Prognostic value of ultra-low-pass whole-genome sequencing of circulating tumor DNA in hepatocellular carcinoma under systemic treatment.

BACKGROUND/AIMS: New prognostic markers are needed to identify patients with hepatocellular carcinoma (HCC) who carry a worse prognosis. Ultra-low-pass whole-genome sequencing (ULP-WGS) (≤0.5× coverage) of cell-free DNA (cfDNA) has emerged as a low-cost promising tool to assess both circulating tumor DNA (ctDNA) fraction and large structural genomic alterations. Here, we studied the performance of ULP-WGS of plasma cfDNA to infer prognosis in patients with HCC. METHODS: Plasma samples were obtained from patients with HCC prior to surgery, locoregional or systemic therapy, and were analyzed by ULP-WGS of cfDNA to an average genome-wide fold coverage of 0.3x. ctDNA and copy number alterations (CNA) were estimated using the software package ichorCNA. RESULTS: Samples were obtained from 73 HCC patients at different BCLC stages (BCLC 0/A: n=37, 50.7%; BCLC B/C: n=36, 49.3%). ctDNA was detected in 18 out of 31 patients who received systemic treatment. Patients with detectable ctDNA showed significantly worse overall survival (median, 13.96 months vs not reached). ctDNA remained an independent predictor of prognosis after adjustment by clinical-pathologic features and type of systemic treatment (hazard ratio 7.69; 95%, CI 2.09-28.27). Among ctDNA-positive patients under systemic treatments, the loss of large genomic regions in 5q and 16q arms was associated with worse prognosis after multivariate analysis. CONCLUSION: ULP-WGS of cfDNA provides clinically relevant information about the tumor biology. The presence of ctDNA and the loss of 5q and 16q arms in ctDNA-positive patients are independent predictors of worse prognosis in patients with advanced HCC receiving systemic therapy.

In vivo screening characterizes chromatin factor functions during normal and malignant hematopoiesis.

Cellular differentiation requires extensive alterations in chromatin structure and function, which is elicited by the coordinated action of chromatin and transcription factors. By contrast with transcription factors, the roles of chromatin factors in differentiation have not been systematically characterized. Here, we combine bulk ex vivo and single-cell in vivo CRISPR screens to characterize the role of chromatin factor families in hematopoiesis. We uncover marked lineage specificities for 142 chromatin factors, revealing functional diversity among related chromatin factors (i.e. barrier-to-autointegration factor subcomplexes) as well as shared roles for unrelated repressive complexes that restrain excessive myeloid differentiation. Using epigenetic profiling, we identify functional interactions between lineage-determining transcription factors and several chromatin factors that explain their lineage dependencies. Studying chromatin factor functions in leukemia, we show that leukemia cells engage homeostatic chromatin factor functions to block differentiation, generating specific chromatin factor-transcription factor interactions that might be therapeutically targeted. Together, our work elucidates the lineage-determining properties of chromatin factors across normal and malignant hematopoiesis.

Multi-Temporal Satellite Investigation of gas Flaring in Iraq and Iran: The DAFI Porting on Collection 2 Landsat 8/9 and Sentinel 2A/B.

The synergic use of satellite data at moderate spatial resolution (i.e., 20-30 m) from the new Collection 2 (C2) Landsat-8/9 (L8/9) Operational Land Imager (OLI) and Sentinel-2 (S2) Multispectral Instrument (MSI) provides a new perspective in the remote sensing applications for gas flaring (GF) identification and monitoring, thanks to a significant improvement in the revisiting time (up to ~3 days). In this study, the daytime approach for gas flaring investigation (DAFI), recently developed for identifying, mapping and monitoring GF sites on a global scale using the L8 infrared radiances, has been ported on a virtual constellation (VC) (formed by C2 L8/9 + S2) to assess its capability in understanding the GF characteristics in the space-time domain. The findings achieved for the regions of Iraq and Iran, ranked at the second and third level among the top 10 gas flaring countries in 2022, demonstrate the reliability of the developed system, with improved levels of accuracy and sensitivity (+52%). As an outcome of this study, a more realistic picture of GF sites and their behavior is achieved. A new step aimed at quantifying the GFs radiative power (RP) has been added in the original DAFI configuration. The preliminary analysis of the daily OLI- and MSI-based RP, provided for all the sites by means of a modified RP formulation, revealed their good matching. An agreement of 90% and 70% between the annual RPs computed in Iraq and Iran and both their gas-flared volumes and carbon dioxide emissions were also recorded. Being that gas flaring is one of the main sources of greenhouse gases (GHG) worldwide, the RP products may concur to infer globally the GHGs GF emissions at finer spatial scales. For the presented achievements, DAFI can be seen as a powerful satellite tool able to automatically assess the gas flaring dimension on a global scale.

