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Book ; Conference proceedings: Crossroads between innate and adaptive immunity IV

Katsikis, Peter D.

[based on the work presented at the Aegean Conference "4th Crossroads between Innate and Adaptive Immunity" ... between September 11 and September 16, 2011 ... in Elia, Mykonos, Greece]

(Advances in experimental medicine and biology ; 785)

2013

Event/congress	International Conference on Crossroads between Innate and Adaptive Immunity (4, 2011, Elia)
Author's details	Peter D. Katsikis ... ed
Series title	Advances in experimental medicine and biology ; 785
Collection
Keywords	Natural immunity ; Immune response--Regulation
Subject code	616.079
Language	English
Size	XII, 136 S. : Ill., 24 cm
Publisher	Springer
Publishing place	New York u.a.
Publishing country	United States
Document type	Book ; Conference proceedings
HBZ-ID	HT017584440
ISBN	978-1-4614-6216-3 ; 9781461462170 ; 1-4614-6216-9 ; 1461462177
Database	Catalogue ZB MED Medicine, Health

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Book ; Conference proceedings: Crossroads between innate and adaptive immunity III

Katsikis, Peter D. / Pulendran, Bali

(Advances in experimental medicine and biology ; 780 ; Biomedicine)

2011

Event/congress	Crossroads Between Innate and Adaptive Immunity Conference (3, 2009, Chania)
Author's details	Bali Pulendran, Peter D. Katsikis ... (ed.)
Series title	Advances in experimental medicine and biology ; 780 Biomedicine
Collection
Language	English
Size	X, 174 S. : Ill., graf. Darst., 24 cm
Publisher	Springer
Publishing place	New York u.a.
Publishing country	United States
Document type	Book ; Conference proceedings
HBZ-ID	HT016946912
ISBN	978-1-441-95631-6 ; 1-441-95631-X ; 9781441956323 ; 1441956328
Database	Catalogue ZB MED Medicine, Health

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Book ; Conference proceedings: Crossroads between innate and adaptive immunity

Katsikis, Peter D.

[proceedings of the "First Crossroads between Innate and Adaptive Immunity" Conference, held in Rhodes, Greece, October 9 - 14, 2005]

(Advances in experimental medicine and biology ; 590)

2007

Event/congress	Crossroads between Innate and Adaptive Immunity Conference (1, 2005)
Author's details	Peter D. Katsikis ..., ed
Series title	Advances in experimental medicine and biology ; 590
Collection
Language	English
Size	XX, 232 S. : Ill., graph. Darst.
Publisher	Springer
Publishing place	New York, NY
Publishing country	United States
Document type	Book ; Conference proceedings
HBZ-ID	HT014791738
ISBN	0387-34813-1 ; 0-387-34813-1 ; 978-0-387-34813-1 ; 978-0387-34813-1
Database	Catalogue ZB MED Medicine, Health

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Article ; Online: Challenges in developing personalized neoantigen cancer vaccines.

Katsikis, Peter D / Ishii, Ken J / Schliehe, Christopher

Nature reviews. Immunology

2023 Volume 24, Issue 3, Page(s) 213–227

Abstract: The recent success of cancer immunotherapies has highlighted the benefit of harnessing the immune system for cancer treatment. Vaccines have a long history of promoting immunity to pathogens and, consequently, vaccines targeting cancer neoantigens have ... ...

Abstract	The recent success of cancer immunotherapies has highlighted the benefit of harnessing the immune system for cancer treatment. Vaccines have a long history of promoting immunity to pathogens and, consequently, vaccines targeting cancer neoantigens have been championed as a tool to direct and amplify immune responses against tumours while sparing healthy tissue. In recent years, extensive preclinical research and more than one hundred clinical trials have tested different strategies of neoantigen discovery and vaccine formulations. However, despite the enthusiasm for neoantigen vaccines, proof of unequivocal efficacy has remained beyond reach for the majority of clinical trials. In this Review, we focus on the key obstacles pertaining to vaccine design and tumour environment that remain to be overcome in order to unleash the true potential of neoantigen vaccines in cancer therapy.
MeSH term(s)	Humans ; Antigens, Neoplasm ; Cancer Vaccines/therapeutic use ; Neoplasms ; Immune System ; Immunotherapy
Chemical Substances	Antigens, Neoplasm ; Cancer Vaccines
Language	English
Publishing date	2023-10-02
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2062776-2
ISSN	1474-1741 ; 1474-1733
ISSN (online)	1474-1741
ISSN	1474-1733
DOI	10.1038/s41577-023-00937-y
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Classification of Inflammation of Unknown Origin patients based on RNA-seq and SomaScan data.

