Twist Bioscience’s Post

Extrachromosomal DNA (ecDNA): Concept and Meaning Extrachromosomal DNA (ecDNA) refers to DNA molecules that exist outside of chromosomes in cells. Unlike chromosomal DNA, which is integrated into the structured genome in the cell nucleus, ecDNA can be circular or linear and is commonly found in prokaryotic and eukaryotic cells. In eukaryotes, ecDNA is often associated with mitochondria (as mitochondrial DNA) or chloroplasts in plants. However, in cancer biology and genetics research, ecDNA specifically refers to DNA fragments that originate from chromosomal DNA but exist independently in the cell nucleus. ecDNA has attracted much attention for its role in tumorigenesis and drug resistance. In cancer cells, ecDNA can carry oncogenes, amplify their expression, and promote tumor growth. Unlike chromosomal DNA, ecDNA replication is not strictly regulated, so genes can be rapidly amplified, resulting in high levels of oncogene expression. This phenomenon leads to tumor heterogeneity and promotes rapid adaptation of cancer cells to environmental stresses, such as drug treatment. Another feature of ecDNA is its ability to escape gene silencing mechanisms that usually occur within chromosomal regions. This makes ecDNA a powerful driver of malignancy, leading to therapeutic resistance and metastasis. Recent advances in sequencing technologies have revealed the prevalence and diversity of ecDNA in various cancers. The study of ecDNA has the potential to innovate therapeutic strategies. Targeting the mechanisms of ecDNA formation, maintenance, or its gene expression pathways could provide new approaches to combat aggressive cancers. Understanding ecDNA also opens avenues for diagnostics, providing biomarkers for tumor progression and therapeutic resistance. In summary, ecDNA represents a dynamic and influential component of the genome, especially in cancer biology, with profound implications for understanding tumor biology and developing targeted therapies. References [1] Rossa WK Chiu et al., Clin Chem 2020 (doi: 10.1093/clinchem/hvaa096) [2] Paul Mischel, TheScientist 2021 (https://lnkd.in/gRgfXQGb) #ecDNA #CancerResearch #GeneTherapy #Oncology #PrecisionMedicine #InnovativeTherapies #CancerBiology #Biomarkers #DrugResistance

🚀 Parean Biotechnologies: Advanced Cancer Research 🚀 For over a year, Parean Biotechnologies has been working alongside the “Oncogenesis Stress Signaling” laboratory (U1242 Inserm/@University of Rennes) and Biotrial as part of the MESHCAP project. Our focus? Developing an innovative model to study lung cancer. It integrates a controlled microbiota, a humanized immune system, and tumor cells from patients to pioneer new immunotherapy strategies for cancer treatment. At Parean Biotechnologies, both our wet lab and data science units are fully involved: - Wet lab expertise: we specialize in managing flow cytometry cell sorting, combined with the 10x Genomics platform, to select, sequence, and analyze tumor cells and their microenvironment at the single-cell level. - Data science expertise: our team manages one of the most comprehensive databases, enabling us to identify immune cell populations, decipher the mechanisms of action of immunotherapies, and uncover the resistance mechanisms of tumor cells. 🔬 At Parean Biotechnologies, we are committed to advancing cancer research and accelerating the development of effective treatments. 🤝 Let's collaborate! Partner with us to leverage our expertise and propel your cancer research projects forward. #CancerResearch #Oncology #Immunotherapy #LungCancer #SingleCellAnalysis #Biotechnology #Innovation #Collaboration Marwan TOUATI, Hang Phuong PHAM, Pierre Barennes, Sergine MONTUY, Remy Pedeux, Ulrich Jarry, 10x Genomics, Parean Biotechnologies, Biotrial, Inserm, Biotech Santé Bretagne

Aviv Regev, PhD, Head of Genentech Research and Early Development, opened her plenary session at AACR 2023 by pointing out the huge problem that cancer research faces. There are > 100 different cancer types, 10,000 known driver mutations, complex circuits driving cancer biology within and between cells in the tumor microenvironment, and an almost unfathomable number of possible small molecules and antibody structures to consider for drug development. With this in mind, the post focuses on: - High-definition spatial transcriptomics and its role in understanding cancer at the molecular level. - Use of single-cell FFPE analysis for identifying unique cancer biomarkers. - Introduction of Xenium technology to improve analysis of the tumor microenvironment. - Computational models aiding in drug discovery and development for cancer treatment. - How these technologies were showcased at the AACR 2024 to illustrate advancements in cancer research and potential impacts on precision medicine. #digitalpathology #pathologynews 10x Genomics Follow the link to read the blog post in full...

Exciting developments in glioblastoma research! @Antonio Iavarone and his team's recent study, leveraging proteomics, uncovered a fascinating discovery: a subset of recurrent GBM tumors exhibiting neuronal-like cells. Published in Cancer Cell, their work sheds light on previously unseen aspects of GBM progression, offering new insights into treatment strategies. Quantum-Si's own Brian Reed says, "By identifying "master kinases" crucial for tumor survival, their findings pave the way for targeted therapies aimed at delaying or treating these treatment-resistant tumors. Discussions for clinical trials targeting master kinases are gaining momentum, representing a crucial step towards personalized therapies for GBM patients. This study underscores the critical role of proteomics in unraveling complexities in cancer biology, closely aligning with our mission at #QSI to accelerate research in proteomics and advance our understanding of disease mechanisms." Read more at Bio-IT World's link below in an article by Deborah Borfitz https://lnkd.in/eFdBF-aH

Interesting read on how long-reads can be used in Oncology.