Photodynamic nasal SARS-CoV-2 decolonization shortens infectivity and influences specific T-Cell responses.

Background: The main objective was to evaluate the efficacy of intranasal photodynamic therapy (PDT) in SARS-CoV-2 mildly symptomatic carriers on decreasing the infectivity period. SARS-CoV-2-specific immune-stimulating effects and safety were also analysed. Methods: We performed a randomized, placebo-controlled, clinical trial in a tertiary hospital (NCT05184205). Patients with a positive SARS-CoV-2 PCR in the last 48 hours were recruited and aleatorily assigned to PDT or placebo. Patients with pneumonia were excluded. Participants and investigators were masked to group assignment. The primary outcome was the reduction in in vitro infectivity of nasopharyngeal samples at days 3 and 7. Additional outcomes included safety assessment and quantification of humoral and T-cell immune-responses. Findings: Patients were recruited between December 2021 and February 2022. Most were previously healthy adults vaccinated against COVID-19 and most carried Omicron variant. 38 patients were assigned to placebo and 37 to PDT. Intranasal PDT reduced infectivity at day 3 post-treatment when compared to placebo with a ß-coefficient of -812.2 (CI95%= -478660 - -1.3, p<0.05) infectivity arbitrary units. The probability of becoming PCR negative (ct>34) at day 7 was higher on the PDT-group, with an OR of 0.15 (CI95%=0.04-0.58). There was a decay in anti-Spike titre and specific SARS-CoV-2 T cell immunity in the placebo group 10 and 20 weeks after infection, but not in the PDT-group. No serious adverse events were reported. Interpretation: Intranasal-PDT is safe in pauci-symptomatic COVID-19 patients, it reduces SARS-CoV-2 infectivity and decelerates the decline SARS-CoV-2 specific immune-responses.

Implementation of the NHI (Normalized Hot Spot Indices) Algorithm on Infrared ASTER Data: Results and Future Perspectives.

The Normalized Hotspot Indices (NHI) tool is a Google Earth Engine (GEE)-App developed to investigate and map worldwide volcanic thermal anomalies in daylight conditions, using shortwave infrared (SWIR) and near infrared (NIR) data from the Multispectral Instrument (MSI) and the Operational Land Imager (OLI), respectively, onboard the Sentinel 2 and Landsat 8 satellites. The NHI tool offers the possibility of ingesting data from other sensors. In this direction, we tested the NHI algorithm for the first time on Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) data. In this study, we show the results of this preliminary implementation, achieved investigating the Kilauea (Hawaii, USA), Klyuchevskoy (Kamchatka; Russia), Shishaldin (Alaska; USA), and Telica (Nicaragua) thermal activities of March 2000-2008. We assessed the NHI detections through comparison with the ASTER Volcano Archive (AVA), the manual inspection of satellite imagery, and the information from volcanological reports. Results show that NHI integrated the AVA observations, with a percentage of unique thermal anomaly detections ranging between 8.8% (at Kilauea) and 100% (at Shishaldin). These results demonstrate the successful NHI exportability to ASTER data acquired before the failure of SWIR subsystem. The full ingestion of the ASTER data collection, available in GEE, within the NHI tool allows us to develop a suite of multi-platform satellite observations, including thermal anomaly products from Landsat Thematic Mapper (TM) and Enhanced Thematic Mapper Plus (ETM+), which could support the investigation of active volcanoes from space, complementing information from other systems.

