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1.
Colorectal Dis ; 26(4): 660-668, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38345176

ABSTRACT

AIM: The optimum surgical approach to splenic flexure cancers (SFCs) remains uncertain. The aim of this survey was to explore the opinions of an international surgical community on the management and outcomes of SFC. METHOD: A questionnaire was constructed comprising five sections (information about respondents; definition and prognosis of SFC; operative approach; approach in specific scenarios; outcomes) and circulated through an international dissemination committee and social media. RESULTS: The survey received 576 responses over 4 weeks across 50 countries. There was no consensus regarding the definition of the splenic flexure, whilst the proportion of respondents who did and did not think that patients with SFC had a worse outcome was equal. The overall preferred operative approach was left hemicolectomy [203 (35.2%)], followed by segmental resection [167 (29%)], extended right hemicolectomy [126 (21.9%)] and subtotal colectomy [7 (12%)]. The stated pedicles for ligation varied between resection types and also within the same resection. One hundred and sixty-six (28.8%) respondents thought a segmental resection was associated with the worst survival and 190 (33%) thought it was associated with the best quality of life. CONCLUSION: This survey confirms a lack of consensus across all aspects SFC treatment. The differing approaches described are likely to represent different beliefs around the variable anatomy of this region and the associated lymphatic drainage. Future studies are required to address such inconsistencies and identify the optimum surgical strategy, whilst also incorporating quality-of-life metrics and patient-reported outcomes. A one-size-fits-all approach is probably not appropriate with SFC, and a more bespoke approach is required.


Subject(s)
Colectomy , Colon, Transverse , Colorectal Neoplasms , Humans , Colectomy/methods , Colon, Transverse/surgery , Surveys and Questionnaires , Colorectal Neoplasms/surgery , Colorectal Neoplasms/pathology , Male , Female , Treatment Outcome , Middle Aged , Prognosis , Aged
2.
Med Phys ; 50(10): 5935-5943, 2023 Oct.
Article in English | MEDLINE | ID: mdl-37665729

ABSTRACT

BACKGROUND: For trans-rectal ultrasound (TRUS)-based high dose rate (HDR) prostate brachytherapy, prostate contouring can be challenging due to artifacts from implanted needles, bleeding, and calcifications. PURPOSE: To evaluate the geometric accuracy and observer preference of an artificial intelligence (AI) algorithm for generating prostate contours on TRUS images with implanted needles. METHODS: We conducted a retrospective study of 150 patients, who underwent HDR brachytherapy. These patients were randomly divided into training (104), validation (26) and testing (20) sets. An AI algorithm was trained/validated utilizing the TRUS image and reference (clinical) contours. The algorithm then provided contours for the test set. For evaluation, we calculated the Dice coefficient between AI and reference prostate contours. We then presented AI and reference contours to eight clinician observers, and asked observers to select their preference. Observers were blinded to the source of contours. We calculated the percentage of cases in which observers preferred AI contours. Lastly, we evaluate whether the presence of AI contours improved the geometric accuracy of prostate contours provided by five resident observers for a 10-patient subset. RESULTS: The median Dice coefficient between AI and reference contours was 0.92 (IQR: 0.90-0.94). Observers preferred AI contours for a median of 57.5% (IQR: 47.5, 65.0) of the test cases. For resident observers, the presence of AI contours was associated with a 0.107 (95% CI: 0.086, 0.128; p < 0.001) improvement in Dice coefficient for the 10-patient subset. CONCLUSION: The AI algorithm provided high-quality prostate contours on TRUS with implanted needles. Further prospective study is needed to better understand how to incorporate AI prostate contours into the TRUS-based HDR brachytherapy workflow.

