Immunogenomics Lab. Department of Pathology. Leiden University Medical Center
Based in Netherlands
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💡 This enables powerful insights into tissue organization, microenvironments & biological processes — while still being compatible with cell-based methods when needed.
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GRIDGENE takes a cell-free approach, using transcript density to define biologically relevant tissue regions such as:
✨ Tissue interfaces
✨ Phenotype-enriched compartments
✨ Gene signature–defined zones
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🚀 Happy to share our new preprint introducing GRIDGENE — a transcript density–based approach for spatial transcriptomics!
biorxiv.org/content/10.1101/…
#SpatialTranscriptomics #CancerResearch #Bioinformatics
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Instead, PENGUIN preserves critical signal intensity variations, cuts down on noise, and boosts accuracy in tasks like cell segmentation & phenotyping. 🧬💻
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📊 What PENGUIN PENGUIN Offers: PENGUIN (Percentile Normalization GUI Image deNoising) stands out with a streamlined, no-fuss approach for preprocessing multiplex imaging data. Unlike other tools, it doesn’t require:
Manual annotation
Complex machine learning models
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🚀 New Tool Alert! 🚀
PENGUIN 🐧is finally published in @CSB_Journal : PENGUIN is a rapid, efficient, and user-friendly tool for denoising and normalizing multiplexed spatial proteomics images! 🔬✨
🔗sciencedirect.com/science/ar…
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By sequentially applying MALDI-MSI and IMC on the same tissue section, we can map the cellular makeup of the tissue microenvironment and simultaneously uncover the metabolic phenotypes of individual cells.
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Imaging mass #cytometry
(SABR was our previous pipeline but led to some loss of real signal)
onlinelibrary.wiley.com/doi/…
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🚀 We just developed a new tool for pre-processing #multiplex #imaging data! 🐧 PENGUIN is an easy, straightforward, and highly effective solution to handle noise while preserving real signals.
biorxiv.org/content/10.1101/…
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In a study spearheaded by @s_vanoost and led by J Bovée's group, we took a deep dive into #chordoma immunity. We unearth intriguing immune responses despite the low mutation burden of chordomas, a rare and complex cancer. #CancerResearch #Immunotherapy
biorxiv.org/content/10.1101/…
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Great work by @Joana_BrasNunes & @MEIjsselsteijn as we delve into the world of single-cell immune and metabolic profiling using imaging #CyTOF and MALDI-MSI. #Cancer #Immunology #metabolism
biorxiv.org/content/10.1101/…
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Today was our group's summer activity. Our survival skills were put to the test during an Expedition Robinson challenge. After science and academia, everything else seems easy ;)
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The @LUMC_Leiden crew @FORTRESSMEETING. Wonderful meeting to advance #sarcoma research and therapy. See you in 2024!
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Great presentation by Debora Meijer, a PhD from the groups of Judith Bovee and our lab @LUMC_Leiden and @mkuijjer on the discovery of #Immunotherapy targets in #osteosarcoma @FORTRESSMEETING
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Last, we showed that #ICB induces profound infiltration of activated, cytotoxic, and proliferating γδ T cells in MMR-d colon cancers with antigen presentation defects, highlighting γδ T cells as effectors of immune checkpoint blockade in this context.🦸
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We demonstrated that γδ T cells from MMR-d colon cancers show preferential reactivity towards HLA class I-negative cancer cell lines and organoids. This reactivity was mainly contained within the PD-1+ Vδ1 and Vδ3 T cells, and partly dependent on NKG2D/NKG2D-L interactions.
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We examined tumor-infiltrating #γδTcells in MMR-d colon cancers by #scRNAseq and #ImagingMassCytometry, and observed that the Vδ1 and Vδ3 T cell subsets display hallmarks of cytotoxic activity and frequently show intraepithelial localization in tumors.🔬
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By using three MMR-deficient cancer cohorts from TCGA, we found that B2M-mutant MMR-deficient cancers show increased levels of Vδ1 and Vδ3 TCRs as well as KIR transcripts.🧬
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First, we showed that in patients with #MMRdeficient cancers, B2M defects are associated with high clinical benefit following PD-1 #CheckpointBlockade. This suggests the involvement of other immune effector cells compensating for the lack of conventional CD8 T cell immunity.
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It’s finally out! Our most recent work published today in @Nature:
γδ T cells are effectors of immunotherapy in cancers with HLA class I defects.
nature.com/articles/s41586-0…
🧵below 👇👇👇
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It seems that cancer-related immune cell populations are not increased in peripheral blood but are enriched in blood isolated from the portal vein. Begs the question whether we can extract immune cells with anti-tumor properties from this source (looking into it).
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Similar to our work in #colorectalcancer, we also pinpointed a tumor-specific ILC1-like cell population, displaying an activated profile. It is still largely a mystery what is the role of these immune cells in the anti-tumor immune response.
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We discovered ta marked reduction in the frequency of "tumor-resident", memory CD8+ T cells, but an increase in the frequency of memory B cells and Tregs in PDAC as compared with non-malignant pancreatic tissues.
