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Article: Recurrent Metastatic Pulmonary Synovial Sarcoma during Pregnancy: A Case Report and Literature Review.

De Rocco, Silvia / Di Biasi, Jasmine / Fantasia, Ilaria / Tabacco, Sara / Ricevuto, Enrico / Palumbo, Pierpaolo / Imbergamo, Ilenia / Ludovisi, Manuela / Guido, Maurizio

Diagnostics (Basel, Switzerland)

2024 Volume 14, Issue 4

Abstract: Primary pulmonary synovial sarcoma is a rare type of soft tissue tumor. Exceptionally it can occur during pregnancy, representing a challenge in management and treatment given its notable aggressiveness and the not infrequent incidence of maternal death. ...

Abstract	Primary pulmonary synovial sarcoma is a rare type of soft tissue tumor. Exceptionally it can occur during pregnancy, representing a challenge in management and treatment given its notable aggressiveness and the not infrequent incidence of maternal death. We report our case of metastatic recurrence of pulmonary synovial sarcoma during pregnancy, with the aim to emphasize the decision-making, diagnostic, and therapeutic multidisciplinary processes and the evolution of the pathology. Besides, we focused on the analysis of the limited literature data available on the topic.
Language	English
Publishing date	2024-02-14
Publishing country	Switzerland
Document type	Case Reports
ZDB-ID	2662336-5
ISSN	2075-4418
ISSN	2075-4418
DOI	10.3390/diagnostics14040424
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Article ; Online: Misclassification bias in estimating clinical severity of SARS-CoV-2 variants - Authors' reply.

Nyberg, Tommy / Ferguson, Neil M / Blake, Joshua / Hinsley, Wes / Bhatt, Samir / De Angelis, Daniela / Thelwall, Simon / Presanis, Anne M

Lancet (London, England)

2022 Volume 400, Issue 10355, Page(s) 809–810

MeSH term(s)	COVID-19 ; Humans ; SARS-CoV-2/genetics
Language	English
Publishing date	2022-09-07
Publishing country	England
Document type	Letter ; Comment
ZDB-ID	3306-6
ISSN	1474-547X ; 0023-7507 ; 0140-6736
ISSN (online)	1474-547X
ISSN	0023-7507 ; 0140-6736
DOI	10.1016/S0140-6736(22)01432-5
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Article ; Online: Waning of 2-Dose BNT162b2 and mRNA-1273 Vaccine Effectiveness Against Symptomatic SARS-CoV-2 Infection Accounting for Depletion-of-Susceptibles Bias.

Andrejko, Kristin L / Pry, Jake M / Myers, Jennifer F / Mehrotra, Megha / Lamba, Katherine / Lim, Esther / Fukui, Nozomi / DeGuzman, Jennifer L / Openshaw, John / Watt, James / Jain, Seema / Lewnard, Joseph A / Covid-Case-Control Study Team, On Behalf Of The California

American journal of epidemiology

2022 Volume 192, Issue 6, Page(s) 895–907

Abstract: ... have arisen in postlicensure evaluations. "Depletion of susceptibles," a bias driven by differential ... estimates, hindering interpretation. We enrolled California residents who received molecular SARS-CoV-2 ... serological study to adjust for "depletion-of-susceptibles" bias and estimated VE for 3 doses, by time ...