3.
Front Oncol ; 13: 1135400, 2023.
Article in English | MEDLINE | ID: mdl-37746299

ABSTRACT

Introduction: Approximately 1.6 million people in the US identify as transgender, many of whom undergo gender-affirming medical or surgical therapies. While transgender individuals are diagnosed with cancer at similar rates as those who are cisgender, the impacts of radiation therapy on outcomes of gender-affirming care in transgender, nonbinary, and gender-expansive people with cancer are understudied. We report on the experiences and outcomes of transgender and gender-expansive patients receiving radiation therapy for cancer treatment. Methods: This study is a multi-institutional retrospective review of patients evaluated from 2005-2019 identified as transgender or gender-expansive in the medical record and treated with radiation therapy. Results: We identified 23 patients who received radiation to 32 sites, including 12 (38%) to the brain, head, or neck, 8 (25%) to the thorax, and 7 (22%) to the pelvis. Seventeen patients (74%) received gender-affirming hormone therapy and 13 patients (57%) underwent gender-affirming surgery. Four patients had pelvic radiation before or after gender-affirming pelvic surgery, including two trans women who had pelvic radiation after vaginoplasty. Four patients had radiation to the chest or thorax and gender-affirming chest or breast surgery, including two trans men with breast cancer. Two pediatric patients developed hypopituitarism and hypogonadism secondary to radiation therapy and, as adults, changed their hormone replacement therapy to affirm their transgender identities. Discussion: Transgender people with cancer undergo radiation therapy for a wide range of cancers. Understanding their prior gender-affirming medical or surgical treatments and future gender affirmation goals may identify important considerations for their oncologic care.

4.
Pituitary ; 26(4): 510-520, 2023 Aug.
Article in English | MEDLINE | ID: mdl-37477853

ABSTRACT

PURPOSE: The quality of life (QoL) impact of multidisciplinary treatment for patients with nonfunctioning pituitary macroadenomas (NFPMA) is unclear. We sought to investigate associations between patient factors, clinical data, and patient-reported QoL in patients with NFPMA. METHODS: Patients with treated NFPMA and > 1 year of follow up after transsphenoidal surgery (TSS) and with no evidence of progressive disease were evaluated utilizing the following patient-reported outcome measures: RAND-36-Item Health Survey, Multidimensional Fatigue Inventory, Cognitive Failures Questionnaire. RESULTS: 229 eligible patients completed QoL questionnaires a median of 7.7 years after initial transsphenoidal surgery (TSS). 25% of participants received radiation therapy (RT) a median of 2.0 years (0.1-22.5) after initial TSS. Patients who received RT were younger (median age 46 v 58, p < 0.0001), had larger tumors (28 mm v 22 mm, p < 0.0001), were more likely to have visual symptoms (65% v 34%, p = 0.0002), and were more likely to have hypopituitarism (93% v 62%, p < 0.0001). Patients with hypopituitarism reported worse energy and fatigue and cognitive function (p < 0.03). Patients who received RT reported significantly worse general health, physical health, physical fatigue and cognitive functioning (p < 0.05). The largest QoL differences were in patients who experienced a financial stressor, independent of treatment type. CONCLUSION: Hypopituitarism, radiation therapy after TSS, and financial stressors are associated with more impaired QoL in patients with NFPMA. Awareness of these factors can better guide use and timing of radiation therapy in addition to identifying patients who can benefit from multidisciplinary surveillance.


Subject(s)
Hypopituitarism , Pituitary Neoplasms , Humans , Middle Aged , Quality of Life , Pituitary Neoplasms/radiotherapy , Pituitary Neoplasms/surgery , Surveys and Questionnaires , Hypopituitarism/diagnosis , Fatigue , Treatment Outcome
5.
Int J Radiat Oncol Biol Phys ; 117(2): 301-311, 2023 10 01.
Article in English | MEDLINE | ID: mdl-37230432

ABSTRACT

Access to gender-affirming surgery is increasing for many transgender and nonbinary people in the United States, and radiation oncologists must be equipped to care for patients who have undergone such surgery in the region of their planned radiation treatment field. There are no guidelines for radiation treatment planning after gender-affirming surgery, and most oncologists do not receive training in the unique needs of transgender people with cancer. We review common gender-affirming genitopelvic surgeries for transfeminine people, including vaginoplasty, labiaplasty, and orchiectomy, and summarize the existing literature on the treatment of cancers of the neovagina, anus, rectum, prostate, and bladder in these patients. We also describe our systematic treatment approach and rationale for pelvic radiation treatment planning.