The short life of the volcanic island New Late'iki (Tonga) analyzed by multi-sensor remote sensing data.

Satellite-based Earth observation plays a key role for monitoring volcanoes, especially those which are located in remote areas and which very often are not observed by a terrestrial monitoring network. In our study we jointly analyzed data from thermal (Moderate Resolution Imaging Spectrometer MODIS and Visible Infrared Imaging Radiometer Suite VIIRS), optical (Operational Land Imager and Multispectral Instrument) and synthetic aperture radar (SAR) (Sentinel-1 and TerraSAR-X) satellite sensors to investigate the mid-October 2019 surtseyan eruption at Late'iki Volcano, located on the Tonga Volcanic Arc. During the eruption, the remains of an older volcanic island formed in 1995 collapsed and a new volcanic island, called New Late'iki was formed. After the 12 days long lasting eruption, we observed a rapid change of the island's shape and size, and an erosion of this newly formed volcanic island, which was reclaimed by the ocean two months after the eruption ceased. This fast erosion of New Late'iki Island is in strong contrast to the over 25 years long survival of the volcanic island formed in 1995.

Analysis of copy number alterations reveals the lncRNA ALAL-1 as a regulator of lung cancer immune evasion.

Cancer is characterized by genomic instability leading to deletion or amplification of oncogenes or tumor suppressors. However, most of the altered regions are devoid of known cancer drivers. Here, we identify lncRNAs frequently lost or amplified in cancer. Among them, we found amplified lncRNA associated with lung cancer-1 (ALAL-1) as frequently amplified in lung adenocarcinomas. ALAL-1 is also overexpressed in additional tumor types, such as lung squamous carcinoma. The RNA product of ALAL-1 is able to promote the proliferation and tumorigenicity of lung cancer cells. ALAL-1 is a TNFα- and NF-κB-induced cytoplasmic lncRNA that specifically interacts with SART3, regulating the subcellular localization of the protein deubiquitinase USP4 and, in turn, its function in the cell. Interestingly, ALAL-1 expression inversely correlates with the immune infiltration of lung squamous tumors, while tumors with ALAL-1 amplification show lower infiltration of several types of immune cells. We have thus unveiled a pro-oncogenic lncRNA that mediates cancer immune evasion, pointing to a new target for immune potentiation.

A lncRNA-SWI/SNF complex crosstalk controls transcriptional activation at specific promoter regions.

LncRNAs have been shown to be direct players in chromatin regulation, but little is known about their role at active genomic loci. We investigate the role of lncRNAs in gene activation by profiling the RNA interactome of SMARCB1-containing SWI/SNF complexes in proliferating and senescent conditions. The isolation of SMARCB1-associated transcripts, together with chromatin profiling, shows prevalent association to active regions where SMARCB1 differentially binds locally transcribed RNAs. We identify SWINGN, a lncRNA interacting with SMARCB1 exclusively in proliferating conditions, exerting a pro-oncogenic role in some tumor types. SWINGN is transcribed from an enhancer and modulates the activation of GAS6 oncogene as part of a topologically organized region, as well as a larger network of pro-oncogenic genes by favoring SMARCB1 binding. Our results indicate that SWINGN influences the ability of the SWI/SNF complexes to drive epigenetic activation of specific promoters, suggesting a SWI/SNF-RNA cooperation to achieve optimal transcriptional activation.

Correction to: SNHG15 is a bifunctional MYC-regulated noncoding locus encoding a lncRNA that promotes cell proliferation, invasion and drug resistance in colorectal cancer by interacting with AIF.

In the original publication of this article,[1] the Funding section needs to be revised, and the corrected Funding section appears below.

SNHG15 is a bifunctional MYC-regulated noncoding locus encoding a lncRNA that promotes cell proliferation, invasion and drug resistance in colorectal cancer by interacting with AIF.

