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1.
J Ovarian Res ; 17(1): 121, 2024 Jun 05.
Article in English | MEDLINE | ID: mdl-38840218

ABSTRACT

BACKGROUND: Polycystic Ovary Syndrome (PCOS) is a widespread endocrine disorder among women, characterized by symptoms like ovarian cysts, hormonal imbalance, and metabolic issues. This research evaluates the therapeutic potential of Bone Marrow Mesenchymal Stem Cell-derived exosomes (BMSC-Exo) in treating PCOS symptoms within a mouse model. METHODS: BMSC-Exo were isolated from NMRI mice, characterized using Transmission Electron Microscopy (TEM) and Nanoparticle Tracking Analysis (NTA), and administered to a PCOS mouse model induced by dehydroepiandrosterone (DHEA). The efficacy of BMSC-Exo was assessed in three groups of mice: a control group, a PCOS group, and a PCOS group treated with intravenous BMSC-Exo. Morphological changes in ovarian tissue were examined by Hematoxylin and Eosin (H&E) staining, apoptosis was determined using the TUNEL assay, and CD31 expression was analyzed through immunofluorescent staining to assess angiogenic activity. RESULTS: The existence of BMSCs-Exo was confirmed via TEM and NTA, revealing their distinct cup-shaped morphology and a size range of 30 to 150 nanometers. H&E staining revealed that BMSCs-Exo treatment improved ovarian morphology in PCOS models, increasing corpora lutea and revitalizing granulosa cell layers, suggesting a reversal of PCOS-induced damage. TUNEL assays showed that BMSCs-Exo treatment significantly reduced apoptosis in PCOS-affected ovarian cells to levels comparable with the control group, highlighting its role in mitigating PCOS-induced cellular apoptosis. Immunofluorescence for CD31 indicated that BMSCs-Exo treatment normalized endothelial marker expression and angiogenic activity in PCOS models, suggesting its effectiveness in modulating the vascular irregularities of PCOS. Collectively, these findings demonstrate the therapeutic potential of BMSCs-Exo in addressing ovarian dysfunction, cellular apoptosis, and aberrant angiogenesis associated with PCOS. CONCLUSION: The study substantiates the role of BMSC-Exo in mitigating the deleterious effects of PCOS on ovarian tissue, with implications for enhanced follicular development and reduced cellular stress. The modulation of CD31 by BMSC-Exo further highlights their potential in normalizing PCOS-induced vascular anomalies. These findings propel the need for clinical investigations to explore BMSC-Exo as a promising therapeutic avenue for PCOS management.


Subject(s)
Apoptosis , Dehydroepiandrosterone , Disease Models, Animal , Exosomes , Mesenchymal Stem Cells , Polycystic Ovary Syndrome , Animals , Female , Polycystic Ovary Syndrome/therapy , Polycystic Ovary Syndrome/metabolism , Exosomes/metabolism , Dehydroepiandrosterone/pharmacology , Mice , Mesenchymal Stem Cells/metabolism , Neovascularization, Physiologic , Ovary/metabolism , Ovary/pathology , Angiogenesis
2.
Ann Diagn Pathol ; 72: 152321, 2024 Oct.
Article in English | MEDLINE | ID: mdl-38759563

ABSTRACT

Retroperitoneal Ewing sarcomas (RES) are very rare and mostly described in case reports. The purpose of this study was to retrospectively analyze the clinicopathology, molecular characteristics, biological behavior, and therapeutic information of 13 cases of primary RES with immunohistochemical staining, fluorescence in situ hybridization, RT-PCR and NGS sequencing detection techniques. The thirteen patients included eight males and five females with a mean age of 34 years. Morphologically, the tumors were comprised of small round or epithelial-like cells with vacuolated cytoplasm (6/13,46 %) arranged in diffuse, nested (8/13,62 %) and perivascular (7/13,54 %) patterns. Unusual morphologic patterns, such as meningioma-like swirling structures and sieve-like structures were relatively novel findings. Immunohistochemical studies showed CD99 (12/13; 92 %), CD56 (11/13; 85 %), NKX2.2 (9/13; 69 %), PAX7 (10/11;91 %) and CD117(6/9;67 %) to be positive.12 cases (92 %) demonstrated EWSR1 rearrangement and 3 cases displayed EWSR1::FLI1 fusion by FISH. ERCC4 splice-site variant, a novel pathogenic variant, was discovered for the first time via RNA sequencing. With a median follow-up duration of 14 months (6 to 79 months), 8/13 (62 %) patients died, while 5/13(38 %) survived. Three cases recurred, and five patients developed metastasis to the liver (2 cases), lung (2 cases) and bone (1 case). RES is an aggressive, high-grade tumor, prone to multiple recurrences and metastases, with distinctive morphologic, immunohistochemical, and molecular genetic features. ERCC4 splicing mutation, which is a novel pathogenic variant discovered for the first time, with possible significance for understanding the disease, as well as the development of targeted drugs.


