dataesr/scientific-paragraphs-categorization huggingface dataset:
The instrument method for the Q Exactive HF was set up in the data dependent acquisition mode. After a survey scan in the Orbitrap (resolution 60 000), the 10 most intense precursor ions were selected for HCD fragmentation with a normalized collision energy set up to 28. Charge state screening was enabled, and precursors with unknown charge state or a charge state of 1, 7, 8 and >8 were excluded. Dynamic exclusion was enabled for 45 s. Tryptic peptides from eFASP digestion were analyzed on a Q Exactive plus instrument (Thermo Fisher Scientific, Bremen) coupled with an EASY nLC 1000 chromatography system (Thermo Fisher Scientific). Sample was loaded on an in--house packed 50 cm nano--HPLC column (75 μm inner diameter) with C18 resin (1. 9 μm particles, 100 Å pore size, Reprosil--Pur Basic C18--HD resin, Dr.
Dynamic exclusion was enabled for 45 s. Data processing for protein identification and quantification. All data were searched using Andromeda 59 against a Human Uniprot database (downloaded in 20150818, 20204 entries), usual known mass spectrometry contaminants and reversed sequences of all entries. Andromeda searches were performed choosing trypsin as specific enzyme with a maximum number of two missed cleavages. Possible modifications included carbamidomethylation (Cys, fixed), oxidation (Met, variable) and Nter acetylation (variable). The mass tolerance in MS was set to 20 ppm for the first search then 4. 5 ppm for the main search and 20 ppm for the MS/MS. Maximum peptide charge was set to seven and five amino acids were required as minimum peptide length. The "match between runs" feature was applied for samples having the same experimental condition with a maximal retention time window of 1 minute.
One unique peptide to the protein group was required for the protein identification. A false discovery rate (FDR) cutoff of 1 % was applied at the peptide and protein levels. Quantification was performed using the XIC--based LFQ algorithm with the Fast LFQ mode as described in ref. 60. Unique and razor peptides, included modified peptides, with at least 2 ratio count were used for quantification. Statistical analysis for proteomic studies. For the differential analyses, proteins identified in the reverse and contaminant databases and proteins "only identified by site" were first discarded from the list of identified proteins. Then, proteins exhibiting fewer than 2 quantified values in at least one condition were discarded from the list. After log2 transformation of the leftover proteins, LFQ values were normalized by median centering within conditions (normalizeD function of the R package DAPAR  61  ).
Note that these two quantities have been computed only when data are available. UpsetR graph and functional association network. The Upset graph (Supplementary Fig. 1c ) represents the distribution of the significant proteins coming from the different statistical analyzes. The Venn diagram represents the numbers of differentially abundant proteins in function of the kind of experiment (Gel or eFASP). Functional association network was determined by STRING  67  and displayed using Cytoscape  68. (e--h) HeLa cells stably expressing CHMP4B-GFP were treated with either control (e), ALIX (f), syntenin (g) or syndecan--4 (h) siRNAs and recorded by spinning--disc confocal time--lapse microscopy every 10 min. Zooms of the intercellular bridges are displayed.
ACKNOWLEDGMENTS We thank  R. Basto ,  G. Hickson ,  J. Mathieu ,  J--R Huyhn ,  R. Shaughnessy  and  T. Wai  for critical reading of the manuscript; the Echard Lab members for helpful discussions; the Recombinant antibodies platform (TAb--IP,  Institut Curie, Paris ) and the  DHSB (University of Iowa ) for antibodies. GFP--MKLP2 cells were from the  Hyman Lab MPI--MCBG Dresden 45. We thank the imaging facilities Imagopole and  Ultrapole, Institut Pasteur. This work has been supported by  Institut Pasteur ,  CNRS , and  ANR (AbCyStem, Cytosign)  to A. E. C. A. and A. P. received a fellowship from the Doctoral School Complexité du Vivant ED515, contrats n°2611 bis/2016 (A. P. ),  2412/2016  and  AMX  (C. A. ).
