Biochemical properties of chromatin domains define genome compartmentalization.

Chromatin three-dimensional (3D) organization inside the cell nucleus determines the separation of euchromatin and heterochromatin domains. Their segregation results in the definition of active and inactive chromatin compartments, whereby the local concentration of associated proteins, RNA and DNA results in the formation of distinct subnuclear structures. Thus, chromatin domains spatially confined in a specific 3D nuclear compartment are expected to share similar epigenetic features and biochemical properties, in terms of accessibility and solubility. Based on this rationale, we developed the 4f-SAMMY-seq to map euchromatin and heterochromatin based on their accessibility and solubility, starting from as little as 10 000 cells. Adopting a tailored bioinformatic data analysis approach we reconstruct also their 3D segregation in active and inactive chromatin compartments and sub-compartments, thus recapitulating the characteristic properties of distinct chromatin states. A key novelty of the new method is the capability to map both the linear segmentation of open and closed chromatin domains, as well as their compartmentalization in one single experiment.

Safety and efficacy of percutaneous image-guided ablation for soft tissue sarcoma metastases to the liver.

PURPOSE: To evaluate outcomes following percutaneous image-guided ablation of soft tissue sarcoma metastases to the liver. MATERIALS AND METHODS: A single-institution retrospective analysis of patients with a diagnosis of metastatic soft tissue sarcoma who underwent percutaneous image-guided ablation of hepatic metastases between January 2011 and December 2021 was performed. Patients with less than 60 days of follow-up after ablation were excluded. The primary outcome was local tumor progression-free survival (LPFS). Secondary outcomes included overall survival, liver-specific progression-free survival. and chemotherapy-free survival. RESULTS: Fifty-five patients who underwent percutaneous ablation for 84 metastatic liver lesions were included. The most common histopathological subtypes were leiomyosarcoma (23/55), followed by gastrointestinal stromal tumor (22/55). The median treated liver lesions was 2 (range, 1-8), whereas the median size of metastases were 1.8 cm (0.3-8.7 cm). Complete response at 2 months was achieved in 90.5% of the treated lesions. LPFS was 83% at 1 year and 80% at 2 years. Liver-specific progression-free survival was 66% at 1 year and 40% at 2 years. The overall survival at 1 and 2 years was 98% and 94%. The chemotherapy-free holiday from the start of ablation was 71.2% at 12 months. The complication rate was 3.6% (2/55); one of the complications was Common Terminology Criteria for Adverse Events grade 3 or higher. LPFS subgroup analysis for leiomyosarcoma versus gastrointestinal stromal tumor suggests histology-agnostic outcomes (2 years, 89% vs 82%, p = .35). CONCLUSION: Percutaneous image-guided liver ablation of soft tissue sarcoma metastases is safe and efficacious.

Clinical outcomes of image-guided therapies in patients with adrenocortical carcinoma: a tertiary referral center retrospective study.

BACKGROUND: Image-guided therapies (IGTs) are commonly used in oncology, but their role in adrenocortical carcinoma (ACC) is not well defined. MATERIALS AND METHODS: A retrospective review of patients with ACC treated with IGTs. We assessed response to therapy using RECIST v1.1, time to next line of systemic therapy, disease control rate (DCR), local tumor progression-free survival (LTPFS), and complications of IGTs (based on the Common Terminology Criteria for Adverse Events [CTCAE] version 5.0). RESULTS: Our cohort included 26 patients (median age 56 years [range 38-76]; n = 18 female) who had 51 IGT sessions to treat 86 lesions. IGTs modalities included cryoablation (n = 49), microwave ablation (n = 21), combined microwave and bland trans-arterial embolization (n = 8), bland trans-arterial embolization alone (n = 3), radio-embolization (n = 3), and radiofrequency ablation (n = 2). DCR was 81.4% (70 out of 86), of which 66.3% of tumors showed complete response, 18.6% showed progressive disease, 8.1% showed partial response, and 7.0% showed stable disease. LTPFS rates were 73% and 63% at 1 and 2 years, respectively. Fourteen lesions underwent re-ablation for incomplete response on initial treatment. Sixteen patients (61.5%) received new systemic therapy following IGTs, with a median time to systemic therapy of 12.5 months (95% CI: 8.6 months upper limit not reached). There was 1 reported CTCAE grade 3 adverse event (biloma) following IGT. CONCLUSIONS: IGT use in properly selected patients with ACC is safe and associated with prolonged disease control and delay in the need for systemic therapy.

