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Article ; Online: SpectiCal:

Zhang, Nathan H / Deutsch, Eric W

2024 Volume 23, Issue 4, Page(s) 1519–1530

Abstract: Most tandem mass spectrometry fragmentation spectra have small calibration errors that can lead to suboptimal interpretation and annotation. We developed SpectiCal, a software tool that can read mzML files from data-dependent acquisition proteomics ... ...

Abstract	Most tandem mass spectrometry fragmentation spectra have small calibration errors that can lead to suboptimal interpretation and annotation. We developed SpectiCal, a software tool that can read mzML files from data-dependent acquisition proteomics experiments in parallel, compute
MeSH term(s)	Calibration ; Peptides/analysis ; Software ; Tandem Mass Spectrometry/methods ; Ions
Chemical Substances	Peptides ; Ions
Language	English
Publishing date	2024-03-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.3c00882
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Article ; Online: Eradicating gross tumor disease: a prerequisite for efficient radioimmunotherapy?

Deutsch, Eric / Levy, Antonin

Journal of the National Cancer Institute

2024

Abstract: Radiotherapy may induce off-target antitumor "abscopal" immunostimulatory but also immunosuppressive effects. Several preclinical and early clinical studies revealed promising results when combining radiation therapy with immunostimulatory agents. ... ...

Abstract	Radiotherapy may induce off-target antitumor "abscopal" immunostimulatory but also immunosuppressive effects. Several preclinical and early clinical studies revealed promising results when combining radiation therapy with immunostimulatory agents. However, most immunoradiotherapy randomized trials showed disappointing results in patients with advanced tumors. On the contrary, encouraging outcomes were suggested when immunotherapy was delivered on top of gross disease elimination with curative-intent radiotherapy. In this review, we highlight available results from randomized trials and discuss the potential impact of overall tumor burden on the observed efficacy of radioimmunotherapy.
Language	English
Publishing date	2024-03-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	2992-0
ISSN	1460-2105 ; 0027-8874 ; 0198-0157
ISSN (online)	1460-2105
ISSN	0027-8874 ; 0198-0157
DOI	10.1093/jnci/djae071
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Article ; Online: Local Immunoradiotherapy in Patients With Metastatic Soft-Tissue Sarcoma.

Levy, Antonin / Deutsch, Eric / Le Péchoux, Cécile

JAMA oncology

2024

Language	English
Publishing date	2024-04-11
Publishing country	United States
Document type	Journal Article
ISSN	2374-2445
ISSN (online)	2374-2445
DOI	10.1001/jamaoncol.2024.0308
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Article ; Online: Translational frontiers and clinical opportunities of immunologically-fitted radiotherapy.

Morel, Daphné / Robert, Charlotte / Paragios, Nikos / Grégoire, Vincent / Deutsch, Eric

Clinical cancer research : an official journal of the American Association for Cancer Research

2024

Abstract: Ionising radiations can have a wide range of impacts on tumour-immune interactions, which are being studied with the greatest interest and at an accelerating pace by the medical community. Despite its undeniable immunostimulatory potential, it clearly ... ...

Abstract	Ionising radiations can have a wide range of impacts on tumour-immune interactions, which are being studied with the greatest interest and at an accelerating pace by the medical community. Despite its undeniable immunostimulatory potential, it clearly appears that radiotherapy as it is prescribed and delivered nowadays often alters the host's immunity towards a suboptimal state. This may impair the full recovery of a sustained and efficient anti-tumour immunosurveillance post-treatment. An emerging concept is arising from this awareness and consists in re-considering the way of designing radiation treatment plannings, notably by taking into account the individualised risks of deleterious radio-induced immune alteration that can be deciphered from the planned beam trajectory through lymphocyte-rich organs. In this review, we critically appraise key aspects to consider while planning immunologically-fitted radiotherapy, including the challenges linked to the identification of new dose constraints to immune-rich structures. We also discuss how pharmacological immunomodulation could be advantageously used in combination with radiotherapy to compensate for the radio-induced loss, for example with (i) agonists of interleukin (IL)-2, IL-4, IL-7, IL-9, IL-15 or IL-21, similarly to G-CSF being used for the prophylaxis of severe chemo-induced neutropenia, or with (ii) myeloid-derived suppressive cells (MDSC) blockers.
Language	English
Publishing date	2024-03-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	1225457-5
ISSN	1557-3265 ; 1078-0432
ISSN (online)	1557-3265
ISSN	1078-0432
DOI	10.1158/1078-0432.CCR-23-3632
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Article ; Online: (Chemo)Radiotherapy-Immunotherapy Combinations: Time to Get Tailored?

