Färkkilä Laboratory

Summer kick-off vibes from the #FärkkiläLab: we celebrated the start of the season (and our *brand new t-shirts👕*) with a BBQ party full of good food, laughs, and reflections. Looking back at a productive first half of the year and feeling motivated for what’s next. Let’s go🚀!

We’ve been a bit quiet from this account, but that’s about to change! Thrilled to share a huge milestone: our first PhD student, @fer-perezv.bsky.social, defended and graduated🎓! We’re sad to see him go, but so proud as he starts a postdoc at @harvardmed.bsky.social
Congrats, Fer💙!
#ProudLabMoment

@afarkkila.bsky.social, Sara, Ada, and Aleksandra are representing the lab at ESSB in Berlin!
Find them to discuss spatial biology!
🟠 Poster #88: Ada presents a spatial study of the cell cycle in #HGSC
🟠 Poster #155: Aleksandra showcases the use of ML to uncover spatial tumor ecosystems

📢Last chance! Final day to apply for our post-doc position!

🔬Join @afarkkila.bsky.social & the team in advancing #CancerResearch w/clinical impact in a collaborative and supportive environment.

📄Details here: farkkilab.org/careers/job-ads

⏳Apply today and/or help us spread the word by sharing!

20/n Finally, thanks to @helsinkiuni.bsky.social, @fimm-uh.bsky.social, HUS, TYKS, and iCAN. We are proud to be part of these amazing and supportive communities.

19/n Also, huge thanks to our funding agencies #ERC (projects SPACE and STRONGER), Sigrid Jusélius Foundation, Research Council of Finland, Cancer Foundation Finland, Foundation for the Finnish Cancer Institute, Instrufoundation. Let's continue fighting #HGSC together💪.

18/n Special thanks to Iga Niemic, @mariamhincapie.bsky.social, @erdoganpekcanerkan.bsky.social, @fer-perezv.bsky.social, and all the other co-authors and collaborators Peter Sorger, Sampsa Hautaniemi, Tuulia Vallius, Anni Virtanen, @ajitjohnson.com, @harvardlab.bsky.social & Johanna Hynninen.

17/n This long-term collab between our lab, @afarkkila.bsky.social and @anna-vaharautio.bsky.social lab was spearheaded by our amazing PhD student Inga-Maria Launonen and could have not been materialized without the help of all our amazing co-authors.

16/n In summary: our study sheds light on chemotherapy-induced myeloid-driven spatial T-cell exhaustion in #HGSC, opening new avenues for novel immunotherapeutic strategies to unleash CD8+ T-cell-mediated anti-tumor immunity.

15/n These results suggest that targeting the NECTIN2-TIGIT axis with ICB post-chemo, can reverse macrophage-driven CD8+ T cell exhaustion in #HGSC. Both TIGIT and NECTIN2 expression, even separately, predict functional response to anti-TIGIT therapy, making them strong biomarker candidates🎯.

14/n 📌TIGIT expression in CD8+ T cells correlates w/NECTIN2+ myeloid cell abundance.
📌TIGIT expression in CD8+ T cells and NECTIN2+ myeloid cell proportion correlated w/ex vivo CD8+ T cell activation after tiragolumab.
📌TIGIT expression predicts ex vivo response to pembro+tira in #iPDCs.

13/n Last but not least, we subjected matched tumors from our #iPDCs to #t-CyCIF single-cell analysis, focusing on NECTIN2 and TIGIT expression. These are our key findings:

12/n Next, we wondered🤔: What happens if we treat chemo-exposed patient cells with immunotherapy vs. chemo-naive cells? Using #iPDCs (immune-competent patient-derived cultures), we showed that immunotherapy after chemo enhances CD8+ T-cell activity, unlocking new therapeutic potential💥.

11/n (continuation)
📌Cancer cell-rich regions in the peritumoral TSI lack NECTIN2 and TIGIT/CD96, emphasizing macrophages' role in spatially regulating T cell exhaustion.

