Enhancer release and retargeting activates disease-susceptibility genes.

The functional engagement between an enhancer and its target promoter ensures precise gene transcription1. Understanding the basis of promoter choice by enhancers has important implications for health and disease. Here we report that functional loss of a preferred promoter can release its partner enhancer to loop to and activate an alternative promoter (or alternative promoters) in the neighbourhood. We refer to this target-switching process as 'enhancer release and retargeting'. Genetic deletion, motif perturbation or mutation, and dCas9-mediated CTCF tethering reveal that promoter choice by an enhancer can be determined by the binding of CTCF at promoters, in a cohesin-dependent manner-consistent with a model of 'enhancer scanning' inside the contact domain. Promoter-associated CTCF shows a lower affinity than that at chromatin domain boundaries and often lacks a preferred motif orientation or a partnering CTCF at the cognate enhancer, suggesting properties distinct from boundary CTCF. Analyses of cancer mutations, data from the GTEx project and risk loci from genome-wide association studies, together with a focused CRISPR interference screen, reveal that enhancer release and retargeting represents an overlooked mechanism that underlies the activation of disease-susceptibility genes, as exemplified by a risk locus for Parkinson's disease (NUCKS1-RAB7L1) and three loci associated with cancer (CLPTM1L-TERT, ZCCHC7-PAX5 and PVT1-MYC).

Transcriptional enhancers at 40: evolution of a viral DNA element to nuclear architectural structures.

Gene regulation by transcriptional enhancers is the dominant mechanism driving cell type- and signal-specific transcriptional diversity in metazoans. However, over four decades since the original discovery, how enhancers operate in the nuclear space remains largely enigmatic. Recent multidisciplinary efforts combining real-time imaging, genome sequencing, and biophysical strategies provide insightful but conflicting models of enhancer-mediated gene control. Here, we review the discovery and progress in enhancer biology, emphasizing the recent findings that acutely activated enhancers assemble regulatory machinery as mesoscale architectural structures with distinct physical properties. These findings help formulate novel models that explain several mysterious features of the assembly of transcriptional enhancers and the mechanisms of spatial control of gene expression.

Long-distance association of topological boundaries through nuclear condensates.

The eukaryotic genome is partitioned into distinct topological domains separated by boundary elements. Emerging data support the concept that several well-established nuclear compartments are ribonucleoprotein condensates assembled through the physical process of phase separation. Here, based on our demonstration that chemical disruption of nuclear condensate assembly weakens the insulation properties of a specific subset (∼20%) of topologically associated domain (TAD) boundaries, we report that the disrupted boundaries are characterized by a high level of transcription and striking spatial clustering. These topological boundary regions tend to be spatially associated, even interchromosomally, segregate with nuclear speckles, and harbor a specific subset of "housekeeping" genes widely expressed in diverse cell types. These observations reveal a previously unappreciated mode of genome organization mediated by conserved boundary elements harboring highly and widely expressed transcription units and associated transcriptional condensates.

High-Mobility Carriers in Epitaxial IrO2 Films Grown using Hybrid Molecular Beam Epitaxy.

Binary rutile oxides of 5d metals such as IrO2 stand out in comparison to their 3d and 4d counterparts due to limited experimental studies, despite rich predicted quantum phenomena. Here, we investigate the electrical transport properties of IrO2 by engineering epitaxial thin films grown using hybrid molecular beam epitaxy. Our findings reveal phonon-limited carrier transport and thickness-dependent anisotropic in-plane resistance in IrO2 (110) films, the latter suggesting a complex relationship between strain relaxation and orbital hybridization. Magnetotransport measurements reveal a previously unobserved nonlinear Hall effect. A two-carrier analysis of this effect shows the presence of minority carriers with mobility exceeding 3000 cm2/(V s) at 1.8 K. These results point toward emergent properties in 5d metal oxides that can be controlled using dimensionality and epitaxial strain.

Isodicentric Philadelphia Chromosome: A Rare Chromosomal Aberration in Imatinib-Resistant Chronic Myelogenous Leukemia Patients - Case Report with Review of the Literature.

