Journal: bioRxiv

Article Title: Multimodal profiling of chordoma immunity reveals distinct immune contextures

doi: 10.1101/2023.09.14.557579

Figure Lengend Snippet: a-b , Heterogeneity in T cell infiltration in chordomas. The images show T cell-related markers (CD4 = red, CD8 = blue), a proliferation marker (Ki-67 = yellow) and a tumour marker (keratin = white) as detected by imaging mass cytometry. a , chordoma with low T cell infiltration (ICR low). b , chordoma with high T cell infiltration and a magnified image of the chordoma with high T cell infiltration (ICR high). c , Heatmap showing the mean cell density Z-Score of all T cell phenotypes in all chordoma samples ( n = 32), hierarchically clustered into a T cell high ( n = 18) and T cell low ( n = 14) group. Samples are annotated with their respective ICR score from the transcriptional analysis. In addition, the samples are annotated for their anatomical location, the follow-up status of the patients as well as whether the sample had received neoadjuvant radiotherapy. d , Boxplots presenting the mean cell densities per mm 2 per classified T cell group (T cell high: n = 18; T cell low: n = 14) for the identified T cell phenotypes. e , Kaplan-Meier curves interrogating the association between T cell infiltration and disease-specific survival. Two-sided log-rank tests were performed for the Kaplan Meier estimates. ICR = immunologic constant of rejection; Tregs = regulatory T cells

Article Snippet: ROIs of 1000×1000 μm were selected with consecutive H&E slides and ablated by using a Hyperion mass cytometry imaging system (Fluidigm) at the Flow Core Facility (LUMC, Leiden) within a month after staining.

Techniques: Marker, Imaging, Mass Cytometry

Journal: bioRxiv

Article Title: Multimodal profiling of chordoma immunity reveals distinct immune contextures

doi: 10.1101/2023.09.14.557579

Figure Lengend Snippet: a , Boxplots comparing cell densities between the T cell high ( n = 18) and T cell low groups ( n = 14). Dendritic cells (CD11c +/- HLA-DR + CD68 - ) and immune cell aggregates (CD45 + and multiple differentiation markers, e.g. CD3 + CD68 + ) are significantly higher in the T cell high group as compared to the T cell low group. Two-sided t-test was performed in R and the P value was adjusted with the Benjamini-Hochberg false discovery rate (FDR). * = P < 0.05; ** = P < 0.01; *** P < 0.001. b , An image generated with imaging mass cytometry displaying co-localisation of dendritic cells (HLA-DR = red) and T cells (CD3 = blue). Tumour cells are only shown in the overview image (top-left image, keratin = white). Other myeloid and T cell-related markers are presented in separate images around the overview image in green (CD4, CD8, CD11c, CD14 and CD163), to show co-localisation of different markers. c , Heatmap displaying the spatial interaction analysis results comparing the microenvironment of T cell high with T cell low chordomas. Only significant interactions are visualised and coloured for the subgroup(s) in which they are enriched. Permutation Z scores below 10 were considered not significant and thus removed for visualisation. Interactions of interest are indicated by black arrows. PDPN = podoplanin.

Article Snippet: ROIs of 1000×1000 μm were selected with consecutive H&E slides and ablated by using a Hyperion mass cytometry imaging system (Fluidigm) at the Flow Core Facility (LUMC, Leiden) within a month after staining.

Techniques: Generated, Imaging, Mass Cytometry

Journal: bioRxiv

Article Title: Multimodal profiling of chordoma immunity reveals distinct immune contextures

doi: 10.1101/2023.09.14.557579

Figure Lengend Snippet: a, Boxplots with the significantly different phenotypes between the T cell high and T cell low groups. Two-sided t-test was performed in R and the P value was adjusted with the Benjamini-Hochberg false discovery rate (FDR). All presented phenotypes were significantly different between the T cell high an T cell low group. * = P < 0.05; ** = P < 0.01; *** P < 0.001. b , Representative images generated with imaging mass cytometry displaying the differentially abundant cell phenotypes in both T cell low and T cell high samples. Images are grouped per row for the displayed cell markers and outlined with their respective T cell group (T cell high = red rectangle & left, T cell low = blue rectangle & right). The top row presents CD11c + macrophages (CD11c = red, CD68 = green, HLA-DR = blue, keratin = white), the middle row displays granulocytes and CD163 + HLA-DR+ macrophages (CD15 = green, CD163 = blue, HLA-DR = red, keratin = white) and the bottom row shows vessels and podoplanin + stromal cells (CD31 = red, PDPN = green, keratin = white). c , Boxplots presenting the cumulative mean cell density per mm 2 of all immune cells, stromal cells and tumour cells in both T cell high and T cell low groups. Two-sided t-test was performed in R. ** = P < 0.01, *** = P < 0.001. PDPN = podoplanin.

Article Snippet: ROIs of 1000×1000 μm were selected with consecutive H&E slides and ablated by using a Hyperion mass cytometry imaging system (Fluidigm) at the Flow Core Facility (LUMC, Leiden) within a month after staining.

Techniques: Generated, Imaging, Mass Cytometry

Journal: bioRxiv

Article Title: Multimodal profiling of chordoma immunity reveals distinct immune contextures

doi: 10.1101/2023.09.14.557579

Figure Lengend Snippet: a , Examples images of Human Leukocyte Antigen (HLA) class I (HCA2 and HC10) expression in a T cell high chordoma as validated by immunohistochemistry. b , A n example image and a corresponding magnitication of the same tissue core as displayed in ( a ) as generated by imaging mass cytometry. The images present intratumoral γδ T cell intiltration as indicated by the magenta arrows (CD3 = red, TCRγδ = blue, keratin = white). TCR = T cell receptor.

Article Snippet: ROIs of 1000×1000 μm were selected with consecutive H&E slides and ablated by using a Hyperion mass cytometry imaging system (Fluidigm) at the Flow Core Facility (LUMC, Leiden) within a month after staining.

Techniques: Expressing, Immunohistochemistry, Generated, Imaging, Mass Cytometry

Journal: Journal of Clinical Medicine

Article Title: Advances in Percutaneous Patent Foramen Ovale Closure: From the Procedure to the Echocardiographic Guidance

doi: 10.3390/jcm11144001

Figure Lengend Snippet: Percutaneous closure of a long and stiff PFO tunnel. A long and stiff tunnel does not allow a correct compaction of the two discs ( A ). The device is pulled back and a trans-septal puncture is performed at the entrance of the tunnel ( B ). The device is deployed again through the trans-septal puncture, with adequate discs compaction and complete closure of the patent foramen ovale ( C , D ).

Article Snippet: Currently, the following devices can also be used: Figulla Flex II PFO Occluder (Occlutech GmbH, Jena, Germany), Figulla Flex II UNI Occluder (Occlutech GmbH, Jena, Germany), Figulla Flex II ASD Occluder (Occlutech GmbH, Jena, Germany), CeraFlex PFO Occluder (Lifetech Scientific Corporation, Shenzhen, China), Ultrasept PFO Occluder (Cardia Inc., Eagan, MN, USA), Hyperion PFO Occluder—II (Comed B.V., Bolsward, The Netherlands), Nit-Occlud PFO (PFM Medical, Cologne, Germany), Amender PFO Occluder (Kewei Rising Medical Co., Ltd., Guangdong, China) and MemoPart PFO Occluder (Lepu Medical Technology Co., Beijing, China).

Techniques: