy is often used in the case of local recurrence after one or more attempts at surgical excision. Dose escalation through intensity-modulated radiotherapy, hyperfractionation, or novel treatment techniques such as high-intensity focused ultrasound may be explored to improve local control of scc lesions. To optimize patient outcomes, cutaneous SCC arising in patients with a history of cll should be managed and followed in a multidisciplinary clinic, with regular skin surveillance and prompt treatment.

9.
Ultrasound Med Biol ; 31(8): 1041-9, 2005 Aug.
Article in English | MEDLINE | ID: mdl-16085095

ABSTRACT

We investigate the use of signal envelope statistics to monitor and quantify structural changes during cell death using an in vitro cell model. Using a f/2.35 transducer (center frequency 20 MHz), ultrasound backscatter data were obtained from pellets of acute myeloid leukemia cells treated with a DNA-intercolating chemotherapy drug, as well as from pellets formed with mixtures of treated and untreated cells. Simulations of signals from pellets of mixtures of cells were generated as a summation of point scatterers. The signal envelope statistics were examined by fitting the Rayleigh and generalized gamma distributions. The fit parameters of the generalized gamma distribution showed sensitivity to structural changes in the cells. The scale parameter showed a 200% increase (p<0.05) between untreated and cells treated for 24 h. The shape parameter showed a 50% increase (p<0.05) over 24 h. Experimental results showed reasonable agreement with simulations. The results indicate that high-frequency ultrasound signal statistics can be used to monitor structural changes within a very low percentage of treated cells in a population, raising the possibility of using this technique in vivo.


Subject(s)
Apoptosis/physiology , Leukemia, Myeloid, Acute/diagnostic imaging , Antineoplastic Agents/pharmacology , Apoptosis/drug effects , Cell Nucleus/diagnostic imaging , Cell Nucleus/physiology , Cisplatin/pharmacology , Computer Simulation , Humans , Leukemia, Myeloid, Acute/physiopathology , Models, Biological , Monitoring, Physiologic/methods , Time Factors , Tumor Cells, Cultured , Ultrasonography
10.
J Acoust Soc Am ; 117(2): 934-43, 2005 Feb.
Article in English | MEDLINE | ID: mdl-15759712

ABSTRACT

Assessing the proportion of biological cells in a volume of interest undergoing structural changes, such as cell death, using high-frequency ultrasound (20-100 MHz), requires the development of a theoretical model of scattering by any arbitrary cell ensemble. A prerequisite to building such a model is to know the scattering by a single cell in different states. In this paper, a simple model for the high-frequency acoustic scattering by one cell is proposed. A method for deducing the backscatter transfer function from a single, subresolution scatterer is also devised. Using this method, experimental measurements of backscatter from homogeneous, subresolution polystyrene microspheres and single, viable eukaryotic cells, acquired across a broad, continuous range of frequencies were compared with elastic scattering theory and the proposed cell scattering model, respectively. The resonant features observed in the backscatter transfer function of microspheres were found to correspond accurately to theoretical predictions. Using the spacing of the major spectral peaks in the transfer functions obtained experimentally, it is possible to predict microsphere diameters with less than 4% error. Such good agreement was not seen between the cell model and the measured backscatter from cells. Possible reasons for this discrepancy are discussed.


Subject(s)
Apoptosis/physiology , Microspheres , Radio Waves , Scattering, Radiation , Tumor Cells, Cultured/physiology , Ultrasonography/instrumentation , Cell Line, Tumor , Humans , Leukemia, Myeloid, Acute , Mathematical Computing , Models, Theoretical , Polystyrenes , Signal Processing, Computer-Assisted , Transducers
11.
Ultrasound Med Biol ; 28(5): 589-97, 2002 May.
Article in English | MEDLINE | ID: mdl-12079696

ABSTRACT

Ultrasound (US) spectral analysis methods are used to analyze the radiofrequency (RF) data collected from cell pellets exposed to chemotherapeutics that induce apoptosis and other chemicals that induce nuclear transformations. Calibrated backscatter spectra from regions-of-interest (ROI) were analyzed using linear regression techniques to calculate the spectral slope and midband fit. Two f/2 transducers, with operating frequencies of 30 and 34 MHz (relative bandwidths of 93% and 78%, respectively) were used with a custom-made imaging system that enabled the collection of the raw RF data. For apoptotic cells, the spectral slope increased from 0.37 dB/MHz before drug exposure to 0.57 dB/MHz 24 h after, corresponding to a change in effective scatterer radius from 8.7 to 3.2 microm. The midband fit increased in a time-dependent fashion, peaking at 13dB 24 h after exposure. The statistical deviation of the spectral parameters was in close agreement with theoretical predictions. The results provide a framework for using spectral parameter methods to monitor apoptosis in in vitro and in in vivo systems and are being used to guide the design of system and signal analysis parameters.


Subject(s)
Apoptosis/physiology , Cells/diagnostic imaging , Cells/ultrastructure , Deoxyribonucleases/metabolism , Humans , Models, Theoretical , Spectrum Analysis , Ultrasonics , Ultrasonography
12.
Br J Cancer ; 81(3): 520-7, 1999 Oct.
Article in English | MEDLINE | ID: mdl-10507779

ABSTRACT

A new non-invasive method for monitoring apoptosis has been developed using high frequency (40 MHz) ultrasound imaging. Conventional ultrasound backscatter imaging techniques were used to observe apoptosis occurring in response to anticancer agents in cells in vitro, in tissues ex vivo and in live animals. The mechanism behind this ultrasonic detection was identified experimentally to be the subcellular nuclear changes, condensation followed by fragmentation, that cells undergo during apoptosis. These changes dramatically increase the high frequency ultrasound scattering efficiency of apoptotic cells over normal cells (25- to 50-fold change in intensity). The result is that areas of tissue undergoing apoptosis become much brighter in comparison to surrounding viable tissues. The results provide a framework for the possibility of using high frequency ultrasound imaging in the future to non-invasively monitor the effects of chemotherapeutic agents and other anticancer treatments in experimental animal systems and in patients.


Subject(s)
Antineoplastic Agents/pharmacology , Apoptosis , Leukemia, Promyelocytic, Acute/diagnostic imaging , Tumor Cells, Cultured/diagnostic imaging , Animals , Apoptosis/drug effects , Brain/pathology , Cell Cycle/drug effects , Cisplatin/pharmacology , DNA, Neoplasm/analysis , Dihematoporphyrin Ether/therapeutic use , Hematoporphyrin Photoradiation , Humans , Leukemia, Promyelocytic, Acute/drug therapy , Leukemia, Promyelocytic, Acute/pathology , Leukemic Infiltration/diagnostic imaging , Leukemic Infiltration/drug therapy , Male , Neoplasm Transplantation , Radiation-Sensitizing Agents/therapeutic use , Rats , Rats, Inbred F344 , Ultrasonography
13.
J Microsc ; 188(Pt 1): 24-35, 1997 Oct.
Article in English | MEDLINE | ID: mdl-9369019

ABSTRACT

The structures of the large and small ribosomal subunits of Escherichia coli were reconstructed using spectroscopic electron microscopy and quaternion-assisted angular reconstitution to resolutions of better than 4 nm. In addition, the distributions of phosphorus within these complexes were reconstructed. The three-dimensional reconstruction of the distribution of this atomic element is an extension of microanalysis (in two dimensions) for phosphorus identification and mapping, as a signature of the arrangement of the phosphate backbones of the constituent ribosomal RNAs. The results on both the phosphorus reconstructions and the total reconstructions (protein and ribosomal RNA) reveal several passageways through both subunits. The structures correspond favourably with other independent reconstructions of the whole E. coli ribosome from cryoelectron micrographs and their accompanying models of translation (Frank et al., Nature, 376, 441-444, 1995; Stark et al., Structure, 3, 815-821, 1995). The overall reconstructions in conjunction with the phosphorus (rRNA) distributions are the first to be achieved synchronously for this nucleoprotein complex.


Subject(s)
Escherichia coli/cytology , Escherichia coli/ultrastructure , RNA, Ribosomal/ultrastructure , Ribosomes/ultrastructure , Electron Probe Microanalysis , Image Processing, Computer-Assisted
14.
J Biol Chem ; 272(7): 4261-8, 1997 Feb 14.
Article in English | MEDLINE | ID: mdl-9020142

ABSTRACT

Myelin basic protein (MBP) plays an integral role in the structure and function of the myelin sheath. In humans and cattle, an 18.5-kDa isoform of MBP predominates and exists as a multitude of charge isomers resulting from extensive and varied post-translational modifications. We have purified the least modified isomer (named C1) of the 18.5-kDa isoform of MBP from fresh bovine brain and imaged this protein as negatively stained single particles adsorbed to a lipid monolayer. Under these conditions, MBP/C1 presented diverse projections whose relative orientations were determined using an iterative quaternion-assisted angular reconstitution scheme. In different buffers, one with a low salt and the other with a high salt concentration, the conformation of the protein was slightly different. In low salt buffer, the three-dimensional reconstruction, solved to a resolution of 4 nm, had an overall "C" shape of outer radius 5.5 nm, inner radius 3 nm, overall circumference 15 nm, and height 4.7 nm. The three-dimensional reconstruction of the protein in high salt buffer, solved to a resolution of 2.8 nm, was essentially the same in terms of overall dimensions but had a somewhat more compact architecture. These results are the first structures achieved directly for this unusual macromolecule, which plays a key role in the development of multiple sclerosis.


