dataesr/scientific-paragraphs-categorization huggingface dataset:
MGT2 (Figure To obtain insights on molecular and cellular functions characterizing "subtype A" from "subtype B," we performed a series of enrichment analyses by applying Enrichr, a web-based tool to highlight enrichments based on gene sets. Both subtypes showed an enrichment in pathways related to DNA repair, cell cycle regulation, and metabolism (Figure  4d ; Figure  S4b , Supporting Information). These enrichments are consistent with enhanced proliferation capacity of MGT4, MGT9, MGT11, and MGT13 cells versus nontumorigenic cells. Moreover, "subtype B" is enriched in pathways related to stemness properties (Figure  4d ; Figure  S4b , Supporting Information), consistent with the enhanced capability of MGT13 to form tumor spheroids in vitro (Figure  3d ,e). Further analysis of RPPA data using the Limma package highlighted differences between the RPPA profiles of subtypes A and B versus the nontumorigenic MGT cells.
Cluster 1: normal tissues; cluster 2: low phospho-MET tumors; cluster 3: "subtype B" cell line (MGT13) and tumors; cluster 4: "subtype A" cell lines (MGT4, MGT9, MGT11) and tumors. Cell lines are indicated by a black dot. c) Graphs reporting the expression levels in "subtype A" (A) and "subtype B" (B) MMTV-R26 Met tumors of the indicated proteins, considered as the hallmark of the "subtype A" cell lines (Table  S5 , Supporting Information). Unpaired Student's t-test was used. * P < 0. 05; *** P < 0. 001. d) Proteomic profiles of cells belonging to the different clusters (shown in (a)) were compared to identify enrichments by applying the Enrichr software. Histograms report the enriched cell signaling pathways, using the Reactome database, ordered according to the combined score. The 20 top ranked enrichments are highlighted.
Note that the majority of the changes are related to signals (indicated by arrowheads) involved in DNA repair (red), metabolism (blue), cell cycle regulation (yellow), and stemness (green) (indicated by colored arrowheads). e) Graph showing the fold change (Log 2 ) of protein phosphorylation or expression between "subtype A" (x-axis) or "subtype B" (y-axis) cell lines versus the nontumorigenic cells (MGT2, MGT7). Proteins among the highest significant differentially expressed in "subtype A" (in blue), "subtype B" (in red), or both (in purple) are indicated (Table  S6 , Supporting Information). p-values were determined by the Limma package in R. f) Western blot analysis of total protein extracts from MMTV-R26 Met MGT cells. Actin and Ponceau S stainings were used as loading controls in all studies.
Discussion In this study, we have developed a new TNBC mouse model that recapitulates primary drug resistance, we uncovered that the combined inhibition of WEE1 and BCL-XL selectively kills mouse and human TNBC cell lines, and provided mechanistic insights into inhibition of WEE1 and BCL-XL in TNBC cells. S7 , Supporting Information). P-values were determined by the Limma package in R. A number of transgenic mice have been engineered to model TNBC, predominantly through drastic genetic manipulations (often combined), such as loss-of-tumor suppressors and overexpression of activated oncogenes. [52] Although they have been instrumental to implicate candidate genes as oncogenes, each model generally recapitulates a fraction of disease features predominantly associated with the genetic manipulation employed.
It is rather surprising that a subtle increase of MET levels, in its wild-type form, spontaneously initiates a destabilization process that fully recapitulates the whole TNBC program. Nevertheless, this sensitivity to MET levels is conditioned by a multiparous context, as females without multiple pregnancies did not develop tumors. Both MET and HGF are dynamically expressed during pregnancy/lactation, as we showed here consistent with previous reports. [37, 38] Moreover, the HGF/MET system regulates mammary gland morphogenesis, especially ductal branching and proliferation of ductal end buds. [62] These data illustrate how a tight regulation of the time and signal input levels required for the mammary gland remodeling is critical to prevent transformation. [31] [32]  The vulnerability of the mammary gland and the liver is contrasted by a remarkable resilience of other tissues, in which a tumorigenic event requires additional genetic alterations, as reported for malignant peripheral nerve sheath tumors.