Subject(s)
Homeobox Protein Nkx-2.2 , RNA-Binding Protein EWS , Retroperitoneal Neoplasms , Sarcoma, Ewing , Humans , Sarcoma, Ewing/genetics , Sarcoma, Ewing/pathology , Sarcoma, Ewing/diagnosis , Sarcoma, Ewing/metabolism , Male , Female , Adult , Retroperitoneal Neoplasms/genetics , Retroperitoneal Neoplasms/pathology , Retroperitoneal Neoplasms/diagnosis , Retrospective Studies , Middle Aged , Young Adult , Adolescent , RNA-Binding Protein EWS/genetics , Biomarkers, Tumor/genetics , Biomarkers, Tumor/metabolism , In Situ Hybridization, Fluorescence/methods , Gene Rearrangement , Immunohistochemistry/methods , Transcription Factors/genetics , Transcription Factors/metabolism , Oncogene Proteins, Fusion/genetics , Child , Nuclear Proteins , Homeodomain Proteins , Zebrafish Proteins
3.
Biomark Res ; 12(1): 20, 2024 Feb 06.
Article in English | MEDLINE | ID: mdl-38321554

ABSTRACT

Multiple primary malignant neoplasms are a rare disease with tumors of different histology or morphology arising in various sites. Next-generation sequencing is essential in the etiology, diagnosis, treatment, and surveillance of this disease. No eight primary malignant neoplasm cases with high variant allele frequencies of RB1, TP53, and TERT have been reported. Herein, we report a 65-year-old male who exhibited eight primary malignancies of the vocal cord, pharynx, kidney, mouth floor, esophagus, and urinary bladder with different pathological types. The first seven tumors were early-stage tumors; the last tumor, small cell carcinoma of urinary bladder, showed liver metastasis at diagnosis. Next-generation sequencing results revealed extremely high somatic variant allele frequencies of RB1 c.1472 T > C, TP53 c.576A > G, and TERT c.-58-u66C > T (95.5%, 95.1%, and 51.0%, respectively). No germline mutations were detected. These findings denoted a heavy tumor burden and poor prognosis. This is the first report of eight primary malignant neoplasm cases with high variant allele frequencies of RB1, TP53, and TERT.

4.
BMC Public Health ; 23(1): 2536, 2023 12 19.
Article in English | MEDLINE | ID: mdl-38114942

ABSTRACT

BACKGROUND: COVID-19, caused by SARS-CoV-2, presents distinct diagnostic challenges due to its wide range of clinical manifestations and the overlapping symptoms with other common respiratory diseases. This study focuses on addressing these difficulties by employing machine learning (ML) methodologies, particularly the XGBoost algorithm, to utilize Complete Blood Count (CBC) parameters for predictive analysis. METHODS: We performed a retrospective study involving 2114 COVID-19 patients treated between December 2022 and January 2023 at our healthcare facility. These patients were classified into fever (1057 patients) and pneumonia groups (1057 patients), based on their clinical symptoms. The CBC data were utilized to create predictive models, with model performance evaluated through metrics like Area Under the Receiver Operating Characteristics Curve (AUC), accuracy, sensitivity, specificity, and precision. We selected the top 10 predictive variables based on their significance in disease prediction. The data were then split into a training set (70% of patients) and a validation set (30% of patients) for model validation. RESULTS: We identified 31 indicators with significant disparities. The XGBoost model outperformed others, with an AUC of 0.920 and high precision, sensitivity, specificity, and accuracy. The top 10 features (Age, Monocyte%, Mean Platelet Volume, Lymphocyte%, SIRI, Eosinophil count, Platelet count, Hemoglobin, Platelet Distribution Width, and Neutrophil count.) were crucial in constructing a more precise predictive model. The model demonstrated strong performance on both training (AUC = 0.977) and validation (AUC = 0.912) datasets, validated by decision curve analysis and calibration curve. CONCLUSION: ML models that incorporate CBC parameters offer an innovative and effective tool for data analysis in COVID-19. They potentially enhance diagnostic accuracy and the efficacy of therapeutic interventions, ultimately contributing to a reduction in the mortality rate of this infectious disease.


