Genome accessibility dynamics in response to phosphate limitation is controlled by the PHR1 family of transcription factors in Arabidopsis.

As phosphorus is one of the most limiting nutrients in many natural and agricultural ecosystems, plants have evolved strategies that cope with its scarcity. Genetic approaches have facilitated the identification of several molecular elements that regulate the phosphate (Pi) starvation response (PSR) of plants, including the master regulator of the transcriptional response to phosphate starvation PHOSPHATE STARVATION RESPONSE1 (PHR1). However, the chromatin modifications underlying the plant transcriptional response to phosphate scarcity remain largely unknown. Here, we present a detailed analysis of changes in chromatin accessibility during phosphate starvation in Arabidopsis thaliana root cells. Root cells undergo a genome-wide remodeling of chromatin accessibility in response to Pi starvation that is often associated with changes in the transcription of neighboring genes. Analysis of chromatin accessibility in the phr1 phl2 double mutant revealed that the transcription factors PHR1 and PHL2 play a key role in remodeling chromatin accessibility in response to Pi limitation. We also discovered that PHR1 and PHL2 play an important role in determining chromatin accessibility and the associated transcription of many genes under optimal Pi conditions, including genes involved in the PSR. We propose that a set of transcription factors directly activated by PHR1 in Pi-starved root cells trigger a second wave of epigenetic changes required for the transcriptional activation of the complete set of low-Pi-responsive genes.

Understanding excited state properties of host materials in OLEDs: simulation of absorption spectrum of amorphous 4,4-bis(carbazol-9-yl)-2,2-biphenyl (CBP).

4,4-Bis(carbazol-9-yl)-2,2-biphenyl (CBP) is widely used as a host material in phosphorescent organic light-emitting diodes (PhOLEDs). In the present study, we simulate the absorption spectra of CBP in gas and condensed phases, respectively, using the efficient time-dependent long-range corrected tight-binding density functional theory (TD-LC-DFTB). The accuracy of the condensed-phase absorption spectra computed using the structures obtained from classical molecular dynamics (MD) and quantum mechanical/molecular mechanical (QM/MM) simulations is examined by comparison with the experimental absorption spectrum. It is found that the TD-LC-DFTB gas-phase spectrum is in good agreement with the GW-BSE spectrum, indicating TD-LC-DFTB is an accurate and robust method in calculating the excitation energies of CBP. For the condensed-phase spectrum, we find that the electrostatic embedding has a minor influence on the excitation energy. Computing accurate absorption spectra is a particular challenge since static and dynamic disorders have to be taken into account. The static disorder results from the molecular packing in the material, which leads to molecule deformations. Since these structural changes sensitively impact the excitation energies of the individual molecules, a proper representation of this static disorder indicates that a reasonable structural model of the material has been generated. The good agreement between computed and experimental absorption spectra is therefore an indicator for the structural model developed. Concerning dynamic disorder, we find that molecular changes occur on long timescales in the ns-regime, which requires the use of fast computation approaches to reach convergence. The structural models derived in this work are the basis for future studies of charge and exciton transfer in CBP and related materials, also concerning the degradation mechanisms of CBP-based PhOLEDs.

Developing in 3D: the role of CTCF in cell differentiation.

CTCF is a highly conserved zinc-finger DNA-binding protein that mediates interactions between distant sequences in the genome. As a consequence, CTCF regulates enhancer-promoter interactions and contributes to the three-dimensional organization of the genome. Recent studies indicate that CTCF is developmentally regulated, suggesting that it plays a role in cell type-specific genome organization. Here, we review these studies and discuss how CTCF functions during the development of various cell and tissue types, ranging from embryonic stem cells and gametes, to neural, muscle and cardiac cells. We propose that the lineage-specific control of CTCF levels, and its partnership with lineage-specific transcription factors, allows for the control of cell type-specific gene expression via chromatin looping.

Epigenetic Effects of an Adenosine Derivative in a Wistar Rat Model of Liver Cirrhosis.