Subject(s)
Neoplasms , Sex Reassignment Surgery , Transgender Persons , Male , Female , Humans , Radiation Oncologists , Vagina , Anal Canal , Neoplasms/surgery
6.
Gynecol Oncol ; 164(1): 27-33, 2022 01.
Article in English | MEDLINE | ID: mdl-34785030

ABSTRACT

OBJECTIVES: To identify patient factors associated with not receiving a recommendation for adjuvant chemotherapy after primary surgery for ovarian cancer. METHODS: This retrospective cohort study used the National Cancer Database (NCDB) data from 2004 to 2015 to identify patients with stage II-III ovarian cancer who underwent primary surgery. Multivariate logistic regression analyses evaluated factors associated with notation in the NCDB that "chemotherapy was not recommended/administered because it was contraindicated due to patient risk factors (i.e., comorbid conditions, advanced age)." Survival data were assessed via Kaplan-Meier analyses. RESULTS: Of the 48,245 patients who met the inclusion criteria, 522 (1.08%) did not receive adjuvant chemotherapy because it was determined to be contraindicated. In multivariate analyses, independent predictors for not receiving a recommendation for adjuvant chemotherapy were age ≥ 70 years old (adjusted odds ratio, aOR = 2.43, p < 0.0001), non-zero Charlson-Deyo comorbidity scores (score 1, aOR = 1.41, p = 0.002; score ≥ 2, aOR = 2.57, p < 0.0001), and Black race (aOR = 2.12, p < 0.0001). For Black patients, recommendation against adjuvant chemotherapy occurred at a younger median age (64.5 years vs. 72 years) and was associated with lower 5-year survival (25.9% vs. 40.3%, p < 0.0001). CONCLUSIONS: Patients with ovarian cancer who underwent surgery but did not receive chemotherapy "because it was contraindicated due to patient risk factors" were older and had higher comorbidity scores. Even after controlling for these differences, Black patients were disproportionately not recommended for chemotherapy, which was associated with worse survival. Determining eligibility for adjuvant chemotherapy requires an individualized approach, and the possible influence of racial bias on risk estimation should be further investigated.


Subject(s)
Antineoplastic Agents/therapeutic use , Chemotherapy, Adjuvant , Healthcare Disparities , Outcome Assessment, Health Care , Ovarian Neoplasms/drug therapy , Adult , Aged , Antineoplastic Agents/administration & dosage , Databases, Factual , Ethnicity , Female , Humans , Kaplan-Meier Estimate , Middle Aged , Neoplasm Staging , Ovarian Neoplasms/ethnology , Ovarian Neoplasms/mortality , Ovarian Neoplasms/pathology , United States
7.
Sci Rep ; 10(1): 918, 2020 01 22.
Article in English | MEDLINE | ID: mdl-31969604

ABSTRACT

Brain penetrant microtubule stabilising agents (MSAs) are being increasingly validated as potential therapeutic strategies for neurodegenerative diseases and traumatic injuries of the nervous system. MSAs are historically used to treat malignancies to great effect. However, this treatment strategy can also cause adverse off-target impacts, such as the generation of debilitating neuropathy and axonal loss. Understanding of the effects that individual MSAs have on neurons of the central nervous system is still incomplete. Previous research has revealed that aberrant microtubule stabilisation can perturb many neuronal functions, such as neuronal polarity, neurite outgrowth, microtubule dependant transport and overall neuronal viability. In the current study, we evaluate the dose dependant impact of epothilone D, a brain penetrant MSA, on both immature and relatively mature mouse cortical neurons in vitro. We show that epothilone D reduces the viability, growth and complexity of immature cortical neurons in a dose dependant manner. Furthermore, in relatively mature cortical neurons, we demonstrate that while cellularly lethal doses of epothilone D cause cellular demise, low sub lethal doses can also affect mitochondrial transport over time. Our results reveal an underappreciated mitochondrial disruption over a wide range of epothilone D doses and reiterate the importance of understanding the dosage, timing and intended outcome of MSAs, with particular emphasis on brain penetrant MSAs being considered to target neurons in disease and trauma.


Subject(s)
Cell Survival/drug effects , Cerebral Cortex/cytology , Epothilones/adverse effects , Microtubules/drug effects , Neuronal Outgrowth/drug effects , Neurons/cytology , Neurons/drug effects , Animals , Cells, Cultured , Dose-Response Relationship, Drug , Epothilones/administration & dosage , In Vitro Techniques , Mice, Inbred C57BL , Mice, Transgenic , Microtubules/physiology , Mitochondria/metabolism , Molecular Targeted Therapy , Neurodegenerative Diseases/drug therapy , Neurodegenerative Diseases/etiology , Neurons/physiology
8.
Nat Commun ; 10(1): 5485, 2019 12 02.
Article in English | MEDLINE | ID: mdl-31792208