Papagiannopoulos, Orestis D / Kourou, Konstantina / Papaloukas, Costas / Karanasiou, Georgia S / van de Werken, Harmen J G / Mueller, Yvonne M / Katsikis, Peter D / Herrero-Saboya, Daniel / Fotiadis, Dimitrios I

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference

2023 Volume 2023, Page(s) 1–4

Abstract: A preliminary analysis was conducted on data acquired from RNA sequencing and SomaScan platforms, for the classification of patients with Inflammation of Unknown Origin. To this end, a multimodal data integration approach was designed, by combining the ... ...

Abstract	A preliminary analysis was conducted on data acquired from RNA sequencing and SomaScan platforms, for the classification of patients with Inflammation of Unknown Origin. To this end, a multimodal data integration approach was designed, by combining the two platforms, in order to assess the potentiality of learning estimators, using the differentially expressed features from the independent profiling experiments of both platforms. The classification framing was the differentiation of Inflammation of Unknown Origin patients against a multitude of Systemic Autoinflammatory disease patients. Separate false discovery rate analyses were performed on each dataset to extract statistically significant features between the two designated sample groups. Genomic analysis managed higher overall classification metrics compared to proteomic analysis, averaging an ~19% increase overall metrics and classifiers, with a ~0.07% increase in standard error. The multimodal data integration approach achieved similar results to the individual platforms' analyses. More specifically, it managed the same classification accuracy, sensitivity, and specificity scores as the best individual analysis, with the simple Logistic Regression estimator.Clinical Relevance- This study highlights the advantage of exploiting RNA sequencing data to identify potential Inflammation of Unknown Origin disease specific biomarkers, even against other Systemic Autoinflammatory diseases. These findings are further emphasized given the non-apparent clinical discrepancy between Inflammation of Unknown Origin and other Systemic Autoinflammatory diseases.
MeSH term(s)	Humans ; Proteomics/methods ; RNA-Seq ; Genomics/methods ; Sequence Analysis, RNA/methods ; Syndrome ; Hereditary Autoinflammatory Diseases
Language	English
Publishing date	2023-12-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2694-0604
ISSN (online)	2694-0604
DOI	10.1109/EMBC40787.2023.10340537
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Article: Targeted multiomics in childhood-onset SLE reveal distinct biological phenotypes associated with disease activity: results from an explorative study.

Wahadat, Mohamed Javad / van Tilburg, Sander J / Mueller, Yvonne M / de Wit, Harm / Van Helden-Meeuwsen, Cornelia G / Langerak, Anton W / Gruijters, Marike J / Mubarak, Amani / Verkaaik, Marleen / Katsikis, Peter D / Versnel, Marjan A / Kamphuis, Sylvia

Lupus science & medicine

2023 Volume 10, Issue 1

Abstract: Objective: To combine targeted transcriptomic and proteomic data in an unsupervised hierarchical clustering method to stratify patients with childhood-onset SLE (cSLE) into similar biological phenotypes, and study the immunological cellular landscape ... ...

Abstract	Objective: To combine targeted transcriptomic and proteomic data in an unsupervised hierarchical clustering method to stratify patients with childhood-onset SLE (cSLE) into similar biological phenotypes, and study the immunological cellular landscape that characterises the clusters. Methods: Targeted whole blood gene expression and serum cytokines were determined in patients with cSLE, preselected on disease activity state (at diagnosis, Low Lupus Disease Activity State (LLDAS), flare). Unsupervised hierarchical clustering, agnostic to disease characteristics, was used to identify clusters with distinct biological phenotypes. Disease activity was scored by clinical SELENA-SLEDAI (Safety of Estrogens in Systemic Lupus Erythematosus National Assessment-Systemic Lupus Erythematosus Disease Activity Index). High-dimensional 40-colour flow cytometry was used to identify immune cell subsets. Results: Three unique clusters were identified, each characterised by a set of differentially expressed genes and cytokines, and by disease activity state: cluster 1 contained primarily patients in LLDAS, cluster 2 contained mainly treatment-naïve patients at diagnosis and cluster 3 contained a mixed group of patients, namely in LLDAS, at diagnosis and disease flare. The biological phenotypes did not reflect previous organ system involvement and over time, patients could move from one cluster to another. Healthy controls clustered together in cluster 1. Specific immune cell subsets, including CD11c+ B cells, conventional dendritic cells, plasmablasts and early effector CD4+ T cells, differed between the clusters. Conclusion: Using a targeted multiomic approach, we clustered patients into distinct biological phenotypes that are related to disease activity state but not to organ system involvement. This supports a new concept where choice of treatment and tapering strategies are not solely based on clinical phenotype but includes measuring novel biological parameters.
MeSH term(s)	Humans ; Lupus Erythematosus, Systemic/drug therapy ; Multiomics ; Proteomics ; Phenotype ; Cytokines
Chemical Substances	Cytokines
Language	English
Publishing date	2023-04-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2779620-6
ISSN	2053-8790
ISSN	2053-8790
DOI	10.1136/lupus-2022-000799
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Article ; Online: Sex-based differences in cardiovascular proteomic profiles and their associations with adverse outcomes in patients with chronic heart failure.