To calculate absolute cell counts, a fixed number of nonfluorescent beads (10000, 10-mm polybead carboxylate microspheres from Polysciences) was added to each tube. The formula number of cells = (number of acquired cells 3 10,000) O (number of acquired beads) was used. Cell counts were finally expressed as a number of cells per milligram of tissue or per milliliter of blood. Data were acquired on a BD LSRFortessa flow cytometer (BD Biosciences) and analyzed with FlowJo software (Tree Star). The dimensionality reduction algorithm tSNE (t-Distributed Stochastic Neighbor Embedding) was run using the plugin integrated in FlowJo. Cell sorting was performed on a BD FACSAria II cell sorter. Liver neutral lipid staining and in situ analysis of Kupffer cells death Livers were collected, fixed in 4% paraformaldehyde solution followed by incubation in a sucrose solution (30% in PBS) at 4 C.
Livers were then embedded in Tissue-Tek OCT compound and sectioned. Frozen sections (8 mm) were rinsed in PBS and incubated with Bodipy (0. 1mg/mL in PBS) for 30 min to label neutral lipids. After washing in PBS, the sections were counterstained for nuclei with DAPI. Frozen liver sections (8 mm) were rinsed in PBS and dead cells were labeled using the In Situ Cell Death Detection Kit (TMR red, Sigma). Kupffer cells were labeled with an anti-CLEC4F antibody (goat polyclonal, R&D Systems) following by anti-goat Cy2 (Jackson ImmunoResearch) while nuclei were stained with DAPI. Images were captured using a Zeiss AxioImagerM2 microscope and the AxioVision Zeiss software. Images were processed using the open-source Fiji software. qPCR analysis of flow cytometry-sorted cells Total RNA preparation was performed from 20 000 sorted cells using the RNeasy Plus micro kit (QIAGEN).
RNA was reverse transcribed using the SuperScript VILO cDNA synthesis kit (Thermo Fisher Scientific). Quantitative PCR analyses were performed using a LightCyclerÒ 480 real-time PCR system and dedicated software (Roche). Initial differences in mRNA quantities were controlled using reference mouse genes Hprt, Rpl13a, and Nono. Gene expression was normalized to those 3 housekeeping genes using the Roche LightCyclerÒ 480 software. Primers sequences are available upon request. qPCR analysis of liver samples Total RNA preparation was performed using the NucleoSpin RNA Plus kit (MACHEREY-NAGEL). RNA was reverse transcribed using the Transcriptor First Strand cDNA Synthesis Kit (Roche). Quantitative PCR analyses were performed using a LightCyclerÒ 480 real-time PCR system and dedicated software (Roche).
ACKNOWLEDGMENTS This work was supported by grants to E. L. G. from the  Agence Nationale de la Recherche  ( ANR-15-CE14-0015-02 ,  ANR-17-CE14-0009-02 , and  ANR-17-CE14-0023-01 ) and from the city of Paris ( Emergence(s) program ). S. T. and M. O. both received a one-year doctoral fellowship from the  Nouvelle Societe Francaise d'Atherosclerose (NSFA).
The goals of targeted maintenance treatment are to maintain the response achieved with chemotherapy and prolong the disease-free interval before recurrence  [15] , delaying the need for further chemotherapies and the associated toxicities that can negatively affect patients' quality of life (QoL)  [16]. In the phase 3 ARIEL3 study (CO-338-014; NCT01968213) which enrolled patients with advanced, recurrent ovarian cancer, maintenance treatment with rucaparib significantly improved investigator-assessed and blinded independent central review (BICR)-assessed progressionfree survival (PFS) versus placebo in all three molecularly defined, nested cohorts: patients with a BRCA-mutated carcinoma (germline, somatic, or unknown origin); patients with a homologous recombination deficient (HRD) carcinoma (BRCA mutation + BRCA wild-type and high loss of heterozygosity [LOH]); and the intent-to-treat (ITT) population  [17].
