1
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Connecting the dots from let-7 to HIC2 to HBG. Blood 2024; 143:1886-1887. [PMID: 38722661 PMCID: PMC11103172 DOI: 10.1182/blood.2024024191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024] Open
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2
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Long noncoding RNA GATA2AS influences human erythropoiesis by transcription factor and chromatin landscape regulation. Blood 2024:blood.2023021287. [PMID: 38447046 DOI: 10.1182/blood.2023021287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 02/29/2024] [Accepted: 03/03/2024] [Indexed: 03/08/2024] Open
Abstract
LncRNAs are extensively expressed in eukaryotic cells and have been revealed to be important for regulating cell differentiation. Many lncRNAs have been found to regulate erythroid differentiation in the mouse. However, given the low sequence conservation of lncRNAs between mouse and human, our understanding of lncRNAs in human erythroid differentiation remains incomplete. LncRNAs are often transcribed opposite to protein coding genes and regulate their expression. Here we characterized a human erythrocyte-expressed lncRNA, GATA2AS, which is transcribed opposite to erythroid transcription regulator GATA2. GATA2AS is a 2080 bp-long, primarily nuclear-localized non-coding RNA that is expressed in erythroid progenitor cells and decreases during differentiation. Knockout of GATA2AS in human HUDEP2 erythroid progenitor cells using CRISPR-Cas9 genome editing to remove the transcription start site accelerated erythroid differentiation and dysregulated erythroblast gene expression. We identified GATA2AS as a novel GATA2 and HBG activator. Chromatin Isolation by RNA Purification (ChIRP) showed that GATA2AS binds to thousands of genomic sites and colocalizes at a subset of sites with erythroid transcription factors including LRF and KLF1. RNA-pulldown and RIP confirmed interaction between GATA2AS and LRF and KLF1. ChIP-sequencing showed that knockout of GATA2AS reduces binding of these transcription factors genome wide. ATAC-seq and H3K27ac ChIP-seq showed that GATA2AS is essential to maintain the chromatin regulatory landscape during erythroid differentiation. Knockdown of GATA2AS in human primary CD34+ cells mimicked results in HUDEP2 cells. Overall, our results implicate human-specific lncRNA GATA2AS as a regulator of erythroid differentiation by influencing erythroid transcription factor binding and the chromatin regulatory landscape.
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Noncoding function of super enhancer derived mRNA in modulating neighboring gene expression and TAD interaction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.05.570115. [PMID: 38105946 PMCID: PMC10723268 DOI: 10.1101/2023.12.05.570115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Super enhancers are important regulators of gene expression that often overlap with protein-coding genes. However, it is unclear whether the overlapping protein-coding genes and the mRNA derived from them contribute to enhancer activity. Using an erythroid-specific super enhancer that overlaps the Cpox gene as a model, we found that Cpox mRNA has a non-coding function in regulating neighboring protein-coding genes, eRNA expression and TAD interactions. Depletion of Cpox mRNA leads to accumulation of H3K27me3 and release of p300 from the Cpox locus, activating an intra-TAD enhancer and gene expression. Additionally, we identified a head-to-tail interaction between the TAD boundary genes Cpox and Dcbld2 that is facilitated by a novel type of repressive loop anchored by p300 and PRC2/H3K27me3. Our results uncover a regulatory role for mRNA transcribed within a super enhancer context and provide insight into head-to-tail inter-gene interaction in the regulation of gene expression and oncogene activation.
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An enhancer RNA recruits MLL1 to regulate transcription of Myb. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.26.559528. [PMID: 37808852 PMCID: PMC10557664 DOI: 10.1101/2023.09.26.559528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The Myb proto-oncogene encodes the transcription factor c-MYB, which is critical for hematopoiesis. Distant enhancers of Myb form a hub of interactions with the Myb promoter. We identified a long non-coding RNA (Myrlin) originating from the -81 kb murine Myb enhancer. Myrlin and Myb are coordinately regulated during erythroid differentiation. Myrlin TSS deletion using CRISPR/Cas9 reduced Myrlin and Myb expression and LDB1 complex occupancy at the Myb enhancers, compromising enhancer contacts and reducing RNA Pol II occupancy in the locus. In contrast, CRISPRi silencing of Myrlin left LDB1 and the Myb enhancer hub unperturbed, although Myrlin and Myb expression were downregulated, decoupling transcription and chromatin looping. Myrlin interacts with the MLL1 complex. Myrlin CRISPRi compromised MLL1 occupancy in the Myb locus, decreasing CDK9 and RNA Pol II binding and resulting in Pol II pausing in the Myb first exon/intron. Thus, Myrlin directly participates in activating Myb transcription by recruiting MLL1.
