Integrating Omics Data for Colorectal Cancer Metastasis

New Post: High‑Resolution Multi‑Omics Graph Integration for Predicting Immune‑Checkpoint Response in Advanced Non‑Small‑Cell Lung Cancer \(NSCLC\) - https://lnkd.in/gnB9raUq Multi‑Omics Graph Integration for Predicting Immune‑Checkpoint Response in Advanced Non‑Small‑Cell Lung Cancer \(NSCLC\) **Abstract** We present a commercially viable framework for integrating spatial transcriptomics, single‑cell proteomics, and bulk genomics to forecast patients’ responses to PD‑1/PD‑L1 blockade therapies. The pipeline constructs a heterogeneous graph of cellular sub‑populations, extracellular matrix \(ECM\) components, and ligand‑receptor interactions, and \[…\]

🔥 #EditorsChoice Articles! 1️⃣ Clinical Impact of High Throughput Sequencing on Liquid Biopsy in Advanced Solid Cancer ➡️ Read now: https://brnw.ch/21x15HM 2️⃣ Comprehensive Genomic Profiling of Circulating Tumor DNA in Patients with Previously Treated Metastatic Colorectal Cancer: Analysis of a Real-World Healthcare Claims Database ➡️ Read now: https://brnw.ch/21x15HN 3️⃣ Consensus Recommendations to Optimize the Detection and Reporting of NTRK Gene Fusions by RNA-Based Next-Generation Sequencing ➡️ Read now: https://brnw.ch/21x15HO 4️⃣ Clinicopathological Features of Non-Small Cell Lung Carcinoma with BRAF Mutation ➡️ Read now: https://brnw.ch/21x15HL 📚 Full Collection: https://brnw.ch/21x15HP #OncologyResearch #MustRead #OpenAccess

🧬 Multiomic Characterization of Small Cell Lung Cancer A large real-world analysis published in Cancer evaluated 944 SCLC tumors using DNA sequencing, RNA sequencing, and immunohistochemistry to better define molecular subtypes and therapeutic targets. Dr. Sonam Puri and colleagues classified tumors by dominant transcription factor expression (ASCL1, NEUROD1, POU2F3, YAP1) and identified meaningful biological differences. The SCLC-Y subtype showed the strongest immune-related gene signatures, suggesting potential relevance for immunotherapy. Subtype-specific targets such as DLL3 and BCL2 (SCLC-A) and SSTR2 (SCLC-N) were also identified. This study reinforces the molecular heterogeneity of SCLC and supports biomarker-driven treatment strategies in a historically uniform disease. https://lnkd.in/ePYXbRcG #SCLC #PrecisionOncology #Immunotherapy #CancerResearch

Two Children's Mercy #CancerResearch projects are getting new support from Braden’s Hope of Childhood Cancer 2025 Super Six grants for “high-impact, translational” research. Both focus on CAR-T therapy, where a patient’s cells are lab-modified to recognize and destroy cancer cells and then transfused back into the patient.  Dr. Todd Bradley, Genomic Medicine Center, is developing immunotherapies that can target multiple tumor antigens at once, which could pave the way for more effective tools for treatment-resistant cancers. Dr. Vivekanand Yadav, Hematology/Oncology/BMT, is studying how adenosine may block CAR T-cell therapy for diffuse intrinsic pontine gliomas (DIPGs) — and whether inhibiting the enzyme that generates adenosine could help. Learn more about their exciting work: https://cmkc.link/4sY5MDj 

Two Children's Mercy #CancerResearch projects are getting new support from Braden’s Hope of Childhood Cancer 2025 Super Six grants for “high-impact, translational” research. Both focus on CAR-T therapy, where a patient’s cells are lab-modified to recognize and destroy cancer cells and then transfused back into the patient.  Dr. Todd Bradley, Genomic Medicine Center, is developing immunotherapies that can target multiple tumor antigens at once, which could pave the way for more effective tools for treatment-resistant cancers. Dr. Vivekanand Yadav, Hematology/Oncology/BMT, is studying how adenosine may block CAR T-cell therapy for diffuse intrinsic pontine gliomas (DIPGs) — and whether inhibiting the enzyme that generates adenosine could help. Learn more about their exciting work: https://cmkc.link/4sY5MDj 