ABSTRACT

Band inversions are key to stabilising a variety of novel electronic states in solids, from topological surface states to the formation of symmetry-protected three-dimensional Dirac and Weyl points and nodal-line semimetals. Here, we create a band inversion not of bulk states, but rather between manifolds of surface states. We realise this by aliovalent substitution of Nb for Zr and Sb for S in the ZrSiS family of nonsymmorphic semimetals. Using angle-resolved photoemission and density-functional theory, we show how two pairs of surface states, known from ZrSiS, are driven to intersect each other near the Fermi level in NbGeSb, and to develop pronounced spin splittings. We demonstrate how mirror symmetry leads to protected crossing points in the resulting spin-orbital entangled surface band structure, thereby stabilising surface state analogues of three-dimensional Weyl points. More generally, our observations suggest new opportunities for engineering topologically and symmetry-protected states via band inversions of surface states.

9.
IUCrJ ; 5(Pt 6): 681-698, 2018 Nov 01.
Article in English | MEDLINE | ID: mdl-30443353

ABSTRACT

Hexaferrites are an important class of magnetic oxides with applications in data storage and electronics. Their crystal structures are highly modular, consisting of Fe- or Ba-rich close-packed blocks that can be stacked in different sequences to form a multitude of unique structures, producing large anisotropic unit cells with lattice parameters typically >100 Šalong the stacking axis. This has limited atomic-resolution structure solutions to relatively simple examples such as Ba2Zn2Fe12O22, whilst longer stacking sequences have been modelled only in terms of block sequences, with no refinement of individual atomic coordinates or occupancies. This paper describes the growth of a series of complex hexaferrite crystals, their atomic-level structure solution by high-resolution synchrotron X-ray diffraction, electron diffraction and imaging methods, and their physical characterization by magnetometry. The structures include a new hexaferrite stacking sequence, with the longest lattice parameter of any hexaferrite with a fully determined structure.

10.
Nature ; 546(7657): 280-284, 2017 06 07.
Article in English | MEDLINE | ID: mdl-28593963

ABSTRACT

The discovery of new materials is hampered by the lack of efficient approaches to the exploration of both the large number of possible elemental compositions for such materials, and of the candidate structures at each composition. For example, the discovery of inorganic extended solid structures has relied on knowledge of crystal chemistry coupled with time-consuming materials synthesis with systematically varied elemental ratios. Computational methods have been developed to guide synthesis by predicting structures at specific compositions and predicting compositions for known crystal structures, with notable successes. However, the challenge of finding qualitatively new, experimentally realizable compounds, with crystal structures where the unit cell and the atom positions within it differ from known structures, remains for compositionally complex systems. Many valuable properties arise from substitution into known crystal structures, but materials discovery using this approach alone risks both missing best-in-class performance and attempting design with incomplete knowledge. Here we report the experimental discovery of two structure types by computational identification of the region of a complex inorganic phase field that contains them. This is achieved by computing probe structures that capture the chemical and structural diversity of the system and whose energies can be ranked against combinations of currently known materials. Subsequent experimental exploration of the lowest-energy regions of the computed phase diagram affords two materials with previously unreported crystal structures featuring unusual structural motifs. This approach will accelerate the systematic discovery of new materials in complex compositional spaces by efficiently guiding synthesis and enhancing the predictive power of the computational tools through expansion of the knowledge base underpinning them.

11.
Nat Chem ; 9(7): 644-652, 2017 07.
Article in English | MEDLINE | ID: mdl-28644481

ABSTRACT

Alkali metal intercalation into polyaromatic hydrocarbons (PAHs) has been studied intensely after reports of superconductivity in a number of potassium- and rubidium-intercalated materials. There are, however, no reported crystal structures to inform our understanding of the chemistry and physics because of the complex reactivity of PAHs with strong reducing agents at high temperature. Here we present the synthesis of crystalline K2Pentacene and K2Picene by a solid-solid insertion protocol that uses potassium hydride as a redox-controlled reducing agent to access the PAH dianions, and so enables the determination of their crystal structures. In both cases, the inserted cations expand the parent herringbone packings by reorienting the molecular anions to create multiple potassium sites within initially dense molecular layers, and thus interact with the PAH anion π systems. The synthetic and crystal chemistry of alkali metal intercalation into PAHs differs from that into fullerenes and graphite, in which the cation sites are pre-defined by the host structure.