The pathological characteristic of cirrhosis is scarring which results in a structurally distorted and dysfunctional liver. Previously, we demonstrated that Col1a1 and Pparg genes are deregulated in CCl4 -induced cirrhosis but their normal expression levels are recovered upon treatment with IFC-305, an adenosine derivative. We observed that adenosine was able to modulate S-adenosylmethionine-dependent trans-methylation reactions, and recently, we found that IFC-305 modulates HDAC3 expression. Here, we investigated whether epigenetic mechanisms, involving DNA methylation processes and histone acetylation, could explain the re-establishment of gene expression mediated by IFC-305 in cirrhosis. Therefore, Wistar rats were CCl4 treated and a sub-group received IFC-305 to reverse fibrosis. Global changes in DNA methylation, 5-hydroxymethylation, and histone H4 acetylation were observed after treatment with IFC-305. In particular, during cirrhosis, the Pparg gene promoter is depleted of histone H4 acetylation, whereas IFC-305 administration restores normal histone acetylation levels which correlates with an increase of Pparg transcript and protein levels. In contrast, the promoter of Col1a1 gene is hypomethylated during cirrhosis but gains DNA methylation upon treatment with IFC-305 which correlates with a reduction of Col1a1 transcript and protein levels. Our results suggest a model in which cirrhosis results in a general loss of permissive chromatin histone marks which triggers the repression of the Pparg gene and the upregulation of the Col1a1 gene. Treatment with IFC-305 restores epigenetic modifications globally and specifically at the promoters of Pparg and Col1a1 genes. These results reveal one of the mechanisms of action of IFC-305 and suggest a possible therapeutic function in cirrhosis. J. Cell. Biochem. 119: 401-413, 2018. © 2017 Wiley Periodicals, Inc.

Chromatin remodeling effects on enhancer activity.

During organism development, a diversity of cell types emerges with disparate, yet stable profiles of gene expression with distinctive cellular functions. In addition to gene promoters, the genome contains enhancer regulatory sequences, which are implicated in cellular specialization by facilitating cell-type and tissue-specific gene expression. Enhancers are DNA binding elements characterized by highly sophisticated and various mechanisms of action allowing for the specific interaction of general and tissue-specific transcription factors (TFs). However, eukaryotic organisms package their genetic material into chromatin, generating a physical barrier for TFs to interact with their cognate sequences. The ability of TFs to bind DNA regulatory elements is also modulated by changes in the chromatin structure, including histone modifications, histone variants, ATP-dependent chromatin remodeling, and the methylation status of DNA. Furthermore, it has recently been revealed that enhancer sequences are also transcribed into a set of enhancer RNAs with regulatory potential. These interdependent processes act in the context of a complex network of chromatin interactions, which together contributes to a renewed vision of how gene activation is coordinated in a cell-type-dependent manner. In this review, we describe the interplay between genetic and epigenetic aspects associated with enhancers and discuss their possible roles on enhancer function.

Epigenetic silencing of miR-181c by DNA methylation in glioblastoma cell lines.

BACKGROUND: Post-transcriptional regulation by microRNAs is recognized as one of the major pathways for the control of cellular homeostasis. Less well understood is the transcriptional and epigenetic regulation of genes encoding microRNAs. In the present study we addressed the epigenetic regulation of the miR-181c in normal and malignant brain cells. METHODS: To explore the epigenetic regulation of the miR-181c we evaluated its expression using RT-qPCR and the in vivo binding of the CCCTC-binding factor (CTCF) to its regulatory region in different glioblastoma cell lines. DNA methylation survey, chromatin immunoprecipitation and RNA interference assays were used to assess the role of CTCF in the miR-181c epigenetic silencing. RESULTS: We found that miR-181c is downregulated in glioblastoma cell lines, as compared to normal brain tissues. Loss of expression correlated with a notorious gain of DNA methylation at the miR-181c promoter region and the dissociation of the multifunctional nuclear factor CTCF. Taking advantage of the genomic distribution of CTCF in different cell types we propose that CTCF has a local and cell type specific regulatory role over the miR-181c and not an architectural one through chromatin loop formation. This is supported by the depletion of CTCF in glioblastoma cells affecting the expression levels of NOTCH2 as a target of miR-181c. CONCLUSION: Together, our results point to the epigenetic role of CTCF in the regulation of microRNAs implicated in tumorigenesis.