de Bakker, Marie / Petersen, Teun B / Akkerhuis, K Martijn / Harakalova, Magdalena / Umans, Victor A / Germans, Tjeerd / Caliskan, Kadir / Katsikis, Peter D / van der Spek, Peter J / Suthahar, Navin / de Boer, Rudolf A / Rizopoulos, Dimitris / Asselbergs, Folkert W / Boersma, Eric / Kardys, Isabella

Biology of sex differences

2023 Volume 14, Issue 1, Page(s) 29

Abstract: Background: Studies focusing on sex differences in circulating proteins in patients with heart failure with reduced ejection fraction (HFrEF) are scarce. Insight into sex-specific cardiovascular protein profiles and their associations with the risk of ... ...

Abstract	Background: Studies focusing on sex differences in circulating proteins in patients with heart failure with reduced ejection fraction (HFrEF) are scarce. Insight into sex-specific cardiovascular protein profiles and their associations with the risk of adverse outcomes may contribute to a better understanding of the pathophysiological processes involved in HFrEF. Moreover, it could provide a basis for the use of circulating protein measurements for prognostication in women and men, wherein the most relevant protein measurements are applied in each of the sexes. Methods: In 382 patients with HFrEF, we performed tri-monthly blood sampling (median follow-up: 25 [13-31] months). We selected all baseline samples and two samples closest to the primary endpoint (PEP: composite of cardiovascular death, heart transplantation, left ventricular assist device implantation, and HF hospitalization) or censoring. We then applied an aptamer-based multiplex proteomic assay identifying 1105 proteins previously associated with cardiovascular disease. We used linear regression models and gene-enrichment analysis to study sex-based differences in baseline levels. We used time-dependent Cox models to study differences in the prognostic value of serially measured proteins. All models were adjusted for the MAGGIC HF mortality risk score and p-values for multiple testing. Results: In 104 women and 278 men (mean age 62 and 64 years, respectively) cumulative PEP incidence at 30 months was 25% and 35%, respectively. At baseline, 55 (5%) out of the 1105 proteins were significantly different between women and men. The female protein profile was most strongly associated with extracellular matrix organization, while the male profile was dominated by regulation of cell death. The association of endothelin-1 (P Conclusion: Baseline cardiovascular protein levels differ between women and men. However, the predictive value of repeatedly measured circulating proteins does not seem to differ except for endothelin-1 and somatostatin.
MeSH term(s)	Humans ; Female ; Male ; Middle Aged ; Heart Failure ; Ventricular Function, Left/physiology ; Stroke Volume/physiology ; Sex Characteristics ; Endothelin-1 ; Proteomics
Chemical Substances	Endothelin-1
Language	English
Publishing date	2023-05-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2587352-0
ISSN	2042-6410 ; 2042-6410
ISSN (online)	2042-6410
ISSN	2042-6410
DOI	10.1186/s13293-023-00516-9
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Article ; Online: HFrEF subphenotypes based on 4210 repeatedly measured circulating proteins are driven by different biological mechanisms.

Petersen, Teun B / de Bakker, Marie / Asselbergs, Folkert W / Harakalova, Magdalena / Akkerhuis, K Martijn / Brugts, Jasper J / van Ramshorst, Jan / Lumbers, R Thomas / Ostroff, Rachel M / Katsikis, Peter D / van der Spek, Peter J / Umans, Victor A / Boersma, Eric / Rizopoulos, Dimitris / Kardys, Isabella

EBioMedicine

2023 Volume 93, Page(s) 104655

Abstract: Background: HFrEF is a heterogenous condition with high mortality. We used serial assessments of 4210 circulating proteins to identify distinct novel protein-based HFrEF subphenotypes and to investigate underlying dynamic biological mechanisms. Herewith ...