Being part of the Bruker team, I've had the opportunity to step out of my usual proteomics background and dive into the world of imaging. What excites me the most? It's the intersection of enabling technology and the new insights it provides into complex biological processes. Rajkumar Savai, at Justus Liebig University and the Max Planck Institute, is tackling the important question why some lung cancers resist treatment. Using Bruker's innovative technologies, combining multiplex immunohistochemistry (mIHC) and MALDI, Savai's team can now precisely identify and localize over 100 targeted protein biomarkers in tissue sections! This spatial biology approach helps to understand the molecular interactions within tumors but also paves the way for developing personalized cancer treatments. Check out the full story and learn how this cutting-edge research is set to transform cancer therapy.

🌟 Thrilled to share a recent milestone on my bioinformatics research journey --> At the American Society of Clinical Oncology (ASCO) 2024 Annual Meeting, my research team presented findings from the study we've been working on: "Individualized Molecular Analyses Guide Efforts in Breast Cancer - Personalized Molecular Profiling in Cancer Treatment" (shortened to IMAGE II). It's very promising research that examines how best to leverage advanced diagnostic methods in the treatment of metastatic breast cancer (mBC). A more in-depth explanation of our research --> 🔬 Traditional tissue biopsies (tbx) provide limited snapshots of tumor DNA from just one site and time. But what if we could capture a fuller picture? Enter liquid biopsies (lbx), which can collect circulating tumor DNA (ctDNA) from blood samples. These allow us to more easily monitor how tumors change over time and respond to treatment—offering a more comprehensive genomic landscape. 🎯 Our study, IMAGE II, compares these two methods to better guide treatment strategies. With 199 participants, our focus was on understanding how tumors evolve and respond to treatment through LBX-based genomic profiling, which presents a potentially easier way to monitor treatment response. (Imagine taking a blood test every few weeks to gauge whether the treatment is working.) 📊 I had the privilege of creating some of the visualizations for this project, specifically the plots that compare the genetic alterations found in both the liquid biopsy and tumor biopsy samples, as well as those unique to either liquid biopsies or tumor biopsies alone. 💡 What we're seeing so far holds a lot of potential: ctDNA can be detected in a high percentage of patients, providing the ability to detect and monitor critical genetic alterations more accessibly than traditional biopsies. This highlights lbx's potential to revolutionize how we approach cancer diagnostics and treatment. 👀 Stay tuned as we continue to analyze and report on our findings, aiming to refine how we combat cancer with precision medicine. And if you're curious about how we can use blood samples for cancer diagnostics—reach out or comment below! Read the abstract here: https://lnkd.in/ep5Nm9VJ. #ASCO2024 #Bioinformatics #CancerResearch #PrecisionMedicine #LiquidBiopsies #HealthTech

Among the thousands of DNA mutations that can be detected in cancer, how to identify the few mutations that matter most? Soufyan Lakbir offers a solution, by developing the tool CIBRA: Computational Identification of Biologically Relevant Alterations. Our study demonstrates that there are still many oncogenes and tumor suppressor genes to be discovered, which deserve to be studied in more detail for their putative impact on treatment of cancer and patient survival. Want to know more? Our paper was just published online in #Bioinformatics, Proceedings of #ECCB2024 https://lnkd.in/e48x5BcU Many thanks to the team: Soufyan Lakbir, Caterina Buranelli, Gerrit Meijer, Jaap Heringa, Sanne Abeln   The Netherlands Cancer Institute, Vrije Universiteit Amsterdam (VU Amsterdam), Utrecht University This work was funded a.o. by Health~Holland #cancer #biomarkers

🚀 Revolutionary Insight into Cancer Genetics: The Role of Extrachromosomal DNA (ecDNA) In a significant advancement in cancer research, a Stanford Medicine-led international team reveals the profound impact of extrachromosomal DNA (ecDNA) on cancer progression and drug resistance. Their findings, published across three papers in Nature, elucidate how these small DNA circles influence tumor behavior and treatment outcomes. 🔑 Key Takeaways: ◾ ecDNA was found in 17.1% of tumors analyzed, indicating a broader presence than previously recognized, which correlates with increased tumor aggression and reduced survival rates. ◾ The studies challenge the conventional understanding of genetic inheritance by demonstrating non-Mendelian distribution of ecDNA during cell division, which contributes to rapid genetic variation and drug resistance in tumors. ◾ An innovative therapy targeting the unique replication and transcription dynamics of ecDNA is currently under clinical trial, showing potential in disrupting these cancer-driving elements. 🌍 Why This Matters: The discovery of ecDNA’s role in enhancing oncogenic features shifts the foundational concepts of genetic behavior in cancer, suggesting new avenues for targeted therapies. This research underscores the importance of ecDNA in not only the onset of cancer but also its ability to evade current treatments, highlighting a critical target for future oncological interventions. This pioneering work sets the stage for potentially transformative therapies that could more effectively combat ecDNA-rich cancers, offering hope for improved management of resistant and aggressive cancer types. 🔗 https://lnkd.in/dHiTDeC6 #GeneticResearch #CancerBiology #StanfordMedicine #NaturePublication #OncologyInnovation #ecDNA #ScientificBreakthrough #MedicalScience

Excellence in our DNA.