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Switch to fulvestrant and palbociclib versus no switch in advanced breast cancer with rising ESR1 mutation during aromatase inhibitor and palbociclib therapy (PADA-1): a randomised, open-label, multicentre, phase 3 trial

Bidard, François-Clément ; Hardy-Bessard, Anne-Claire ; Dalenc, Florence ; [et al.]

Elsevier BV ; 2022

In: The Lancet Oncology Vol. 23, No. 11 ( 2022-11), p. 1367-1377

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In: The Lancet Oncology, Elsevier BV, Vol. 23, No. 11 ( 2022-11), p. 1367-1377

Type of Medium: Online Resource

ISSN: 1470-2045

URL: Article

DOI: 10.1016/S1470-2045(22)00555-1

Language: English

Publisher: Elsevier BV

Publication Date: 2022

detail.hit.zdb_id: 2049730-1

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PADA-1: A randomized, open label, multicentric phase III trial to evaluate the safety and efficacy of palbociclib in combination with hormone therapy driven by circulating DNA ESR1 mutation monitoring in ER-positive, HER2-negative metastatic breast cancer patients.

Bidard, Francois Clement ; Sabatier, Renaud ; Berger, Frederique ; [et al.]

American Society of Clinical Oncology (ASCO) ; 2018

In: Journal of Clinical Oncology Vol. 36, No. 15_suppl ( 2018-05-20), p. TPS1105-TPS1105

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In: Journal of Clinical Oncology, American Society of Clinical Oncology (ASCO), Vol. 36, No. 15_suppl ( 2018-05-20), p. TPS1105-TPS1105

Type of Medium: Online Resource

ISSN: 0732-183X , 1527-7755

URL: Article

DOI: 10.1200/JCO.2018.36.15_suppl.TPS1105

RVK:

XA 52760

RVK:

XA 10000

Language: English

Publisher: American Society of Clinical Oncology (ASCO)

Publication Date: 2018

detail.hit.zdb_id: 2005181-5

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BRANEnet: embedding multilayer networks for omics data integration

Jagtap, Surabhi ; Pirayre, Aurélie ; Bidard, Frédérique ; [et al.]

Springer Science and Business Media LLC ; 2022

In: BMC Bioinformatics Vol. 23, No. 1 ( 2022-10-17)

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In: BMC Bioinformatics, Springer Science and Business Media LLC, Vol. 23, No. 1 ( 2022-10-17)

Abstract: Gene expression is regulated at different molecular levels, including chromatin accessibility, transcription, RNA maturation, and transport. These regulatory mechanisms have strong connections with cellular metabolism. In order to study the cellular system and its functioning, omics data at each molecular level can be generated and efficiently integrated. Here, we propose BRANEnet , a novel multi-omics integration framework for multilayer heterogeneous networks. BRANEnet is an expressive, scalable, and versatile method to learn node embeddings, leveraging random walk information within a matrix factorization framework. Our goal is to efficiently integrate multi-omics data to study different regulatory aspects of multilayered processes that occur in organisms. We evaluate our framework using multi-omics data of Saccharomyces cerevisiae , a well-studied yeast model organism. Results We test BRANEnet on transcriptomics (RNA-seq) and targeted metabolomics (NMR) data for wild-type yeast strain during a heat-shock time course of 0, 20, and 120 min. Our framework learns features for differentially expressed bio-molecules showing heat stress response. We demonstrate the applicability of the learned features for targeted omics inference tasks: transcription factor (TF)-target prediction, integrated omics network (ION) inference, and module identification. The performance of BRANEnet is compared to existing network integration methods. Our model outperforms baseline methods by achieving high prediction scores for a variety of downstream tasks.

Type of Medium: Online Resource

ISSN: 1471-2105

URL: Article

DOI: 10.1186/s12859-022-04955-w

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2022

detail.hit.zdb_id: 2041484-5

SSG: 12

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Actionability of HER2-amplified circulating tumor cells in HER2-negative metastatic breast cancer: the CirCe T-DM1 trial

Jacot, William ; Cottu, Paul ; Berger, Frederique ; [et al.]