Organophotoredox Catalysis: Switchable Radical Generation from Alkyl Sodium Sulfinates for Sulfonylation and Alkylative Activation of C-C Bonds of Cyclopropenes.

Generating alkyl radicals from the sulfonyl radicals remains challenging in synthetic chemistry. Here, we report an efficient photocatalyzed strategy using alkyl sodium sulfinates as both sulfonylating and alkylating reagents by controlling the reaction temperature. This methodology provides a versatile protocol for synthesizing diastereoselective sulfonylated cyclopropanes and poly-substituted styrene derivatives. This methodology is successfully demonstrated with a wide variety of cyclopropenes and alkyl sulfinates, showcasing its broad substrate scope, high diastereo- and E/Z selectivity, and yielding good to excellent yields.

A Single-Center Experience with a Shear-Thinning Conformable Embolic.

The purpose of this study was to evaluate the technical success, effectiveness, and safety of transarterial embolization for acute bleeding management with a shear-thinning conformable embolic. This single-center retrospective study evaluated outcomes after embolization using Obsidio conformable embolic (OCE). Technical success was defined as performing transarterial embolization within the target vessel to complete stasis of antegrade flow. Treatment effectiveness was defined as cessation of bleeding for patients. Eleven patients underwent 11 embolization procedures. A total of 16 arteries were embolized. Indications for embolization were spontaneous tumor bleeding (6/11), hematuria (2/11), active duodenal bleeding (1/11), portal hypertensive bleeding (1/11), and rectus sheath hematoma (1/11). The technical success rate was 100%. The median vessel diameter was 2 mm (range, 1-3 mm). There were no adverse events or off-target embolization. OCE demonstrated technical success and treatment effectiveness with a short-term safety profile for transarterial embolization interventions.

Visible light-induced organo-photocatalyzed route to synthesize substituted pyrazoles.

The synthesis of tetra-substituted pyrazoles holds significant synthetic value and has been accomplished through an organo-photocatalyzed decarboxylative intramolecular cyclization using readily available 1,2-diaza-1,3-dienes and α-ketoacids. This method allows for the systematic synthesis of substituted pyrazole derivatives. Notably, this approach is characterized by its metal-free and oxidant-free nature, offering distinct advantages such as short reaction times and exceptionally mild reaction conditions. The developed methodology enables the efficient construction of tetra-substituted pyrazoles, expanding the available chemical space for exploration and opening up potential applications in various scientific fields.

Organophotocatalyzed Mono- and Bis-Alkyl/Difluoroalkylative Thio/Selenocyanation of Alkenes.

Organophotocatalyzed three-component 1,2-difluoroacetyl/alkyl/perfluoroalkylative thio/selenocyanation of styrene derivatives under stoichiometric, transition metal-, oxidant-, and additive-free, and mild redox-neutral conditions is reported. Organophotocatalyst 4CzIPN operates the overall radical-polar-crossover mechanistic cycle via initial oxidative luminescence quenching, and the key intermediates were experimentally detected. Selective mono-alkylative thiocyanation of alkenes using dibromoalkanes is also demonstrated. This one-pot synthetic methodology is suitable for primary, secondary, and tertiary alkyl halides and also extended for double alkylative thiocyanation of the dibromoalkanes with excellent yields.

Leveraging three-dimensional chromatin architecture for effective reconstruction of enhancer-target gene regulatory interactions.