Abstract	Concerns about the duration of protection conferred by coronavirus disease 2019 (COVID-19) vaccines have arisen in postlicensure evaluations. "Depletion of susceptibles," a bias driven by differential accrual of infection among vaccinated and unvaccinated individuals, may obscure vaccine effectiveness (VE) estimates, hindering interpretation. We enrolled California residents who received molecular SARS-CoV-2 tests in a matched, test-negative design, case-control study to estimate VE of mRNA-based COVID-19 vaccines between February 23 and December 5, 2021. We analyzed waning protection following 2 vaccine doses using conditional logistic regression models. Additionally, we used data from a population-based serological study to adjust for "depletion-of-susceptibles" bias and estimated VE for 3 doses, by time since second dose receipt. Pooled VE of BNT162b2 and mRNA-1273 against symptomatic SARS-CoV-2 infection was 91.3% (95% confidence interval (CI): 83.8, 95.4) at 14 days after second-dose receipt and declined to 50.8% (95% CI: 19.7, 69.8) at 7 months. Adjusting for depletion-of-susceptibles bias, we estimated VE of 53.2% (95% CI: 23.6, 71.2) at 7 months after primary mRNA vaccination series. A booster dose of BN162b2 or mRNA-1273 increased VE to 95.0% (95% CI: 82.8, 98.6). These findings confirm that observed waning of protection is not attributable to epidemiologic bias and support ongoing efforts to administer additional vaccine doses to mitigate burden of COVID-19.
MeSH term(s)	Humans ; 2019-nCoV Vaccine mRNA-1273 ; BNT162 Vaccine ; COVID-19/epidemiology ; COVID-19/prevention & control ; COVID-19 Vaccines ; Case-Control Studies ; Vaccine Efficacy ; SARS-CoV-2/genetics ; RNA, Messenger
Chemical Substances	2019-nCoV Vaccine mRNA-1273 (EPK39PL4R4) ; BNT162 Vaccine ; COVID-19 Vaccines ; RNA, Messenger
Language	English
Publishing date	2022-04-29
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	2937-3
ISSN	1476-6256 ; 0002-9262
ISSN (online)	1476-6256
ISSN	0002-9262
DOI	10.1093/aje/kwad017
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Article: Recruitment location influences bias and uncertainty in SARS-CoV-2 seroprevalence estimates.

medRxiv : the preprint server for health sciences

2021

Abstract: ... to rapidly estimate a community's seroprevalence. However, biases and uncertainty due to site selection and ... use of convenience samples are poorly understood. Using data from a SARS-CoV-2 serosurveillance study ... of bias. Our results demonstrated that study-site selection informed by mobility patterns can markedly ...

Abstract	The initial phase of the COVID-19 pandemic in the US was marked by limited diagnostic testing, resulting in the need for seroprevalence studies to estimate cumulative incidence and define epidemic dynamics. In lieu of systematic representational surveillance, venue-based sampling was often used to rapidly estimate a community's seroprevalence. However, biases and uncertainty due to site selection and use of convenience samples are poorly understood. Using data from a SARS-CoV-2 serosurveillance study we performed in Somerville, Massachusetts, we found that the uncertainty in seroprevalence estimates depends on how well sampling intensity matches the known or expected geographic distribution of seropositive individuals in the study area. We use GPS-estimated foot traffic to measure and account for these sources of bias. Our results demonstrated that study-site selection informed by mobility patterns can markedly improve seroprevalence estimates. Such data should be used in the design and interpretation of venue-based serosurveillance studies.
Language	English
Publishing date	2021-10-05
Publishing country	United States
Document type	Preprint
DOI	10.1101/2021.02.03.21251011
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Article: Circulating and Tumor-Associated Neutrophils in the Era of Immune Checkpoint Inhibitors: Dynamics, Phenotypes, Metabolism, and Functions.

Gibellini, Lara / Borella, Rebecca / Santacroce, Elena / Serattini, Eugenia / Boraldi, Federica / Quaglino, Daniela / Aramini, Beatrice / De Biasi, Sara / Cossarizza, Andrea

Cancers

2023 Volume 15, Issue 13

Abstract: Neutrophils are the most abundant myeloid cells in the blood and are a considerable immunological component of the tumor microenvironment. However, their functional importance has often been ignored, as they have always been considered a mono-dimensional ...

Abstract	Neutrophils are the most abundant myeloid cells in the blood and are a considerable immunological component of the tumor microenvironment. However, their functional importance has often been ignored, as they have always been considered a mono-dimensional population of terminally differentiated, short-living cells. During the last decade, the use of cutting-edge, single-cell technologies has revolutionized the classical view of these cells, unmasking their phenotypic and functional heterogeneity. In this review, we summarize the emerging concepts in the field of neutrophils in cancer, by reviewing the recent literature on the heterogeneity of both circulating neutrophils and tumor-associated neutrophils, as well as their possible significance in tumor prognosis and resistance to immune checkpoint inhibitors.
Language	English
Publishing date	2023-06-24
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers15133327
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Article ; Online: Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable.