Subject(s)
COVID-19 , Humans , COVID-19/diagnosis , Public Health , COVID-19 Testing , Retrospective Studies , SARS-CoV-2
5.
Diagn Pathol ; 18(1): 14, 2023 Feb 06.
Article in English | MEDLINE | ID: mdl-36740682

ABSTRACT

BACKGROUND: Although epithelioid angiomyolipoma of the kidney has been studied by several groups, the reported prevalence of malignant behavior remains uncertain and there are not yet definitive predictive biomarkers. We evaluated the behavior of renal epithelioid angiomyolipoma in a consecutive series in a single institution and investigated the prognostic value of aberrant p53 expression and TFE3 gene abnormality. METHODS: We retrospectively reviewed 14 epithelioid angiomyolipomas, most with pure or close to pure epithelioid components, comprising 12 consecutive cases who had attended our institution and two consultation cases. Fluorescence in situ hybridization with TFE3 break-apart probe was performed on 14 cases. The 14 cases were also labeled for p53 and TFE3 by immunohistochemistry. All cases were followed up. RESULTS: Three of the epithelioid angiomyolipomas were strongly positive for TFE3 and two had a mutant expression of p53. Although no TFE3 gene rearrangement was found, the two tumors with strong TFE3 expression showed TFE3 gene amplification. Follow-up details were available for seven of the 12 consecutive cases: two of them had developed metastases and died (29%), their mean overall survival was 41 months, and both had mutant p53 expression. The two consultation cases with TFE3 gene amplification developed recurrence/metastasis within 1 year after surgery. CONCLUSIONS: Our series study from a single institution presented the prevalence of malignant behavior in pure epithelioid angiomyolipomas, although the small number of cases with follow-up data greatly reduced the accuracy. p53 may be a prognostic marker for epithelioid angiomyolipoma. Cases with TFE3 gene amplification had poor prognoses.


Subject(s)
Angiomyolipoma , Basic Helix-Loop-Helix Leucine Zipper Transcription Factors , Kidney Neoplasms , Perivascular Epithelioid Cell Neoplasms , Humans , Angiomyolipoma/genetics , Angiomyolipoma/pathology , Angiomyolipoma/surgery , Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/genetics , Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/metabolism , Biomarkers, Tumor/genetics , Biomarkers, Tumor/metabolism , Gene Amplification , In Situ Hybridization, Fluorescence , Kidney/pathology , Kidney Neoplasms/pathology , Perivascular Epithelioid Cell Neoplasms/genetics , Perivascular Epithelioid Cell Neoplasms/metabolism , Perivascular Epithelioid Cell Neoplasms/pathology , Prognosis , Retrospective Studies , Tumor Suppressor Protein p53/genetics , Tumor Suppressor Protein p53/metabolism
6.
Transl Cancer Res ; 11(6): 1850-1860, 2022 Jun.
Article in English | MEDLINE | ID: mdl-35836519