A growing amount of evidence in literature suggests that germline sequence variants and somatic mutations in non-coding distal regulatory elements may be crucial for defining disease risk and prognostic stratification of patients, in genetic disorders as well as in cancer. Their functional interpretation is challenging because genome-wide enhancer-target gene (ETG) pairing is an open problem in genomics. The solutions proposed so far do not account for the hierarchy of structural domains which define chromatin three-dimensional (3D) architecture. Here we introduce a change of perspective based on the definition of multi-scale structural chromatin domains, integrated in a statistical framework to define ETG pairs. In this work (i) we develop a computational and statistical framework to reconstruct a comprehensive map of ETG pairs leveraging functional genomics data; (ii) we demonstrate that the incorporation of chromatin 3D architecture information improves ETG pairing accuracy and (iii) we use multiple experimental datasets to extensively benchmark our method against previous solutions for the genome-wide reconstruction of ETG pairs. This solution will facilitate the annotation and interpretation of sequence variants in distal non-coding regulatory elements. We expect this to be especially helpful in clinically oriented applications of whole genome sequencing in cancer and undiagnosed genetic diseases research.

Comparison of computational methods for Hi-C data analysis.

Hi-C is a genome-wide sequencing technique used to investigate 3D chromatin conformation inside the nucleus. Computational methods are required to analyze Hi-C data and identify chromatin interactions and topologically associating domains (TADs) from genome-wide contact probability maps. We quantitatively compared the performance of 13 algorithms in their analyses of Hi-C data from six landmark studies and simulations. This comparison revealed differences in the performance of methods for chromatin interaction identification, but more comparable results for TAD detection between algorithms.

HiCBricks: building blocks for efficient handling of large Hi-C datasets.

SUMMARY: Genome-wide chromosome conformation capture based on high-throughput sequencing (Hi-C) has been widely adopted to study chromatin architecture by generating datasets of ever-increasing complexity and size. HiCBricks offers user-friendly and efficient solutions for handling large high-resolution Hi-C datasets. The package provides an R/Bioconductor framework with the bricks to build more complex data analysis pipelines and algorithms. HiCBricks already incorporates functions for calling domain boundaries and functions for high quality data visualization. AVAILABILITY: http://bioconductor.org/packages/devel/bioc/html/HiCBricks.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Giant magnetoresistance resulting from superzone gap in spin-frustrated rare-earth-based aluminide: DyFe2Al10.

The magnetic properties of orthorhombic aluminides have recently been the subject of investigation, revealing several intriguing phenomena within this class of materials. However, the exploration of their magnetic and electrical transport phenomena has remained somewhat limited. In this study, we delve into the magnetic and electrical transport characteristics of one such material from that group which is DyFe2Al10(DFA). Our findings go beyond classifying this material as a simple antiferromagnet; but it posses a short range ferromagnetic ordering apart from helical spin structure of Dy3+. It exhibits a metamagnetic transition and spin glass behavior below its Néel temperature (TN). Our analysis of electrical magnetotransport behavior indicates the emergence of an antiferromagnetic superzone gap, resulting in a significant enhancement in magnetoresistance effect. This discovery paves the way for a class of materials with complex interactions and notable magnetoresistance properties.

Impact of social determinants of health on progression from potentially life-threatening complications to near miss events and death during pregnancy and post partum in a middle-income setting: an observational study.