Three independent experiments were performed. Data are expressed as means ± s. e. m. For multiple comparisons, statistical significance was assessed by one-way ANOVA followed by Tukey test. not significant (ns) P > 0. 05; ** P < 0. 01; *** P < 0. 001. Bioinformatic Analysis: Random Forest was performed using the ran-domForest package in R. RPPA data for 152 TNBC patients in the TCGA dataset (TCPA: The Cancer Proteome Atlas) was split into training (80%) and test (20%) sets. The expression levels of 105 proteins (protein without missing data in the TCGA and whose expression was also evaluated in RPPA) were scaled to have an average of 0 and standard deviation of 1, and were used to train a random forest model for TNBCtype-4 classification by optimizing the number of proteins randomly selected at each split, using tenfold cross validation.
RPPA analyses of drug perturbation effects were done in duplicates (Figure  6 ). Expression levels of proteins were Log2 transformed before analysis. Analysis of fold-change proteins and p-values to determine significantly differentially expressed proteins were done by the Limma package in R. The cumulative overall disease-free survival rates were calculated using the Kaplan-Meier method. P values are indicated in figures. P < 0. 05 was considered significant. * P < 0. 05; ** P < 0. 01; *** P < 0. 001.
Cell lines are indicated by a black dot. c) Graphs reporting the expression levels in "subtype A" (A) and "subtype B" (B) MMTV-R26 Met tumors of the indicated proteins, considered as the hallmark of the "subtype A" cell lines (Table S5, Supporting Information). Unpaired Student's t-test was used. * P < 0. 05; *** P < 0. 001. d) Proteomic profiles of cells belonging to the different clusters (shown in (a)) were compared to identify enrichments by applying the Enrichr software. Histograms report the enriched cell signaling pathways, using the Reactome database, ordered according to the combined score. The 20 top ranked enrichments are highlighted. Note that the majority of the changes are related to signals (indicated by arrowheads) involved in DNA repair (red), metabolism (blue), cell cycle regulation (yellow), and stemness (green) (indicated by colored arrowheads).
e) Graph showing the fold change (Log 2 ) of protein phosphorylation or expression between "subtype A" (x-axis) or "subtype B" (y-axis) cell lines versus the nontumorigenic cells (MGT2, MGT7). Proteins among the highest significant differentially expressed in "subtype A" (in blue), "subtype B" (in red), or both (in purple) are indicated (TableS6, Supporting Information). p-values were determined by the Limma package in R. f) Western blot analysis of total protein extracts from MMTV-R26 Met MGT cells. Actin and Ponceau S stainings were used as loading controls in all studies. At least two independent experiments were performed.
Acknowledgements F. L. and F. A. contributed equally as joint first authors. S. L. and F. M. contributed equally as joint senior authors. The authors thank all members of labs for helpful discussions and comments,  R. Dono  and  F. Helmbacher  for extremely valuable feedback on the study,  A. Furlan  for initial work with MMTV-R26 Met mice,  S. Richelme  for in vivo bioluminescence imaging reported in Figure 1B and for work on a first cohort of mice,  E. Marechal  for her contribution to the MMTV-R26 Met characterization,  C. Sequera  for the analysis of overall survival of TNBC patients according to MET expression levels,  M. Buferne  for in vivo bioluminescence imaging, and the animal house platform for excellent help with mouse husbandry. This research was supported by a grant from the  Ministry of Foreign Affairs and International Development (MAEDI)  and the  Ministry of National Education, Higher Education and Research (MENESR) of France  and by the  Ministry of Science and Technology of Israel  (Grant # 3-14002 ) to F.
M. and S. L. This study was supported in part by research funding from  Institut National du Cancer, Région Provence-Alpes-Côte d'Azur , and  Canceropôle Provence-Alpes-Côte d'Azur  to F. M. F. A. was supported by the  Higher Education Commission (HEC) of Pakistan. U. A. K. was supported by the  Rising Tide Foundation Cancer Research Postdoctoral Fellowship , the  Dean Fellowship of the Faculty of Biology of the Weizmann Institute of Science (WIS) , and the  Postdoctoral Fellowship of the Swiss Society of Friends  of the WIS. J. -P. B. is a scholar of  Institut Universitaire de France. V. G. was supported by the  "Ligue Nationale Contre le Cancer" (Equipe Labellisée ). The contribution of the  Region Provence Alpes Côtes d'Azur and of the Aix-Marseille University  to the IBDM animal facility and of the  France-BioImaging/PICsL infrastructure  ( ANR-10-INBS-04-01 ) to the imaging facility is also acknowledged.