ABSTRACT

Background: NUT carcinoma (NC) is a rapidly progressing and rare neoplasm that primarily affects younger patients and has a survival time of about 1 year. Most of these neoplasms express epithelial markers with no neuroendocrine markers observed. Retrospective studies have shown that pathologists and clinicians do not have a sufficient understanding of the disease due to the lack of common clinical manifestations, imaging, and morphological features. Case Description: A 60-year-old female presented at Beijing Friendship Hospital, showing repetitive epistaxis, nasal pain, and nasal congestion with obvious masses in the right nasal sinus and frontal sinus. Microscope analysis revealed two unique morphological changes which have not been previously reported in the existing literature: (I) small spindle cells with sparse cytoplasm and densely stained nuclei and (II) large tumor cells with abundant cytoplasm, some cells resembling plasma cells. The sudden appearance of keratinization was also a prominent feature. Immunohistochemical staining showed differences between the two cell morphologies. Small spindle cells simultaneously expressed CK5/6 and P40, and the Ki67 proliferation index was 40%. The large round cells did not express CK5/6 and P40 but were focal positive for synaptophysin and the Ki67 index was 10%. NUT and P63 were strongly expressed in both cell types and fluorescence in situ hybridization (FISH) revealed BRD4-NUTM1 translocation. Following 20 rounds of postoperative radiation treatment, the patient was alive and no recurrence or metastasis was observed during a 5-month follow-up. Conclusions: We present novel information from the oldest known and surviving patient of NC originating in the nasal cavity with unique morphological features and different immunohistochemical results. NUT antibody testing should be performed in undifferentiated or poorly differentiated malignancies, particularly those with either or both cytoplasmic vacuolation of medium-sized cells and abrupt keratinization, irrespective of patient age.

7.
J Chem Phys ; 153(10): 104510, 2020 Sep 14.
Article in English | MEDLINE | ID: mdl-32933292

ABSTRACT

The self-diffusion coefficient of water shows an anomalous increase with increasing hydrostatic pressure up to a broad maximum (PmD) near 1 kbar at 298 K, which has been attributed to pressure effects on the tetrahedral hydrogen bond network of water. Moreover, the ability of a water model to reproduce anomalous properties of water is a signature that it is reproducing the network. Here, water was simulated between 1 bar and 5 kbar using three water models, two four-site (with all charges in the molecular plane) and one single-site multipole (which accounts for out-of-molecular plane charge), that have reasonable pressure-temperature properties. For these three models, the diffusion coefficients display a maximum in the pressure dependence and the radial distribution functions show good agreement with the limited experimental structural data at high pressure that are available. In addition, a variety of properties associated with the network are examined, including hydrogen bond lifetimes and occupancies, three-body angle distributions, and tetrahedral order parameters. Results suggest that the initial increasing diffusion with pressure is because hydrogen bonds are distorted and thus weakened by pressure, but above PmD, the hydrogen bonds are weakened to the point it behaves more like a normal liquid. In other words, the PmD may be a measure of the angular strength of hydrogen bonds. In addition, since the four-site models over-predict the values of PmD while the multipole model under-predicts it, out-of-plane charge may improve four-site models.

8.
J Phys Chem B ; 124(10): 1978-1986, 2020 03 12.
Article in English | MEDLINE | ID: mdl-32059113

ABSTRACT

Of cosolutes found in living cells, urea denatures and trimethylamine N-oxide (TMAO) stabilizes proteins; furthermore, these effects cancel at a 2:1 ratio of urea to TMAO. Interestingly, cartilaginous fish use urea and TMAO as osmolytes at similar ratios at the ocean surface but with increasing fractions of TMAO at increasing depths. Here, molecular dynamics simulations of aqueous solutions with different urea:TMAO ratios show that the diffusion coefficients of water in the solutions vary with pressure if the urea:TMAO ratio is constant, but strikingly, they are almost pressure independent at the ratio found in these fish as a function of depth. This suggests that this ratio may be maintaining a homeostasis of water dynamics. In addition, diffusion is determined by hydrogen-bond lifetimes of the different species in the solution. Based on these observations, a dynamical model in terms of hydrogen-bond lifetimes is developed for the hydrogen bonding propensities of cosolutes and water in an aqueous solution to proteins. This model provides an explanation for both the counteracting effects of TMAO on urea denaturation and the depth-dependent urea:TMAO ratio found in cartilaginous fish.