Subject(s)
Myelin Basic Protein/chemistry , Animals , Cattle , Microscopy, Electron , Models, Molecular , Protein Conformation
15.
Ultrasound Med Biol ; 23(6): 961-5, 1997.
Article in English | MEDLINE | ID: mdl-9301000

ABSTRACT

Ultrasonic imaging is frequently used in medical diagnosis to differentiate normal and tumour tissues. Here we investigate if distinct types of cell death can be discriminated through the use of ultrasound biomicroscopy. By using a well-controlled system in vitro, we demonstrate that this imaging modality can be used to differentiate living cells, dead cells and cells that have died by programmed cell death or apoptosis. The results indicate a greater than twofold ultrasound backscatter signal from apoptotic cells in comparison to viable cells, whereas heat-killed cells exhibit an intermediate level of ultrasound backscatter. The results have potential implications in the study of disease-related biological processes involving apoptosis.


Subject(s)
Apoptosis , DNA, Neoplasm/drug effects , Leukemia, Monocytic, Acute/diagnostic imaging , Leukemia, Monocytic, Acute/pathology , Antineoplastic Agents/pharmacology , Cell Count , Cell Survival , Cisplatin/pharmacology , DNA Damage/drug effects , Humans , Microscopy , Tumor Cells, Cultured , Ultrasonography
16.
Micron ; 28(6): 419-31, 1997 Dec.
Article in English | MEDLINE | ID: mdl-9519470

ABSTRACT

The nucleosome is the ubiquitous and fundamental DNA-protein complex of the eukaryotic chromosome, participating in the packaging of DNA and in the regulation of gene expression. Biophysical studies have implicated changes in nucleosome structure from chromatin that is quiescent to active in transcription. Since DNA within the nucleosome contains a high concentration of phosphorus whereas histone proteins do not, the nucleosome structure is amenable to microanalytical electron energy loss mapping of phosphorus to delineate the DNA within the protein-nucleic acid particle. Nucleosomes associated with transcriptionally active genes were separated from nucleosomes associated with quiescent genes using mercury-affinity chromatography. The three-dimensional image reconstruction methods for the total nucleosome structure and for the 3D DNA-phosphorus distribution combined quaternion-assisted angular reconstitution of sets of single particles at random orientations and electron spectroscopic imaging. The structure of the active nucleosome has the conformation of an open clam-shell, C- or U-shaped in one view, elongated in another, and exhibits a protein asymmetry. A three-dimensional phosphorus map reveals a conformational change in nucleosomal DNA compared to DNA in the canonical nucleosome structure. It indicates an altered superhelicity and is consistent with unfolding of the particle. The results address conformational changes of the nucleosome and provide a direct structural linkage to biochemical and physiological changes which parallel gene expression.


Subject(s)
Chromatin/metabolism , Nucleosomes/chemistry , Nucleosomes/ultrastructure , DNA/chemistry , DNA/metabolism , Electron Probe Microanalysis , Gene Expression , Histones/metabolism , Image Processing, Computer-Assisted , Microscopy, Electron , Molecular Structure , Nucleosomes/metabolism , Transcription, Genetic , Tumor Cells, Cultured
17.
J Biol Chem ; 271(7): 3677-83, 1996 Feb 16.
Article in English | MEDLINE | ID: mdl-8631980

ABSTRACT

The nucleosome is the fundamental component of the eukaryotic chromosome, participating in the packaging of DNA and in the regulation of gene expression. Its numerous interactions imply a structural dynamism. Previous biophysical studies under limited sets of conditions have not been able to reconcile structural differences and transitions observed. We have determined a series of nucleosome conformations over a >10,000-fold range in salt concentration using a combination of biochemical methods, spectroscopic electron microscopy, and three-dimensional reconstruction techniques for randomly oriented single particles. This study indicates several ionic strength-dependent nucleosome conformations and also reconciles the differences between currently existing divergent models for the nucleosome. At low ionic environments, the particle appears highly elongated, becoming more compact and prolate ellipsoidal as ionic strength is increased to 10 mm NaCl. At 30 mM NaCl, the particle exhibits a spheroidal conformation. As ionic strength is increased to 150 mM NaCl, the nucleosome conformation changes and becomes oblate. Above 450 mM NaCl, the structure becomes highly elongated again. The result of this study is a unifying concept in which the three-dimensional structure of the nucleosome is inferred to be dynamic in response to ionic interactions and in accord with biochemical and genetic studies.


