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Kadir Akdemir

@kcakdemir.bsky.social

250 followers 370 following 40 posts

Husband & father | Asst prof at MD Anderson Cancer Center | Our lab focuses on tumor evolution, chromatin folding & instability akdemirlab.github.io

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Kadir Akdemir @kcakdemir.bsky.social · Feb 28

Really excited to share our lab's first manuscript! I cant be more proud of our team, especially @nora-mae.bsky.social who diligently worked on this project.
It will be a long thread but I promise it's worth it!
#Oncology #BrainMets

Reposted by Kadir Akdemir

Benjamin Werner @benjaminwerner.bsky.social · Jul 9

Very happy that the review article by @magnushaughey.bsky.social and Imran Noorani on the evolutionary role of extra-chromosomal DNA in cancers just came out.

authors.elsevier.com/sd/article/S...

ScienceDirect.com | Science, health and medical journals, full text articles and books.

authors.elsevier.com

Reposted by Kadir Akdemir

Darío Lupiáñez @dariloops.bsky.social · May 13

🚨The formation of 3D chromatin hubs is a poorly understood
phenomenon.

I wrote a N&V about the excellent work Karpinska, Zhu and colleagues, from @mariekeoudelaar.bsky.social lab, who shed new light on the formation and function of these structures.

rdcu.be/elPt3

Decoupling chromatin hubs from gene control

Nature Structural & Molecular Biology - Chromatin hubs, which are formed during cell differentiation, are characterized by simultaneous interactions between multiple regulatory elements and...

Kadir Akdemir @kcakdemir.bsky.social · May 22

Thanks for reading and we would be delighted to hear your comments/suggestions.

Kadir Akdemir @kcakdemir.bsky.social · May 22

I’m also incredibly proud of our multi-institutional, collaborative team—this work reflects the efforts of researchers across disciplines and career stages, including three undergraduate students who are co-authors on this study!

Kadir Akdemir @kcakdemir.bsky.social · May 22

We are deeply grateful to all the patients and their families whose generosity made this study possible.

Kadir Akdemir @kcakdemir.bsky.social · May 22

This supports the conclusion that joint Hi-C/ONT-based reconstructions yield more accurate structural predictions than those based solely on short-read WGS.

Kadir Akdemir @kcakdemir.bsky.social · May 22

We compared ecDNA structure and transcription in two tumors: in P59, EGFR and CDK4 were predicted to be on separate ecDNAs; in P68, on the same ecDNA. Xenium data showed stronger EGFR-CDK4 expression correlation in P68 compared to p59.

Kadir Akdemir @kcakdemir.bsky.social · May 22

We found that ecDNA+ tumors form nuclear EGFR transcriptional hubs.
EGFR FISH on post-Xenium slides showed >70% of these hubs localized to the nucleus and overlapped with EGFR copy number - unlike control gene FABP7 with similar expression but no hub formation.

Kadir Akdemir @kcakdemir.bsky.social · May 22

We found that EGFR ecDNA tumors are hypoxic, mesenchymal-rich, and pericyte-enriched.

Kadir Akdemir @kcakdemir.bsky.social · May 22

Given our comprehensive whole-genome sequnecing datasets, we compared the spatial organization of ecDNA vs Linear Amplification GBMs

Kadir Akdemir @kcakdemir.bsky.social · May 22

We found that IDH-mutant gliomas frequently harbored inflammatory microglia expressing CX3CR1 specifically within AC-like malignant neighborhoods, rather than OPC-like niches—despite the OPC-like malignant cell state being more prevalent in IDH-mutant gliomas.

Kadir Akdemir @kcakdemir.bsky.social · May 22

To investigate the spatial tumor microenvironment of our glioma samples, we applied a single-cell spatial transcriptomics approach (10x Xenium), generating 4.6 million cells and over 775 million transcripts.
We identified distinct cell states in IDH-wildtype vs mutant gliomas

Kadir Akdemir @kcakdemir.bsky.social · May 22

We next asked whether treatment contributed to ecDNA loss in recurrences. Recurrent tumors arose from residual regions of the primary site, suggesting ecDNAs were spatially restricted subclones eliminated during initial surgery.

Kadir Akdemir @kcakdemir.bsky.social · May 22

We also examined EGFR expression levels, which showed a marked reduction in the recurrent tumors. Similarly, single-nucleus whole-genome analysis revealed the disappearance of the focal amplification on chromosome 7, while clonal alterations were retained.

