Pioneer-like factor GAF cooperates with PBAP (SWI/SNF) and NURF (ISWI) to regulate transcription.

Transcriptionally silent genes must be activated throughout development. This requires nucleosomes be removed from promoters and enhancers to allow transcription factor (TF) binding and recruitment of coactivators and RNA polymerase II (Pol II). Specialized pioneer TFs bind nucleosome-wrapped DNA to perform this chromatin opening by mechanisms that remain incompletely understood. Here, we show that GAGA factor (GAF), a Drosophila pioneer-like factor, functions with both SWI/SNF and ISWI family chromatin remodelers to allow recruitment of Pol II and entry to a promoter-proximal paused state, and also to promote Pol II's transition to productive elongation. We found that GAF interacts with PBAP (SWI/SNF) to open chromatin and allow Pol II to be recruited. Importantly, this activity is not dependent on NURF as previously proposed; however, GAF also synergizes with NURF downstream from this process to ensure efficient Pol II pause release and transition to productive elongation, apparently through its role in precisely positioning the +1 nucleosome. These results demonstrate how a single sequence-specific pioneer TF can synergize with remodelers to activate sets of genes. Furthermore, this behavior of remodelers is consistent with findings in yeast and mice, and likely represents general, conserved mechanisms found throughout eukarya.

An improved auxin-inducible degron system preserves native protein levels and enables rapid and specific protein depletion.

Rapid perturbation of protein function permits the ability to define primary molecular responses while avoiding downstream cumulative effects of protein dysregulation. The auxin-inducible degron (AID) system was developed as a tool to achieve rapid and inducible protein degradation in nonplant systems. However, tagging proteins at their endogenous loci results in chronic auxin-independent degradation by the proteasome. To correct this deficiency, we expressed the auxin response transcription factor (ARF) in an improved inducible degron system. ARF is absent from previously engineered AID systems but is a critical component of native auxin signaling. In plants, ARF directly interacts with AID in the absence of auxin, and we found that expression of the ARF PB1 (Phox and Bem1) domain suppresses constitutive degradation of AID-tagged proteins. Moreover, the rate of auxin-induced AID degradation is substantially faster in the ARF-AID system. To test the ARF-AID system in a quantitative and sensitive manner, we measured genome-wide changes in nascent transcription after rapidly depleting the ZNF143 transcription factor. Transcriptional profiling indicates that ZNF143 activates transcription in cis and regulates promoter-proximal paused RNA polymerase density. Rapidly inducible degradation systems that preserve the target protein's native expression levels and patterns will revolutionize the study of biological systems by enabling specific and temporally defined protein dysregulation.

Kinetic networks identify TWIST2 as a key regulatory node in adipogenesis.

Adipocytes contribute to metabolic disorders such as obesity, diabetes, and atherosclerosis. Prior characterizations of the transcriptional network driving adipogenesis have overlooked transiently acting transcription factors (TFs), genes, and regulatory elements that are essential for proper differentiation. Moreover, traditional gene regulatory networks provide neither mechanistic details about individual regulatory element-gene relationships nor temporal information needed to define a regulatory hierarchy that prioritizes key regulatory factors. To address these shortcomings, we integrate kinetic chromatin accessibility (ATAC-seq) and nascent transcription (PRO-seq) data to generate temporally resolved networks that describe TF binding events and resultant effects on target gene expression. Our data indicate which TF families cooperate with and antagonize each other to regulate adipogenesis. Compartment modeling of RNA polymerase density quantifies how individual TFs mechanistically contribute to distinct steps in transcription. The glucocorticoid receptor activates transcription by inducing RNA polymerase pause release, whereas SP and AP-1 factors affect RNA polymerase initiation. We identify Twist2 as a previously unappreciated effector of adipocyte differentiation. We find that TWIST2 acts as a negative regulator of 3T3-L1 and primary preadipocyte differentiation. We confirm that Twist2 knockout mice have compromised lipid storage within subcutaneous and brown adipose tissue. Previous phenotyping of Twist2 knockout mice and Setleis syndrome Twist2 -/- patients noted deficiencies in subcutaneous adipose tissue. This network inference framework is a powerful and general approach for interpreting complex biological phenomena and can be applied to a wide range of cellular processes.

Molecular mechanisms driving transcriptional stress responses.