Role of the funding source ARIEL3 was designed by Elizabeth M. Swisher, Jonathan A. Ledermann, and Robert L. Coleman in collaboration with the funder. This article was written by the authors, with medical writing and copyediting support paid for by the funder. Data were collected by the investigators, analyzed by the funder, and interpreted by all authors. All authors had full access to all trial data and had final responsibility for the decision to submit these data for publication.
The Mac-1 and Mac-2A cell lines were grown in RPMI 1640 medium supplemented with Glutamax, penicillinstreptomycin, and 10% FBS. The human BeWo chorioncarcinoma cell line was maintained in Ham's F12 medium supplemented with Glutamax, penicillin-streptomycin, and 10% FBS. Normal T cells were isolated from a buffy coat of a healthy blood donor (Finnish Red Cross Blood Service, Helsinki, Finland) with the Lympholyte-H gradient separation method (CL5015, Cedarlane Corporation, Burlington, ON, Canada) followed by enrichment with a Pan T cell Isolation Kit (130-096-535, Milteney Biotec, Auburn, CA) according to the manufacturer's instructions. The enriched cells were immunostained with CD3 and CD19 antibodies and analyzed by flow cytometry (Biomedicum Flow Cytometry Core, Helsinki, Finland) and immunocytochemistry staining with CD3 antibody (MF7254, Dako, Glostrup, Denmark) to confirm the T cell nature of the enriched cells (data not shown).
5 cm on top of the pellet, and sterile filtered (0. 1 mm filter) into aliquots stored at e20 C until use. For EV purification, cell supernatants were centrifuged at 3,000g at 4 C for 25 minutes, followed by centrifugation at 100,000g at 4 C for 2 hours to isolate the microvesicle and exosome fractions. EV pellets were washed with 0. 1 mm filtered Dulbecco's PBS, followed by centrifugation at 100,000g at 4 C for 2 hours. Purified EV samples were analyzed by nanoparticle tracking analysis using Nanosight model LM14 (Malvern Panalytical Ltd, Malvern, United Kingdom) equipped with blue (404 nm, 70 mW) laser and a Scientific Complementary metal-oxide-semiconductor camera. The samples were diluted in Dulbecco's PBS, and three 60-second videos were recorded using camera level 13. The data were analyzed using Nanoparticle Tracking Analysis software 3.
Membranes were incubated with antieASCT-1 (1:200, SC-134846, Santa Cruz Biotechnology), antieASCT-2 (1:200, 5100, Cell Signaling Technology), and antiesyncytin-1 (1:200, SC-50369, Santa Cruz Biotechnology) antibodies overnight at 4 C. Incubation with antieb-actin antibodies (4970L, 1:1,000, Cell Signaling Technology) served as a loading control. After washing, the membranes were incubated with antierabbit horseradish peroxidase-conjugated secondary antibody (PO448, Dako) for 1 hour at room temperature. The proteins were detected using Clarity ECL reagent (Bio-Rad), and expression values were normalized against b-actin using the ChemiDoc MP Imaging System (Bio-Rad). Adjusted density values were calculated using Image Lab software (Bio-Rad). Western blot analyses of EVs were performed using 5 mg of protein.
ACKNOWLEDGMENTS We thank  Mrs. Alli Tallqvist  and  Ms. Inga Liukko  for their skillful technical assistance. We thank  Professor Robert Gniadecki ,  Bispebjerg Hospital, Copenhagen University , for the kind gift of the MyLa, Mac-1, and Mac-2A cell lines. We thank the  Extracellular Vesicle Core Facility  at the  University of Helsinki, Finland , for providing nanoparticle tracking analysis and preparation of immunoelectron microscopy samples. Biomedicum Imaging Unit and Biomedicum Flow Cytometry Core  facilities at the  University of Helsinki , Finland, were used for imaging and flow cytometry analyses. This work was supported by grants from the  Cancer Foundation Finland  and the  Finnish Dermatological Society.