12.
J Med Entomol ; 54(4): 1055-1060, 2017 07 01.
Article in English | MEDLINE | ID: mdl-28399208

ABSTRACT

Measuring rates of acquisition of the Lyme disease pathogen, Borrelia burgdorferi sensu lato Johnson, Schmid, Hyde, Steigerwalt & Brenner, by the larval stage of Ixodes scapularis Say is a useful tool for xenodiagnoses of B. burgdorferi in vertebrate hosts. In the nymphal and adult stages of I. scapularis, the duration of attachment to hosts has been shown to predict both body engorgement during blood feeding and the timing of infection with B. burgdorferi. However, these relationships have not been established for the larval stage of I. scapularis. We sought to establish the relationship between body size during engorgement of larval I. scapularis placed on B. burgdorferi-infected, white-footed mice (Peromyscus leucopus Rafinesque) and the presence or absence of infection in larvae sampled from hosts over time. Body size, time, and their interaction were the best predictors of larval infection with B. burgdorferi. We found that infected larvae showed significantly greater engorgement than uninfected larvae as early as 24 h after placement on a host. These findings may suggest that infection with B. burgdorferi affects the larval feeding process. Alternatively, larvae that engorge more rapidly on hosts may acquire infections faster. Knowledge of these relationships can be applied to improve effective xenodiagnosis of B. burgdorferi in white-footed mice. Further, these findings shed light on vector-pathogen-host interactions during an understudied part of the Lyme disease transmission cycle.


Subject(s)
Borrelia burgdorferi/physiology , Ixodes/microbiology , Ixodes/physiology , Lyme Disease/veterinary , Peromyscus , Rodent Diseases/transmission , Animals , Body Size , Feeding Behavior , Host-Parasite Interactions , Ixodes/growth & development , Larva/growth & development , Larva/microbiology , Larva/physiology , Lyme Disease/microbiology , Lyme Disease/transmission , Nymph/growth & development , Nymph/microbiology , Nymph/physiology , Rodent Diseases/microbiology , Time Factors
13.
J Thromb Haemost ; 15(2): 375-387, 2017 02.
Article in English | MEDLINE | ID: mdl-27925685

ABSTRACT

Essentials Platelet transfusion suffers from availability, portability, contamination, and short shelf-life. SynthoPlate™ (synthetic platelet technology) can resolve platelet transfusion limitations. SynthoPlate™ does not activate resting platelets or stimulate coagulation systemically. SynthoPlate™ significantly improves hemostasis in thrombocytopenic mice dose-dependently. SUMMARY: Background Platelet transfusion applications face severe challenges, owing to the limited availability and portability, high risk of contamination and short shelf-life of platelets. Therefore, there is significant interest in synthetic platelet substitutes that can provide hemostasis while avoiding these issues. Platelets promote hemostasis by injury site-selective adhesion and aggregation, and propagation of coagulation reactions on their membranes. On the basis of these mechanisms, we have developed a synthetic platelet technology (SynthoPlate™) that integrates platelet-mimetic site-selective 'adhesion' and 'aggregation' functionalities via heteromultivalent surface decoration of lipid vesicles with von Willebrand factor-binding, collagen-binding and active platelet integrin glycoprotein (GP) IIb-IIIa-binding peptides. Objective To evaluate SynthoPlate for its effects on platelets and plasma in vitro, and for systemic safety and hemostatic efficacy in severely thrombocytopenic mice in vivo. Methods In vitro, SynthoPlate was evaluated with aggregometry, fluorescence microscopy, microfluidics, and thrombin and fibrin generation assays. In vivo, SynthoPlate was evaluated for systemic safety with prothrombin and fibrin assays on plasma, and for hemostatic effects on tail-transection bleeding time in severely thrombocytopenic (TCP) mice. Results SynthoPlate did not aggregate resting platelets or spontaneously promote coagulation in plasma, but could amplify the recruitment and aggregation of active platelets at the bleeding site, and thereby site-selectively enhance fibrin generation. SynthoPlate dose-dependently reduced bleeding time in TCP mice, to levels comparable to those in normal mice. SynthoPlate has a reasonable circulation residence time, and is cleared mostly by the liver and spleen. Conclusion The results demonstrate the promise of SynthoPlate as a synthetic platelet substitute in transfusion treatment of platelet-related bleeding complications.