Mondini, Michele / Deutsch, Eric

Clinical cancer research : an official journal of the American Association for Cancer Research

2021 Volume 27, Issue 14, Page(s) 3815–3817

Abstract: Chemoradiotherapy is considered an immunogenic anticancer treatment. Data obtained during the course of chemoradiotherapy treatment of patients with cervical cancer show heterogeneous changes in the tumor immune landscape, highlighting the need for ... ...

Abstract	Chemoradiotherapy is considered an immunogenic anticancer treatment. Data obtained during the course of chemoradiotherapy treatment of patients with cervical cancer show heterogeneous changes in the tumor immune landscape, highlighting the need for patient selection to rationally design successful combined immunotherapies. Blood-based biomarkers could be valuable to perform such stratification.
MeSH term(s)	Chemoradiotherapy ; Drug Therapy, Combination ; Female ; Humans ; Immunologic Factors ; Immunotherapy ; Uterine Cervical Neoplasms
Chemical Substances	Immunologic Factors
Language	English
Publishing date	2021-05-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Comment
ZDB-ID	1225457-5
ISSN	1557-3265 ; 1078-0432
ISSN (online)	1557-3265
ISSN	1078-0432
DOI	10.1158/1078-0432.CCR-21-1173
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Article ; Online: Does the Ubiquitination Degradation Pathway Really Reach inside of the Chloroplast? A Re-Evaluation of Mass Spectrometry-Based Assignments of Ubiquitination.

van Wijk, Klaas J / Leppert, Tami / Sun, Zhi / Deutsch, Eric W

Journal of proteome research

2023 Volume 22, Issue 6, Page(s) 2079–2091

Abstract: A recent paper in Science Advances by Sun et al. claims that intra-chloroplast proteins in the model plant Arabidopsis can be polyubiquitinated and then extracted into the cytosol for subsequent degradation by the proteasome. Most of this conclusion ... ...

Abstract	A recent paper in Science Advances by Sun et al. claims that intra-chloroplast proteins in the model plant Arabidopsis can be polyubiquitinated and then extracted into the cytosol for subsequent degradation by the proteasome. Most of this conclusion hinges on several sets of mass spectrometry (MS) data. If the proposed results and conclusion are true, this would be a major change in the proteolysis/proteostasis field, breaking the long-standing dogma that there are no polyubiquitination mechanisms within chloroplast organelles (nor in mitochondria). Given its importance, we reanalyzed their raw MS data using both open and closed sequence database searches and encountered many issues not only with the results but also discrepancies between stated methods (e.g., use of alkylating agent iodoacetamide (IAA)) and observed mass modifications. Although there is likely enrichment of ubiquitination signatures in a subset of the data (probably from ubiquitination in the cytosol), we show that runaway alkylation with IAA caused extensive artifactual modifications of N termini and lysines to the point that a large fraction of the desired ubiquitination signatures is indistinguishable from artifactual acetamide signatures, and thus, no intra-chloroplast polyubiquitination conclusions can be drawn from these data. We provide recommendations on how to avoid such perils in future work.
MeSH term(s)	Ubiquitination ; Proteolysis ; Chloroplasts/metabolism ; Proteasome Endopeptidase Complex/metabolism ; Arabidopsis/metabolism ; Mass Spectrometry
Chemical Substances	Proteasome Endopeptidase Complex (EC 3.4.25.1)
Language	English
Publishing date	2023-04-24
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.3c00178
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Article: How to Improve SBRT Outcomes in NSCLC: From Pre-Clinical Modeling to Successful Clinical Translation.

Milic, Marina / Mondini, Michele / Deutsch, Eric

Cancers

2022 Volume 14, Issue 7

Abstract: Despite major research and clinical efforts, lung cancer remains the leading cause of cancer-related death. While the delivery of conformal radiotherapy and image guidance of stereotactic body radiotherapy (SBRT) have revolutionized the treatment of ... ...

Abstract	Despite major research and clinical efforts, lung cancer remains the leading cause of cancer-related death. While the delivery of conformal radiotherapy and image guidance of stereotactic body radiotherapy (SBRT) have revolutionized the treatment of early-stage non-small-cell lung cancer (NSCLC), additional research is needed to elucidate underlying mechanisms of resistance and identify novel therapeutic combinations. Clinical progress relies on the successful translation of pre-clinical work, which so far has not always yielded expected results. Improved clinical modelling involves characterizing the preclinical models and selecting appropriate experimental designs that faithfully mimic precise clinical scenarios. Here, we review the current role of SBRT and the scope of pre-clinical armamentarium at our disposal to improve successful clinical translation of pre-clinical research in the radiation oncology of NSCLC.
Language	English
Publishing date	2022-03-27
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers14071705
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Article ; Online: Is DIA proteomics data FAIR? Current data sharing practices, available bioinformatics infrastructure and recommendations for the future.