The first demonstration of a clinically meaningful activity of olaparib in BRCA -proficient ovarian tumors was provided by Gelmon and colleagues in a phase II study (NCT00679783)  [41]. Moreover, therapeutic interventions in BRCA proficient tumors and in tumors without BRCAness that could result in HR impairment with subsequent sensitization to PARP inhibitors is an approach that merits further investigation. Ongoing efforts are directed towards the clinical application of synthetic lethality and the development of novel inhibitors that target the various components of the DNA repair mechanisms. Indeed, blocking of the BER pathway with PARP inhibitors significantly improves survival of cancer patients. Within this context, it has been demonstrated that Αtaxia telangiectasia and Rad3-related protein (ATR) inhibitor NU6027 inhibits RAD51 foci formation and exhibits a synthetic lethal relationship with BER inactivation in ovarian cancer cell line  [42].
The tablet formulation of olaparib has been approved by both agencies for the maintenance therapy of platinum-sensitive recurrent ovarian cancer regardless of BRCA mutational status  [40, 45]. Due to the enhanced bioavailability, the approved dose of the tablet is 300 mg twice daily  [46]. The FDA approved olaparib maintenance treatment on December 19, 2018, based on the results of the SOLO-1 trial (NCT01844986), examined the efficacy of olaparib versus placebo in subjects with BRCA -mutated advanced EOC, fallopian tube, or primary peritoneal carcinoma, who responded to first-line platinum-based chemotherapy  [47]. The estimated median PFS was not met in the olaparib arm and was 13. 8 months in the placebo arm [hazard ratio (HazR) 0. 30, 95% confidence interval (CI) 0. 23-0. 41; p < 0. 001].
Overall survival (OS) data were not yet realized in the study. Very recently, the phase III PAOLA-1/ENGOT-ov25 trial (NCT02477644) assessed the addition of olaparib to bevacizumab maintenance therapy in unselected patients with advanced EOC, fallopian tube, or primary peritoneal carcinoma, who achieved complete response (CR) or partial response (PR), following first-line platinum-based therapy accompanied by bevacizumab  [48]. As presented at the 2019 European Society for Medical Oncology (ESMO) congress, overall median PFS was significantly longer with the doublet compared with bevacizumab monotherapy (22. 1 vs 16. 6 months, respectively; HazR 0. 59, 95% CI 0. 49-0. 72; p < 0. 001). The cohorts with a BRCA mutation or HR deficiency achieved even longer PFS. Following approval of olaparib, rucaparib and niraparib received authorization for the treatment of relapsed BRCA -mutated ovarian cancer.
The median PFS was significantly longer in the BRCA mutated subgroup (12. 8 months; HazR 0. 27; p < 0. 0001) and in the BRCA wild-type/LOH high (5. 7 months; HazR 0. 62; p = 0. 011), as compared with BRCA wild-type/LOH low subgroup (5. 2 months). Similarly, the objective response rate (ORR) was higher in the BRCA1/2 mutated and BRCA wild-type/LOH high, than the BRCA wildtype/LOH low subgroup (80, 29, and 10%, respectively). In March 2017, the FDA approved niraparib at a dosage of 300 mg daily as maintenance treatment of recurrent EOC, fallopian tube, or primary peritoneal carcinoma in patients obtaining CR or PR to platinum-based chemotherapy. The EMA's approval for the same indication was established in November 2017. In October 2019, the FDA approved niraparib for patients with advanced HR-deficient EOC, or primary peritoneal cancer treated with at least three prior chemotherapy regimens, based on the results of the Quadra trial (NCT02354586)  [52].