Subject(s)
Models, Structural , Nucleosomes/ultrastructure , Thymus Gland/ultrastructure , Animals , Cattle , Microscopy, Electron , Nucleosomes/drug effects , Osmolar Concentration , Sodium Chloride/pharmacology
18.
Nucleic Acids Res ; 24(2): 321-9, 1996 Jan 15.
Article in English | MEDLINE | ID: mdl-8628657

ABSTRACT

We have characterized the structure of transcriptionally active nucleosome subunits using electron spectroscopic imaging. Individual nucleosomes were analyzed in terms of total mass, DNA and protein content, while the ensemble of images of active nucleosomes was used to calculate a three-dimensional reconstruction. Transcriptionally active nucleosomes were separated from inactive nucleosomes by mercury-affinity chromatography thus making it possible to compare their structures. The chromatographic results combined with electron spectroscopic imaging confirm that active nucleosomes unfold to form extended U-shaped particles. Phosphorus mapping indicated that the nucleosomal DNA also underwent a conformational change consistent with particle unfolding. The three-dimensional structure of the Hg-affinity purified nucleosomes determined using quaternion-assisted angular reconstitution methods unites and resolves the different electron microscopic views of the particle and is concordant with a sulphydryl-exposing disruption of the H3-H4 tetramer.


Subject(s)
Nucleosomes/ultrastructure , Chromatin , Chromatography, Affinity/methods , DNA/analysis , Humans , Image Processing, Computer-Assisted/methods , Mercury , Microscopy, Electron/methods , Molecular Conformation , Molecular Weight , Nuclear Proteins/analysis , Nucleosomes/chemistry , Phosphorus/analysis , Spectrum Analysis/methods , Transcription, Genetic
19.
J Struct Biol ; 113(1): 35-46, 1994.
Article in English | MEDLINE | ID: mdl-7880651

ABSTRACT

The 54-kDa subunit SRP54 of the signal recognition particle in eukaryotic cells is responsible for the recognition of nascent proteins destined for secretion or membrane integration. The three-dimensional structure of this protein was determined using computational techniques applied to images of the molecule obtained via high-resolution, low-dose, scanning transmission electron microscopy at low temperature. The reconstructions at spatial resolutions between 12 and 15 A feature two unequal domains joined by a slender linker. The two-domain structure is in agreement with genetic and biochemical data indicating organization of SRP54 into a larger N-terminal GTP-binding region and a smaller C-terminal peptide-binding region. The structure has similarities to other protein domains with related functions and similar amino acid sequences. The larger domain of the 3D reconstruction is consistent in shape and size with the GTP-binding domains of EF-Tu and p21-RAS, while the smaller domain is compatible in structure with part of the peptide-binding protein calmodulin. The overall shape of SRP54 and the deduced location of critical functional regions of the molecule provide a structural framework for its known biochemical properties in the targeting cycle of the signal recognition particle.


Subject(s)
Protein Conformation , Protein Structure, Secondary , Signal Recognition Particle/chemistry , Signal Recognition Particle/ultrastructure , Amino Acid Sequence , Calmodulin/chemistry , Computer Simulation , GTP-Binding Proteins/chemistry , GTP-Binding Proteins/ultrastructure , Microscopy, Electron, Scanning Transmission/methods , Models, Molecular , Molecular Sequence Data , Peptide Elongation Factor Tu/chemistry , Peptide Elongation Factor Tu/ultrastructure , Structure-Activity Relationship
20.
J Microsc ; 172(Pt 3): 205-14, 1993 Dec.
Article in English | MEDLINE | ID: mdl-8120881

ABSTRACT

Optimized fixation conditions were determined for protein-protein and protein-DNA crosslinking within calf-thymus nucleosomes in low monovalent salt concentrations. Nucleosomes were examined without heavy-atom staining by darkfield electron microscopy. The dimensions of these macromolecular complexes and those of HeLa core particles optimally fixed in divalent salt were analysed using principal component analysis. According to this analysis the structure of the calf-thymus nucleosomes was best presented by a prolate ellipsoid. Particle images had average major and minor axis lengths of 14.1 and 10.5 nm, respectively. In contrast, the HeLa nucleosomes were best modelled by an oblate ellipsoid from the analysis of their images, which had average major and minor axes of 13.3 and 11.5 nm. The applicability of this multivariate statistical analysis to the interpretation of macromolecular images is illustrated and discussed.


Subject(s)
Nucleosomes/ultrastructure , Tissue Fixation/methods , Animals , Cattle , Cross-Linking Reagents , Formaldehyde/pharmacology , Glutaral/pharmacology , HeLa Cells/ultrastructure , Humans , Image Processing, Computer-Assisted , Microscopy, Electron/methods , Models, Structural , Nucleosomes/drug effects , Thymus Gland/ultrastructure
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