Assessment and relevance of the putative DNA/RNA helicase Schlafen-11 in ovarian and breast cancer

Abstract in English Schlafen 11 (SLFN11) is a putative DNA/RNA helicase, first described for its role in thymocyte development and differentiation in mouse models [1]. SLFN11 is part of a family of proteins with various degree of homology across species, but intriguingly being consistently present only in vertebrates and especially in mammals. Recently the role of this putative DNA/RNA helicase, SLFN11, was causal association with sensitivity to DNA damaging agents, such as platinum salts, topoisomerase I and II inhibitors, and other alkylators in the NCI-60 panel of cancer cell lines.13 In the first study, we validate an anti-SLFN11 antibody in formalin-fixed paraffin-embedded (FFPE) high-grade serous ovarian carcinoma (HGSOC) samples, developing a immunohistochemistry (IHC) protocol in order to determinate the expression of SLFN11 in our series of HGSOC. Indeed, we tested and validated a reliable SLFN 11 antibody (Ab) in IHC choosing between two anti-SLFN11 Ab used normally for Western Blot (WB) in culture cell block (CCB) of ovarian carcinoma and in an independent series of HGSOCs tissue micro-array (TMA). For each case, we evaluated both the Intensity Score (IS) and the Distribution Score (DS) evaluating at least 300 cells. A Histological Score (HS) was obtained as follow: HS=IS x DS. Successively, we applied our protocol to a large case series of HGSOC samples to confirm our preliminary results. We found one antibody to be reliable in CCB and TMA series allowing to determinate clearly IHC expression of SLFN11. These results were confirmed in our large case series of FFPE HGSOC samples. Briefly, as for TMA independent series, we found that the HS for SLFN11 expression presents a normal distribution with a prevalent ( 48 60%) intermediate expression. Parallel SLFN11 was not expressed in practically 40% of cases that clinically corresponded to the platinum resistant patients in about 60% of cases (16/27). So, we believe that low IHC expression of SLFN 11 should be correlated to response to the platinum based chemotherapy. In the second study, we investigate the transcriptional landscape of SLFN11 in breast cancer performing a gene expression microarray meta-analysis of more than 7000 cases from 35 publicly available data sets. By correlation analysis, we identified 537 transcripts in the top 95th percentile of Pearson\u2019s coef- ficients with SLFN11 identifying \u201cimmune response\u201d, \u201clymphocyte activation\u201dand \u201cT cell activation\u201d as top Gene Ontology enriched processes. Furthermore, we reported very strong association of SLFN11 with immune signatures in breast cancer through penalized maximum like-lihood lasso regression Finally, through multiple corresponde analysis we discovered a subgroup of patients, defined \u201cSLF11-hot cluster\u201d, characterized by high SLFN11 levels, estrogen receptor negativity, basal-like phenotype, elevated CD3D, STAT1 signature, and young age and using Cox proportional hazard regression, we characterized SLFN11 high levels, high proliferation index, and ER negativity as independent parameters for longer disease-free interval in patients undergoing chemotherapy. We believe that our work supports proof of concept that: i) A clear and specific role for SLFN11 in breast cancer, in likely connection with the immune system modulation in such disease entity, ii) a strong correlation between high SFLN 11 and specific molecular subtype of breast cancer (estrogen receptor negativity, basal-like phenotype)

Accelerating global parameter estimation of gravitational waves from Galactic binaries using a genetic algorithm and GPUs

The Laser Interferometer Space Antenna (LISA) is a planned space-based gravitational wave telescope with the goal of measuring gravitational waves in the milli-Hertz frequency band, which is dominated by millions of Galactic binaries. While some of these binaries produce signals that are loud enough to stand out and be extracted, most of them blur into a confusion foreground. Current methods for analyzing the full frequency band recorded by LISA to extract as many Galactic binaries as possible and to obtain Bayesian posterior distributions for each of the signals are computationally expensive. We introduce a new approach to accelerate the extraction of the best fitting solutions for Galactic binaries across the entire frequency band from data with multiple overlapping signals. Furthermore, we use these best fitting solutions to omit the burn-in stage of a Markov chain Monte Carlo method and to take full advantage of GPU-accelerated signal simulation, allowing us to compute posterior distributions in 2 seconds per signal on a laptop-grade GPU.Comment: 13 pages, 11 figure

Bayesian parameter-estimation of Galactic binaries in LISA data with Gaussian Process Regression

The Laser Interferometer Space Antenna (LISA), which is currently under construction, is designed to measure gravitational wave signals in the milli-Hertz frequency band. It is expected that tens of millions of Galactic binaries will be the dominant sources of observed gravitational waves. The Galactic binaries producing signals at mHz frequency range emit quasi monochromatic gravitational waves, which will be constantly measured by LISA. To resolve as many Galactic binaries as possible is a central challenge of the upcoming LISA data set analysis. Although it is estimated that tens of thousands of these overlapping gravitational wave signals are resolvable, and the rest blurs into a galactic foreground noise; extracting tens of thousands of signals using Bayesian approaches is still computationally expensive. We developed a new end-to-end pipeline using Gaussian Process Regression to model the log-likelihood function in order to rapidly compute Bayesian posterior distributions. Using the pipeline we are able to solve the Lisa Data Challange (LDC) 1-3 consisting of noisy data as well as additional challenges with overlapping signals and particularly faint signals.Comment: 12 pages, 10 figure

Low-Grade Uterine Endometrial Stromal Sarcoma: Prognostic Analysis of Clinico-Pathological Characteristics, Surgical Management, and Adjuvant Treatments. Experience From Two Referral Centers