Mavian, Carla / Pond, Sergei Kosakovsky / Marini, Simone / Magalis, Brittany Rife / Vandamme, Anne-Mieke / Dellicour, Simon / Scarpino, Samuel V / Houldcroft, Charlotte / Villabona-Arenas, Julian / Paisie, Taylor K / Trovão, Nídia S / Boucher, Christina / Zhang, Yun / Scheuermann, Richard H / Gascuel, Olivier / Lam, Tommy Tsan-Yuk / Suchard, Marc A / Abecasis, Ana / Wilkinson, Eduan /

de Oliveira, Tulio / Bento, Ana I / Schmidt, Heiko A / Martin, Darren / Hadfield, James / Faria, Nuno / Grubaugh, Nathan D / Neher, Richard A / Baele, Guy / Lemey, Philippe / Stadler, Tanja / Albert, Jan / Crandall, Keith A / Leitner, Thomas / Stamatakis, Alexandros / Prosperi, Mattia / Salemi, Marco

Proceedings of the National Academy of Sciences of the United States of America

2020 Volume 117, Issue 23, Page(s) 12522–12523

MeSH term(s)	Betacoronavirus ; COVID-19 ; Coronavirus Infections ; Humans ; Pandemics ; Phylogeny ; Pneumonia, Viral ; Severe acute respiratory syndrome-related coronavirus ; SARS-CoV-2 ; Selection Bias
Keywords	covid19
Language	English
Publishing date	2020-05-07
Publishing country	United States
Document type	Letter ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Comment
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2007295117
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Article ; Online: Immunosenescence and vaccine efficacy revealed by immunometabolic analysis of SARS-CoV-2-specific cells in multiple sclerosis patients.

De Biasi, Sara / Lo Tartaro, Domenico / Neroni, Anita / Rau, Moritz / Paschalidis, Nikolaos / Borella, Rebecca / Santacroce, Elena / Paolini, Annamaria / Gibellini, Lara / Ciobanu, Alin Liviu / Cuccorese, Michela / Trenti, Tommaso / Rubio, Ignacio / Vitetta, Francesca / Cardi, Martina / Argüello, Rafael José / Ferraro, Diana / Cossarizza, Andrea

Nature communications

2024 Volume 15, Issue 1, Page(s) 2752

Abstract: ... can influence immune responses to SARS-CoV-2 and vaccine efficacy. However, data on the detailed phenotypic ... the phenotype, function and the single-cell metabolic profile of SARS-CoV-2-specific T and B cells up to 8 ... ocrelizumab. Almost all patients display functional immune response to SARS-CoV-2. Different ...

Abstract	Disease-modifying therapies (DMT) administered to patients with multiple sclerosis (MS) can influence immune responses to SARS-CoV-2 and vaccine efficacy. However, data on the detailed phenotypic, functional and metabolic characteristics of antigen (Ag)-specific cells following the third dose of mRNA vaccine remain scarce. Here, using flow cytometry and 45-parameter mass cytometry, we broadly investigate the phenotype, function and the single-cell metabolic profile of SARS-CoV-2-specific T and B cells up to 8 months after the third dose of mRNA vaccine in a cohort of 94 patients with MS treated with different DMT, including cladribine, dimethyl fumarate, fingolimod, interferon, natalizumab, teriflunomide, rituximab or ocrelizumab. Almost all patients display functional immune response to SARS-CoV-2. Different metabolic profiles characterize antigen-specific-T and -B cell response in fingolimod- and natalizumab-treated patients, whose immune response differs from all the other MS treatments.
MeSH term(s)	Humans ; Multiple Sclerosis ; Immunosuppressive Agents/therapeutic use ; Fingolimod Hydrochloride/therapeutic use ; SARS-CoV-2 ; Natalizumab/therapeutic use ; Vaccine Efficacy ; mRNA Vaccines ; COVID-19/prevention & control ; Immunosenescence
Chemical Substances	Immunosuppressive Agents ; Fingolimod Hydrochloride (G926EC510T) ; Natalizumab ; mRNA Vaccines
Language	English
Publishing date	2024-03-29
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-47013-0
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Article ; Online: Gene Expression Analysis of T-Cells by Single-Cell RNA-Seq.

Lo Tartaro, Domenico / De Biasi, Sara / Forcato, Mattia / Gibellini, Lara / Cossarizza, Andrea

Methods in molecular biology (Clifton, N.J.)

2021 Volume 2285, Page(s) 277–296

Abstract: During the last decade, the rapid progress in the development of next-generation sequencing (NGS) technologies has provided relevant insights into complex biological systems, ranging from cancer genomics to microbiology. Among NGS technologies, single- ... ...