Kadir Akdemir @kcakdemir.bsky.social · May 22

Hi-C and WGS data revealed the loss of ecDNA signals in recurrent tumor (P-12r1) while preserving other structural variations, such as chromothripsis on chr 3

Kadir Akdemir @kcakdemir.bsky.social · May 22

We also identified two GBM patients (P12 and P29) in whom ecDNA molecules were not implicated in tumor recurrence and were absent in both subsequent surgical specimens.

Kadir Akdemir @kcakdemir.bsky.social · May 22

Hi-C and long-read data were essential to improve ecDNA reconstructions.
For example, for p59, the short-read reconstruction suggested EGFR and CDK4 genes are on the same ecDNA circle.
However, Hi-C and ONT WGS-based reconstructions suggested these genes reside on two distinct circles.

Kadir Akdemir @kcakdemir.bsky.social · May 22

🔹 Resolving ecDNA Structure and Function
We used short- and long-read whole-genome sequencing plus Hi-C to reconstruct complex extrachromosomal DNA (ecDNA) structures. This revealed:

Tumors can harbor multiple ecDNA circles with distinct oncogenes.

Kadir Akdemir @kcakdemir.bsky.social · May 22

We performed an integrative multi-omic and spatial transcriptomic analysis of 93 gliomas, leveraging 449 unique specimens to uncover how oncogenic drivers reshape tumor architecture and the surrounding microenvironment in human gliomas.

Kadir Akdemir @kcakdemir.bsky.social · May 22

Excited to share our latest manuscript www.biorxiv.org/content/10.1...
This was a great collaboration with Drs. Huse, Lang, @jesserdixon.bsky.social

Reposted by Kadir Akdemir

Eileen Parkes @eileenparkes.bsky.social · May 12

Incoming - new preprint alert from the Parkes lab led by @brunobeernaert.bsky.social Full bluetutorial follows! 1/ 11 www.biorxiv.org/content/10.1...

Model figure - in EAC cancers, as chromosomal instability (CIN) increases, we found that a CIN-driven cGAS-dependent axis drives myeloid directed chemokine expression and recruitment of tumor-favoring myeloid populations

Reposted by Kadir Akdemir

Emre Kocakavuk @ekocakavuk.bsky.social · May 7

🧪 We’re Hiring: Lab Technician 🧪

I’m happy to share that our newly established Emmy Noether Group in Essen is looking for a Lab Technician to join our team!

🔗 Apply here: karriere.ume.de/job-finder/?...
📅 Start: At the earliest possible date
💻 Homepage: kocakavuklab.vercel.app/overview

Job Finder - Karriereportal - Universitätsklinikum Essen

Finden Sie eine Stelle am Universitätsklinikum Essen

karriere.ume.de

Kadir Akdemir @kcakdemir.bsky.social · May 3

Omg, this is super funny but also very painful!!!

Reposted by Kadir Akdemir

Costa Samaras @costasamaras.com · Apr 26

that’s right

Kat O’Brien @lavidagata.bsky.social · Apr 18

I knew the U.S. higher education system was a massive draw for foreigners, but I did not know the U.S. sold more educational services to the rest of the world than it did natural gas and coal combined. Great piece by @crampell.bsky.social

Colleges and universities are among America's most competitive international exporters. In dollar terms, last year, the United States sold more educational services to the rest of the world than it sold in natural gas and coal combined.
Make sense of the latest news and debates with our daily newsletter
What are America's most competitive exports? By dollars, not coal or corn.
Dollar value of exports in select sectors, 2024
Education-related travel
$56B
Natural gas
34B

Reposted by Kadir Akdemir

Carolyn Bertozzi @carolynbertozzi.bskyverified.social · Apr 25

Huge opportunity for postdocs gearing up for an academic job search, hosted by @stanford-chemh.bsky.social @berkeleymcb.bsky.social and UCSF!

Flora Rutaganira @frutag33.bsky.social · Apr 21

Hello Community!
Are you a postdoc/grad student preparing to launch a faculty search? Do you have a track record of excellence in research, leadership, mentorship & community engagement? Apply to the 2025 Next Generation Faculty Symposium: www.berkeleystanfordnextgensymposium.com! Pls repost! (1/3)

Flyer for the 2025 Next Generation Faculty Symposium (including QR code in top right corner). This symposium highlights the work of exceptional early-career scientists in the broad field of quantitative biological and biomedical sciences, with a track record of excellence in research, leadership, mentorship, and community engagement. These early career scientists are preparing to launch a faculty search. Applications are due May 30th, 2025.