Copper Coordination Features of Human Islet Amyloid Polypeptide: The Type 2 Diabetes Peptide.

Human islet amyloid polypeptide (hIAPP) is the major component of amyloid deposits found in pancreatic ß-cells of patients with type 2 diabetes (T2D). Copper ions have an inhibitory effect on the amyloid aggregation of hIAPP, and they may play a role in the etiology of T2D. However, deeper knowledge of the structural details of the copper-hIAPP interaction is required to understand the molecular mechanisms involved. Here, we performed a spectroscopic study of Cu(II) binding to hIAPP and several variants, using electron paramagnetic resonance (EPR), nuclear magnetic resonance (NMR), electronic absorption, and circular dichroism (CD) in the UV-vis region in combination with Born-Oppenheimer molecular dynamics (BOMD) and density functional theory geometry optimizations. We find that Cu(II) binds to the imidazole N1 of His18, the deprotonated amides of Ser19 and Ser20, and an oxygen-based ligand provided by Ser20, either via its hydroxyl group or its backbone carbonyl, while Asn22 might also play a role as an axial ligand. Ser20 plays a crucial role in stabilizing Cu(II) coordination toward the C-terminal, providing a potential link between the S20G mutation associated with early onset of T2D, its impact in Cu binding properties, and hIAPP amyloid aggregation. Our study defines the nature of the coordination environment in the Cu(II)-hIAPP complex, revealing that the amino acid residues involved in metal ion binding are also key residues for the formation of ß-sheet structures and amyloid fibrils. Cu(II) binding to hIAPP may lead to the coexistence of more than one coordination mode, which in turn could favor different sets of Cu-induced conformational ensembles. Cu-induced hIAPP conformers would display a higher energetic barrier to form amyloid fibrils, hence explaining the inhibitory effect of Cu ions in hIAPP aggregation. Overall, this study provides further structural insights into the bioinorganic chemistry of T2D.

Cytoreductive surgery and Hyperthermic Intraperitoneal Chemotherapy (HIPEC) for children, adolescents, and young adults: the first 50 cases.

BACKGROUND: Extensive peritoneal metastatic disease is rare in children. Although usually manifested as carcinomatosis in adults, sarcomatosis is more common in children. The authors began a pediatric hyperthermic intraperitoneal chemotherapy (HIPEC) program, and this report describes their initial results from the first 50 pediatric, adolescent, and young adult patients. METHODS: A single-institution, retrospective study investigated the first 50 cytoreductive surgeries and HIPEC by one surgeon for patients 3-21 years of age. The HIPEC was added to chemotherapy and radiotherapy treatment. Demographics, outcome, and complications were recorded. RESULTS: The median follow-up period for the surviving patients was 21.9 months. The most common diagnoses were desmoplastic small round cell tumor (n = 21), rhabdomyosarcoma (n = 7), mesothelioma (n = 4), and other carcinoma (n = 17). Multivariate analysis showed that patients treated with HIPEC and an incomplete cytoreduction had a greater risk for recurrence than those who had a complete cytoreduction (p = 0.0002). The patients with a higher peritoneal cancer index (PCI) (i.e., a large tumor burden) had a median overall survival (OS) time of 19.9 months relative to the patients with a lower PCI score, who had a median OS of 34 months (p = 0.049). The patients without complete cytoreduction had a median OS of 7.1 months compared with 31.4 months for the patients with complete cytoreduction (p = 0.012). No perioperative mortalities occurred. The incidence of major complications was 28 %. CONCLUSION: Cytoreductive surgery and HIPEC with a programmatic approach for patients 3-21 years of age is unique. The best outcome was experienced by patients with desmoplastic small round cell tumor and those with complete cytoreduction. Complete cytoreduction for patients without disease outside the abdominal cavity at the time of surgery affords the best outcome.

Complete cytoreduction and HIPEC improves survival in desmoplastic small round cell tumor.