Abstract	Background: HFrEF is a heterogenous condition with high mortality. We used serial assessments of 4210 circulating proteins to identify distinct novel protein-based HFrEF subphenotypes and to investigate underlying dynamic biological mechanisms. Herewith we aimed to gain pathophysiological insights and fuel opportunities for personalised treatment. Methods: In 382 patients, we performed trimonthly blood sampling during a median follow-up of 2.1 [IQR:1.1-2.6] years. We selected all baseline samples and two samples closest to the primary endpoint (PEP; composite of cardiovascular mortality, HF hospitalization, LVAD implantation, and heart transplantation) or censoring, and applied an aptamer-based multiplex proteomic approach. Using unsupervised machine learning methods, we derived clusters from 4210 repeatedly measured proteomic biomarkers. Sets of proteins that drove cluster allocation were analysed via an enrichment analysis. Differences in clinical characteristics and PEP occurrence were evaluated. Findings: We identified four subphenotypes with different protein profiles, prognosis and clinical characteristics, including age (median [IQR] for subphenotypes 1-4, respectively:70 [64, 76], 68 [60, 79], 57 [47, 65], 59 [56, 66]years), EF (30 [26, 36], 26 [20, 38], 26 [22, 32], 33 [28, 37]%), and chronic renal failure (45%, 65%, 36%, 37%). Subphenotype allocation was driven by subsets of proteins associated with various biological functions, such as oxidative stress, inflammation and extracellular matrix organisation. Clinical characteristics of the subphenotypes were aligned with these associations. Subphenotypes 2 and 3 had the worst prognosis compared to subphenotype 1 (adjHR (95%CI):3.43 (1.76-6.69), and 2.88 (1.37-6.03), respectively). Interpretation: Four circulating-protein based subphenotypes are present in HFrEF, which are driven by varying combinations of protein subsets, and have different clinical characteristics and prognosis. Clinical trial registration: ClinicalTrials.gov Identifier: NCT01851538https://clinicaltrials.gov/ct2/show/NCT01851538. Funding: EU/EFPIA IMI2JU BigData@Heart grant n°116074, Jaap Schouten Foundation and Noordwest Academie.
MeSH term(s)	Humans ; Infant ; Child, Preschool ; Heart Failure/diagnosis ; Heart Failure/therapy ; Stroke Volume ; Proteomics ; Biomarkers ; Prognosis
Chemical Substances	Biomarkers
Language	English
Publishing date	2023-06-14
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2851331-9
ISSN	2352-3964
ISSN (online)	2352-3964
DOI	10.1016/j.ebiom.2023.104655
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Article ; Online: The timing of differentiation and potency of CD8 effector function is set by RNA binding proteins.

Petkau, Georg / Mitchell, Twm J / Chakraborty, Krishnendu / Bell, Sarah E / D Angeli, Vanessa / Matheson, Louise / Turner, David J / Saveliev, Alexander / Gizlenci, Ozge / Salerno, Fiamma / Katsikis, Peter D / Turner, Martin

Nature communications

2022 Volume 13, Issue 1, Page(s) 2274

Abstract: ... ...

Abstract	CD8
MeSH term(s)	CD28 Antigens/metabolism ; CD8-Positive T-Lymphocytes ; Cell Differentiation ; RNA-Binding Proteins/metabolism ; Signal Transduction
Chemical Substances	CD28 Antigens ; RNA-Binding Proteins
Language	English
Publishing date	2022-04-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-29979-x
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Article ; Online: Ibrutinib directly reduces CD8+T cell exhaustion independent of BTK.

Li, Ling / Zhao, Manzhi / Kiernan, Caoimhe H / Castro Eiro, Melisa D / van Meurs, Marjan / Brouwers-Haspels, Inge / Wilmsen, Merel E P / Grashof, Dwin G B / van de Werken, Harmen J G / Hendriks, Rudi W / Mueller, Yvonne M / Katsikis, Peter D

Frontiers in immunology

2023 Volume 14, Page(s) 1201415

Abstract: Introduction: Cytotoxic CD8+ T cell (CTL) exhaustion is a dysfunctional state of T cells triggered by persistent antigen stimulation, with the characteristics of increased inhibitory receptors, impaired cytokine production and a distinct transcriptional ...

Abstract	Introduction: Cytotoxic CD8+ T cell (CTL) exhaustion is a dysfunctional state of T cells triggered by persistent antigen stimulation, with the characteristics of increased inhibitory receptors, impaired cytokine production and a distinct transcriptional profile. Evidence from immune checkpoint blockade therapy supports that reversing T cell exhaustion is a promising strategy in cancer treatment. Ibrutinib, is a potent inhibitor of BTK, which has been approved for the treatment of chronic lymphocytic leukemia. Previous studies have reported improved function of T cells in ibrutinib long-term treated patients but the mechanism remains unclear. We investigated whether ibrutinib directly acts on CD8+ T cells and reinvigorates exhausted CTLs. Methods: We used an established Results: We found that ibrutinib reduced exhaustion-related features of CTLs in an Discussion: Our study demonstrates that ibrutinib directly ameliorates CTL exhaustion, and provides evidence for its synergistic use with cancer immunotherapy.
Language	English
Publishing date	2023-09-12
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2023.1201415
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