Proteotoxic stress, that is, stress caused by protein misfolding and aggregation, triggers the rapid and global reprogramming of transcription at genes and enhancers. Genome-wide assays that track transcriptionally engaged RNA polymerase II (Pol II) at nucleotide resolution have provided key insights into the underlying molecular mechanisms that regulate transcriptional responses to stress. In addition, recent kinetic analyses of transcriptional control under heat stress have shown how cells 'prewire' and rapidly execute genome-wide changes in transcription while concurrently becoming poised for recovery. The regulation of Pol II at genes and enhancers in response to heat stress is coupled to chromatin modification and compartmentalization, as well as to co-transcriptional RNA processing. These mechanistic features seem to apply broadly to other coordinated genome-regulatory responses.

Heart rate score in remote monitoring: An additional tool for predicting outcomes in heart failure with reduced ejection fraction.

BACKGROUND: Heart rate score (HRS) ≥ 70% has been associated with arrhythmic events and mortality but these studies were not specific for heart failure (HF) patients. We hypothesized that HRS ≥ 70% obtained from remote monitoring (RM) is associated with HF hospitalizations and arrhythmic events in HF with reduced ejection fraction (HFrEF). METHODS: HRS was calculated from RM in patients with HFrEF and ICD or CRT-D. Two groups were defined: HRS ≥ 70% (G1, n = 55) and HRS < 70% (G2, n = 48) RESULTS: A total of 103 patients were included (64.4 ± 13.04 years, 69.9% male, mean left ventricular ejection fraction (LVEF) 33.62 ± 11.97% and FUP 61.7 ± 38.87 months). The device was CRT-D in 59.2% and ICD in 40.8% and the majority (90.3%) had the device implanted in primary prevention. G1 patients were more frequently male (p = .017) and had more coronary disease (p = .035). HRS ≥70% was an independent predictor for unplanned HF hospitalizations (OR: 1.905 (95% CI: 1.328-3.649), p < .001)). The indication for device implantation (primary vs. secondary prevention), type of device, NYHA class, age, gender and LVEF were not independent predictors of the outcome. VF (4.9 ± 20.0 G1 vs. 1.1 ± 5.47 G2, p = .046) and VT episodes were more prevalent in G1 (3.1 ± 8.93 G1 vs. 0.3 ± 1.59 G2, p = .026), as well as appropriate device shocks (4.3 ± 12.06 G1 vs. 0.3 ± 1.49 G2, p = .023). There was no difference in inappropriate shocks or mortality outcomes between groups. CONCLUSION: HRS ≥70% obtained from RM was an independent predictor of HF hospitalizations and was associated with arrhythmic events with VT and VF episodes and appropriate device shocks in HFrEF patients.

Mammalian Heat Shock Response and Mechanisms Underlying Its Genome-wide Transcriptional Regulation.

The heat shock response (HSR) is critical for survival of all organisms. However, its scope, extent, and the molecular mechanism of regulation are poorly understood. Here we show that the genome-wide transcriptional response to heat shock in mammals is rapid and dynamic and results in induction of several hundred and repression of several thousand genes. Heat shock factor 1 (HSF1), the "master regulator" of the HSR, controls only a fraction of heat shock-induced genes and does so by increasing RNA polymerase II release from promoter-proximal pause. Notably, HSF2 does not compensate for the lack of HSF1. However, serum response factor appears to transiently induce cytoskeletal genes independently of HSF1. The pervasive repression of transcription is predominantly HSF1-independent and is mediated through reduction of RNA polymerase II pause release. Overall, mammalian cells orchestrate rapid, dynamic, and extensive changes in transcription upon heat shock that are largely modulated at pause release, and HSF1 plays a limited and specialized role.

Transcription factors GAF and HSF act at distinct regulatory steps to modulate stress-induced gene activation.