Subject(s)
Blood Platelets/cytology , Blood Substitutes , Platelet Adhesiveness , Thrombocytopenia/therapy , Animals , Bleeding Time , Blood Coagulation , Hemorrhage , Hemostasis , Humans , Light , Mice , Microfluidics , Microscopy, Electron, Scanning , Microscopy, Fluorescence , Platelet Transfusion , Scattering, Radiation , Thrombin/metabolism
15.
Cell Death Dis ; 7(6): e2249, 2016 06 02.
Article in English | MEDLINE | ID: mdl-27253413

ABSTRACT

We have used polysome profiling coupled to microarray analysis to examine the translatome of a panel of peripheral blood (PB) B cells isolated from 34 chronic lymphocytic leukaemia (CLL) patients. We have identified a 'ribosome-related' signature in CLL patients with mRNAs encoding for ribosomal proteins and factors that modify ribosomal RNA, e.g. DKC1 (which encodes dyskerin, a pseudouridine synthase), showing reduced polysomal association and decreased expression of the corresponding proteins. Our data suggest a general impact of dyskerin dysregulation on the translational apparatus in CLL and importantly patients with low dyskerin levels have a significantly shorter period of overall survival following treatment. Thus, translational dysregulation of dyskerin could constitute a mechanism by which the CLL PB B cells acquire an aggressive phenotype and thus have a major role in oncogenesis.


Subject(s)
Gene Expression Profiling , Leukemia, Lymphocytic, Chronic, B-Cell/blood , Leukemia, Lymphocytic, Chronic, B-Cell/genetics , Ribosomes/metabolism , Cell Cycle Proteins/genetics , Cell Cycle Proteins/metabolism , Cell Nucleolus/metabolism , Down-Regulation/genetics , Eukaryotic Initiation Factors/genetics , Eukaryotic Initiation Factors/metabolism , Gene Expression Regulation, Leukemic , Humans , Immunoblotting , Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy , Leukemia, Lymphocytic, Chronic, B-Cell/pathology , Nuclear Proteins/genetics , Nuclear Proteins/metabolism , Polyribosomes/metabolism , Protein Biosynthesis , RNA, Ribosomal/metabolism , Ribosomal Proteins/genetics , Ribosomal Proteins/metabolism , Survival Analysis , Treatment Outcome
16.
Leukemia ; 30(11): 2179-2186, 2016 11.
Article in English | MEDLINE | ID: mdl-27282254

ABSTRACT

Histone methyltransferases (HMTs) are important epigenetic regulators of gene transcription and are disrupted at the genomic level in a spectrum of human tumours including haematological malignancies. Using high-resolution single nucleotide polymorphism (SNP) arrays, we identified recurrent deletions of the SETD2 locus in 3% (8/261) of chronic lymphocytic leukaemia (CLL) patients. Further validation in two independent cohorts showed that SETD2 deletions were associated with loss of TP53, genomic complexity and chromothripsis. With next-generation sequencing we detected mutations of SETD2 in an additional 3.8% of patients (23/602). In most cases, SETD2 deletions or mutations were often observed as a clonal event and always as a mono-allelic lesion, leading to reduced mRNA expression in SETD2-disrupted cases. Patients with SETD2 abnormalities and wild-type TP53 and ATM from five clinical trials employing chemotherapy or chemo-immunotherapy had reduced progression-free and overall survival compared with cases wild type for all three genes. Consistent with its postulated role as a tumour suppressor, our data highlight SETD2 aberration as a recurrent, early loss-of-function event in CLL pathobiology linked to aggressive disease.


Subject(s)
Genomics , Histone-Lysine N-Methyltransferase/genetics , Leukemia, Lymphocytic, Chronic, B-Cell/genetics , Mutation , Ataxia Telangiectasia Mutated Proteins/genetics , Disease-Free Survival , Female , Genes, Tumor Suppressor , Histone Methyltransferases , Humans , Leukemia, Lymphocytic, Chronic, B-Cell/enzymology , Leukemia, Lymphocytic, Chronic, B-Cell/mortality , Male , Prognosis , Survival Rate , Tumor Suppressor Protein p53/genetics
17.
J Chem Phys ; 142(10): 101916, 2015 Mar 14.
Article in English | MEDLINE | ID: mdl-25770505