BACKGROUND: Thousands of long noncoding RNAs (lncRNAs) are aberrantly expressed in various types of cancers, however our understanding of their role in the disease is still very limited. METHODS: We applied RNAseq analysis from patient-derived data with validation in independent cohort of patients. We followed these studies with gene regulation analysis as well as experimental dissection of the role of the identified lncRNA by multiple in vitro and in vivo methods. RESULTS: We analyzed RNA-seq data from tumors of 456 CRC patients compared to normal samples, and identified SNHG15 as a potentially oncogenic lncRNA that encodes a snoRNA in one of its introns. The processed SNHG15 is overexpressed in CRC tumors and its expression is highly correlated with poor survival of patients. Interestingly, SNHG15 is more highly expressed in tumors with high levels of MYC expression, while MYC protein binds to two E-box motifs on SNHG15 sequence, indicating that SNHG15 transcription is directly regulated by the oncogene MYC. The depletion of SNHG15 by siRNA or CRISPR-Cas9 inhibits cell proliferation and invasion, decreases colony formation as well as the tumorigenic capacity of CRC cells, whereas its overexpression leads to opposite effects. Gene expression analysis performed upon SNHG15 inhibition showed changes in multiple relevant genes implicated in cancer progression, including MYC, NRAS, BAG3 or ERBB3. Several of these genes are functionally related to AIF, a protein that we found to specifically interact with SNHG15, suggesting that the SNHG15 acts, at least in part, by regulating the activity of AIF. Interestingly, ROS levels, which are directly regulated by AIF, show a significant reduction in SNHG15-depleted cells. Moreover, knockdown of SNHG15 increases the sensitiveness of the cells to 5-FU, while its overexpression renders them more resistant to the chemotherapeutic drug. CONCLUSION: Altogether, these results describe an important role of SNHG15 in promoting colon cancer and mediating drug resistance, suggesting its potential as prognostic marker and target for RNA-based therapies.

Investigating Volcanic Plumes from Mt. Etna Eruptions of December 2015 by Means of AVHRR and SEVIRI Data.

In early December 2015, a rapid sequence of strong paroxysmal events took place at the Mt. Etna crater area (Sicily, Italy). Intense paroxysms from the Voragine crater (VOR) generated an eruptive column extending up to an altitude of about 15 km above sea level. In the following days, other minor ash emissions occurred from summit craters. In this study, we present results achieved by monitoring Mt. Etna plumes by means of RSTASH (Robust Satellite Techniques-Ash) algorithm, running operationally at the Institute of Methodologies for Environmental Analysis (IMAA) on Advanced Very High Resolution Radiometer (AVHRR) data. Results showed that RSTASH detected an ash plume dispersing from Mt. Etna towards Ionian Sea starting from 3 December at 08:40 UTC, whereas it did not identify ash pixels on satellite data of same day at 04:20 UTC and 04:40 UTC (acquired soon after the end of first paroxysm from VOR), due to a mixed cloud containing SO2 and ice. During 8⁻10 December, the continuity of RSTASH detections allowed us to estimate the mass eruption rate (an average value of about 1.5 × 10³ kg/s was retrieved here), quantitatively characterizing the eruptive activity from North East Crater (NEC). The work, exploiting information provided also by Spinning Enhanced Visible and Infrared Imager (SEVIRI) data, confirms the important contribution offered by RSTASH in identifying and tracking ash plumes emitted from Mt. Etna, despite some operational limitations (e.g., cloud coverage). Moreover, it shows that an experimental RST product, tailored to SEVIRI data, for the first time used and preliminarily assessed here, may complement RSTASH detections providing information about areas mostly affected by volcanic SO2.

A "Counter-Enhancer" in Tumor Suppression.

The role of the noncoding genome in cancer biology is continually expanding. Cho et al. reveal a new and unexpected mechanism for the regulation of MYC expression mediated by the promoter sequence of its neighbor gene PVT1. This DNA element acts as a promoter-enhancer competitor and a candidate tumor suppressor.