Recently, Wang et al. tested chloroquine in vitro on a clinical isolate of SARS-CoV-2; one of their conclusions was that "chloroquine (is) very effective in controlling 2019-nCoV ( rst name ofSARS-CoV-2) infection in vitro"  [23]. Gautretet al. were the rst to report in vivo data on hydroxychloroquine in a non-randomised, uncontrolled clinical trial  [24]. However, the results of these initial clinical studies do not make it possible to reach a conclusion on the e cacy of this drug in patients with COVID-19 due to major methodological weaknesses. French and European clinical trials are currently testing this therapy in randomised controlled trials at different stages of the disease, without major respiratory manifestations at inclusion (HYCOVID NCT04325893, OUTCOV NCT04365582) or with respiratory complications (CORIMMUNO-VIRO NCT04341870, DISCOVERY NCT04315948).
The inclusion period may be 3 to 6 months depending on the recruitment rate post-decon nement. The treatment time is 14 days per patient and the last patient visit will be 28 days (+/-2 days) from the start of treatment. Patients cannot be included in any other interventional research; unless they are hospitalised, provided that there is no drug interaction with any other experimental treatment. Patients included in the study who will receive an investigational treatment (e. g. IL inhibitor or anti-IL6) during hospitalisation will be kept in the study. Their data will be analysed for the primary endpoint assessment only. Their data will not be analysed for the evaluation of secondary endpoints, except for the safety endpoint.
Clinical data related to hospitalisation will be reported in the CRF. For patients hospitalised after 28 days and until 90 days post-treatment, follow-up will be carried out until discharge. This follow-up will allow the collection of vigilance data, some hospitalisation data (date of end of hospitalisation, length of hospitalisation in intensive care unit, duration of mechanical respiratory assistance, possible death). During the trial, any drug judged to be necessary for the well-being of the patient, which should not interfere with the evaluation of the test drug, may be administered at the discretion of the investigator. Absorption of doxycycline is impaired by antacids containing aluminium, calcium, as well as magnesium, bismuth subsalicylate and iron-zinc-containing preparations. The study drug should be taken at a different time to antacids.
Outcomes The main criterion is an e cacy criterion corresponding to the percentage of patients with clinical respiratory aggravation (SaO2 ≤ 93%) after at least 48 hours of treatment and the percentage of patients hospitalised for COVID-19 after at least 48 hours of experimental treatment. The criterion corresponding to the embedded second main objective corresponds to the percentage of patients requiring mechanical ventilator assistance. These three criteria aremonitored in the 2 arms from 48hoursof treatment to 28 days corresponding to the end-of-study visit. For the secondary outcomes: Safety: Report of the number of Adverse Events (AE) and Serious Adverse Events (SAE) over 28 days Apart from the rst and the last secondary criterion, the other criteria will be noted at 28 days. If the patient is hospitalised during the duration of the study,this data will be noted 3 months after the beginning of the treatment.
data. gouv. fr/fr/datasets/donnees-hospitalieres-relatives-a-lepidemie-de-covid-19/) of the hospitalisedpatients are admitted to intensive care units. With the recruitment we have, we will have a power of 80% to show a decrease of 23 to 10%. Under these hypotheses, with a 5% alpha risk in a bilateral situation and a power of 80%, we would have to evaluate 280 patients in total in both arms. If the rst hypothesis is rejected, the power of the test of the second hypothesis would then be 83. 5%. Three hundred and thirty (330) patients will be included to compensate for study exits and non-assessable patients.
Randomisation Randomisation will be strati ed by centre and by severity factors (1 versus ≥2). It will be performed according to a 1:1 ratio and balanced by blocks. The random numbers will be generated by computer. Subjects are randomised into blocks as the allocation progresses, a block being a sub-group of predetermined size within which there is a random allocation of patients. The software used for the randomisation is SAS version 9. 4. The randomisation key is known only to the biostatistician and the data managers, to make it impossible for the investigator to assign a particular treatment. It should be noted that the biostatistician who carries out the randomisation is different to the biostatistician who will carry out the statistical analysis.
The amended protocol should be a dated and updated version. If necessary, the information form and consent form should be amended. The updated protocol is version 1. 2 on 11 May 2020. The trial is not yet recruiting and the anticipated date of enrolment of the rst participant is expected on 1 June 2020. The anticipated study completion is anticipated to be on 1 January 2021. All the submissions/declarations were made by the Sponsor Department at CHU Nantes, which of course, manages the quality of the data collected. The data collected during the study will be processed electronically in accordance with the requirements of the CNIL, the French Data Protection Authority (in compliance with the French Reference Methodology MR001). The data-sharing will be only between the investigators. However, the datasets analysed during the current study will be available from the corresponding author on reasonable request.