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5
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Help on the way to unsilence HbF. Blood 2023; 141:2670-2672. [PMID: 37261855 DOI: 10.1182/blood.20(23)020345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023] Open
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6
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Help on the way to unsilence HbF. Blood 2023; 141:2670-2672. [PMID: 37530647 PMCID: PMC10273155 DOI: 10.1182/blood.2023020345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023] Open
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7
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Enhancer looping protein LDB1 regulates hepatocyte gene expression by cooperating with liver transcription factors. Nucleic Acids Res 2022; 50:9195-9211. [PMID: 36018801 PMCID: PMC9458430 DOI: 10.1093/nar/gkac707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/22/2022] [Indexed: 12/24/2022] Open
Abstract
Enhancers establish proximity with distant target genes to regulate temporospatial gene expression and specify cell identity. Lim domain binding protein 1 (LDB1) is a conserved and widely expressed protein that functions as an enhancer looping factor. Previous studies in erythroid cells and neuronal cells showed that LDB1 forms protein complexes with different transcription factors to regulate cell-specific gene expression. Here, we show that LDB1 regulates expression of liver genes by occupying enhancer elements and cooperating with hepatic transcription factors HNF4A, FOXA1, TCF7 and GATA4. Using the glucose transporter SLC2A2 gene, encoding GLUT2, as an example, we find that LDB1 regulates gene expression by mediating enhancer-promoter interactions. In vivo, we find that LDB1 deficiency in primary mouse hepatocytes dysregulates metabolic gene expression and changes the enhancer landscape. Conditional deletion of LDB1 in adult mouse liver induces glucose intolerance. However, Ldb1 knockout hepatocytes show improved liver pathology under high-fat diet conditions associated with increased expression of genes related to liver fatty acid metabolic processes. Thus, LDB1 is linked to liver metabolic functions under normal and obesogenic conditions.
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User involvement throughout development of technology to support diabetes foot care: a case illustration of the devices for dignity PPIE model. J Med Eng Technol 2022; 46:558-566. [PMID: 36062509 DOI: 10.1080/03091902.2022.2089259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The successful development and implementation of any healthcare technology requires input from multiple stakeholders including clinical leads, trust information technology directorates as well as project management and procurement. In this process however, a key stakeholder that is often overlooked is the patient.This paper illustrates the crucial importance of patient involvement to avoid poor design and poor uptake of technology and subsequently poor health outcomes.To highlight this, we share a case example evidencing involvement of people with lived experience of foot ulcers resulting from Diabetic foot neuropathy throughout identification of unmet technology needs, design requirements for the device and iterative device development and evaluation.
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P.25 Improving antenatal anaesthetic assessment and dissemination of information to parturients with a high body mass index. Int J Obstet Anesth 2021. [DOI: 10.1016/j.ijoa.2021.103023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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10
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P.37 “To PIE (B) or not to PIE (B)?” A prospective audit of patient controlled epidural analgesia (PCEA) efficacy for labour at a large tertiary centre. Int J Obstet Anesth 2021. [DOI: 10.1016/j.ijoa.2021.103035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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P.103 Programmed intermittent epidural bolus protocols: an international survey of programmes currently used. Int J Obstet Anesth 2021. [DOI: 10.1016/j.ijoa.2021.103101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Abstract
How transcriptional enhancers function to activate distant genes has been the subject of lively investigation for decades. "Enhancers, gene regulation, and genome organization" was the subject of a virtual meeting held November 16-17, 2020, under sponsorship of the National Cancer Institute (NCI), the National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), and the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) at the National Institutes of Health (NIH). The goal of the meeting was to advance an understanding of how transcriptional enhancers function within the framework of the folded genome as we understand it, emphasizing how levels of organization may influence each other and may contribute to the spatiotemporal specification of transcription. Here we focus on broad questions about enhancer function that remain unsettled and that we anticipate will be central to work in this field going forward. Perforce, we cover contributions of only some speakers and apologize to other contributors in vital areas that we could not include because of space constraints.