OBJECTIVE: To assess the potential associations between social determinants of health (SDH) and severe maternal outcomes (SMO), to better understand the social structural framework and the contributory, non-clinical mechanisms associated with SMO. STUDY DESIGN: Prospective observational study. STUDY SETTING: Tertiary referral centre in south-eastern region of India. PARTICIPANTS: One thousand and thirty-three women with potentially life-threatening complications (PLTC) were identified using WHO criteria. RISK FACTORS ASSESSED: Social Determinants of Health (SDH). PRIMARY OUTCOMES: Severe maternal outcomes, which include maternal near-miss and maternal death. STATISTICAL ANALYSIS: Logistic regression to assess the association between SDH and clinical factors on SMO, expressed as adjusted ORs (aOR) with a 95% CI. RESULTS: Of the 37 590 live births, 1833 (4.9%) sustained PLTC, and 380 (20.7%) developed SMO. Risk of SMO was higher with increasing maternal age (adjusted OR (aOR) 1.04 (95% CI 1.01 to 1.07)), multiparity (aOR 1.44 (1.10 to 1.90)), medical comorbidities (aOR 1.50 (1.11 to 2.02)), obstetric haemorrhage (aOR 4.63 (3.10 to 6.91)), infection (aOR 2.93 (1.83 to 4.70)), delays in seeking care (aOR 3.30 (2.08 to 5.23)), and admissions following a referral (aOR 2.95 (2.21 to 3.93)). SMO was lower in patients from socially backward community (aOR 0.45 (0.33 to 0.61)), those staying more than 10 km from hospital (aOR 0.56 (0.36 to 0.78)), those attending at least four antenatal visits (aOR=0.53 (0.36 to 0.78)) and those referred from resource-limited facilities (aOR=0.62 (0.46 to 0.84)). CONCLUSION: This study demonstrates the independent contribution of SDH to SMO among those sustaining PLTC in a middle-income setting, highlighting the need to formulate preventive strategies beyond clinical considerations.

Mechanical Venous Thrombectomy for Deep Venous Thrombosis in Cancer Patients: A Single-Center Retrospective Study.

PURPOSE: Venous thromboembolism (VTE) is a major contributor to the mortality of cancer patients. Mechanical thrombectomy (MT) is an endovascular technique that physically removes a thrombus without thrombolytics. The purpose of this study was to evaluate safety, efficacy, and clinical outcomes following MT for lower extremity DVT in cancer patients. METHODS: This single-center, retrospective study evaluated outcomes following MT of lower extremity DVT in cancer patients from November 2019 to May 2023. The primary outcome measure was clinical success, defined as a decrease in Villalta score by at least 2 points following the intervention. Secondary outcomes included repeat intervention-free survival and overall survival. Technical success was defined as restoring venous flow with mild (< 10%) or no residual filling defect. RESULTS: In total, 90 patients and 113 procedures were included. Technical and clinical success was achieved in 81% and 87% of procedures performed. Repeat intervention-free survival at 1 month, 3 months, and 6 months post-procedure was 92%, 82%, and 77%, respectively. The complication rate was 2.7%. Pathologic analysis of the extracted thrombus revealed tumor thrombus in 18.4% (18/98) samples. Overall survival for the study cohort was 87% at 1 month, 74% at 3 months, and 62% at 6 months. Patients who were found to have tumor thrombi were noted to have a decreased overall survival compared to patients with non-tumor thrombi (P = 0.012). CONCLUSION: MT is safe and efficacious in reducing cancer patients' VTE-related symptoms. The high rate of tumor thrombus in thrombectomy specimens suggests this phenomenon is more common than suspected.

A Sticky Situation: Glue Migration during Hepatic Vein Embolization.

The addition of hepatic venous embolization to portal venous embolization to achieve ipsilateral liver venous deprivation before major hepatectomy has been suggested to increase the extent of hypertrophy of the future liver remnant. The presented case discusses a hepatic vein embolization procedure complicated by the unintended migration of a glue cast used to achieve hepatic venous occlusion and subsequent management with endovascular retrieval of the glue cast from the inferior vena cava. The emerging role of hepatic venous embolization and associated complications are also discussed.

Carotid blowout into the trachea: unusual entity with unexpected management outcome.

We present a case report of a patient with a history of aggressive thyroid cancer managed by surgery, chemotherapy, and radiation to the neck. A year later, he presented with hemoptysis. Endobronchial ultrasound showed a pulsatile vessel; however, a CT scan and conventional angiogram were negative. Three days later, a repeat angiogram revealed a pseudoaneurysm arising from the right common carotid artery. Carotid sacrifice was performed after passing balloon test occlusion. Three years later the patient presented with coil herniation into the trachea. The carotid stump was closed with a vascular plug to prevent rebleeding from coil removal. Four months later the patient experienced an intractable cough and underwent laryngoscopy-assisted removal of the residual coil mass. This case report discusses the rare scenario of a carotid blowout into the trachea and the subsequent course of events.