The coordinated regulation of gene expression at the transcriptional level is fundamental to development and homeostasis. Inducible systems are invaluable when studying transcription because the regulatory process can be triggered instantaneously, allowing the tracking of ordered mechanistic events. Here, we use precision run-on sequencing (PRO-seq) to examine the genome-wide heat shock (HS) response in Drosophila and the function of two key transcription factors on the immediate transcription activation or repression of all genes regulated by HS. We identify the primary HS response genes and the rate-limiting steps in the transcription cycle that GAGA-associated factor (GAF) and HS factor (HSF) regulate. We demonstrate that GAF acts upstream of promoter-proximally paused RNA polymerase II (Pol II) formation (likely at the step of chromatin opening) and that GAF-facilitated Pol II pausing is critical for HS activation. In contrast, HSF is dispensable for establishing or maintaining Pol II pausing but is critical for the release of paused Pol II into the gene body at a subset of highly activated genes. Additionally, HSF has no detectable role in the rapid HS repression of thousands of genes.

Chronic constrictive pericarditis: a rare cardiac involvement in primary Sjögren's syndrome.

BACKGROUND: Constrictive pericarditis represents a chronic condition and systemic inflammatory diseases are a known, yet uncommon, cause. Pericardial involvement is seldom reported in primary Sjögren's syndrome, usually occurring in association with pericardial effusion or pericarditis. We report a case of constrictive pericarditis with an insidious course and unusual evolution associated with primary Sjögren's syndrome. Due to the challenging nature of the diagnosis, clinical suspicion and multimodality imaging are essential for early identification and prompt initiation of treatment. Long-term outcomes remain uncertain. To the best of our knowledge, no other cases linking this autoimmune disease to constrictive pericarditis have been reported. CASE PRESENTATION: We present the case of a 48-year-old male patient with moderate alcohol habits and a history of two prior hospitalizations. On the first, the patient was diagnosed with primary Sjögren's syndrome after presenting with pleural effusion and ascites, and empirical corticosteroid regiment was initiated. On the second, two-years later, he was readmitted with complaints of dyspnea and abdominal distension. Thoracic computed tomography revealed a localized pericardial thickening and a thin pericardial effusion, both of which were attributed to his rheumatic disease. A liver biopsy showed hepatic peliosis, which was considered to be a consequence of glucocorticoid therapy. Diuretic therapy was adjusted to symptom-relief, and a tapering corticosteroid regimen was adopted. Four years after the initial diagnosis, the patient was admitted again with recurrent dyspnea, orthopnea and ascites. At this time, constrictive pericarditis was diagnosed and a partial pericardiectomy was performed. Although not completely asymptomatic, the patient reported clinical improvement since the surgery, but still with a need for baseline diuretic therapy. CONCLUSION: Albeit uncommon, connective tissue disorders, such as primary Sjögren's syndrome, should be considered as a potential cause of constrictive pericarditis, especially in young patients with no other classical risk factors for constriction. In this case, after excluding possible infectious, neoplastic and autoimmune conditions, a primary Sjögren´s syndrome in association with constrictive pericarditis was assumed. This case presents an interesting and challenging clinical scenario, highlighting the importance of clinical awareness and the use of multimodal cardiac imaging for early recognition and treatment.

Contact allergy to a subcutaneous implantable cardiac defibrillator - A rare problem with a golden solution.

Contact allergy to implantable cardiac defibrillators (ICD) is an uncommon and underdiagnosed complication. We report a case of a 20-years-old man patient that was resuscitated from sudden cardiac death. Workup imaging study was unremarkable, but genetic testing identified a mutation in the KCNH2 gene of uncertain significance. The patient underwent a subcutaneous implantable cardiac defibrillator (S-ICD) implantation, with no complications. The patient suffered two hospital re-admissions due to a device-related inflammatory reaction, leading to two device re-implantations. At the first time, it was considered a bacterial infection and the S-ICD was replaced by an endovascular device. At the second time, a tissue-device interaction, with hypersensitivity reaction and device rejection was suspected. The skin patch-tests were inconclusive, but it was decided to implant a custom-made gold-coated endovascular ICD. Indeed, the tendency is an initial misdiagnosis as an infection and a high clinical suspicion is essential to an early diagnosis.

Defining data-driven primary transcript annotations with primaryTranscriptAnnotation in R.