10/n Here’s what we found:
📌Chemo induces activated NECTIN2+ M1-like macrophages and exhausted, immune-checkpoint-positive CD8+ T cells, both co-localizing in the peritumoral stroma.
📌M1-like macrophages drive T cell exhaustion in #Myelonets, confirmed at the gene expression level.

9/n To integrate findings from both #t-CycIF and #scRNA-seq, we performed *t-CyCIF-guided spatial transcriptomics (GeoMx)* and deconvolution algorithms.

8/n From 22 paired patient samples (pre/post chemo)📊 we found that macrophage-dominated signaling is a key feature post-chemo, aligning with our spatial findings. Wondering what was the strongest induced interaction? NECTIN2 binding to CD226, & the inhibitory receptors CD96 & TIGIT on CD8+ T cells.

7/n To dig deeper, we turned to #scRNAseq 🧬! Chemotherapy induces not only spatial changes but also shifts in immune cell states. Post-treatment, we observe new states emerging for macrophages and T cells, while the diversity of cancer cells decreases. A dynamic TME ecosystem in action 🌌!

6/n However, these immune cells gain exhaustion markers, limiting anti-tumor immunity🛑. Notably, chemotherapy drives exhaustion in CD8+ T cells within M1-like myeloid neighborhoods.

5/n On the other hand, chemo reshapes the spatial landscape of #HGSC, transforming an spatially confined immunophenotype into a more infiltrated one. CD8+ T cells migrate from their “private” neighbourhoods toward cancer cell-hubs and #Myelonets.

4/n In summary, we showed that M2-like macrophage interactions limit CD8+ T cell interactions with tumor cells, resulting in inferior prognosis.

3/n Moreover, interactions between CD8+ T cells and M2-like macrophages at the TSI were mutually exclusive with sustained CD8+ T cell-tumor cell interactions and associated with shorter treatment responses.

2/n Spatial and molecular profiling of 117 #HGSC tumors pre- and post-chemo revealed a dynamic tumor ecosystem🔍. Using a high-plexed (30+🚨) antibody panel and #t-CycIF we identified #myelonets, interconnected networks of myeloid cells, as key drivers CD8+ T cell exhaustion upon chemotherapy.

Chemotherapy induces myeloid-driven spatially confined T cell exhaustion in ovarian cancer Anti-tumor immunity is crucial for high-grade serous ovarian cancer (HGSC) prognosis, yet its adaptation upon standard chemotherapy remains poorly und…

1/n New paper alert 🚨 We're thrilled to share our just published paper in #CancerCell
Do you ever wonder how the #TME in #HGSC changes during chemotherapy? Check it here: www.sciencedirect.com/science/arti... and let’s dive into the highlights together #spatialbiology #ovariancancer #cancerresarch

A thread on our findings is coming later today—stay tuned! 📢

New preprint from our team is live🚨! Don’t miss it—read the preprint and send your thoughts our way: www.biorxiv.org/content/10.1...

Congrats to Fernando and all the co-authors for the hard work 👏

#SpatialBiology #CancerResearch #OvarianCancer

Mathematical modeling framework enhances clinical trial design for maintenance treatment in oncology - Scientific Reports Scientific Reports - Mathematical modeling framework enhances clinical trial design for maintenance treatment in oncology

New paper published! We modelled PARPi maintenance therapy in #ovariancancer www.nature.com/articles/s41...

Matilda presenting her PhD work at NSGO Annual meeting 🎉💪🏼 #ovariancancer #clinicalcancerresrarch @farkkilab.bsky.social

We are looking for a postdoc (Please share 🙏)!
Are you passionate about spatial biology, proteomics, and the TME? Join our culturally diverse, multidisciplinary, and friendly team in 🇫🇮 to make impactful discoveries in ovarian cancer
🧬Details: farkkilab.org/careers/job-...
📅Apply by Dec 11

Hi there👋! We’re the Systems Medicine of Tumor Microenvironment Lab. Our passion? Exploring the #TME through #SystemsOncology. Harnessing the power of our diverse and multidisciplinary team, we use innovative approaches to uncover #Biomarkers and transform these insights into clinical applications.