Springer Science and Business Media LLC ; 2019

In: Breast Cancer Research Vol. 21, No. 1 ( 2019-12)

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In: Breast Cancer Research, Springer Science and Business Media LLC, Vol. 21, No. 1 ( 2019-12)

Abstract: In this prospective phase 2 trial, we assessed the efficacy of trastuzumab-emtansine (T-DM1) in HER2-negative metastatic breast cancer (MBC) patients with HER2-positive CTC. Methods Main inclusion criteria for screening were as follows: women with HER2-negative MBC treated with ≥ 2 prior lines of chemotherapy and measurable disease. CTC with a HER2 /CEP17 ratio of ≥ 2.2 by fluorescent in situ hybridization (CellSearch) were considered to be HER2 -amplified ( HER2 amp ). Patients with ≥ 1 HER2 amp CTC were eligible for the treatment phase (T-DM1 monotherapy). The primary endpoint was the overall response rate. Results In 154 screened patients, ≥ 1 and ≥ 5 CTC/7.5 ml of blood were detected in N = 118 (78.7%) and N = 86 (57.3%) patients, respectively. ≥1 HER2 amp CTC was found in 14 patients (9.1% of patients with ≥ 1 CTC/7.5 ml). Among 11 patients treated with T-DM1, one achieved a confirmed partial response. Four patients had a stable disease as best response. Median PFS was 4.8 months while median OS was 9.5 months. Conclusions CTC with HER2 amplification can be detected in a limited subset of HER2-negative MBC patients. Treatment with T-DM1 achieved a partial response in only one patient. Trial registration NCT01975142 , Registered 03 November 2013

Type of Medium: Online Resource

ISSN: 1465-542X

URL: Article

DOI: 10.1186/s13058-019-1215-z

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2019

detail.hit.zdb_id: 2041618-0

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The cellulase induction system in Trichoderma reesei strains remains well conserved despite several generations of random mutagenesis and screening

Poggi-Parodi, Dante ; Pirayre, Aurelie ; Portnoy, Thomas ; [et al.]

Elsevier BV ; 2014

In: New Biotechnology Vol. 31 ( 2014-07), p. S216-

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In: New Biotechnology, Elsevier BV, Vol. 31 ( 2014-07), p. S216-

Type of Medium: Online Resource

ISSN: 1871-6784

URL: Article

DOI: 10.1016/j.nbt.2014.05.1006

Language: English

Publisher: Elsevier BV

Publication Date: 2014

detail.hit.zdb_id: 2400836-9

SSG: 12

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Correction to: Genome and transcriptome of the natural isopropanol producer Clostridium beijerinckii DSM6423

de Gérando, Hadrien Máté ; Wasels, François ; Bisson, Angélique ; [et al.]

Springer Science and Business Media LLC ; 2018

In: BMC Genomics Vol. 19, No. 1 ( 2018-12)

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In: BMC Genomics, Springer Science and Business Media LLC, Vol. 19, No. 1 ( 2018-12)

Type of Medium: Online Resource

ISSN: 1471-2164

URL: Article

DOI: 10.1186/s12864-018-4799-2

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2018

detail.hit.zdb_id: 2041499-7

SSG: 12

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BRANE Cut: biologically-related a priori network enhancement with graph cuts for gene regulatory network inference

Pirayre, Aurélie ; Couprie, Camille ; Bidard, Frédérique ; [et al.]

Springer Science and Business Media LLC ; 2015

In: BMC Bioinformatics Vol. 16, No. 1 ( 2015-12)

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In: BMC Bioinformatics, Springer Science and Business Media LLC, Vol. 16, No. 1 ( 2015-12)

Type of Medium: Online Resource

ISSN: 1471-2105

URL: Article

DOI: 10.1186/s12859-015-0754-2

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2015

detail.hit.zdb_id: 2041484-5

SSG: 12

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The ß‐importin KAP 8 ( P se1/ K ap121) is required for nuclear import of the cellulase transcriptional regulator XYR 1, asexual sporulation and stress resistance in T richoderma reesei

Ghassemi, Sara ; Lichius, Alexander ; Bidard, Fréderique ; [et al.]

Wiley ; 2015

In: Molecular Microbiology Vol. 96, No. 2 ( 2015-04), p. 405-418

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In: Molecular Microbiology, Wiley, Vol. 96, No. 2 ( 2015-04), p. 405-418