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A Zinc Finger Transcription Factor Faithfully Dedicated to Only a Single Target Gene in Erythroid Cells. Mol Cell 2021; 81:218-219. [PMID: 33482089 DOI: 10.1016/j.molcel.2020.12.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Lan et al. carry out a CRISPR-mediated genetic screen and discover that ZNF410 uniquely regulates the NuRD component CHD4 to repress γ-globin transcription in erythroid cells, establishing a novel fetal hemoglobin regulatory mechanism.
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Embryonic erythropoiesis and hemoglobin switching require transcriptional repressor ETO2 to modulate chromatin organization. Nucleic Acids Res 2020; 48:10226-10240. [PMID: 32960220 DOI: 10.1093/nar/gkaa736] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/19/2020] [Accepted: 09/18/2020] [Indexed: 11/14/2022] Open
Abstract
The underlying mechanism of transcriptional co-repressor ETO2 during early erythropoiesis and hemoglobin switching is unclear. We find that absence of ETO2 in mice interferes with down-regulation of PU.1 and GATA2 in the fetal liver, impeding a key step required for commitment to erythroid maturation. In human β-globin transgenic Eto2 null mice and in human CD34+ erythroid progenitor cells with reduced ETO2, loss of ETO2 results in ineffective silencing of embryonic/fetal globin gene expression, impeding hemoglobin switching during erythroid differentiation. ETO2 occupancy genome-wide occurs virtually exclusively at LDB1-complex binding sites in enhancers and ETO2 loss leads to increased enhancer activity and expression of target genes. ETO2 recruits the NuRD nucleosome remodeling and deacetylation complex to regulate histone acetylation and nucleosome occupancy in the β-globin locus control region and γ-globin gene. Loss of ETO2 elevates LDB1, MED1 and Pol II in the locus and facilitates fetal γ-globin/LCR looping and γ-globin transcription. Absence of the ETO2 hydrophobic heptad repeat region impairs ETO2-NuRD interaction and function in antagonizing γ-globin/LCR looping. Our results reveal a pivotal role for ETO2 in erythropoiesis and globin gene switching through its repressive role in the LDB1 complex, affecting the transcription factor and epigenetic environment and ultimately restructuring chromatin organization.
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191P First-line liposomal irinotecan + 5 fluorouracil/leucovorin + oxaliplatin in patients with pancreatic ductal adenocarcinoma: Results from a phase I/II study. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.10.455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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16
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805O ICON8: Overall survival results in a GCIG phase III randomised controlled trial of weekly dose-dense chemotherapy in first line epithelial ovarian, fallopian tube or primary peritoneal carcinoma treatment. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.08.944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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17
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821P Timing of adverse events during maintenance treatment with rucaparib for recurrent ovarian cancer in the phase III ARIEL3 study. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.08.960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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18
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P-256 Survival rates of locally advanced and metastatic pancreatic cancer in Western Australia. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.04.338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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19
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P-249 Resecting the unresectable: Superior survival of tri-modality pancreatic adenocarcinoma patients. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.04.331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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20
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LBA-1 First-line liposomal irinotecan + 5 fluorouracil/leucovorin + oxaliplatin in patients with pancreatic ductal adenocarcinoma: Long-term follow-up results from a phase 1/2 study. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.04.076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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21
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Custom design for special needs client. JOURNAL OF VISUAL IMPAIRMENT & BLINDNESS 2020. [DOI: 10.1177/0145482x8908300704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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22
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1209 Effect Of Wearables On Sleep In Healthy Individuals: A Randomized Cross-over Trial And Validation Study. Sleep 2020. [DOI: 10.1093/sleep/zsaa056.1203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Introduction
To determine whether a wearable sleep-tracker improves perceived sleep quality in healthy subjects. To test whether wearables reliably measure sleep quantity and quality compared to polysomnography.