Abstract	During the last decade, the rapid progress in the development of next-generation sequencing (NGS) technologies has provided relevant insights into complex biological systems, ranging from cancer genomics to microbiology. Among NGS technologies, single-cell RNA sequencing is currently used to decipher the complex heterogeneity of several biological samples, including T cells. Even if this technique requires specialized equipment and expertise, nowadays it is broadly applied in research. In this chapter, we will provide an optimized protocol for the isolation of T cells and the preparation of RNA sequencing libraries by using droplet digital technology (ddSEQ, Bio-Rad Laboratories). We will also illustrate a guide to the main steps of data processing and options for data interpretation. This protocol will support users in building a single-cell experimental framework, from sample preparation to data interpretation.
MeSH term(s)	CD8-Positive T-Lymphocytes/immunology ; CD8-Positive T-Lymphocytes/metabolism ; Cell Separation ; Gene Expression Regulation ; Gene Library ; Humans ; Lab-On-A-Chip Devices ; Microfluidic Analytical Techniques/instrumentation ; RNA-Seq ; Research Design ; Single-Cell Analysis ; Workflow
Language	English
Publishing date	2021-04-30
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1311-5_22
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Article ; Online: Advances and Challenges in Sepsis Management: Modern Tools and Future Directions.

Santacroce, Elena / D'Angerio, Miriam / Ciobanu, Alin Liviu / Masini, Linda / Lo Tartaro, Domenico / Coloretti, Irene / Busani, Stefano / Rubio, Ignacio / Meschiari, Marianna / Franceschini, Erica / Mussini, Cristina / Girardis, Massimo / Gibellini, Lara / Cossarizza, Andrea / De Biasi, Sara

Cells

2024 Volume 13, Issue 5

Abstract: Sepsis, a critical condition marked by systemic inflammation, profoundly impacts both innate and adaptive immunity, often resulting in lymphopenia. This immune alteration can spare regulatory T cells (Tregs) but significantly affects other lymphocyte ... ...

Abstract	Sepsis, a critical condition marked by systemic inflammation, profoundly impacts both innate and adaptive immunity, often resulting in lymphopenia. This immune alteration can spare regulatory T cells (Tregs) but significantly affects other lymphocyte subsets, leading to diminished effector functions, altered cytokine profiles, and metabolic changes. The complexity of sepsis stems not only from its pathophysiology but also from the heterogeneity of patient responses, posing significant challenges in developing universally effective therapies. This review emphasizes the importance of phenotyping in sepsis to enhance patient-specific diagnostic and therapeutic strategies. Phenotyping immune cells, which categorizes patients based on clinical and immunological characteristics, is pivotal for tailoring treatment approaches. Flow cytometry emerges as a crucial tool in this endeavor, offering rapid, low cost and detailed analysis of immune cell populations and their functional states. Indeed, this technology facilitates the understanding of immune dysfunctions in sepsis and contributes to the identification of novel biomarkers. Our review underscores the potential of integrating flow cytometry with omics data, machine learning and clinical observations to refine sepsis management, highlighting the shift towards personalized medicine in critical care. This approach could lead to more precise interventions, improving outcomes in this heterogeneously affected patient population.
MeSH term(s)	Humans ; Adaptive Immunity ; Biomarkers ; Inflammation ; Precision Medicine/methods ; Sepsis
Chemical Substances	Biomarkers
Language	English
Publishing date	2024-03-02
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2661518-6
ISSN	2073-4409 ; 2073-4409
ISSN (online)	2073-4409
ISSN	2073-4409
DOI	10.3390/cells13050439
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Article ; Online: SARS-CoV-2, the Virus that Causes COVID-19: Cytometry and the New Challenge for Global Health.

Cossarizza, Andrea / De Biasi, Sara / Guaraldi, Giovanni / Girardis, Massimo / Mussini, Cristina

Cytometry. Part A : the journal of the International Society for Analytical Cytology

2020 Volume 97, Issue 4, Page(s) 340–343

MeSH term(s)	Betacoronavirus ; COVID-19 ; Coronavirus Infections/immunology ; Flow Cytometry ; Global Health ; Humans ; Pandemics ; Pneumonia, Viral/immunology ; SARS-CoV-2 ; Severe Acute Respiratory Syndrome ; T-Lymphocytes/virology
Keywords	covid19
Language	English
Publishing date	2020-03-18
Publishing country	United States
Document type	Editorial
ZDB-ID	2099868-5
ISSN	1552-4930 ; 0196-4763 ; 1552-4922
ISSN (online)	1552-4930
ISSN	0196-4763 ; 1552-4922
DOI	10.1002/cyto.a.24002
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Zs.A 1688: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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