Subject(s)
Methylamines , Urea , Hydrogen Bonding , Water
9.
J Phys Chem B ; 123(5): 1108-1115, 2019 02 07.
Article in English | MEDLINE | ID: mdl-30638025

ABSTRACT

Trimethylamine N-oxide (TMAO) stabilizes protein structures, whereas urea destabilizes proteins, and their opposing effects can be counteracted at a 1:2 ratio of TMAO to urea. To investigate how they affect solution dynamics, molecular dynamics simulations have been carried out for aqueous solutions of TMAO and urea at different concentrations. In the binary solutions, urea mainly slows the diffusion of waters that are hydrogen bonded to it (i.e., hydration water), whereas TMAO dramatically slows the diffusion of both hydration water and bulk water because of long-lived TMAO-water hydrogen bonds. In the ternary solutions, because TMAO decreases the diffusion rate of bulk water, the lifetimes of not only water-water but also urea-water hydrogen bonds increase. In addition, the constant forming and breaking of short lifetime hydrogen bonds between urea and water appears to impart energy into the bulk, whereas the long lifetime hydrogen bonds between TMAO and water slows down the bulk, resulting in the compensating effects on bulk water in the ternary solution. This suggests that the counteracting effects of TMAO on urea denaturation may be both to make longer lived hydrogen bonds to water and to counter the energizing effects of urea on bulk water.


Subject(s)
Methylamines/chemistry , Urea/chemistry , Water/chemistry , Diffusion , Hydrogen Bonding , Molecular Dynamics Simulation , Solutions/chemistry
10.
Dig Dis Sci ; 64(1): 68-75, 2019 01.
Article in English | MEDLINE | ID: mdl-30311151

ABSTRACT

BACKGROUND: Esophageal squamous cell precursor lesions remain one of the most controversial topics in pathology and clinical management. AIMS: To analyze the dysregulation of human telomerase RNA component (hTERC) in esophageal squamous cell precursor lesions and the clinicopathological correlations with the characteristics of esophageal squamous cell precursor lesions. METHODS: Florescence in situ hybridization was performed to detect hTERC amplification in different gradings of esophageal squamous cell precursor lesions. With retrospective follow-up data, clinicopathological correlations between hTERC and esophageal squamous cell precursor lesions were subjected to logistic regression analysis. RESULTS: hTERC amplification gradually increased with upgrading of dysplasia, reaching the highest level in high-grade intraepithelial neoplasia, and there was a significant difference between the low-grade intraepithelial neoplasia group and the high-grade intraepithelial neoplasia group (P = 0.00). Logistic regression analysis showed that hTERC amplification was correlated with both dysplasia grading and ulcer characteristics of esophageal squamous cell precursor lesions (P < 0.05). CONCLUSIONS: hTERC amplification with increasing grading of esophageal squamous cell precursor lesions and the presence of ulcer characteristics might provide an important molecular and pathological marker for the diagnosis and clinical prognosis of esophageal squamous cell precursor lesions, especially for those ambiguous cases with more divergence in classification.


Subject(s)
Biomarkers, Tumor/genetics , Esophageal Neoplasms/genetics , Esophageal Squamous Cell Carcinoma/genetics , Gene Amplification , Precancerous Conditions/genetics , RNA/genetics , Telomerase/genetics , Adult , Aged , Aged, 80 and over , Biopsy , Esophageal Neoplasms/enzymology , Esophageal Neoplasms/pathology , Esophageal Squamous Cell Carcinoma/enzymology , Esophageal Squamous Cell Carcinoma/pathology , Female , Genetic Predisposition to Disease , Humans , In Situ Hybridization, Fluorescence , Male , Middle Aged , Neoplasm Grading , Phenotype , Precancerous Conditions/enzymology , Precancerous Conditions/pathology , Retrospective Studies , Risk Factors
11.
J Chem Phys ; 148(22): 222827, 2018 Jun 14.
Article in English | MEDLINE | ID: mdl-29907024