Methods
A single-center randomized cross-over trial of community-based participants without medical conditions or sleep disorders. Wearable device (WHOOP, Inc.) that provided feedback regarding sleep information to the participant for 1-week and maintaining sleep logs versus 1-week of maintaining sleep logs alone. Self-reported daily sleep behaviors were documented in sleep logs. Polysomnography was performed on one night when wearing the wearable. PROMIS Sleep disturbance sleep scale was measured at baseline, 7, and 14 days of study participation.
Results
In 32 participants (21 women; 23.8 + 5 years), wearables improved nighttime sleep quality (PROMIS sleep disturbance; B= -1.69; 95% Confidence Interval -3.11, -0.27; P=0.021) after adjusting for age, sex, baseline, and order effect. There was a small increase in self-reported daytime naps when wearing the device (B = 3.2; SE 1.4; P=0.023) but total daily sleep remained unchanged (P=0.43). The wearable had low bias (2.5 minutes) and low precision (5.6 minutes) errors for measuring sleep duration and measured dream sleep and slow wave sleep accurately (Intra-class coefficient 0.74 + 0.28 and 0.85 + 0.15, respectively). Bias and precision error for heart rate (bias -0.17%; precision 1.5%) and respiratory rate (bias 1.8%’ precision 6.7%) were very low when compared to that measured by electrocardiogram and inductance plethysmography during polysomnography.
Conclusion
In healthy people, wearables can improve sleep quality and accurately measure sleep and cardiorespiratory variables.
Support
WHOOP Inc.
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The mRNA-Binding Protein IGF2BP1 Restores Fetal Hemoglobin in Cultured Erythroid Cells from Patients with β-Hemoglobin Disorders. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 17:429-440. [PMID: 32154328 PMCID: PMC7056608 DOI: 10.1016/j.omtm.2020.01.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 01/22/2020] [Indexed: 12/12/2022]
Abstract
Sickle cell disease (SCD) and β-thalassemia are caused by structural abnormality or inadequate production of adult hemoglobin (HbA, α2β2), respectively. Individuals with either disorder are asymptomatic before birth because fetal hemoglobin (HbF, α2γ2) is unaffected. Thus, reversal of the switch from HbF to HbA could reduce or even prevent symptoms these disorders. In this study, we show that insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) is one factor that could accomplish this goal. IGF2BP1 is a fetal factor that undergoes a transcriptional switch consistent with the transition from HbF to HbA. Lentivirus delivery of IGF2BP1 to CD34+ cells of healthy adult donors reversed hemoglobin production toward the fetal type in culture-differentiated erythroid cells. Analogous studies using patient-derived CD34+ cells revealed that IGF2BP1-dependent HbF induction could ameliorate the chain imbalance in β-thalassemia or potently suppress expression of sickle β-globin in SCD. In all cases, fetal γ-globin mRNA increased and adult β-globin decreased due, in part, to formation of contacts between the locus control region (LCR) and γ-globin genes. We conclude that expression of IGF2BP1 in adult erythroid cells has the potential to maximize HbF expression in patients with severe β-hemoglobin disorders by reversing the developmental γ- to β-globin switch.