BACKGROUND: Desmoplastic small round cell tumor (DSRCT) is a rare tumor of adolescents and young adults. Less than 100 cases per year are reported in North America. Extensive peritoneal metastases are characteristic of this disease. We performed cytoreductive surgery and hyperthermic peritoneal perfusion with chemotherapy (HIPEC) using cisplatin (CDDP) for DSRCT. METHODS: A retrospective cohort study was performed on 26 pediatric and adult patients who underwent cytoreduction/HIPEC using CDDP for DSRCT at a single cancer center. Neoadjuvant chemotherapy, adjuvant chemotherapy, and postoperative enteral nutrition were given to all patients. Postoperative radiation therapy was given to most patients. Follow-up was from 6 months to 6 years. Outcome variables were evaluated for disease-free and overall survival (OS). RESULTS: Five patients (19 %) were less than 12 years of age at surgery. Patients who had disease outside the abdomen at surgery had a larger risk of recurrence or death than those who did not (p = 0.0158, p = 0.0393 time from surgery to death respectively). Age, liver metastasis, and peritoneal cancer index level did not significantly predict disease-free or OS. Patients who had CR0 or CR1 and HIPEC had significantly longer median survival compared with patients who had HIPEC and CR2 cytoreduction (63.4 vs. 26.7 months). CONCLUSIONS: HIPEC may be an effective therapy for children and young adults with DSRCT. Patients with DSRCT require complete cytoreduction before HIPEC to optimize outcome. Patients with DSRCT and disease outside the abdomen at the time of surgery do not benefit from HIPEC.

The epigenome under pressure: On regulatory adaptation to chronic stress in the brain.

Chronic stress (CS) can have long-lasting consequences on behavior and cognition, that are associated with stable changes in gene expression in the brain. Recent work has examined the role of the epigenome in the effects of CS on the brain. This review summarizes experimental evidence in rodents showing that CS can alter the epigenome and the expression of epigenetic modifiers in brain cells, and critically assesses their functional effect on genome function. It discusses the influence of the developmental time of stress exposure on the type of epigenetic changes, and proposes new lines of research that can help clarify these changes and their causal involvement in the impact of CS.

Remembering through the genome: the role of chromatin states in brain functions and diseases.

Chromatin is the physical substrate of the genome that carries the DNA sequence and ensures its proper functions and regulation in the cell nucleus. While a lot is known about the dynamics of chromatin during programmed cellular processes such as development, the role of chromatin in experience-dependent functions remains not well defined. Accumulating evidence suggests that in brain cells, environmental stimuli can trigger long-lasting changes in chromatin structure and tri-dimensional (3D) organization that can influence future transcriptional programs. This review describes recent findings suggesting that chromatin plays an important role in cellular memory, particularly in the maintenance of traces of prior activity in the brain. Inspired by findings in immune and epithelial cells, we discuss the underlying mechanisms and the implications for experience-dependent transcriptional regulation in health and disease. We conclude by presenting a holistic view of chromatin as potential molecular substrate for the integration and assimilation of environmental information that may constitute a conceptual basis for future research.

Pain and Analgesia in Children with Cancer after Hemipelvectomy: A Retrospective Analysis.

A paucity of data exists centering on the pain experience of children following hemipelvectomy performed for primary bone and soft tissue sarcomas. In this study, we aimed to describe the incidence, severity, and evolution of perioperative pain and function in pediatric oncology patients undergoing hemipelvectomy, and, additionally, we sought to detail the analgesic regimens used for these patients perioperatively. A retrospective chart review was conducted, studying cancer patients, aged 21 years and under, who underwent hemipelvectomy at MD Anderson Cancer Center (MDACC) from 2018 to 2021. Primary outcomes included the evolution of pain throughout the perioperative course, as well as the route, type, dose, and duration of analgesic regimens. Eight patients were included in the analysis. The mean age at operation was 13 ± 2.93 years. All patients received opioids and acetaminophen. The mean pain scores were highest on post-operative day (POD)0, POD5, and POD 30. The mean opioid use was highest on POD5. A total of 75% of patients were noted to be ambulating after hemipelvectomy. The mean time to ambulation was 5.33 ± 2.94 days. The combination of acetaminophen with opioids, as well as adjunctive regional analgesia, non-steroidal anti-inflammatory drugs, gabapentin, and/or ketamine in select patients, appeared to be an effective analgesic regimen, and functional outcomes were excellent in 75% of patients.