The BCR-ABL1 fusion gene derived from the Philadelphia chromosome, resulting from a classical translocation event t(9;22)(q34.13;q11.23), is responsible for the pathogenesis of chronic myeloid leukemia (CML) in more than 90% of the patients. The isoderivative chromosome 22, ider(22), and relative amplification or duplication of the BCR-ABL1 gene have been considered as one of the major reasons associated with the resistance to chemotherapy with imatinib mesylate, but the data remain unclear. GTG-banding together with FISH were performed to identify the presence of the ider(22) chromosome. Reverse transcription-polymerase chain reaction (RT-PCR) for the detection of BCR-ABL1 fusion transcripts and BCR-ABL1 kinase domain mutation analysis were carried out in this study. Conventional and molecular cytogenetic analysis on metaphase chromosomes confirmed the presence of ider(22) chromosomes in both patients. Molecular characterization revealed the presence of a 210-kDa BCR-ABL1 type b3a2 and lack of mutations at the kinase domain region on the fusion product in both patients. The occurrence of the ider(22) chromosome could be considered as an important marker correlated with the aggressive progression of CML as well as the emergence of drug-resistant cell clones.

Quantifying Intracellular Platinum Accumulation Using Inductively Coupled Mass Spectrometry.

The platinum-based anticancer drug cisplatin and its analog carboplatin are the most used chemotherapeutic agents worldwide. It is estimated that approximately half of all cancer patients are treated with platinum drugs at some point during the therapy regimen. Cisplatin covalently binds to purine nucleobases to form DNA adducts. Cisplatin therapy is faced with two key challenges. First, despite the initial response, many patients develop cisplatin resistance. Reduced cellular accumulation of cisplatin is one common cause of therapy resistance. Second, cisplatin treatment causes general cytotoxicity, leading to severe side effects. Monitoring the subcellular concentration of platinum chemotherapeutics will help yield clinical efficacy with the minimum possible dose. Inductively coupled plasma-mass spectrometry (ICP-MS) is an analytical technique to quantify the elemental composition of various types of liquified bulk samples with high sensitivity. This article describes quantifying cisplatin accumulation in chromatin and total cell lysate using ICP-MS. The method involves treating cells with cisplatin, isolating RNA-free DNA, digesting samples, ICP-MS instrumentation, and data analysis. Although we describe these steps in one cancer cell line, the protocol can be adapted to any cell line or tissue. The protocol should be a valuable resource for investigators interested in accurate measurement of subcellular concentration of platinum and other metallo-drugs. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Cell culture conditions for A2780 cells and cisplatin treatment Basic Protocol 2: Isolating cellular fractions and sample quantitation Basic Protocol 3: Sample digestion, ICP-MS data collection, and analysis.

Quantum Insights into Partially Molecular Imprinted Microspheres for Anticancer Therapeutics: Experimental and Theoretical Studies.

Drug solubility is a determining factor for controlled release, and solubility-dependent release kinetics can be modified by changing the drug's state in the polymer matrix through partial molecular imprinting (PMI), although research in this area remains limited. This novel PMI approach creates nanocavities within the polymer by partially retaining the imprinting molecule and trapping the drug. Such a method holds promise for developing advanced biomaterial-based drug delivery systems for anticancer therapies. In this study, we developed microspheres designed for anticancer drug delivery utilizing PMI to enhance controlled release properties. Poly(vinyl alcohol) (PVA) microspheres were partially imprinted with aspirin (ASP) to create nanocavities for gemcitabine (GEM) molecules, inducing a polymorphic shift of GEM within the polymer matrix. This novel PMI approach enhanced drug release properties by enabling control over the drug crystallinity and release rate. The PVA-ASP-GEM complex showed zero-order release kinetics, releasing 21.6% of GEM over 48 h, maintaining steady state release profile. In contrast, nonimprinted PVA-GEM microspheres exhibited first-order kinetics with a faster release of 46.85% in the same period. Quantum insights from density functional theory (DFT) calculations revealed the superior stability of the PVA-ASP-GEM complex, with a binding free energy of -56.03 kcal/mol, compared to -29.07 kcal/mol for PVA-GEM. Molecular dynamics (MD) simulations demonstrated that ASP's presence created nanocavities that restricted GEM's movement, further contributing to the controlled release. Experimental validation through differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), X-ray diffraction (XRD), and Raman spectroscopy confirmed the polymorphic transitions within the PVA-ASP-GEM complex. This PMI-based approach offers a promising method for modulating drug release kinetics and improving the stability of anticancer therapeutics, paving the way for innovative biomaterial-based drug delivery systems.