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24
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The tolerability and efficacy of FOLFIRINOX in gastro-oesophageal carcinoma. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz422.072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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25
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Durable response to second-line m-FOLFIRINOX for advanced pancreatic adenocarcinoma in patients with performance status of two or less. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz422.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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26
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The emerging role of third-line gemcitabine plus nab-paclitaxel in advanced pancreatic adenocarcinoma. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz422.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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27
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P.83Vacuolar myopathy with valosin containing protein (VCP)-positive intranuclear and cytoplasmic inclusions: report of two cases with early and late childhood-onset disease. Neuromuscul Disord 2019. [DOI: 10.1016/j.nmd.2019.06.112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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28
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Integrated population pharmacokinetic modelling of liposomal irinotecan in patients with various tumour types, including untreated metastatic pancreatic cancer (mPC). Ann Oncol 2019. [DOI: 10.1093/annonc/mdz247.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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29
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Effect of response to last platinum-based chemotherapy in patients (pts) with platinum-sensitive, recurrent ovarian carcinoma in the phase III study ARIEL3 of rucaparib maintenance treatment. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz250.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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30
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Patient demographics and management landscape of metastatic colorectal cancer in the third-line setting: Real-world data in an Australian population. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz246.134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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31
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A phase 1/2, open-label, dose-expansion study of liposomal irinotecan (nal-IRI) plus 5-fluorouracil/leucovorin (5-FU/LV) and oxaliplatin (OX) in patients with previously untreated metastatic pancreatic cancer. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz157.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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32
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Modified FOLFIRINOX as a second-line treatment in pancreatic adenocarcinoma following gemcitabine plus nab-paclitaxel failure in patients with performance status two or less. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz155.303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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33
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Prospective evaluation of FOLFIRINOX in Neo-adjuvant treatment of gastro-oesophageal junction carcinomas. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz155.301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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34
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Third-line re-treatment of advanced pancreatic adenocarcinoma with gemcitabine and nab-paclitaxel. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz155.302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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35
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Post hoc exploratory analysis of rucaparib in patients with platinum-sensitive recurrent ovarian carcinoma from the randomized, placebo-controlled phase III study ARIEL3: Effect of a deleterious germline or no germline mutation on efficacy. Gynecol Oncol 2019. [DOI: 10.1016/j.ygyno.2019.04.549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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36
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The effect of age on efficacy and safety outcomes with rucaparib: A post hoc exploratory analysis of ARIEL3, a phase III, randomized, placebo-controlled maintenance study in patients with recurrent ovarian carcinoma. Gynecol Oncol 2019. [DOI: 10.1016/j.ygyno.2019.04.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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37
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Alarming levels of multidrug-resistant tuberculosis in Ukraine: results from the first national survey. Int J Tuberc Lung Dis 2019; 22:197-205. [PMID: 29506617 DOI: 10.5588/ijtld.17.0254] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
SETTING The true prevalence of multidrug-resistant tuberculosis (MDR-TB) in Ukraine is not known. Available data are a decade old and limited to only one province. OBJECTIVE To determine the prevalence of MDR-TB among new and previously treated TB cases in Ukraine and explore the risk factors associated with drug resistance. METHODS A total of 1550 sputum smear-positive pulmonary TB patients were recruited from 40 clusters throughout Ukraine. Sputum specimens were examined using culture, drug susceptibility testing and pncA gene sequencing. RESULTS The proportion of MDR-TB among new and previously treated TB cases was respectively 24.1% (95%CI 20.7-27.6) and 58.1% (95%CI 52.1-64.1). More than one third (38.0%) of MDR-TB or rifampicin (RMP) resistant cases showed resistance to either a fluoroquinolone (FQ) or a second-line injectable agent or both. Resistance to pyrazinamide and FQs was low in patients with RMP-susceptible TB. Among new TB cases, the odds of MDR-TB were higher among patients who were younger, female and living in south-eastern provinces, as well as among human immunodeficiency virus-positive patients who belonged to a low socio-economic group. CONCLUSIONS Our study showed that the burden of MDR-TB in Ukraine was much greater than previously assumed. Urgent actions are needed to prevent further spread of drug-resistant TB in Ukraine.
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CRISPR/Cas9 offers a new tool for studying the role of chromatin architecture in disease pathogenesis. Genome Biol 2018; 19:185. [PMID: 30400943 PMCID: PMC6219166 DOI: 10.1186/s13059-018-1569-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
A recent study used CRISPR/Cas9 to reveal long-range looping between disease-related genes and their regulatory elements that is mediated by the CCCTC-binding factor (CTCF) in prostate cancer.