ABSTRACT

The properties of aqueous solutions of ionic, zwitterionic, and polar solutes are of interest to many fields. For instance, one of the many anomalous properties of aqueous solutions is the behavior of water diffusion in different monovalent salt solutions. In addition, solutes can affect the stabilities of macromolecules such as proteins in aqueous solution. Here, the diffusivities of aqueous solutions of sodium chloride, potassium chloride, tri-methylamine oxide (TMAO), urea, and TMAO-urea are examined in molecular dynamics simulations. The decrease in the diffusivity of water with the concentration of simple ions and urea can be described by a simple model in which the water molecules hydrogen bonded to the solutes are considered to diffuse at the same rate as the solutes, while the remainder of the water molecules are considered to be bulk and diffuse at almost the same rate as pure water. On the other hand, the decrease in the diffusivity of water with the concentration of TMAO is apparently affected by a decrease in the diffusion rate of the bulk water molecules in addition to the decrease due to the water molecules hydrogen bonded to TMAO. In other words, TMAO enhances the viscosity of water, while urea barely affects it. Overall, this separation of water molecules into those that are hydrogen bonded to solute and those that are bulk can provide a useful means of understanding the short- and long-range effects of solutes on water.

12.
Biophys J ; 114(8): 1791-1803, 2018 04 24.
Article in English | MEDLINE | ID: mdl-29694859

ABSTRACT

Cytosine methylation affects mechanical properties of DNA and potentially alters the hydration fingerprint for recognition by proteins. The atomistic origin for these effects is not well understood, and we address this via all-atom molecular dynamics simulations. We find that the stiffness of the methylated dinucleotide step changes marginally, whereas the neighboring steps become stiffer. Stiffening is further enhanced for consecutively methylated steps, providing a mechanistic origin for the effect of hypermethylation. Steric interactions between the added methyl groups and the nonpolar groups of the neighboring nucleotides are responsible for the stiffening in most cases. By constructing hydration maps, we found that methylation also alters the surface hydration structure in distinct ways. Its resistance to deformation may contribute to the stiffening of DNA for deformational modes lacking steric interactions. These results highlight the sequence- and deformational-mode-dependent effects of cytosine methylation.


Subject(s)
DNA Methylation , DNA/chemistry , DNA/metabolism , Mechanical Phenomena , Water/metabolism , Biomechanical Phenomena , DNA/genetics , Molecular Dynamics Simulation , Nucleic Acid Conformation
13.
Int J Clin Exp Pathol ; 11(3): 1281-1288, 2018.
Article in English | MEDLINE | ID: mdl-31938223

ABSTRACT

The Epstein-Barr virus (EBV) is a ubiquitous lymphotropic herpesvirus that infects the human body through the respiratory tract. Usually, primary infection with EBV is asymptomatic and occurs early in life, however adolescents or young adults are more likely to develop a self-limited symptomatic infection, which manifests as acute infectious mononucleosis (IM). Systemic EBV-positive lymphoproliferative disease (EBV + T/NK-LPD) has been described as a disease related to chronic or persistent EBV infection after acute EBV infection, with severe IM-like symptoms. EBV + T/NK-LPD is associated with high mortality and morbidity with life-threatening complications. Information on its prognostic factors remains limited, therefore in this study, we aimed to evaluate the association between prognostic factors and mortality and complications of EBV + T/NK-LPD in China by retrospectively reviewing 173 EBV + T/NK-LPD cases. We observed that the high mortality rate of EBV + T/NK-LPD was mainly due to serious and fatal complications. Fever, lymphadenopathy, hepatosplenomegaly, EBV-encoded RNA (EBER) > 50/HPF, Ki-67 > 30%, and other visible complications were closely associated with EBV + T/NK-LPD prognosis. In addition, fever, hepatosplenomegaly, decreased WBC count, and a Ki-67 index of > 30% were risk factors for complications. Thus, disease prognosis should be based on a comprehensive analysis of pathological and clinical data. Such data will help pathologists and clinicians to pay close attention to the changes in the clinical condition of the patients as well as take precautionary measures against the occurrence of fatal complications.