Ewing's sarcoma in adolescents and adults - 10-year experience from a tertiary cancer center in India.

BACKGROUND: Ewing's sarcoma (EWS) is an aggressive small round cell tumor, affecting bone and soft tissues and is mostly seen in childhood and second decade of life. EWS accounts for 10-12% of bone tumors in more than 15 years age group and is even rarer after 40 years of age. MATERIALS AND METHODS: This retrospective analysis was conducted among patients aged more than 15 years with histologically proven EWS. RESULTS: Among 240 cases of EWS treated at our center during 2001-2010, 130 (54%) were more than 15 years of age. The median age was 20 years with a male: female ratio of 2.4:1. Ninety percent had skeletal EWS, 10% had extra skeletal EWS, and 37% patients were metastatic at presentation. Eighty-two received curative treatment with chemotherapy (vincristine, doxorubicin, cyclophosphamide, ifosfamide, etoposide (VAC/IE)) along with local treatment, radiotherapy (RT) in 61, surgery alone in seven, and RT plus surgery in 14. Two- and 5-year overall survival (OS) was 43.3% and 25.5%, respectively, for the entire series. The OS for the non-metastatic group was 63.2% at 2 years and 36.5% at 5 years, and the progression free survival was 53.7% at 2 years and 37.8% at 5 years. High lactate dehydrogenase was found to be a significant poor prognostic factor (P = 0.001). Median OS for localized central EWS was 49.2 months and that for peripheral EWS was 24 months. Patients more than 20 years of age with non-metastatic disease had better OS compared to those with 15-20 years of age. CONCLUSION: Treatment of EWS requires a multidisciplinary approach with radical surgery and/or radiation to control local disease and multiagent chemotherapy to control systemic disease. Long-term follow-up is essential because of disease relapse and treatment-related complications.

Recruitment of CTCF to the SIRT1 promoter after Oxidative Stress mediates Cardioprotective Transcription.

Because most DNA-binding transcription factors (dbTFs), including the architectural regulator CTCF, bind RNA and exhibit di-/multimerization, a central conundrum is whether these distinct properties are regulated post-transcriptionally to modulate transcriptional programs. Here, investigating stress-dependent activation of SIRT1, encoding an evolutionarily-conserved protein deacetylase, we show that induced phosphorylation of CTCF acts as a rheostat to permit CTCF occupancy of low-affinity promoter DNA sites to precisely the levels necessary. This CTCF recruitment to the SIRT1 promoter is eliciting a cardioprotective cardiomyocyte transcriptional activation program and provides resilience against the stress of the beating heart in vivo . Mice harboring a mutation in the conserved low-affinity CTCF promoter binding site exhibit an altered, cardiomyocyte-specific transcriptional program and a systolic heart failure phenotype. This transcriptional role for CTCF reveals that a covalent dbTF modification regulating signal-dependent transcription serves as a previously unsuspected component of the oxidative stress response.

Mending cracks atom-by-atom in rutile TiO2 with electron beam radiolysis.

Rich electron-matter interactions fundamentally enable electron probe studies of materials such as scanning transmission electron microscopy (STEM). Inelastic interactions often result in structural modifications of the material, ultimately limiting the quality of electron probe measurements. However, atomistic mechanisms of inelastic-scattering-driven transformations are difficult to characterize. Here, we report direct visualization of radiolysis-driven restructuring of rutile TiO2 under electron beam irradiation. Using annular dark field imaging and electron energy-loss spectroscopy signals, STEM probes revealed the progressive filling of atomically sharp nanometer-wide cracks with striking atomic resolution detail. STEM probes of varying beam energy and precisely controlled electron dose were found to constructively restructure rutile TiO2 according to a quantified radiolytic mechanism. Based on direct experimental observation, a "two-step rolling" model of mobile octahedral building blocks enabling radiolysis-driven atomic migration is introduced. Such controlled electron beam-induced radiolytic restructuring can be used to engineer novel nanostructures atom-by-atom.