SUMMARY: Nascent transcript measurements derived from run-on sequencing experiments are critical for the investigation of transcriptional mechanisms and regulatory networks. However, conventional mRNA gene annotations significantly differ from the boundaries of primary transcripts. New primary transcript annotations are needed to accurately interpret run-on data. We developed the primaryTranscriptAnnotation R package to infer the transcriptional start and termination sites of primary transcripts from genomic run-on data. We then used these inferred coordinates to annotate transcriptional units identified de novo. This package provides the novel utility to integrate data-driven primary transcript annotations with transcriptional unit coordinates identified in an unbiased manner. Highlighting the importance of using accurate primary transcript coordinates, we demonstrate that this new methodology increases the detection of differentially expressed transcripts and provides more accurate quantification of RNA polymerase pause indices. AVAILABILITY AND IMPLEMENTATION: https://github.com/WarrenDavidAnderson/genomicsRpackage/tree/master/primaryTranscriptAnnotation. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

High-throughput binding characterization of RNA aptamer selections using a microplate-based multiplex microcolumn device.

We describe a versatile 96-well microplate-based device that utilizes affinity microcolumn chromatography to complement downstream plate-based processing in aptamer selections. This device is reconfigurable and is able to operate in serial and/or parallel mode with up to 96 microcolumns. We demonstrate the utility of this device by simultaneously performing characterizations of target binding using five RNA aptamers and a random library. This was accomplished through 96 total selection tests. Three sets of selections tested the effects of target concentration on aptamer binding compared to the random RNA library using aptamers to the proteins green fluorescent protein (GFP), human heat shock factor 1 (hHSF1), and negative elongation factor E (NELF-E). For all three targets, we found significant effects consistent with steric hindrance with optimum enrichments at predictable target concentrations. In a fourth selection set, we tested the partitioning efficiency and binding specificity of our three proteins' aptamers, as well as two suspected background binding sequences, to eight targets running serially. The targets included an empty microcolumn, three affinity resins, three specific proteins, and a non-specific protein control. The aptamers showed significant enrichments only on their intended targets. Specifically, the hHSF1 and NELF-E aptamers enriched over 200-fold on their protein targets, and the GFP aptamer enriched 750-fold. By utilizing our device's plate-based format with other complementary plate-based systems for all downstream biochemical processes and analysis, high-throughput selections, characterizations, and optimization were performed to significantly reduce the time and cost for completing large-scale aptamer selections.

Systemic disease presenting as cardiac tamponade: a case report.

Background: Systemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by multisystem inflammation and is a common cause of pericarditis and pericardial effusion, but significant pericardial effusion and cardiac tamponade are rare and even rarer as the first manifestation. Case summary: We report the case of a young male who presented with fever, recurrent pericarditis, and polyserositis with pericardial and bilateral pleural effusion. On examination, he was haemodynamically unstable and the pericardial effusion had considerable dimensions and an urgent pericardiocentesis was performed. Antinuclear antibody with a speckled pattern was positive, complement C4 levels were low, and the remaining autoimmunity and infectious study was unremarkable. Considering the European League Against Rheumatism/American College of Rheumatology classification criteria for SLE, a score of 11 points was obtained, confirming the diagnosis of SLE. Discussion: This case report illustrates a rare form of presentation of SLE, in which the first manifestation was pericarditis with polyserositis and cardiac tamponade.

Heart surgery waiting list management in an ultra-peripheral region: impact of a risk-stratified queuing method.

BACKGROUND: The management of heart surgery waiting list is essential, particularly in ultraperipheral regions. We aimed to characterise a cohort of patients awaiting surgery in such a region, and to assess the occurrence of adverse events and causative factors. METHODS: A retrospective, multicentre analysis from 2016 to 2020. Patients were divided into "Urgent group" vs "Priority group" based on surgical priority. A composite outcome of death or hospital admission was determined. RESULTS: We included 329 patients, 18.2% in the Urgent group. Baseline characteristics were similar, except for a higher prevalence of smoking habits in the Urgent group (56.7% vs 38.7%, p = 0.016), as well as the CCS class (p = 0.014) and EuroScore surgical risk (p < 0.001). Disease acuity indicated highest priority for coronary artery bypass grafting patients. Myocardial revascularization and aortic valvular replacement were the main procedures. Overall, 15.2% of patients received treatment within recommended waiting time, with 50.8% being Urgent patients. Urgent patients had higher risk for composite outcome (HR 3.92, 95% CI 1.26-12.22; p = 0.019), with fewer events reported (5% vs 17.8%, p = 0.051). Chronic kidney disease and previous open-heart surgery were independent predictors of this outcome. Chronic kidney disease remained as independent predictor at 1-year follow-up, while surgical priority did not affect outcomes. CONCLUSIONS: Despite similar occurrences of adverse events on the waiting list, longer waiting times for patients in the Urgent group increase their risk of adverse events. The priority level had no impact on outcomes. Chronic kidney disease and open-heart surgery were independent predictors for events, highlighting their significance in the triage process.