Epigenetic Inheritance: Impact for Biology and Society-recent progress, current questions and future challenges.

Epigenetic inheritance has emerged as a new research discipline that aims to study the mechanisms underlying the transmission of acquired traits across generations. Such transmission is well established in plants and invertebrates but remains not well characterized and understood in mammals. Important questions are how life experiences and environmental factors induce phenotypic changes that are passed to the offspring of exposed individuals, sometimes across several successive generations, what is the contribution of germ cells and what are the consequences for health and disease. These questions were recently discussed at the symposium Epigenetic Inheritance: Impact for Biology and Society organized every 2 years in Zürich, Switzerland. This review provides a summary of the research presented during the symposium and discusses current important questions, perspectives and challenges for the field in the future.

Implementing Rounding Checklists in a Pediatric Oncologic Intensive Care Unit.

Standardized rounding checklists during multidisciplinary rounds (MDR) can reduce medical errors and decrease length of pediatric intensive care unit (PICU) and hospital stay. We added a standardized process for MDR in our oncologic PICU. Our study was a quality improvement initiative, utilizing a four-stage Plan-Do-Study-Act (PDSA) model to standardize MDR in our PICU over 3 months, from January 2020 to March 2020. We distributed surveys to PICU RNs to assess their understanding regarding communication during MDR. We created a standardized rounding checklist that addressed key elements during MDR. Safety event reports before and after implementation of our initiative were retrospectively reviewed to assess our initiative's impact on safety events. Our intervention increased standardization of PICU MDR from 0% to 70% over three months, from January 2020 to March 2020. We sustained a rate of zero for CLABSI, CAUTI, and VAP during the 12-month period prior to, during, and post-intervention. Implementation of a standardized rounding checklist may improve closed-loop communication amongst the healthcare team, facilitate dialogue between patients' families and the healthcare team, and reduce safety events. Additional staffing for resource RNs, who assist with high acuity patients, has also facilitated bedside RN participation in MDR, without interruptions in clinical care.

Signaling epigenetics: novel insights on cell signaling and epigenetic regulation.

Cells must be able to respond rapidly and precisely not only to changes in their external environment but also to developmental and differentiation cues to determine when to divide, die, or acquire a particular cell fate. Signal transduction pathways are responsible for the integration and interpretation of most of such signals into specific transcriptional states. Those states are achieved by the modulation of chromatin structure that activates or represses transcription at particular loci. Although a large variety of signal transduction pathways have already been described, much less is known about the crosstalk between signal transduction and its consequent changes in chromatin structure and, therefore, gene expression. Here we present some examples of the relationship between chromatin-associated proteins and important signal transduction pathways during critical processes like development, differentiation, and disease. There is a great diversity of epigenetic mechanisms that have unexpected interactions with signaling pathways to establish transcriptional programs. Moreover, there are also particular cases where signaling pathways directly affect important components of the epigenetic machinery. Based on such examples, we further propose future research directions linking cell signaling and epigenetics. It is foreseeable that analyzing the relationship between cell signaling and epigenetics will be a huge area for future development that will help us understand the complex process by which a cell is able to induce transcriptional changes in response to external and internal signals.

In-Nucleus Hi-C in Drosophila Cells.

The genome is organized into topologically associating domains (TADs) delimited by boundaries that isolate interactions between domains. In Drosophila, the mechanisms underlying TAD formation and boundaries are still under investigation. The application of the in-nucleus Hi-C method described here helped to dissect the function of architectural protein (AP)-binding sites at TAD boundaries isolating the Notch gene. Genetic modification of domain boundaries that cause loss of APs results in TAD fusion, transcriptional defects, and long-range topological alterations. These results provided evidence demonstrating the contribution of genetic elements to domain boundary formation and gene expression control in Drosophila. Here, the in-nucleus Hi-C method has been described in detail, which provides important checkpoints to assess the quality of the experiment along with the protocol. Also shown are the required numbers of sequencing reads and valid Hi-C pairs to analyze genomic interactions at different genomic scales. CRISPR/Cas9-mediated genetic editing of regulatory elements and high-resolution profiling of genomic interactions using this in-nucleus Hi-C protocol could be a powerful combination for the investigation of the structural function of genetic elements.