Adsorption-Controlled Growth and Magnetism in Epitaxial SrRuO3 Films.

Controlling defect densities in SrRuO3 films is the cornerstone for probing the intricate relationship among its structural, electrical, and magnetic properties. We combine film growth, electrical transport, and magnetometry to demonstrate the adsorption-controlled growth of phase-pure, epitaxial, and stoichiometric SrRuO3 films on SrTiO3 (001) substrates using solid source metal-organic molecular beam epitaxy. Across the growth window, we show that the anomalous Hall curves arise from two distinct magnetic domains. Domains with similar anomalous Hall polarities generate the stepped feature observed within the growth window, and those with opposite polarities produce the hump-like feature present exclusively in the highly Ru-poor film. We achieve a residual resistivity ratio (RRR = ρ300K/ρ2K) of 87 in a 50 nm-thick, coherently strained, and stoichiometric SrRuO3 film, the highest reported value to date on SrTiO3 (001) substrates. We hypothesize further improvements in the RRR through strain engineering to control the tetragonal-to-orthorhombic phase transformation and the domain structure of SrRuO3 films.

Castleman disease: Experience from a single institution.

Castleman disease (CD) describes a group of rare heterogeneous lymphoproliferative disorders characterized by enlarged hyperplastic lymph nodes. It is classified into unicentric CD (UCD) and multicentric CD (MCD). The present retrospective study examined the data of 11 patients with CD diagnosed and treated at a tertiary cancer center from 2017 to 2022. The median age of the study group was 41 years (range, 24 to 68 years). There were 8 males and 3 females. In total, 7 patients were diagnosed with UCD and 4 patients with MCD. The hyaline-vascular variant was the most common histology in both UCD and MCD. Among the 7 patients with UCD, 5 patients underwent excision, 1 patient underwent debulking followed by radiotherapy and 1 patient received single agent rituximab. Of the patients with UCD, 6 had a complete response (CR) and 1 patient had a partial response (PR). All 4 patients with MCD received systemic treatment, which included single agent rituximab (2 patients), rituximab, cyclophosphamide, doxorubicin, vincristine and prednisolone (RCHOP) (1 patient) and CHOP (1 patient). Among the patients with MCD, 1 patient attained a CR, 2 patients had a PR and 1 patient succumbed. The 3-year survival rate for the study population was 91%. In summary, CD is a rare disease occurring in immunodeficient patients. UCD is more common and is associated with better outcomes. Surgery is the mainstay of management in UCD whereas MCD requires combination chemotherapy.

Signal-induced enhancer activation requires Ku70 to read topoisomerase1-DNA covalent complexes.

Enhancer activation serves as the main mechanism regulating signal-dependent transcriptional programs, ensuring cellular plasticity, yet central questions persist regarding their mechanism of activation. Here, by successfully mapping topoisomerase I-DNA covalent complexes genome-wide, we find that most, if not all, acutely activated enhancers, including those induced by 17ß-estradiol, dihydrotestosterone, tumor necrosis factor alpha and neuronal depolarization, are hotspots for topoisomerase I-DNA covalent complexes, functioning as epigenomic signatures read by the classic DNA damage sensor protein, Ku70. Ku70 in turn nucleates a heterochromatin protein 1 gamma (HP1γ)-mediator subunit Med26 complex to facilitate acute, but not chronic, transcriptional activation programs. Together, our data uncover a broad, unappreciated transcriptional code, required for most, if not all, acute signal-dependent enhancer activation events in both mitotic and postmitotic cells.

Engineering metal oxidation using epitaxial strain.