Nonbacterial thrombotic endocarditis of mitral valve associated with a lymphoproliferative malignancy: case report and literature review.

BACKGROUND: Non-bacterial thrombotic endocarditis (NBTE) is a rare condition marked by sterile vegetations on cardiac valves, often linked to rheumatologic diseases, autoimmune disorders, and advanced solid malignancies. An early diagnosis and treatment of the associated clinical condition are mandatory, although they do not usually eliminate valvular vegetations, making anticoagulation essential to prevent embolic events. Despite variability, the prognosis of NBTE is usually unfavorable due to recurrent embolic events and the severity of the primary condition, typically advanced cancer. CASE PRESENTATION: We present a case of a 57 years-old male who presented to the emergency department with a 5-day history of painful bilateral digital edema and color change episodes (from pallor to cyanosis). Physical examination revealed erythrocyanosis in the distal extremities, prompting consideration of secondary Raynaud syndrome. Despite medical therapy, progressive digital ischemia led to multiple finger amputations. During etiological investigation, anticoagulation tests and autoimmune analysis yielded negative results. A transesophageal echocardiogram was performed, revealing an irregular hyperechogenic mass on the anterior leaflet of the mitral valve without valve dysfunction, and a thoracic computed tomography scan with contrast showed an enlarged right paratracheal lymph node. Histopathological analysis from a transthoracic needle biopsy of the paratracheal lymph node revealed diffuse large B-cell lymphoma. The patient underwent aggressive R-CHOP chemotherapy, achieving a favorable complete response. CONCLUSION: This is a particular case involving the occurrence of NBTE and Raynaud phenomenon as the initial paraneoplastic manifestations in a previously healthy young man. Reports of NBTE associated with lymphoproliferative conditions are quite rare, with fewer than ten cases described in the literature. To our knowledge, this is the first case of NBTE specifically associated with diffuse large B-cell lymphoma.

Cell of origin epigenetic priming determines susceptibility to Tet2 mutation.

Hematopoietic stem cell (HSC) mutations can result in clonal hematopoiesis (CH) with heterogeneous clinical outcomes. Here, we investigate how the cell state preceding Tet2 mutation impacts the pre-malignant phenotype. Using an inducible system for clonal analysis of myeloid progenitors, we find that the epigenetic features of clones at similar differentiation status are highly heterogeneous and functionally respond differently to Tet2 mutation. Cell differentiation stage also influences Tet2 mutation response indicating that the cell of origin's epigenome modulates clone-specific behaviors in CH. Molecular features associated with higher risk outcomes include Sox4 that sensitizes cells to Tet2 inactivation, inducing dedifferentiation, altered metabolism and increasing the in vivo clonal output of mutant cells, as confirmed in primary GMP and HSC models. Our findings validate the hypothesis that epigenetic features can predispose specific clones for dominance, explaining why identical genetic mutations can result in different phenotypes.

Multiplexed microcolumn-based process for efficient selection of RNA aptamers.

We describe a reusable microcolumn and process for the efficient discovery of nucleic acid aptamers for multiple target molecules. The design of our device requires only microliter volumes of affinity chromatography resin-a condition that maximizes the enrichment of target-binding sequences over non-target-binding (i.e., background) sequences. Furthermore, the modular design of the device accommodates a multiplex aptamer selection protocol. We optimized the selection process performance using microcolumns filled with green fluorescent protein (GFP)-immobilized resin and monitoring, over a wide range of experimental conditions, the enrichment of a known GFP-binding RNA aptamer (GFPapt) against a random RNA aptamer library. We validated the multiplex approach by monitoring the enrichment of GFPapt in de novo selection experiments with GFP and other protein preparations. After only three rounds of selection, the cumulative GFPapt enrichment on the GFP-loaded resin was greater than 10(8) with no enrichment for the other nonspecific targets. We used this optimized protocol to perform a multiplex selection to two human heat shock factor (hHSF) proteins, hHSF1 and hHSF2. High-throughput sequencing was used to identify aptamers for each protein that were preferentially enriched in just three selection rounds, which were confirmed and isolated after five rounds. Gel-shift and fluorescence polarization assays showed that each aptamer binds with high-affinity (KD < 20 nM) to the respective targets. The combination of our microcolumns with a multiplex approach and high-throughput sequencing enables the selection of aptamers to multiple targets in a high-throughput and efficient manner.