Comparing Two Independent Satellite-Based Algorithms for Detecting and Tracking Ash Clouds by Using SEVIRI Sensor.

The Eyjafjallajökull (Iceland) volcanic eruption of April-May 2010 caused unprecedented air-traffic disruption in Northern Europe, revealing some important weaknesses of current operational ash-monitoring and forecasting systems and encouraging the improvement of methods and procedures for supporting the activities of Volcanic Ash Advisory Centers (VAACs) better. In this work, we compare two established satellite-based algorithms for ash detection, namely RSTASH and the operational London VAAC method, both exploiting sensor data of the spinning enhanced visible and infrared imager (SEVIRI). We analyze similarities and differences in the identification of ash clouds during the different phases of the Eyjafjallajökull eruption. The work reveals, in some cases, a certain complementary behavior of the two techniques, whose combination might improve the identification of ash-affected areas in specific conditions. This is indicated by the quantitative comparison of the merged SEVIRI ash product, achieved integrating outputs of the RSTASH and London VAAC methods, with independent atmospheric infrared sounder (AIRS) DDA (dust-detection algorithm) observations.

The multidimensional mechanisms of long noncoding RNA function.

A major shift in our understanding of genome regulation has emerged recently. It is now apparent that the majority of cellular transcripts do not code for proteins, and many of them are long noncoding RNAs (lncRNAs). Increasingly, studies suggest that lncRNAs regulate gene expression through diverse mechanisms. We review emerging mechanistic views of lncRNAs in gene regulation in the cell nucleus. We discuss the functional interactions that lncRNAs establish with other molecules as well as the relationship between lncRNA transcription and function. While some of these mechanisms are specific to lncRNAs, others might be shared with other types of genes.

A Long Noncoding RNA Regulates Sister Chromatid Cohesion.

Long noncoding RNAs (lncRNAs) are involved in diverse cellular processes through multiple mechanisms. Here, we describe a previously uncharacterized human lncRNA, CONCR (cohesion regulator noncoding RNA), that is transcriptionally activated by MYC and is upregulated in multiple cancer types. The expression of CONCR is cell cycle regulated, and it is required for cell-cycle progression and DNA replication. Moreover, cells depleted of CONCR show severe defects in sister chromatid cohesion, suggesting an essential role for CONCR in cohesion establishment during cell division. CONCR interacts with and regulates the activity of DDX11, a DNA-dependent ATPase and helicase involved in DNA replication and sister chromatid cohesion. These findings unveil a direct role for an lncRNA in the establishment of sister chromatid cohesion by modulating DDX11 enzymatic activity.

Association between long-term erectile dysfunction and biochemical recurrence after permanent seed I(125) implant brachytherapy for prostate cancer. A longitudinal study of a single-institution.

We aimed to investigate the predictive factor of erectile dysfunction (ED) in prostate cancer (PCa) patients who underwent low-dose permanent I(125) seed implant brachytherapy and to investigate if ED could represent a patient's reported outcome measures (PROMs) of efficacy of BT and indirectly associated with biochemical recurrence free survival (BRFS). From 2000 to 2012, 176 consecutive patients with low-risk PCa underwent BT. ED was evaluated with the International Index of Erectile Function (IIEF-5). Cox regression analysis was performed to assess significant predictors of mild-to-severe ED and BRFS after BT, including covariates. The 10-year actuarial rate of ED was 66%. Subjects with severe ED had higher values of D90 (183.0 versus 177.0; p < 0.05) and V100% (40.1 versus 31.4; p < 0.05) compared with normal. At the multivariate logistic regression analysis, D90 (OR: 1.10; p < 0.05) was an independent predictor of ED. Multivariate Cox-regression analysis did not demonstrate significant association between erectile preservation and biochemical recurrence (BCR) after 10 years of follow up (HR: 2.15; p = 0.20), while D90 ≤ 180 Gy independently predicted BCR (HR: 4.65; [95%CI: 1.25-17.34]; p < 0.05). Erectile preservation should be addressed as valuable PROMs after permanent seed I(125) implant, but it is not associated with better BRFS.