The oxides of platinum group metals are promising for future electronics and spintronics due to the delicate interplay of spin-orbit coupling and electron correlation energies. However, their synthesis as thin films remains challenging due to their low vapour pressures and low oxidation potentials. Here we show how epitaxial strain can be used as a control knob to enhance metal oxidation. Using Ir as an example, we demonstrate the use of epitaxial strain in engineering its oxidation chemistry, enabling phase-pure Ir or IrO2 films despite using identical growth conditions. The observations are explained using a density-functional-theory-based modified formation enthalpy framework, which highlights the important role of metal-substrate epitaxial strain in governing the oxide formation enthalpy. We also validate the generality of this principle by demonstrating epitaxial strain effect on Ru oxidation. The IrO2 films studied in our work further revealed quantum oscillations, attesting to the excellent film quality. The epitaxial strain approach we present could enable growth of oxide films of hard-to-oxidize elements using strain engineering.

Genetic and genomic analyses of RNA polymerase II-pausing factor in regulation of mammalian transcription and cell growth.

Many mammalian genes are occupied by paused RNA polymerase II (pol II) in the promoter-proximal region on both sides of the transcription start site. However, the impact of pol II pausing on gene expression and cell biology is not fully understood. In this study, we used a Cre-Lox system to conditionally knock out the b subunit of mouse negative elongation factor (Nelf-b), a key pol II-pausing factor, in mouse embryonic fibroblasts. We found that Nelf-b was associated with the promoter-proximal region of the majority of expressed genes, yet genetic ablation of Nelf-b only affected the steady-state mRNA levels of a small percentage of the Nelf-b-associated genes. Interestingly, Nelf-b deletion also increased levels of transcription start site upstream transcripts at multiple negative elongation factor-associated genes. The direct target genes of Nelf-b were highly enriched with those involved in the control of cell growth and cell death. Correspondingly, Nelf-b knock-out mouse embryonic fibroblasts exhibited slower progression from quiescence to proliferation, as well as in a cycling cell population. Furthermore, Nelf-b deletion also resulted in increased apoptosis. Thus, the genetic and genomic studies provide new physiological and molecular insight into Nelf-mediated pol II pausing.

Serum Free Light Chain Assay as a Prognostic Marker in Patients with Aggressive B-Cell Non-Hodgkin's Lymphoma: Impact on Survival Outcome.

T.M. AnoopBackground The role of serum free light chain (FLC) as a prognostic biomarker in lymphoproliferative diseases is being increasingly studied. In this study we present the 5-year survival outcome for patients with aggressive B-cell non-Hodgkin's lymphoma (NHL) and their relation to FLC and other known prognostic markers. Materials and Methods This is a prospective study conducted in patients diagnosed with aggressive B-cell NHL. Serum FLC level and ratio were estimated prior to initiation of treatment. Results A total of 100 patients were included in the study from December 2013 to December 2015 with a median age of 53 years. Thirty-eight patients (38%) had elevated FLC level of which 26% were polyclonal and 12% were monoclonal elevations. Abnormal FLC ratio was noted in 12% patients. Median follow-up duration of the study was 75 months. Five-year relapse-free survival (RFS) for the study population was 54.4%. Five-year RFS was 64.1% for early stage and 48.2% for advanced stage diseases ( p = 0.05). The RFS was significantly better in age less than 60 years (59.5% vs 43.8%, p < 0.001). Five-year overall survival (OS) was 61.3%. OS was significantly better in younger patients (73.6% vs 33.4%, p < 0.001), with International Prognosis Index score of 0 to 2 (87.4% vs 26.7%, p < 0.001). Patients with elevated FLC had inferior RFS (50% vs 71.4%, p = 0.04). Abnormal FLC ratio also strongly corresponded to inferior RFS (54.5% vs 66.2%, p = 0.001). OS was also significantly inferior in patients with abnormal FLC ratio (72.6% vs 63.6%, p = 0.001). Conclusion In patients with newly diagnosed aggressive B-cell NHL, elevated FLC levels and abnormal FLC ratio were significantly associated with inferior survival.

Synchronous Primary Multifocal Skeletal Chondrosarcoma of Extremity: A Report of 2 Cases.