14.
Virchows Arch ; 470(5): 567-573, 2017 May.
Article in English | MEDLINE | ID: mdl-28238098

ABSTRACT

Fluorescence in situ hybridisation (FISH) is a molecular cytogenetic technique, which is regularly applied to formalin-fixed paraffin-embedded (FFPE) tissue sections of a variety of cancers to assess chromosomal aberrations. However, high-quality FISH requires optimal enzymatic digestion, and insufficient digestion is not noted until the hybridisation signals are evaluated in the fluorescence microscope. As a consequence, FISH results may be unreliable, and the experiment might have to be repeated. To solve this problem, we developed a new method for real-time evaluation of enzymatic tissue digestion. Termination of enzyme activity at the proper time facilitates successful hybridisation, and experiments do not have to be repeated. We first performed FISH on 20 FFPE samples, which had been pepsin digested for different times, and this revealed distinct morphological changes within the nucleus and perinuclear space that were detectable by light microscopy. These observations suggested that the presence of intact and clear bare nuclei, surrounded by a translucent perinuclear space, might serve as an indicator of adequate digestion. We developed a protocol for assessment of this indicator, based on morphological features, and applied this to a collection of 400 tissue samples, partly of breast cancer and partly of different types of lymphoma, prior to FISH. The FISH success rate was 99.5% (398/400), which was significantly higher than that of the conventional method. In all successful cases, morphological signs of adequate digestion were paralleled by easily interpretable FISH signals. This new method for the real-time assessment of digestion quality improved the success rate of FISH and in addition was simple and rapid.


Subject(s)
Histocytological Preparation Techniques , In Situ Hybridization, Fluorescence/methods , Pepsin A , Humans , Neoplasms/diagnosis , Neoplasms/genetics , Paraffin Embedding
15.
ACS Nano ; 10(1): 170-80, 2016 Jan 26.
Article in English | MEDLINE | ID: mdl-26638896

ABSTRACT

We study the elasticity of DNA based on local principal axes of bending identified from over 0.9-µs all-atom molecular dynamics simulations of DNA oligos. The calculated order parameters describe motion of DNA as an elastic rod. In 10 possible dinucleotide steps, bending about the two principal axes is anisotropic yet linearly elastic. Twist about the centroid axis is largely decoupled from bending, but DNA tends to overtwist for unbending beyond the typical range of thermal motion, which is consistent with experimentally observed twist-stretch coupling. The calculated elastic stiffness of dinucleotide steps yield sequence-dependent persistence lengths consistent with previous single-molecule experiments, which is further analyzed by performing coarse-grained simulations of DNA. Flexibility maps of oligos constructed from simulation also match with those from the precalculated stiffness of dinucleotide steps. These support the premise that base pair interaction at the dinucleotide-level is mainly responsible for the elasticity of DNA. Furthermore, we analyze 1381 crystal structures of protein-DNA complexes. In most structures, DNAs are mildly deformed and twist takes the highest portion of the total elastic energy. By contrast, in structures with the elastic energy per dinucleotide step greater than about 4.16 kBT (kBT: thermal energy), the major bending becomes dominant. The extensional energy of dinucleotide steps takes at most 35% of the total elastic energy except for structures containing highly deformed DNAs where linear elasticity breaks down. Such partitioning between different deformational modes provides quantitative insights into the conformational dynamics of DNA as well as its interaction with other molecules and surfaces.


Subject(s)
DNA Topoisomerases, Type II/chemistry , DNA-Binding Proteins/chemistry , DNA/chemistry , Oligodeoxyribonucleotides/chemistry , Base Pairing , Databases, Factual , Elasticity , Humans , Molecular Dynamics Simulation , Motion , Nucleic Acid Conformation , Thermodynamics
16.
Am J Surg Pathol ; 39(11): 1493-501, 2015 Nov.
Article in English | MEDLINE | ID: mdl-26457354

ABSTRACT

In some cases, long-term tumor-free survival might be possible for untreated primary diffuse large B-cell lymphoma (DLBCL) of the tonsil. Here, we report of 9 untreated patients who had primary tonsil DLBCL with long-term tumor-free survival. All these patients were children or young adults (4 male and 5 female individuals; ages: 6 to 38 y, median age: 25 y) with clinically evident swollen tonsils or papillary neoplasms. Tonsillectomy and biopsies indicated partial structural destruction of the tonsils with diffuse infiltration of large lymphoid cells. The large cells expressed CD20 with a Ki-67 proliferative index >50%. All samples were negative for CD5, Epstein-Barr virus-encoded RNA, and t(14;18) translocation. Except for cases 2 and 4, all samples showed monoclonal immunoglobulin gene rearrangements. Although chemotherapy and radiotherapy had not been administered after tonsillectomy (for various reasons), periodic imaging and clinical evaluation showed that none of the 9 patients developed or died of lymphoma (median follow-up: 40 mo). In conclusion, primary tonsil DLBCL does not always behave in a malignant manner, and some patients can achieve long-term tumor-free survival without chemotherapy or radiotherapy. On the basis of this case series, we concluded that close follow-up and observation might be possible for pediatric and young-adult patients who have undergone complete tonsillectomy for primary tonsil DLBCL with the following features: short disease course, morphologically early lesions, negativity for Epstein-Barr virus-encoded RNA and t(14;18) translocation, and no involvement of any other sites, after careful clinical evaluation.


