Neha Jain, Ph.D.’s Post

Liquid biopsy is revolutionizing how we detect and monitor cancer — but it’s not a replacement for tissue What are we really sequencing? Cell-free DNA (cfDNA), a mixture of: Tumor-derived fragments (ctDNA) Normal DNA (hematopoietic, apoptotic cells) Why use liquid biopsy? Non-invasive — when tissue is unavailable or risky to obtain Real-time monitoring — track resistance mutations and clonal shifts Faster turnaround — useful in time-sensitive treatment decisions Key limitations: Low tumor fraction → variants may be missed (esp. early stage or brain tumors) Background noise → harder to distinguish true low-VAF variants Clonal hematopoiesis (CHIP) → false positives from non-tumor mutations (e.g. DNMT3A, TET2) Clinical applications: Detecting EGFR T790M in NSCLC for TKI resistance Monitoring KRAS dynamics in mCRC under therapy Identifying resistance markers post-immunotherapy A negative liquid biopsy result ≠ no mutation — it may just mean no detectable ctDNA. Tissue testing remains essential for definitive diagnosis and in low-shedding tumors. Bottom line: liquid biopsy complements tissue, it doesn’t replace it. Use it wisely — in the right setting, at the right time. In the next post, we’ll talk about structural variants: what they are, how to detect them, and why they’re harder to find in routine pipelines. Are you routinely using cfDNA in your workflow? How do you confirm findings from liquid biopsy? #liquidbiopsy #cfDNA #ctDNA #NGS #cancerdiagnostics #precisiononcology #somaticvariants #moleculardiagnostics #VAF #tumorprofiling

Universal Tumor Classifier Showcased at CTOS 2025   We’re excited to announce that Joshua Nash, PhD student at The Hospital for Sick Children, will present new findings on the utility of our AI-powered universal tumor classifier at the Connective Tissue Oncology Society conference in Boca Raton, Florida. 📍 Paper 61: UNBIASED TRANSCRIPTOME-WIDE ANALYSIS OF SARCOMA REVEALS PROGNOSTIC SUBTYPES OF LIPOSARCOMA AND OSTEOSARCOMA 🗓️ Saturday, Nov. 15 | 🕘 9:00–10:30 a.m. EST 📌 Royal Palm Ballroom This work demonstrates how transcriptome-wide, unbiased analysis can uncover prognostic subtypes in challenging sarcoma entities, leveraging the classifier’s ability to generalize across diverse tumor types and sample preparations. The findings highlight the potential for AI-driven RNA-Seq diagnostics to inform prognosis and guide clinical decision-making in rare cancers. We invite sarcoma researchers, molecular pathologists, and clinicians to join the session and explore how this technology is advancing precision oncology. #CTOS2025 #NewCodeOncology #RNASeq #AIinDiagnostics #MolecularPathology #PrecisionOncology #CancerGenomics #PrecisionMedicine #SickKidsResearch #SarcomaResearch Adam Shlien

Recent research from Arizona State University reveals that SerpinB3 (squamous cell carcinoma antigen-1), widely known as a biomarker for aggressive epithelial cancers, also plays an essential role as an endogenous skin injury response element. The study demonstrates that SerpinB3 expression is induced during skin wound healing where it promotes epithelial cell migration, supports extracellular matrix remodeling, and accelerates wound closure. This dual function links SerpinB3’s roles in cancer progression and tissue repair, highlighting it as a promising therapeutic target for improving chronic wound healing and tailoring cancer treatments. These findings open exciting avenues for regenerative medicine and cancer biology by targeting a common molecular pathway underlying tissue regeneration and disease. This breakthrough positions SerpinB3 not only as a cancer marker but as a vital driver of skin repair, with therapeutic potential extending to chronic wounds, inflammatory diseases, and possibly other epithelial tissues. https://lnkd.in/gheWfwxH