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The most recent paper from the lab has been published at @jitcancer. We employed single-cell mass cytometry to delineate tumor-associated and systemic immune profiles in #PancreaticCancer.
jitc.bmj.com/content/10/7/e0…
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@Joana_BrasNunes, a postdoc in the group, presented a poster with her work on #immunometabolism at the Cell Symposium Translational Immunometabolism @CellSymposia #CSimmunomet22. She also spotted the Pathology Dept. from the Universitatsspital #Basel #immunity #Cancer
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The final contribution of the group to the DTIM was the presentation by @NFdeMiranda. He presented our work on gamma-delta T cells in colorectal cancer, spearheaded by @NLdeVries
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Second day of DTIM, where @MEIjsselsteijn showed her work on the tumourmicroenvironment of colorectal cancer using #imagingmasscytometry #cancer
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In the following laptop session at the DTIM, @JessicaRoelands showed her work applying spatial transcriptomics to colorectal cancer to determine hallmarks of CRC tumorigenesis #cancer #immunemicroenvironment
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At the DTIM, our Postdocs had the chance to show their data in the fast-paced laptop sessions, first @Joana_BrasNunes shared her project on the immunometabolism of colorectal cancercells and the immunemicroenvironment #immunometabolism #cancer
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Next Ricki Krog got the opportunity to share his very interesting data on the immunemicroenvironment of pancreatic cancer at the DTIM #cancerimmunology #Imagingmasscytometry
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Our contributions to the DTIM were started of by Siddh van Oost who presented his work on multi-omics analyses of chordomas #CancerGenomics #Cancerimmunology
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Today and tomorrow we are at the Dutch Tumour Immunology Meeting (DTIM) in Breukelen. Very interesting talks and lovely weather! Oh and 6 of us are presenting our data!
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Induced pluripotent stem cells (#iPSCs) hold great potential to advance the treatment options for #pancreatic #cancer patients. Clinical trials are ongoing. Great collaboration with Green Light Leiden @LUMC_Leiden. #Immunotherapy @Cancers_MDPI @PAVEH2020
mdpi.com/2072-6694/13/22/578…
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We've employed spatially-resolved gene expression with #GeoMx_DSP from @nanostringtech to revisit and redefine the multistep model of #colorectal #cancer onset and progression. Bonus: we may have found clinically-relevant biomarkers!! biorxiv.org/content/10.1101/…
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A new Review from our group on successes, failures, and promises of cancer immunotherapy in pancreatic cancer:
link.springer.com/content/pd…
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A new pre-print from our lab in collaboration with @ThomasHollt group to make the best of your IMC data!
biorxiv.org/content/10.1101/… #masscytometry @fluidigm @MEIjsselsteijn
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Researchers and clinicians from the @LUMC_Leiden and @NKI_nl got together at the 1st immuno-oncology symposium co-organized by both institutes. Excellent talks demonstrating a huge potential to work together on #Cancer #immunology and #immunotherapy
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Ziena Abdulrahman did a #research project at our lab where she found #immune signatures predictive of response to #HPVvaccine in patients affected by lesions that precede #vulvar #cancer. For that, she got the Nijbakker-Morra award! Her work will be in the press soon!
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Time to go back to @LUMC_Leiden after two very successful days of scientific discussions but also socializing between the lab members. We have great plans for the coming year! #Immunogenomics #lab #retreat 1st edition. #cancer #research #immunology #genomics #immunotherapy
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Already well underway in the scientific activities of @deMirandaLab retreat. First day dedicated to the projects from the #PhD students. All projects/ideas are being discussed and priorities are being defined.
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1st day of the @deMirandaLab retreat's 1st edition. Austrian mountains in the background and getting together for breakfast before starting our discussions. #oberaudorf #immunogenomics #CancerResearch #Immunology
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We can find anti-cancer immune responses in #colorectalcancer patients that are currently not considered for #Immunotherapy Congratulations to @JvandenBulk et al. for a lot of work Next step: develop specific approaches for these patients! genomemedicine.biomedcentral… @GenomeMedicine
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Great to see our collaborative work out. P.S. always re-characterize your models ;)
#cancer #immunotherapy #Checkpoint #blockade #MC38
tandfonline.com/doi/full/10.…
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Our paper describing how we set up a 40-marker panel for #imaging mass #cytometry is accepted @FrontImmunol. Full-text will follow soon! Congrats @MEIjsselsteijn and colleagues! @fluidigm
@CellSignal
frontiersin.org/articles/10.…
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The lab is participating at the @transcoloncan #COSTaction meeting in Krakow with presentations by @NLdeVries and @JvandenBulk on their work in #colorectalcancer #immunology and #Immunotherapy . We look forward to increase the collaborations and networking from the lab!
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During two weeks we hosted @JoãoSilva from the @adbeggs lab to work together on immune contextures influencing the treatment of #rectalcancer. Great support from @EACRnews @CR_UK @LUMC_Leiden @unibirmingham for collaborative #cancerresearch. #Cytometry #Cancerimmunology
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Both @NLdeVries and @JvandenBulk presented their work at the Dutch Tumor Immunology Meeting on novel #Immunotherapy approaches for #colorectalcancer
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3 very talented BSc. Biomedicine students that did their traineeship at our lab presenting their #science @LUMC_Leiden @UniLeiden #nextgeneration
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Our group was brilliantly represented by our PhD students thay presented 4 posters and gave 2 short-talks at #CIMT2019 #Cancer #Immunotherapy @MEIjsselsteijn @JvandenBulk
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@deMirandaLab @NFdeMiranda @MEIjsselsteijn attending a great meeting on spatial protein multiplexing @abcam
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Jitske van de Bulk & @NLdeVries got a travel award and poster prize respectively for their work presented at #DITBA19. Great work! @EACRnews @LUMC_Leiden #cancerimmunology #ColorectalCancer
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Jitske van den Bulk from @deMirandaLab gave a great talk at #DITBA19 on neoantigen-specific responses to support #personalized #immunotherapy in #ColorectalCancer @EACRnews @LUMC_Leiden
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@NLdeVries showing her great work on the characterization of the #immune landscape of #colorectalcancer at #DITBA19 @EACRnews @LUMC_Leiden
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