Subject(s)
Lymphoma, Large B-Cell, Diffuse/pathology , Survivors , Tonsillar Neoplasms/pathology , Adolescent , Adult , Biomarkers, Tumor/analysis , Biomarkers, Tumor/genetics , Biopsy , Child , Chromosomes, Human, Pair 14 , Chromosomes, Human, Pair 18 , Disease-Free Survival , Female , Herpesvirus 4, Human/genetics , Humans , Lymphoma, Large B-Cell, Diffuse/chemistry , Lymphoma, Large B-Cell, Diffuse/genetics , Lymphoma, Large B-Cell, Diffuse/surgery , Lymphoma, Large B-Cell, Diffuse/virology , Male , Molecular Diagnostic Techniques , Multimodal Imaging , Predictive Value of Tests , RNA, Viral/genetics , Retrospective Studies , Risk Factors , Survival Analysis , Time Factors , Tonsillar Neoplasms/chemistry , Tonsillar Neoplasms/genetics , Tonsillar Neoplasms/surgery , Tonsillar Neoplasms/virology , Tonsillectomy , Translocation, Genetic , Young Adult
17.
Biomacromolecules ; 15(8): 3019-29, 2014 Aug 11.
Article in English | MEDLINE | ID: mdl-24964130

ABSTRACT

Degradation of fibrillar collagen is critical for tissue maintenance. Yet, understanding collagen catabolism has been challenging partly due to a lack of atomistic picture for its load-dependent conformational dynamics, as both mechanical load and local unfolding of collagen affect its cleavage by matrix metalloproteinase (MMP). We use molecular dynamics simulation to find the most cleavage-prone arrangement of α chains in a collagen triple helix and find amino acids that modulate stability of the MMP cleavage domain depending on the chain registry within the molecule. The native-like state is mechanically inhomogeneous, where the cleavage site interfaces a stiff region and a locally unfolded and flexible region along the molecule. In contrast, a triple helix made of the stable glycine-proline-hydroxyproline motif is uniformly flexible and is dynamically stabilized by short-lived, low-occupancy hydrogen bonds. These results provide an atomistic basis for the mechanics, conformation, and stability of collagen that affect catabolism.


Subject(s)
Collagen/chemistry , Protein Conformation , Humans , Hydrogen Bonding , Matrix Metalloproteinases/chemistry , Models, Theoretical , Molecular Dynamics Simulation , Proline/chemistry
19.
Sheng Wu Yi Xue Gong Cheng Xue Za Zhi ; 27(2): 429-34, 2010 Apr.
Article in Chinese | MEDLINE | ID: mdl-20481333

ABSTRACT

The implantation of endovascular stents is currently one of the main treatments for cardiovascular occlusion diseases. However, the problem of arterial restenosis after implantation has not been completely solved. It has been well documented that the disturbed local blood flow and abnormal flow environment due to the deployment of the stent is one of the major causes of restenosis. Based on the principle of swirling flow in the arterial system, in this research, a spiral flow guider for endovascular stent was proposed to induce the blood flow in the stent to rotate. Then a computational fluid dynamics (CFD) method was employed to optimize the design of the guider. The numerical simulation showed that the optimized guider could create sufficiently strong spiral flow that, we believe, can efficiently subdue the adverse disturbance to blood flow by the stent so that the arterial restenosis due to the stent implantation might be suppressed.


Subject(s)
Blood Flow Velocity/physiology , Blood Vessel Prosthesis , Coronary Restenosis/prevention & control , Prosthesis Design/methods , Stents/adverse effects , Arteries/physiopathology , Humans , Pulsatile Flow , Shear Strength
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