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39
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Subgroup analysis of rucaparib in platinum-sensitive recurrent ovarian carcinoma: Effect of prior chemotherapy regimens in ARIEL3. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy285.155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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40
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Response to neoadjuvant chemotherapy in ICON8: A GCIG phase III randomised trial evaluating weekly dose-dense chemotherapy integration in first-line epithelial ovarian/ fallopian tube/ primary peritoneal carcinoma (EOC) treatment. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy285.151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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NAPOLI-1 phase III trial outcomes by prior surgery, and disease stage, in patients with metastatic pancreatic ductal adenocarcinoma (mPDAC). Ann Oncol 2018. [DOI: 10.1093/annonc/mdy282.116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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42
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Process to Improve the Consistency and Accuracy of Diagnosing Malnutrition in a Large Pediatric Academic Hospital. J Acad Nutr Diet 2018. [DOI: 10.1016/j.jand.2018.06.235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Prognostic value of baseline biliary stents on outcomes in patients with metastatic pancreatic ductal adenocarcinoma (mPDAC) in the NAPOLI-1 trial. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy151.150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Use of gemcitabine and nab-paclitaxel as a third-line treatment following failure of first line gemcitabine for advanced pancreatic adenocarcinoma. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy151.146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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The effect of best response to prior anticancer therapy on efficacy outcomes in the NAPOLI-1 trial of patients with metastatic pancreatic ductal adenocarcinoma (mPDAC) previously treated with gemcitabine-based therapy. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy151.151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Prognostic effect of primary tumor location in the NAPOLI-1 phase 3 study in metastatic pancreatic ductal adenocarcinoma (mPDAC). Ann Oncol 2018. [DOI: 10.1093/annonc/mdy151.149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Correlation of neutrophil lymphocyte ratio, platelet lymphocyte ratio and rate of change of CA 19.9 in predicting outcome for metastatic pancreatic cancer. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy151.157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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The use of NLR, PLR and CA19.9 as prognostic markers for locally advanced pancreatic cancer. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy151.132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Understanding the microbiome of diabetic foot osteomyelitis: insights from molecular and microscopic approaches. Clin Microbiol Infect 2018; 25:332-339. [PMID: 29787888 DOI: 10.1016/j.cmi.2018.04.036] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/30/2018] [Accepted: 04/30/2018] [Indexed: 01/13/2023]
Abstract
OBJECTIVES Rigorous visual evidence on whether or not biofilms are involved in diabetic foot osteomyelitis (DFO) is lacking. We employed a suite of molecular and microscopic approaches to investigate the microbiome, and phenotypic state of microorganisms involved in DFO. METHODS In 20 consecutive subjects with suspected DFO, we collected intraoperative bone specimens. To explore the microbial diversity present in infected bone we performed next generation DNA sequencing. We used scanning electron microscopy (SEM) and peptide nucleic acid fluorescent in situ hybridization (PNA-FISH) with confocal microscopy to visualize and confirm the presence of biofilms. RESULTS In 19 of 20 (95%) studied patients presenting with DFO, it was associated with an infected diabetic foot ulcer. By DNA sequencing of infected bone, Corynebacterium sp. was the most commonly identified microorganism, followed by Finegoldia sp., Staphylococcus sp., Streptococcus sp., Porphyromonas sp., and Anaerococcus sp. Six of 20 bone samples (30%) contained only one or two pathogens, while the remaining 14 (70%) had polymicrobial communities. Using a combination of SEM and PNA-FISH, we identified microbial aggregates in biofilms in 16 (80%) bone specimens and found that they were typically coccoid or rod-shaped aggregates. CONCLUSIONS The presence of biofilms in DFO may explain why non-surgical treatment of DFO, relying on systemic antibiotic therapy, may not resolve some chronic infections caused by biofilm-producing strains.
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Abstract
Chromatin immunoprecipitation (ChIP) allows determination of the locations to which a select protein is bound in chromatin. Chemical crosslinking of DNA and protein with bi-functional reagents such as formaldehyde and precipitation of the protein with a specific antibody permit PCR amplification (ChIP) or sequencing (ChIP-seq) to identify the bound sites. Here, we present methodology for these approaches that are widely applicable to erythroid cell lines, progenitor cells, and tissues.
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