Efficacy was investigated in 98 patients with either tumor BRCA -mutated (n = 63) and/or a genomic instability score ≥ 42 (n = 35). The ORR was 24% (95% CI  [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] , whereas the estimated median duration of response reached 8. 3 months (95% CI 6. 5-not estimable). In the subset of BRCA -mutated EOC, the ORR was 39% (95% CI 17-64) in patients with platinum-sensitive disease, compared with 29% (95% CI 11-52) and 19% (95% CI 4-46) in those with platinum-resistant and platinum-refractory disease, respectively. Adverse events led to dose reduction or interruption in 73% of patients treated with niraparib in Quadra. Furthermore, the phase III PRIMA study (NCT02655016) compared niraparib with placebo in newly diagnosed, advanced, platinum-sensitive EOC regardless of BRCA mutation status.
Niraparib extended PFS significantly more than placebo in both the overall population and the subset of patients with HR deficiency  [53]. As far as veliparib is concerned, the phase III VELIA trial (NCT02470585) presented at the 2019 ESMO congress demonstrated that patients with high-grade serous EOC, fallopian tube, or primary peritoneal carcinoma experienced a 32% reduction in the risk of progression or death with frontline combination veliparib plus carboplatin and paclitaxel followed by veliparib maintenance treatment  [54]. The VELIA study randomized patients in three arms. The control arm consisted of carboplatin and paclitaxel with placebo followed by placebo as maintenance (n = 375). In the second arm, veliparib was added at 150 mg twice daily to carboplatin and paclitaxel as induction therapy followed by placebo maintenance (n = 383).
Additional assays illustrating the burden of genomic instability include telomeric allelic imbalance (TAI), large-scale transition (LST) and LOH. They have been tested as predictive biomarkers of sensitivity to PARP inhibitors  [66]. Among them, two have been approved by the FDA as companion diagnostics for PARP inhibitors in ovarian cancer. 'FoundationFocus CDx BRCA LOH' evaluates the frequency of LOH events throughout the genome, whereas 'myChoice HRD' (Myriad) is a composite signature of LOH, TAI, and LST events  [67]. The ARIEL2 trial (NCT01891344) suggests that an assay using LOH to identify genomic scarring may be useful to predict PARP inhibitor response in ovarian cancer without BRCA1/2 mutations  [50]. The study demonstrated significant difference in PFS between the rucaparib-treated high genomic LOH and biomarker-negative groups (HazR 0.
Development of Talazoparib in Ovarian Cancer Evidence supporting the use of talazoparib specifically in the treatment of EOC is limited in comparison with other PARP inhibitors and it is still at an early stage of clinical development. However, some studies have evaluated the activity of talazoparib in several solid tumors. Chronologically, talazoparib therapy was evaluated in a two-part, phase I, first-in-human trial in 2017, in patients with germline BRCA1/2 mutated advanced or recurrent solid tumors, or selected sporadic cancers (NCT01286987)  [13]. Thirty-four ovarian cancer patients were enrolled in nine cohorts and received doses of 25-1100 μg daily. A sustained PARP inhibition was observed at doses ≥ 60 μg daily. The recommended MTD was 1 mg daily. Seventeen patients with BRCA1/2-mutant high-grade serous EOC were treated at doses of at least 0.
Grade 3/4 toxicities included fatigue (13%), neutropenia (63%), thrombocytopenia (29%), and anemia (38%). Neutropenia was more prominent in germline BRCA carriers. Three patients (14%) showed a PR or CR among BRCA -mutated patients. Among 21 evaluable patients, 11 (52%) experienced disease stabilization (range 7-22 weeks; median 10. 5 weeks). Furthermore, POSITION is a phase I study evaluating the effects of talazoparib on DNA copy number, RNA expression and protein levels in patients with stage IIIA-IV ovarian cancer (NCT02316834)  [73]. Additionally, two trials have already been withdrawn. NCT02326844 was a phase II single-arm study of talazoparib in women with recurrent BRCA1/2-mutated ovarian cancer who have progressed on prior PARP inhibitor therapy after attaining a response  [74]. The rationale was to establish whether re-challenge with an alternative PARP inhibitor can induce a further clinical response.