Maternal and perinatal outcome in pregnancies complicated with portal hypertension: a systematic review and meta-analysis.

BACKGROUND: Portal hypertension is secondary to either cirrhotic or non-cirrhotic causes, and complicating pregnancy poses a challenge to the treating team. A systematic review was performed to determine maternal and perinatal outcomes in women with portal hypertension. Outcomes were compared among those with cirrhotic (CPH) with non-cirrhotic portal hypertension (NCPH) as well as non-cirrhotic portal fibrosis (NCPF) with extra-hepatic portal vein obstruction (EHPVO). METHODS: Medline and EMBASE databases were searched for studies reporting outcomes among pregnant women with portal hypertension. Reference lists from relevant papers and reviews were hand-searched for appropriate citations. Data were extracted to describe maternal complications, obstetric and neonatal outcomes. A random-effects model was used to derive pooled estimates of various outcomes, and final estimates were reported as percentages with a 95% confidence interval (CI). Cumulative, sequential and sensitivity analysis was studied to assess the temporal trends of outcomes over the period. RESULTS: Information on 895 pregnancies among 581 patients with portal hypertension was included from 26 studies. Portal hypertension was diagnosed during pregnancy in 10% (95% CI 4-24%). There were 22 maternal deaths (0%, 95% CI 0-1%), mostly following complications from variceal bleeding or hepatic decompensation. Variceal bleeding complicated in 14% (95% CI 9-20%), and endoscopic interventions were performed in 12% (95% CI 8-17%) during pregnancy. Decompensation of liver function occurred in 7% (95% CI 3-12%). Thrombocytopenia was the most common complication (41%, 95% CI 23-60%). Miscarriages occurred in 14% (95% CI 8-20%), preterm birth in 27% (95% CI 19-37%), and low birth weights in 22% (95% CI 15-30%). Risk of postpartum hemorrhage was higher (RR 5.09, 95% CI 1.84-14.12), and variceal bleeding was lower (RR 0.51, 95% CI 0.30-0.86) among those with CPH compared to NCPH. Risk of various outcomes was comparable between NCPF and EHPVO. CONCLUSION: One in ten pregnancies complicated with portal hypertension is diagnosed during pregnancy, and thrombocytopenia is the most common complication. Hepatic decompensation and variceal bleeding remain the most common cause of maternal deaths, with reduced rates of bleeding and its complications reported following the introduction of endoscopic procedures during pregnancy. CPH increases the risk of postpartum hemorrhage, whereas variceal bleeding is higher among NCPH.

Phenolic Phytochemicals for Prevention and Treatment of Colorectal Cancer: A Critical Evaluation of In Vivo Studies.

Colorectal cancer (CRC) is the third most diagnosed and second leading cause of cancer-related death worldwide. Limitations with existing treatment regimens have demanded the search for better treatment options. Different phytochemicals with promising anti-CRC activities have been reported, with the molecular mechanism of actions still emerging. This review aims to summarize recent progress on the study of natural phenolic compounds in ameliorating CRC using in vivo models. This review followed the guidelines of the Preferred Reporting Items for Systematic Reporting and Meta-Analysis. Information on the relevant topic was gathered by searching the PubMed, Scopus, ScienceDirect, and Web of Science databases using keywords, such as "colorectal cancer" AND "phenolic compounds", "colorectal cancer" AND "polyphenol", "colorectal cancer" AND "phenolic acids", "colorectal cancer" AND "flavonoids", "colorectal cancer" AND "stilbene", and "colorectal cancer" AND "lignan" from the reputed peer-reviewed journals published over the last 20 years. Publications that incorporated in vivo experimental designs and produced statistically significant results were considered for this review. Many of these polyphenols demonstrate anti-CRC activities by inhibiting key cellular factors. This inhibition has been demonstrated by antiapoptotic effects, antiproliferative effects, or by upregulating factors responsible for cell cycle arrest or cell death in various in vivo CRC models. Numerous studies from independent laboratories have highlighted different plant phenolic compounds for their anti-CRC activities. While promising anti-CRC activity in many of these agents has created interest in this area, in-depth mechanistic and well-designed clinical studies are needed to support the therapeutic use of these compounds for the prevention and treatment of CRC.