CASE: Multifocal synchronous primary skeletal chondrosarcomas of an extremity are rarely reported. In this study, we report 2 such cases. The first case is a 32-year-old woman who presented with extensive right femoral and tibial diaphysis lesions. The second case is a 36-year-old woman with lesions in the left proximal humerus, the coracoid process of scapula and sternum. Both patients underwent limb salvage surgery and were disease-free at the 38- and 20-month follow-up. CONCLUSION: Athough rare, the possibility of multifocal chondrosarcoma should be kept in mind during the workup of a patient with chondrosarcoma.

Soybean cyst nematode detection and management: a review.

Soybeans play a key role in global food security. U.S. soybean yields, which comprise [Formula: see text] of the total soybeans planted in the world, continue to experience unprecedented grain loss due to the soybean cyst nematode (SCN) plant pathogen. SCN remains one of the primary disruptive pests despite the existence of advanced management techniques such as crop rotation and SCN-resistant varieties. SCN detection is a key step in managing this disease; however, early detection is challenging because soybeans do not show any above ground symptoms unless they  are significantly damaged. Direct soil sampling remains the most common method for SCN detection, however, this method has several problems. For example, the threshold damage methods-adopted by most of the laboratories to make recommendations-is not reliable as it does not consider soil pH, N, P, and K values and relies solely on the egg count instead of assessment of the root infection. To overcome the challenges of manual soil sampling methods, deep learning and hyperspectral imaging are important current topics in precision agriculture for plant disease detection and have been proposed as cost-effective and efficient detection methods that can work at scale. We have reviewed more than 150 research papers focusing on soybean cyst nematodes with an emphasis on deep learning techniques for detection and management. First: we describe soybean vegetation and reproduction stages, SCN life cycles, and factors influencing this disease. Second: we highlight the impact of SCN on soybean yield loss and the challenges associated with its detection. Third: we describe direct sampling methods in which the soil samples are procured and analyzed to evaluate SCN egg counts. Fourth: we highlight the advantages and limitations of these direct methods, then review computer vision- and remote sensing-based detection methods: data collection using ground, aerial, and satellite approaches followed by a review of machine learning methods for image analysis-based soybean cyst nematode detection. We highlight the evaluation approaches and the advantages of overall detection workflow in high-performance and big data environments. Lastly, we discuss various management approaches, such as crop rotation, fertilization, SCN resistant varieties such as PI 88788, and SCN's increasing resistance to these strategies. We review machine learning approaches for soybean crop yield forecasting as well as the influence of pesticides, herbicides, and fertilizers on SCN infestation reduction. We provide recommendations for soybean research using deep learning and hyperspectral imaging to accommodate the lack of the ground truth data and training and testing methodologies, such as data augmentation and transfer learning, to achieve a high level of detection accuracy while keeping costs as low as possible.

Histiocytic Sarcoma: Clinical Features and Outcomes of Patients Treated at a Tertiary Cancer Care Center.

Histiocytic sarcoma (HS) is an extremely rare histiocytic disorder of unknown etiology. It is not a true sarcoma and is named so, due to the pathological resemblance to mature histiocytes. The clinical presentation of HS is diverse and is related to the involved organs. Due to its aggressive nature, with poor prognosis and lack of a standard treatment regimen of choice, its diagnosis and management pose a challenge to the clinician. Limited literature is available on the management of this entity. Here, we report four patients with HS, diagnosed over 15 years in a tertiary cancer center, with varied clinical presentation, management, and outcomes. The first patient presented with a localized unresectable esophageal mass. He was treated with cyclophosphamide, doxorubicin, vincristine, and prednisone (CHOP) combination chemotherapy and attained complete remission. The second patient had a painless mass of the hand, treated with wide excision and adjuvant Radiotherapy. She is disease-free for the past 12 years. The third patient had presented with an anterior mediastinal mass. He had progressive disease on chemotherapy. The fourth patient had multifocal disease with generalized lymphadenopathy. She was treated with CHOP chemotherapy and is now disease-free at 13 months. To summarize, the patients with the localized resectable disease did well, with surgical excision and adjuvant radiotherapy, while patients with the multifocal disease did well on CHOP chemotherapy. The take-home message from this case series is - CHOP off whenever you can and if not give CHOP to chop off the disease.