🔥 #EditorsChoiceArticles 1️⃣ Clinical Impact of High Throughput Sequencing on Liquid Biopsy in Advanced Solid Cancer ➡️ Read now: https://brnw.ch/21x0mLM 2️⃣ Comprehensive Genomic Profiling of Circulating Tumor DNA in Patients with Previously Treated Metastatic Colorectal Cancer: Analysis of a Real-World Healthcare Claims Database ➡️ Read now: https://brnw.ch/21x0mLL 3️⃣ Consensus Recommendations to Optimize the Detection and Reporting of NTRK Gene Fusions by RNA-Based Next-Generation Sequencing ➡️ Read now: https://brnw.ch/21x0mLO 4️⃣ Clinicopathological Features of Non-Small Cell Lung Carcinoma with BRAF Mutation ➡️ Read now: https://brnw.ch/21x0mLK 📚 Full Collection: https://brnw.ch/21x0mLN #OncologyResearch #OpenAccess #CallForReading

New Post: DeepGraph: End‑to‑End Graph Neural Network Approach for Predicting SIRT7‑Dependent rRNA Transcriptional Regulation Networks and Therapeutic Target Identification in Triple‑Negative Breast Cancer - https://lnkd.in/gWz4Yjm6 ### Abstract Sirtuin 7 \(SIRT7\) is a NAD⁺‑dependent histone deacetylase that directly regulates ribosomal RNA \(rRNA\) transcription and ribosome biogenesis. Dysregulation of SIRT7 has been implicated in the aggressive phenotype of triple‑negative breast cancer \(TNBC\). However, the full complement of SIRT7 co‑factors, their dynamic chromatin states, and the therapeutic vulnerabilities tethered to the SIRT7 \[…\]

New preprint from the lab: how does genetic variation within a tumor shape its phenotype? Spearheaded by talented PhD student Sólrún Kolbeinsdóttir, with the help of several dedicated teams of clinical researchers, we have performed whole genome and mRNA co-sequencing on single cells from many patients across six cancer types. Using this highly diverse dataset, we chart cancer-type specific dosage compensation across the different cancer types, and find both general sequence-specific mechanisms as well as tissue-specific compensatory effects. We also describe a class of very weakly subclonal solid tumors (“transient clonality”) with extremely high turnover of large genomic segments. Transient clonality appears in several cancer types, and the copy number turnover has large-scale transcriptional effects. https://lnkd.in/d_af-k8U Kolbeinsdóttir et al, Principles of subclonal gene dosage across human cancer.

New preprint from the National Cancer Institute (NCI) using the 6-base genome! 🎉 Adam Sowalsky, Chennan Li, Fatima Karzai, MD, and team at the NCI asked whether 6-base whole-genome sequencing that jointly quantifies 5mC and 5hmC could infer gene expression directly from plasma. Read their findings “Integrative dual ctDNA 5mC/5hmC methylomics and clonal reconstruction infer tumor transcription and resistance phenotypes in metastatic prostate cancer” here: https://lnkd.in/gMhFgWqg biomodal

Colorectal cancer research continues to evolve as sequencing technologies provide deeper insight into tumor biology. Next-generation sequencing is helping researchers identify key molecular pathways involved in colorectal cancer, including WNT, RAS-MAPK, PI3K, TGF-β, and DNA mismatch repair mechanisms. These discoveries are shaping how tumors are classified, studied, and ultimately treated. In this blog post, we explore how genomic and transcriptomic approaches are supporting colorectal cancer research, from biomarker discovery to targeted therapy development. Read the article: https://lnkd.in/ggRR7kDw #ScienceofSignals #ColorectalCancer #CancerResearch #Genomics #NGS