OBJECTIVE: Low-grade uterine endometrial stromal sarcoma (LG-ESS) is a rare tumor characterized by an overall good survival but showing a indolent behavior and a variable risk of recurrence. There is no clear consensus on the optimal management of these tumors and no prognostic or predictive factors have been established. With this study, we evaluated the prognostic relevance of several clinical, surgical, and pathological features in patients affected by LG-ESS to identify risk factors associated with recurrence. METHODS: We retrospectively analyzed 52 LG-ESS cases, treated from January 1st, 1994, to May 31st, 2020, in two referral centers. The relationship between recurrence and clinicopathological characteristics as well as surgical treatment was investigated. Risk of recurrence and disease-free survival (DFS) were estimated by Cox regression and the Kaplan-Meier analysis, respectively. RESULTS: Of 52 patients with LG-ESS, 8 experienced recurrence (15%). The median follow-up was 100 months (SD ± 96, range: 15–336). By univariate analysis, fragmentation/morcellation, tumor size, FIGO stage, higher mitotic count, presence of necrosis, and lymphovascular space invasion (LSVI) resulted associated with a poorer outcome. Conversely, the surgical modality (laparotomic vs laparoscopic and hysterectomy with bilateral salpingo-oophorectomy vs local excision) and pelvic lymphadenectomy were not. Even the different modalities of adjuvant therapy (hormonal therapy, radiotherapy, and chemotherapy) showed no prognostic significance. Tumor fragmentation/morcellation and higher mitotic count resulted independent prognostic variables at multivariate analysis. CONCLUSIONS: This data supports the avoidance of any type of morcellation if LG-ESS is suspected preoperatively. Higher mitotic count and, possibly, tumor size, advanced FIGO stage, necrosis, and LVSI could be exploited to tailor the adjuvant therapy, but these results need to be confirmed in larger prospective studies

Her2 assessment using quantitative reverse transcriptase polymerase chain reaction reliably identifies Her2 overexpression without amplification in breast cancer cases

Background: Immunohistochemistry (IHC) and fluorescent-in situ hybridization (FISH) are standard methods to assess human epidermal growth factor receptor 2 (HER2) status in breast cancer (BC) patients. Real-time quantitative polymerase-chain-reaction (qRT-PCR) is able to detect HER2 overexpression. Here we compared FISH, IHC, quantitative PCR (qPCR), and qRT-PCR to determine the concordance rates and evaluate their relative roles in HER2 determination. Patients and methods: We determined HER2 status in 153 BC patients, using IHC, FISH, Q-PCR and qRT-PCR. In discordant cases, we directly measured HER2 protein levels using Western blotting. Results: The overall agreement (OA) between FISH and Q-PCR was 94.1, with a k value of 0.87. Assuming FISH as the standard reference, Q-PCR showed an 86.1% sensitivity and a 99.0% specificity with a global accuracy of 91.6%. OA between FISH and qRT-PCR was 90.8% with a k value of 0.81. Of interest, the disagreement between FISH and qRT-PCR was mostly restricted to equivocal cases. HER2 protein analysis suggested that qRT-PCR correlates better than FISH with HER2 protein levels, particularly where FISH fails to provide conclusive results. Significance: qRT-PCR may outperform FISH in identifying patients overexpressing HER2 protein. Q-PCR cannot be used for HER2 status assessment, due to its suboptimal level of agreement with FISH. Both FISH and Q-PCR may be less accurate than qRT-PCR as surrogates of HER2 protein determination

Sub-Femto- g Free Fall for Space-Based Gravitational Wave Observatories: LISA Pathfinder Results

We report the first results of the LISA Pathfinder in-flight experiment. The results demonstrate that two free-falling reference test masses, such as those needed for a space-based gravitational wave observatory like LISA, can be put in free fall with a relative acceleration noise with a square root of the power spectral density of 5.2±0.1  fm s−2/Hz, or (0.54±0.01)×10−15  g/Hz, with g the standard gravity, for frequencies between 0.7 and 20 mHz. This value is lower than the LISA Pathfinder requirement by more than a factor 5 and within a factor 1.25 of the requirement for the LISA mission, and is compatible with Brownian noise from viscous damping due to the residual gas surrounding the test masses. Above 60 mHz the acceleration noise is dominated by interferometer displacement readout noise at a level of (34.8±0.3)  fm/Hz, about 2 orders of magnitude better than requirements. At f≤0.5  mHz we observe a low-frequency tail that stays below 12  fm s−2/Hz down to 0.1 mHz. This performance would allow for a space-based gravitational wave observatory with a sensitivity close to what was originally foreseen for LISA.CNES 1316634/CNRS 103747UnivEarthS Labex program/ANR-10-LABX-0023UnivEarthS Labex program/ANR-11-IDEX-0005-02DLRFederal Ministry for Economic Affairs and Energy/FKZ 50OQ0501Federal Ministry for Economic Affairs and Energy/FKZ 50OQ1601Agenzia Spaziale ItalianaInstituto Nazionale di Fisica NucleareAYA2010-15709 (MICINN)ESP2013-47637-P (MINECO)ESP2015-67234-P (MINECO)Fundacion General CSICSwiss Space Office (SSO)Swiss National Science FoundationUnited Kingdom Space Agency (UKSA)University of GlasgowUniversity of BirminghamImperial CollegeScottish Universities Physics Alliance (SUPA)U.S. National Aeronautics and Space Administration (NASA