Development of Talazoparib in Breast Cancer Among solid tumors, talazoparib has mostly been investigated in breast cancer. At the 2017 San Antonio Breast Cancer Symposium, the results of the EMBRACA study (NCT01945775) were presented. This open-label, randomized, two-arm, phase III trial compared the efficacy and safety of talazoparib with the physician's choice of chemotherapy, which included eribulin, vinorelbine, capecitabine, or gemcitabine  [56]. Patients with advanced and unresectable or metastatic HER2-negative breast cancer and a germline BRCA1/2 mutation were randomly assigned in a 2:1 was associated with higher rates of grade 3/4 neutropenia (63%). Non-hematologic toxicity was minimal and patients experienced fewer grade 3/4 gastrointestinal side effects with talazoparib as compared with chemotherapy (5.
6 vs 11. 9%, respectively). The FDA granted priority review designation for talazoparib based on the results of the EMBRACA study. Efficacy of talazoparib in the EMBRACA study was comparable to that observed in a similar phase III, OlympiAD trial (NCT02000622), which compared olaparib versus single-agent chemotherapy in metastatic breast cancer  [55]. The primary endpoint of median PFS in the OlympiAD trial was 7. 0 months in the olaparib group versus 4. 2 months in the standard therapy group (HazR 0. 58, 95% CI 0. 43-0. 80; p < 0. 001); nevertheless, there was no difference in OS between the two arms (19. 3 vs 19. 6 months, respectively; HazR 0. 90, 95% CI 0. 63-1. 29; p = 0. 57), likely due to a high degree of cross over. Patients previously treated with platinum chemotherapy were less likely to benefit from olaparib (HazR 0.
67, 95% CI 0. 48-1. 14), suggesting overlap in the mechanisms of resistance to olaparib and platinum agents. Encouraging signs of efficacy of talazoparib came also from the phase II ABRAZO trial (NCT02034916), conducted in patients with germline BRCA1/2 mutated, locally advanced or metastatic breast cancers with or without prior exposure to platinum agents  [76]. Those who were enrolled on the platinum-exposed arm were further required to have a platinum-sensitive disease with a documented PR or CR to platinum agents and no history of disease progression on a platinum agent. Patients who had not been exposed to platinum were required to have had two or more non-platinum regimens in the metastatic setting. The primary outcome was ORR, whereas CBR, PFS, and OS were among the secondary outcome measures.
As with other PARP inhibitors, myelosuppression was the predominant toxicity [anemia (52%), thrombocytopenia (33%), and neutropenia (27%)], in addition to nausea (42%), and diarrhea (33%). Currently, there is a trend for investigation of PARP inhibitors in earlier stages of the disease, given that fewer resistance mechanisms will be present in this setting. Singleagent talazoparib has been assessed preoperatively in BRCA -mutated metastatic breast cancer in a small phase II trial (NCT03499353)  [77]. The treatment produced significant pathologic CR with manageable toxicity. Clinical trials exploring talazoparib in ovarian cancer are listed in Table  2.
In the previously reported study by de Bono et al. [13] , 4 out of 13 patients with pancreatic cancer treated with talazoparib at 1. 0 mg once daily experienced CBR of 31% for at least 16 weeks. Among those responders, one harbored a PALB2 mutation, Beyond that, Table  3  depicts two additional trials of single-agent talazoparib that are currently recruiting patients with solid tumors. Phase II study NCT02286687 will explore talazoparib activity in advanced neoplasms with BRCA1/2 germline or somatic alterations, PTEN mutations or PTEN loss and HR deficiency defect  [82] , whilst the phase I/II NCT01989546 study will evaluate talazoparib efficacy in platinum-sensitive BRCA1/2-mutant tumors  [83]. In this study, tumor biopsies for DNA damage response markers are taken prior to treatment, during cycle 1, and if the disease progresses.