Abstract: The ascomycete T richoderma reesei is an industrial producer of cellulolytic and hemicellulolytic enzymes, and serves as a prime model for their genetic regulation. Most of its (hemi‐)cellulolytic enzymes are obligatorily dependent on the transcriptional activator XYR 1. Here, we investigated the nucleo‐cytoplasmic shuttling mechanism that transports XYR 1 across the nuclear pore complex. We identified 14 karyopherins in T . reesei , of which eight were predicted to be involved in nuclear import, and produced single gene‐deletion mutants of all. We found KAP 8, an ortholog of A spergillus nidulans KapI , and S accharomyces cerevisiae K ap121/ P se1, to be essential for nuclear recruitment of GFP ‐ XYR 1 and cellulase gene expression. Transformation with the native gene rescued this effect. Transcriptomic analyses of Δ kap8 revealed that under cellulase‐inducing conditions 42 CAZ ymes, including all cellulases and hemicellulases known to be under XYR 1 control, were significantly down‐regulated. Δ kap8 strains were capable of forming fertile fruiting bodies but exhibited strongly reduced conidiation both in light and darkness, and showed enhanced sensitivity towards abiotic stress, including high osmotic pressure, low pH and high temperature. Together, these data underscore the significance of nuclear import of XYR 1 in cellulase and hemicellulase gene regulation in T . reesei , and identify KAP 8 as the major karyopherin required for this process.

Type of Medium: Online Resource

ISSN: 0950-382X , 1365-2958

URL: Issue

URL: Article

DOI: 10.1111/mmi.2015.96.issue-2

DOI: 10.1111/mmi.12944

Language: English

Publisher: Wiley

Publication Date: 2015

detail.hit.zdb_id: 1501537-3

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Wood Utilization Is Dependent on Catalase Activities in the Filamentous Fungus Podospora anserina

Bourdais, Anne ; Bidard, Frederique ; Zickler, Denise ; [et al.]

Public Library of Science (PLoS) ; 2012

In: PLoS ONE Vol. 7, No. 4 ( 2012-4-27), p. e29820-

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In: PLoS ONE, Public Library of Science (PLoS), Vol. 7, No. 4 ( 2012-4-27), p. e29820-

Type of Medium: Online Resource

ISSN: 1932-6203

URL: Article

DOI: 10.1371/journal.pone.0029820

DOI: 10.1371/journal.pone.0029820.g001

DOI: 10.1371/journal.pone.0029820.g002

DOI: 10.1371/journal.pone.0029820.g003

DOI: 10.1371/journal.pone.0029820.g004

DOI: 10.1371/journal.pone.0029820.g005

DOI: 10.1371/journal.pone.0029820.t001

DOI: 10.1371/journal.pone.0029820.t002

DOI: 10.1371/journal.pone.0029820.s001

DOI: 10.1371/journal.pone.0029820.s002

DOI: 10.1371/journal.pone.0029820.s003

DOI: 10.1371/journal.pone.0029820.s004

DOI: 10.1371/journal.pone.0029820.s005

DOI: 10.1371/journal.pone.0029820.s006

DOI: 10.1371/journal.pone.0029820.s007

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2012

detail.hit.zdb_id: 2267670-3

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Genome-Wide Gene Expression Profiling of Fertilization Competent Mycelium in Opposite Mating Types in the Heterothallic Fungus Podospora anserina

Bidard, Frédérique ; Aït Benkhali, Jinane ; Coppin, Evelyne ; [et al.]

Public Library of Science (PLoS) ; 2011

In: PLoS ONE Vol. 6, No. 6 ( 2011-6-28), p. e21476-

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In: PLoS ONE, Public Library of Science (PLoS), Vol. 6, No. 6 ( 2011-6-28), p. e21476-

Type of Medium: Online Resource

ISSN: 1932-6203

URL: Article

DOI: 10.1371/journal.pone.0021476

DOI: 10.1371/journal.pone.0021476.g001

DOI: 10.1371/journal.pone.0021476.g002

DOI: 10.1371/journal.pone.0021476.g003

DOI: 10.1371/journal.pone.0021476.g004

DOI: 10.1371/journal.pone.0021476.g005

DOI: 10.1371/journal.pone.0021476.t001

DOI: 10.1371/journal.pone.0021476.t002

DOI: 10.1371/journal.pone.0021476.t003

DOI: 10.1371/journal.pone.0021476.t004

DOI: 10.1371/journal.pone.0021476.t005

DOI: 10.1371/journal.pone.0021476.s001

DOI: 10.1371/journal.pone.0021476.s002

DOI: 10.1371/journal.pone.0021476.s003

DOI: 10.1371/journal.pone.0021476.s004

DOI: 10.1371/journal.pone.0021476.s005

DOI: 10.1371/journal.pone.0021476.s006

DOI: 10.1371/journal.pone.0021476.s007

DOI: 10.1371/journal.pone.0021476.s008

DOI: 10.1371/journal.pone.0021476.s009

DOI: 10.1371/journal.pone.0021476.s010

DOI: 10.1371/journal.pone.0021476.s011

DOI: 10.1371/journal.pone.0021476.s012

DOI: 10.1371/journal.pone.0021476.s013

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2011

detail.hit.zdb_id: 2267670-3

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