An electronic Case Report Form (eCRF) shall be drawn up for each included patient. The identi cation of the subject will be performed using the rst letter of the family name, the rst letter of the rst name, the centre number and the inclusion number. This code should be the only information featuring on the eCRF enabling a retrospective link to the patient. The investigator, or their team, shall also encode the patient data on any documents that may be in their possession (imaging, biology test reports, etc. ) attached to the eCRF. At the end of the study, database reconciliation is carried out between the CRF database and the safety database. This reconciliation is performed before database locking. Similarly, an annual reconciliation is carried out when updating the Annual Safety Report (ASR).
Discussion The COVID-19pandemic is affecting all continents. Saturation of the hospital care system is feared in many countries. On 11 May 2020, there were 4,238,140 cases and 286,078 deaths (https://www. worldometers. info/coronavirus/). The con nement of the French population and practically the whole world was decided to try to avoid hospital overcrowding. However, in France, according to gures provided by the Ministry of Health on 16 March 2020, 97 hospitals out of the 650 -public or private -that have an emergency structure had, by 13 March 2020, activated the "hospital under stress" plan, highlighting the saturation of the emergency services. Researchers are looking for a life-saving drug. So far, 1,410 clinical studies have been published in https://clinicaltrials. gov/since the beginning of the pandemic.
Acknowledgement: In March 2020 , Pierre Gandon  submitted an opinion to the  Nouvelle-Aquitaine French regional public health authority (AgenceRégionale de Santé -ARS ) regarding the potential interest of doxycycline in COVID-19, having noticed that acne sufferers on doxycycline escaped seasonal viral infections. Laboratoires  Pierre Fabre and Bailleul  and the  University Hospital of Nantes (CHU Nantes ) are supporting this clinical trial nancially.
BIBR has been demonstrated to reduce telomerase activity in several human cancer cell lines  [9] [10] [11] [12] [13] [14] [15] , but no data are available on zebrafish. Therefore, we tested the effect of BIBR on telomerase activity in zebrafish embryos. As shown in Figure  S2 , 12 h of treatment with 2 µM BIBR induced a 75. 7 ± 8. 4% decrease in the level of telomerase activity compared to that of the control (p < 0. 001). As expected, no evidence of telomerase activity was observed in protein extracts from tert-/zebrafish embryos (Figure  S2 ). To assess the in vivo modulatory effect of Tert inhibition on cell proliferation, we evaluated the expression of phosphohistone H3 (pHH3), a mitosis molecular marker, in short-term treated zebrafish embryos. Twelve hours of BIBR treatment reduced the proliferation rate in wt embryos, as indicated by the significant decrease in the mitotic foci, counted in the caudal portion, from the apex of the tail to the anus, compared to those observed in control DMSO-treated embryos (91 ± 5 vs.
18 ± 0. 8% vs. 0. 60 ± 0. 37%; p = 0. 011). Similarly, at 72 hpx DMSO-pretreated cells proliferated up to 3. 51%, whereas the percentage of cells pretreated with BIBR was significantly lower (0. 52%; p = 0. 004) (Figure  4a ). These results reflect our previous in vitro data on anti-proliferative effect of BIBR treatment in these cell lines  [15]. Xenotransplantation of BL41 cells pretreated with BIBR or DMSO showed a behavior similar to that of 4134/Late cells, displaying higher percentage of DMSO pretreated cells compared to BIBR pretreated ones at each considered time point (Figure  S5 ). We analyzed the percentage of apoptotic cells xenografted in zebrafish at 72 hpx, when the percentage of cells pre-treated with DMSO or BIBR in dissociated embryos showed the largest difference. Apoptotic rate was detected by TUNEL assay positivity in enzymatically dissociated embryos by flow cytometry selecting CM-DiI fluorescent population (Figure  S4b ).
S-phase was analyzed employing the anti-PCNA antibody (DAKO, Glostrup, Denmark) followed by Alexa Fluor 594 secondary antibody goat antimouse (Life Technologies, Carlsbad, CA, USA) and visualized at the fluorescence Leica M165FC dissecting microscope and then with a Nikon C2 H600L confocal microscope. All images were analyzed with ImageJ software  [36].