What are the clinical and molecular features of neurofibromatosis type 1 (NF1)-associated breast cancers? Our new study reveals that breast cancers in Neurofibromatosis type 1 (NF1) patients emerge earlier, tend to be more aggressive, and bear distinct NF1‑gene mutation patterns. This was proved from the computational front as well. Our team applied in‑silico structural workflows including Missense3D to flag structural rearrangements, introduced amino‑acid substitutions in ChimeraX, performed energy minimisation in Amber/SANDER, and calculated ΔΔG values via FoldX 5.0 to identify destabilising variants. Read it at: https://lnkd.in/dZYDgu3N Powered by: Paola Daniele, Francesco Petrizzelli, Chiara Iacovino, Chiara Canciani, Maria Luisa Garau, Claudia Santoro, Valentina Trevisan, Arianna Panfili, Stefania Cavone, Valentina Guida, Maria Cecilia D'Asdia, Laura Bernardini, Silvia Majore, Alessandro Ferraris, Michele Valiante, Francesca Gensini, Francesca Clementina Radio, Giada Tortora, Matteo Cassina, Giuseppina Miele, Manuela Priolo, Fabio sirchia, Ludovica Piccinno, Elisabetta Flex, Giuseppe Zampino, Maurizio Genuardi, Vincenzo Nigro, Leonardo Salviati, Laura Papi, Paola Grammatico, Chiara Leoni, Giulio Piluso, Sandra Giustini, Tommaso Mazza, Meena Upadhyaya, Marco Tartaglia, Eva Trevisson, Alessandro De Luca #BreastCancer #NF1 #Bioinformatics #StructuralBioinformatics #ComputationalGenomics Fondazione Policlinico Universitario Agostino Gemelli IRCCS

Artificial Intelligence is entering a new era in oncology. At #ESMO25, several studies highlighted how AI-based pathology, imaging, and multiomic analyses can predict treatment benefit and guide clinical decision-making across tumor types. In the AtezoTRIBE study, AI-driven pathology identified patients who truly benefited from adding atezolizumab to FOLFOXIRI + bevacizumab — 📈 Median PFS: 13.3 vs 11.5 months 📈 Median OS: 46.9 vs 24.7 months Only AI-biomarker–high patients derived benefit (HR for OS 0.54). Similar results were confirmed in AVETRIC, while NERO, AEGEAN, and CROWN demonstrated how combining AI-based imaging, ctDNA, and genomic data can refine response prediction in mesothelioma and lung cancer. 💡 These studies mark a significant step toward data-driven precision oncology, where algorithms complement clinical expertise to personalise care and minimise toxicity. #OncoDaily #OncoAlert #OncoLive #ClinicalResearch #ClinicalTrials #PrecisionOncology #ESMO25

I’m very excited to share that our paper, “Prostate-specific membrane antigen positron emission tomography/computed tomography imaging as a precision diagnostic at prostate cancer recurrence after radical prostatectomy: Modeling long-term survival,” has just been published in CANCER, part of the American Cancer Society Journals. PSMA-PET/CT is affecting the management of patients with prostate cancer with biochemical recurrence after radical prostatectomy. However, the long-term outcomes of tailoring salvage treatment on the basis of PSMA-PET/CT status remain to be determined. In this study, we developed a decision-analytic modeling framework to project long-term outcomes based on short-term PSMA-PET/CT findings and corresponding treatment decisions. In the absence of survival outcomes by PSMA-PET/CT status, this framework permits the projection of a range over the expected incremental survival benefit under tailored management strategies.The modeling framework we present here also applies more broadly to precision oncology settings, where a novel diagnostic enables additional risk stratification and treatment personalization. Our model projections might also complement emerging data on the corresponding economic costs and health-related quality of life. While we await results from empirical studies on long-term outcomes, our modeling framework may help clarify key factors driving the impact of precision diagnostics like PSMA-PET/CT. You can access the article here: https://lnkd.in/g_zKZCjS #PSMAPET #ProstateCancer #PrecisionOncology #DecisionModeling #OutcomesResearch