Acute Chest Pain and Electrical Alternans.

A young man presented with acute stabbing chest pain. A 12-lead electrocardiogram revealed electrical alternans with phasic variation of the QRS amplitude in all leads. Lung auscultation revealed absent left hemithorax breath sounds. Chest radiography confirmed a left-sided tension pneumothorax. Tension pneumothorax is a very rare cause for electrical alternans. (Level of Difficulty: Intermediate.).

Primary cardiac lymphoma: The unusual suspect and the importance of a multimodality approach.

Primary cardiac lymphomas are rare tumors with heterogeneous presentation, often difficult to diagnose, requiring a high level of clinical suspicion. An attempted diagnosis is fundamental for effective treatment. We report a very rare case of a primary cardiac lymphoma in a middle-age female patient that presented with atrial flutter, atrioventricular conduction disorder, and a secondary autoimmune hemolytic anemia with cold agglutinin syndrome. The investigation was challenging and a definite diagnosis was achieved by histopathological study and corroborated by regression after chemotherapy. Learning objectives: Primary cardiac tumors are rare, often difficult to diagnose, and a multimodality imaging approach is essential for diagnosis. Although complete atrioventricular (AV) block is often an indication for permanent pacemaker, reversible causes should be considered. AV blocks caused by infiltration of lymphoma can resolve after effective treatment and so it may be reasonable to delay pacemaker implantation until after treatment. A multidisciplinary approach is fundamental in complex cases.

Single-cell multi-scale footprinting reveals the modular organization of DNA regulatory elements.

Cis-regulatory elements control gene expression and are dynamic in their structure, reflecting changes to the composition of diverse effector proteins over time1-3. Here we sought to connect the structural changes at cis-regulatory elements to alterations in cellular fate and function. To do this we developed PRINT, a computational method that uses deep learning to correct sequence bias in chromatin accessibility data and identifies multi-scale footprints of DNA-protein interactions. We find that multi-scale footprints enable more accurate inference of TF and nucleosome binding. Using PRINT with single-cell multi-omics, we discover wide-spread changes to the structure and function of candidate cis-regulatory elements (cCREs) across hematopoiesis, wherein nucleosomes slide, expose DNA for TF binding, and promote gene expression. Activity segmentation using the co-variance across cell states identifies "sub-cCREs" as modular cCRE subunits of regulatory DNA. We apply this single-cell and PRINT approach to characterize the age-associated alterations to cCREs within hematopoietic stem cells (HSCs). Remarkably, we find a spectrum of aging alterations among HSCs corresponding to a global gain of sub-cCRE activity while preserving cCRE accessibility. Collectively, we reveal the functional importance of cCRE structure across cell states, highlighting changes to gene regulation at single-cell and single-base-pair resolution.

Systematic benchmarking of single-cell ATAC-sequencing protocols.

Single-cell assay for transposase-accessible chromatin by sequencing (scATAC-seq) has emerged as a powerful tool for dissecting regulatory landscapes and cellular heterogeneity. However, an exploration of systemic biases among scATAC-seq technologies has remained absent. In this study, we benchmark the performance of eight scATAC-seq methods across 47 experiments using human peripheral blood mononuclear cells (PBMCs) as a reference sample and develop PUMATAC, a universal preprocessing pipeline, to handle the various sequencing data formats. Our analyses reveal significant differences in sequencing library complexity and tagmentation specificity, which impact cell-type annotation, genotype demultiplexing, peak calling, differential region accessibility and transcription factor motif enrichment. Our findings underscore the importance of sample extraction, method selection, data processing and total cost of experiments, offering valuable guidance for future research. Finally, our data and analysis pipeline encompasses 169,000 PBMC scATAC-seq profiles and a best practices code repository for scATAC-seq data analysis, which are freely available to extend this benchmarking effort to future protocols.