Jones, Andrew R / Deutsch, Eric W / Vizcaíno, Juan Antonio

Proteomics

2022 Volume 23, Issue 7-8, Page(s) e2200014

Abstract: Data independent acquisition (DIA) proteomics techniques have matured enormously in recent years, thanks to multiple technical developments in, for example, instrumentation and data analysis approaches. However, there are many improvements that are still ...

Abstract	Data independent acquisition (DIA) proteomics techniques have matured enormously in recent years, thanks to multiple technical developments in, for example, instrumentation and data analysis approaches. However, there are many improvements that are still possible for DIA data in the area of the FAIR (Findability, Accessibility, Interoperability and Reusability) data principles. These include more tailored data sharing practices and open data standards since public databases and data standards for proteomics were mostly designed with DDA data in mind. Here we first describe the current state of the art in the context of FAIR data for proteomics in general, and for DIA approaches in particular. For improving the current situation for DIA data, we make the following recommendations for the future: (i) development of an open data standard for spectral libraries; (ii) make mandatory the availability of the spectral libraries used in DIA experiments in ProteomeXchange resources; (iii) improve the support for DIA data in the data standards developed by the Proteomics Standards Initiative; and (iv) improve the support for DIA datasets in ProteomeXchange resources, including more tailored metadata requirements.
MeSH term(s)	Proteomics/methods ; Proteome ; Mass Spectrometry/methods ; Computational Biology/methods
Chemical Substances	Proteome
Language	English
Publishing date	2022-09-13
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2032093-0
ISSN	1615-9861 ; 1615-9853
ISSN (online)	1615-9861
ISSN	1615-9853
DOI	10.1002/pmic.202200014
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Article ; Online: Extending Comet for Global Amino Acid Variant and Post-Translational Modification Analysis Using the PSI Extended FASTA Format.

Eng, Jimmy K / Deutsch, Eric W

Proteomics

2020 Volume 20, Issue 21-22, Page(s) e1900362

Abstract: Protein identification by tandem mass spectrometry sequence database searching is a standard practice in many proteomics laboratories. The de facto standard for the representation of sequence databases used as input to sequence database search tools is ... ...

Abstract	Protein identification by tandem mass spectrometry sequence database searching is a standard practice in many proteomics laboratories. The de facto standard for the representation of sequence databases used as input to sequence database search tools is the FASTA format. The Human Proteome Organization's Proteomics Standards Initiative has developed an extension to the FASTA format termed the proteomics standards initiative extended FASTA format or PSI extended FASTA format (PEFF) where additional information such as structural annotations are encoded in the protein description lines. Comet has been extended to automatically analyze the post translational modifications and amino acid substitutions encoded in PEFF databases. Comet's PEFF implementation and example analysis results searching a HEK293 dataset against the neXtProt PEFF database are presented.
MeSH term(s)	Amino Acids ; Databases, Protein ; HEK293 Cells ; Humans ; Protein Processing, Post-Translational ; Proteome ; Proteomics ; Software
Chemical Substances	Amino Acids ; Proteome
Language	English
Publishing date	2020-04-02
Publishing country	Germany
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2032093-0
ISSN	1615-9861 ; 1615-9853
ISSN (online)	1615-9861
ISSN	1615-9853
DOI	10.1002/pmic.201900362
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Article: Cytofluorometric characterization of the myeloid compartment of irradiated mouse tumors.

De Thoré, Marine Gerbé / Meziani, Lydia / Deutsch, Eric / Mondini, Michele

Methods in cell biology

2022 Volume 174, Page(s) 17–30

Abstract: The use of ionizing radiation (IR) is a cornerstone for the treatment of cancer and radiotherapy (RT) is used in roughly 50% of cancer patients. It is now well established that RT exerts widespread effects on the tumor stroma, including the immune ... ...

Abstract	The use of ionizing radiation (IR) is a cornerstone for the treatment of cancer and radiotherapy (RT) is used in roughly 50% of cancer patients. It is now well established that RT exerts widespread effects on the tumor stroma, including the immune environment. Together with its deeply characterized effects on the lymphoid compartment, RT also deeply affects the myeloid cell compartment. Fluorescence-activated flow cytometry is one of the most widely used technologies in immunology, allowing the multiparametric analysis of cells on a cell-by-cell basis. Here, we provide a detailed flow cytometry protocol to analyze the myeloid cell populations of human papillomavirus (HPV)-positive TC1/Luc tumors engrafted in the oral mucosa of immunocompetent mice, and to evaluate their modulations in response to RT. The same method, with slight modifications, can be used to study the tumor myeloid cells from a variety of other mouse tumors.
MeSH term(s)	Animals ; Humans ; Mice ; Neoplasms/radiotherapy ; Radiation, Ionizing ; Myeloid Cells/radiation effects ; Flow Cytometry
Language	English
Publishing date	2022-12-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	0091-679X
ISSN	0091-679X
DOI	10.1016/bs.mcb.2022.08.004
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