Metamorphic Effect of Angiogenic Switch in Tumor Development: Conundrum of Tumor Angiogenesis Toward Progression and Metastatic Potential 🌱🧫 by Moshe, D. L., et al. (2023). Biomedicines, 11(8), 2142. 📚 Read the full text here: https://brnw.ch/21wWR03 🧠 This review explores molecular mechanisms driving angiogenesis in tumors, emphasizing its pivotal role in cancer growth, immune modulation, and metastasis. 🌿 The article provides a comprehensive overview of angiogenic control systems and therapeutic strategies targeting tumor vascular remodeling. ✨ #MDPI #OpenAccess #Biomedicines #Angiogenesis #TumorMicroenvironment #CancerProgression #AntiAngiogenicTherapy

We are thrilled to announce our participation in the ESMO - European Society for Medical Oncology AI & Digital Oncology Congress 2025, where we will unveil Negedia Pathology Breast RUO, our new AI-powered transcriptomic solution designed to bring whole-transcriptome insights directly into pathology. 💥 Negedia Pathology Breast bridges the translational gap between NGS innovation and clinical practice, enabling comprehensive molecular profiling from FFPE tissue with clinical-grade robustness and reproducibility. Built on our Digital mRNAseq technology and validated on over 800 breast cancer samples, the solution provides: • Automated tumor cellularity assessment • Quantitative analysis of ESR1, PGR, HER2, and refined classification of HR+  • Identification of HER2-low activity  • Clear, clinically oriented report ready to support diagnostic and translational decisions 🎤 Don’t miss Dr. Beatrice Salvatori presenting “Machine Learning meets transcriptomics: Negedia Pathology an innovative tool bridging clinical practice and biomarker discovery” 📍 Vintura’s On-Stage Presentation Slot (November 13, 16:15-16:45) #NegediaPathologyBreast #GenomicsAndBeyond

Cytology is often the only viable sample for patients with lung, liver, and other solid tumors—yet it remains underused for molecular profiling. Mayo Clinic Laboratories highlights new evidence showing cytology performs on par with FFPE for comprehensive next-generation sequencing and is available across validated oncology panels. Why it matters: - Cytology samples are frequently the only specimen available—or the most practical—when tissue is limited. - In practice, there’s a gap: internal ordering used cytology in 29% of comprehensive cases vs 2% externally—suggesting many patients could benefit if cytology were leveraged more often. - Alcohol-fixed smear slides often preserve cellular integrity better than FFPE sections, supporting reliable sequencing. Mayo Clinic experts also share practical steps to ensure molecular adequacy (e.g., rapid on-site evaluation) and offer quick-reference guides plus a deeper dive e-book for clinicians. Worth a look if you’re aiming to reduce “insufficient tissue” roadblocks and get more patients to actionable results. #cytology #molecularpathology #oncology #precisionmedicine

AI is shifting from “nice-to-have” to “must-use” in oncology, with models now forecasting relapse, immunotherapy benefit and survival years before conventional imaging or staging can. 🔍 New deep-learning models already outperform classic scores for pan-cancer survival prediction [1]. NCI’s LORIS tools estimate checkpoint-inhibitor response from routine clinical data [2], and FDA authorization of ArteraAI Prostate makes AI prognosis for localised prostate cancer a clinical reality [3]. Paired with ctDNA-driven liquid biopsies that detect breast-cancer recurrence up to three years before scans [4], AI-driven prognostics are moving us from static staging to continuously updated risk estimates across the patient journey. 🧬 For oncologists, the task now is to stress-test these models in real-world cohorts, embed them into MDT workflows and consent, and build governance for bias, calibration and ongoing monitoring. 🤔 When survival curves come with an AI confidence band, will ignoring those predictions ever be ethically—or legally—defensible? Sources [1] https://lnkd.in/dB2WCsw9 [2] https://lnkd.in/dXCzabCW [3] https://lnkd.in/dc4EY3rK [4] https://lnkd.in/dfqF8Dvq #Oncology #AIinMedicine #CancerPrognostics Sciqst: AI-powered literature reviews in minutes.  Generate comprehensive, up-to-date scientific reviews from the latest papers with one click.  https://www.sciqst.com