Visualizing and Annotating Hi-C Data.

Epigenomics studies require the combined analysis and integration of multiple types of data and annotations to extract biologically relevant information. In this context, sophisticated data visualization techniques are fundamental to identify meaningful patterns in the data in relation to the genomic coordinates. Data visualization for Hi-C contact matrices is even more complex as each data point represents the interaction between two distant genomic loci and their three-dimensional positioning must be considered. In this chapter we illustrate how to obtain sophisticated plots showing Hi-C data along with annotations for other genomic features and epigenomics data. For the example code used in this chapter we rely on a Bioconductor package able to handle even high-resolution Hi-C datasets. The provided examples are explained in details and highly customizable, thus facilitating their extension and adoption by end users for other studies.

Engineering the Tumor Immune Microenvironment through Minimally Invasive Interventions.

The tumor microenvironment (TME) is a unique landscape that poses several physical, biochemical, and immune barriers to anti-cancer therapies. The rapidly evolving field of immuno-engineering provides new opportunities to dismantle the tumor immune microenvironment by efficient tumor destruction. Systemic delivery of such treatments can often have limited local effects, leading to unwanted offsite effects such as systemic toxicity and tumor resistance. Interventional radiologists use contemporary image-guided techniques to locally deliver these therapies to modulate the immunosuppressive TME, further accelerating tumor death and invoking a better anti-tumor response. These involve local therapies such as intratumoral drug delivery, nanorobots, nanoparticles, and implantable microdevices. Physical therapies such as photodynamic therapy, electroporation, hyperthermia, hypothermia, ultrasound therapy, histotripsy, and radiotherapy are also available for local tumor destruction. While the interventional radiologist can only locally manipulate the TME, there are systemic offsite recruitments of the immune response. This is known as the abscopal effect, which leads to more significant anti-tumoral downstream effects. Local delivery of modern immunoengineering methods such as locoregional CAR-T therapy combined with immune checkpoint inhibitors efficaciously modulates the immunosuppressive TME. This review highlights the various advances and technologies available now to change the TME and revolutionize oncology from a minimally invasive viewpoint.

Prostate cancer: Therapeutic prospect with herbal medicine.

Prostate cancer (PCa) is a major cause of morbidity and mortality in men worldwide. A geographic variation on the burden of the disease suggested that the environment, genetic makeup, lifestyle, and food habits modulate one's susceptibility to the disease. Although it has been generally thought to be an older age disease, and awareness and timely execution of screening programs have managed to contain the disease in the older population over the last decades, the incidence is still increasing in the population younger than 50. Existing treatment is efficient for PCa that is localized and responsive to androgen. However, the androgen resistant and metastatic PCa are challenging to treat. Conventional radiation and chemotherapies are associated with severe side effects in addition to being exorbitantly expensive. Many isolated phytochemicals and extracts of plants used in traditional medicine are known for their safety and diverse healing properties, including many with varying levels of anti-PCa activities. Many of the phytochemicals discussed here, as shown by many laboratories, inhibit tumor cell growth and proliferation by interfering with the components in the pathways responsible for the enhanced proliferation, metabolism, angiogenesis, invasion, and metastasis in the prostate cells while upregulating the mechanisms of cell death and cell cycle arrest. Notably, many of these agents simultaneously target multiple cellular pathways. We analyzed the available literature and provided an update on this issue in this review article.