Retrospective Review of Flexible Bronchoscopy in Pediatric Cancer Patients.

The use of flexible bronchoscopy (FB) with bronchoalveolar lavage (BAL) to diagnose and manage pulmonary complications has been shown to be safe in adult cancer patients, but whether its use is safe in pediatric cancer patients remains unclear. Thus, to describe the landscape of FB outcomes in pediatric cancer patients and to help define the populations most likely to benefit from the procedure, we undertook a retrospective review of FBs performed in patients younger than 21 years treated at our institution from 2002 to 2017. We found that a greater volume of total fluid instilled during BAL was significantly associated with increased probabilities of positive BAL culture (p=0.042), positive bacterial BAL culture (p=0.037), and positive viral BAL culture (p=0.0496). In more than half of the FB cases, findings resulted in alterations in antimicrobial treatment. Our study suggests that for pediatric cancer patients, FB is safe, likely provides diagnostic and/or therapeutic benefits, and has implications for treatment decisions.

Case Discussion and Literature Review: Cancer Immunotherapy, Severe Immune-Related Adverse Events, Multi-Inflammatory Syndrome, and Severe Acute Respiratory Syndrome Coronavirus 2.

Pediatric, adolescent and young adult (AYA) patients receiving novel cancer immunotherapies may develop associated toxicities with overlapping signs and symptoms that are not always easily distinguished from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection/clinical sequelae. We describe 2 diagnostically challenging cases of SARS-CoV-2 and Multi-Inflammatory Syndrome-Adult (MIS-A), in patients with a history of acute lymphoblastic leukemia following cellular therapy administration and review evolving characterization of both the natural course of SARS-CoV-2 infection and toxicities experienced in younger cancer immunotherapy patients. Vigilant monitoring for unique presentations and epidemiologic surveillance to promptly detect changes in incidence of either condition may be warranted.

The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle.

BACKGROUND: Circadian gene expression is essential for organisms to adjust their physiology and anticipate daily changes in the environment. The molecular mechanisms controlling circadian gene transcription are still under investigation. In particular, how chromatin conformation at different genomic scales and regulatory elements impact rhythmic gene expression has been poorly characterized. RESULTS: Here we measure changes in the spatial chromatin conformation in mouse liver using genome-wide and promoter-capture Hi-C alongside daily oscillations in gene transcription. We find topologically associating domains harboring circadian genes that switch assignments between the transcriptionally active and inactive compartment at different hours of the day, while their boundaries stably maintain their structure over time. To study chromatin contacts of promoters at high resolution over time, we apply promoter capture Hi-C. We find circadian gene promoters displayed a maximal number of chromatin contacts at the time of their peak transcriptional output. Furthermore, circadian genes, as well as contacted and transcribed regulatory elements, reach maximal expression at the same timepoints. Anchor sites of circadian gene promoter loops are enriched in DNA binding sites for liver nuclear receptors and other transcription factors, some exclusively present in either rhythmic or stable contacts. Finally, by comparing the interaction profiles between core clock and output circadian genes, we show that core clock interactomes are more dynamic compared to output circadian genes. CONCLUSION: Our results identify chromatin conformation dynamics at different scales that parallel oscillatory gene expression and characterize the repertoire of regulatory elements that control circadian gene transcription through rhythmic or stable chromatin configurations.

Long-Term Impact of Social Isolation and Molecular Underpinnings.

Prolonged periods of social isolation can have detrimental effects on the physiology and behavior of exposed individuals in humans and animal models. This involves complex molecular mechanisms across tissues in the body which remain partly identified. This review discusses the biology of social isolation and describes the acute and lasting effects of prolonged periods of social isolation with a focus on the molecular events leading to behavioral alterations. We highlight the role of epigenetic mechanisms and non-coding RNA in the control of gene expression as a response to social isolation, and the consequences for behavior. Considering the use of strict quarantine during epidemics, like currently with COVID-19, we provide a cautionary tale on the indiscriminate implementation of such form of social isolation and its potential damaging and lasting effects in mental health.