ABSTRACT

Adsorption of thymine on a defined Cu(110) surface was studied using reflection-absorption infrared spectroscopy (RAIRS), temperature programmed desorption (TPD), and scanning tunnelling microscopy (STM). In addition, density functional theory (DFT) calculations were undertaken in order to further understand the energetics of adsorption and self-assembly. The combination of RAIRS, TPD, and DFT results indicates that an upright, three-point-bonded adsorption configuration is adopted by the deprotonated thymine at room temperature. DFT calculations show that the upright configuration adopted by individual molecules arises as a direct result of strong O-Cu and N-Cu bonds between the molecule and the surface. STM data reveal that this upright thymine motif self-assembles into 1D chains, which are surprisingly oriented along the open-packed [001] direction of the metal surface and orthogonal to the alignment of the functional groups that are normally implicated in H-bonding interactions. DFT modelling of this system reveals that the molecular organisation is actually driven by dispersion interactions, which cause a slight tilt of the molecule and provide the major driving force for assembly into dimers and 1D chains. The relative orientations and distances of neighbouring molecules are amenable for π-π stacking, suggesting that this is an important contributor in the self-assembly process.


Subject(s)
Copper/chemistry , Quantum Theory , Thymine/chemistry , Adsorption , Molecular Structure , Surface Properties , Vibration
18.
Oncogene ; 34(41): 5207-15, 2015 Oct 08.
Article in English | MEDLINE | ID: mdl-25639868

ABSTRACT

Pediatric solid tumors are remarkably diverse in their cellular origins, developmental timing and clinical features. Over the last 5 years, there have been significant advances in our understanding of the genetic lesions that contribute to the initiation and progression of pediatric solid tumors. To date, over 1000 pediatric solid tumors have been analyzed by Next-Generation Sequencing. These genomic data provide the foundation to launch new research efforts to address one of the fundamental questions in cancer biology-why are some cells more susceptible to malignant transformation by particular genetic lesions at discrete developmental stages than others? Because of their developmental, molecular, cellular and genetic diversity, pediatric solid tumors provide an ideal platform to begin to answer this question. In this review, we highlight the diversity of pediatric solid tumors and provide a new framework for studying the cellular and developmental origins of pediatric cancer. We also introduce a new unifying concept called cellular pliancy as a possible explanation for susceptibility to cancer and the developmental origins of pediatric solid tumors.


Subject(s)
Neoplasms/genetics , Child , Epigenesis, Genetic , Gene Expression Regulation, Neoplastic , Genes, Neoplasm , Genomics , Humans , Mutation , Neoplasms/pathology
19.
Leukemia ; 29(3): 598-605, 2015 Mar.
Article in English | MEDLINE | ID: mdl-25151957

ABSTRACT

Prospective identification of patients with chronic lymphocytic leukemia (CLL) destined to progress would greatly facilitate their clinical management. Recently, whole-genome DNA methylation analyses identified three clinicobiologic CLL subgroups with an epigenetic signature related to different normal B-cell counterparts. Here, we developed a clinically applicable method to identify these subgroups and to study their clinical relevance. Using a support vector machine approach, we built a prediction model using five epigenetic biomarkers that was able to classify CLL patients accurately into the three subgroups, namely naive B-cell-like, intermediate and memory B-cell-like CLL. DNA methylation was quantified by highly reproducible bisulfite pyrosequencing assays in two independent CLL series. In the initial series (n=211), the three subgroups showed differential levels of IGHV (immunoglobulin heavy-chain locus) mutation (P<0.001) and VH usage (P<0.03), as well as different clinical features and outcome in terms of time to first treatment (TTT) and overall survival (P<0.001). A multivariate Cox model showed that epigenetic classification was the strongest predictor of TTT (P<0.001) along with Binet stage (P<0.001). These findings were corroborated in a validation series (n=97). In this study, we developed a simple and robust method using epigenetic biomarkers to categorize CLLs into three subgroups with different clinicobiologic features and outcome.


Subject(s)
B-Lymphocytes/metabolism , Biomarkers, Tumor/genetics , Epigenesis, Genetic , Immunoglobulin Heavy Chains/genetics , Leukemia, Lymphocytic, Chronic, B-Cell/genetics , Transcriptome , Adult , Aged , Aged, 80 and over , Antineoplastic Agents/therapeutic use , B-Lymphocytes/classification , B-Lymphocytes/pathology , DNA Methylation , Disease Progression , Female , High-Throughput Nucleotide Sequencing , Humans , Leukemia, Lymphocytic, Chronic, B-Cell/classification , Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy , Leukemia, Lymphocytic, Chronic, B-Cell/mortality , Male , Middle Aged , Proportional Hazards Models , Support Vector Machine , Survival Analysis , Time-to-Treatment , Treatment Outcome
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