Cdc48-independent proteasomal degradation coincides with a reduced need for ubiquitylation.

Ubiquitin fusion degradation (UFD) substrates are delivered at the proteasome by a handover mechanism involving the ubiquitin-selective chaperone Cdc48 and the ubiquitin shuttle factor Rad23. Here, we show that introduction of a 20 amino acid peptide extension not only rendered degradation independent of Cdc48, in line with the model that this chaperone is involved in early unfolding events of tightly folded substrates, but at the same time relieved the need for efficient polyubiquitylation and the ubiquitin shuttle factor Rad23. Removal of the ubiquitylation sites in the N-terminal UFD signal made the degradation of this substrate strictly dependent on the peptide extension and also on Cdc48 and, importantly the presence of a functional ubiquitylation machinery. This suggests that the extension in the absence of N-terminal ubiquitylation sites is not properly positioned to engage the unfoldase machinery of the proteasome. Thus the need for efficient ubiquitylation and Cdc48 in facilitating proteasomal degradation are tightly linked but can be bypassed in the context of UFD substrates by the introduction of an unstructured extension. Our data suggest that polyubiquitin-binding complexes acting upstream of the proteasome, rather than the proteasome itself, can be primary determinants for the level of ubiquitylation required for protein degradation.

Genome-wide analysis of the human p53 transcriptional network unveils a lncRNA tumour suppressor signature.

Despite the inarguable relevance of p53 in cancer, genome-wide studies relating endogenous p53 activity to the expression of lncRNAs in human cells are still missing. Here, by integrating RNA-seq with p53 ChIP-seq analyses of a human cancer cell line under DNA damage, we define a high-confidence set of 18 lncRNAs that are p53 transcriptional targets. We demonstrate that two of the p53-regulated lncRNAs are required for the efficient binding of p53 to some of its target genes, modulating the p53 transcriptional network and contributing to apoptosis induction by DNA damage. We also show that the expression of p53-lncRNAs is lowered in colorectal cancer samples, constituting a tumour suppressor signature with high diagnostic power. Thus, p53-regulated lncRNAs establish a positive regulatory feedback loop that enhances p53 tumour suppressor activity. Furthermore, the signature defined by p53-regulated lncRNAs supports their potential use in the clinic as biomarkers and therapeutic targets.

PARP-14 combines with tristetraprolin in the selective posttranscriptional control of macrophage tissue factor expression.

Tissue factor (TF) (CD142) is a 47 kDa transmembrane cell surface glycoprotein that triggers the extrinsic coagulation cascade and links thrombosis with inflammation. Although macrophage TF expression is known to be regulated at the RNA level, very little is known about the mechanisms involved. Poly(adenosine 5'-diphosphate [ADP]-ribose)-polymerase (PARP)-14 belongs to a family of intracellular proteins that generate ADP-ribose posttranslational adducts. Functional screening of PARP-14-deficient macrophages mice revealed that PARP-14 deficiency leads to increased TF expression and functional activity in macrophages after challenge with bacterial lipopolysaccharide. This was related to an increase in TF messenger RNA (mRNA) stability. Ribonucleoprotein complex immunoprecipitation and biotinylated RNA pull-down assays demonstrated that PARP-14 forms a complex with the mRNA-destabilizing protein tristetraprolin (TTP) and a conserved adenylate-uridylate-rich element in the TF mRNA 3' untranslated region. TF mRNA regulation by PARP-14 was selective, as tumor necrosis factor (TNF)α mRNA, which is also regulated by TTP, was not altered in PARP-14 deficient macrophages. Consistent with the in vitro data, TF expression and TF activity, but not TNFα expression, were increased in Parp14(-/-) mice in vivo. Our study provides a novel mechanism for the posttranscriptional regulation of TF expression, indicating that this is selectively regulated by PARP-14.