TUNEL Assay Apoptosis rate was evaluated by employing the DeadEnd™ Fluorometric TUNEL System (Promega, Madison, WI, USA). Shortly after manual dechorionation, embryos were fixed with 4% PFA and stored in 100% methanol at -20 • C. Rehydrated samples were then treated with proteinase K, incubated in 2:1 ethanol:acetic acid and then subjected to TUNEL assay, according to the manufacturer's instructions. Apoptotic foci were visualized using the fluorescence Leica M165FC dissecting microscope and then with a Nikon C2 H600L confocal microscope. All images were analyzed with ImageJ software  [36]. DeadEnd™ Fluorometric TUNEL System was also employed to detect apoptotic cells in cell suspensions from enzymatically dissociated xenograft embryos (see below) according to the manufacturer's instructions.
Apoptotic rate was quantitated by flow cytometry analyses in an LSR II cytofluorimeter (Becton-Dickinson, San Jose, CA, USA). Data were processed with FACSDiva™ Software (Becton-Dickinson, San Jose, CA, USA) and analyzed using Kaluza ® Analyzing Software v. 1. 2 (Beckman Coulter, Fullerton, CA, USA).
Louis, MO, USA) antibodies, respectively. Blots were incubated with appropriate peroxidase-conjugated secondary antibody and stained with chemiluminescent detection kit (SuperSignal West Pico Chemiluminescent Substrate, Pierce). Quantitation of the signal was performed with ImageJ software  [36]. The uncropped blots and densitometric analysis are shown in the Supplementary Materials (Figure  S6 ).
Cell Cycle Analysis To evaluate cell cycle profile, 50 wt and tert-/embryos, treated with BIBR or DMSO, were manually dechorionated and disaggregated using small pellet pestle in 500 µl of Dulbecco's Modified Eagle Medium (DMEM) (Sigma-Aldrich, St. Louis, MO, USA)-10% fetal bovine serum (FBS) (Gibco, Milano, Italy). Subsequently, cell suspensions were filtered through 70 µm nylon mesh and cell viability was assessed by Trypan blue exclusion in a Countess automated cell counter (Invitrogen, Life Technologies, Carlsbad, CA, USA) and was always higher than 80%. Cell suspensions were then employed for PI staining as previously described  [15]. Samples were analyzed by flow cytometry and cell cycle profiles were analyzed with ModFit LT Cell Cycle Analysis software (version 2. 0) (Verity software House, Topsham, ME, USA).
A combination of such datasets provides sufficient information to restrain the relative position of several molecules within a multisubunit complex. In our case we acquired SANS curves for 2 H-L7Ae, 2 H-Nop5, 2 H-Fib, 2 H-RNA, 2 H-Fib/ 2 H-RNA and 2 H(70%)-Nop5/ 2 H-RNA in 42%:58% D 2 O:H 2 O (Figure  2 -figure supplement 3b). In addition, we also collected SAXS curves, which report on the shape of the entire complexes. These data were then incorporated into a structure-calculation protocol adapted from that developed in our previous study  (Lapinaite et al. , 2013)  (for a description of the adapted protocol, refer to Methods and Figure  3 -figure supplement 1). We used the conformations of the modules L7Ae-K-turn-sRNA-Nop5-CTD and Nop5-NTD-fibrillarin observed in previous crystal structures, and restricted our conformational search to the relative orientations of the three domains of Nop5, the conformation of the sRNA in parts other than the K-turn motifs and A-form helices and the relative positions of the two copies of each protein in the mono-RNP.
The two final structure ensembles corresponding to the [on,off]-states (Figure  3 ) are defined to a precision of better than 2. 5 A ˚(root-mean-square-deviation, RMSD, of the protein Ca and RNA P atoms, excluding flexible regions). When compared to the existing structure of the holo mono-RNP from Sulfolobus solfataricus (PDB entry 3pla,  Lin et al. , 2011) , the substrate D-and substrate D'-loaded complexes show a reasonable similarity (Figure  3 figure supplement 2). All major features of the substrate-bound site are conserved: the RNA-guide sequences lie on the coiled-coil Nop5 domain at an angle of about 70˚and the C-terminal tip of L7Ae is in proximity to the short Nop5 b-sheet 77-79 and a-helix 64-73. However, the solution structures differ from the crystallographic structure in many details, demonstrating that the sRNP architecture is flexible enough to adapt to different guide-and substrate-RNAs.