Zaklina Strezoska’s Post

📃Scientific paper: A comparison of DNA sequencing and gene expression profiling to assist tissue of origin diagnosis in cancer of unknown primary Abstract: Cancer of unknown primary (CUP) is a syndrome defined by clinical absence of a primary cancer after standardised investigations. Gene expression profiling (GEP) and DNA sequencing have been used to predict primary tissue of origin (TOO) in CUP and find molecularly guided treatments; however, a detailed comparison of the diagnostic yield from these two tests has not been described. Here, we compared the diagnostic utility of RNA and DNA tests in 215 CUP patients (82% received both tests) in a prospective Australian study. Based on retrospective assessment of clinicopathological data, 77% (166/215) of CUPs had insufficient evidence to support TOO diagnosis (clinicopathology unresolved). The remainder had either a latent primary diagnosis (10%) or clinicopathological evidence to support a likely TOO diagnosis (13%) (clinicopathology resolved). We applied a microarray (CUPGuide) or custom NanoString 18‐class GEP test to 191 CUPs with an accuracy of 91.5% in known metastatic cancers for high–medium confidence predictions. Classification performance was similar in clinicopathology‐resolved CUPs – 80% had high–medium predictions and 94% were concordant with pathology. Notably, only 56% of the clinicopathology‐unresolved CUPs had high–medium confidence GEP predictions. Diagnostic DNA features were interrogated in 201 CUP tumours guided by the cancer type specificity of mutations observed across 22 cancer types from the AACR Project GENIE database (77,058 tumours) as well as... Continued on ES/IODE ➡️ https://etcse.fr/zOtQ1 ------- If you find this interesting, feel free to follow, comment and share. We need your help to enhance our visibility, so that our platform continues to serve you.

Colorectal cancer (CRC) is a leading cause of cancer mortality, driven by genetic and environmental factors. Genomics and differential expression analysis offer crucial insights into CRC's molecular mechanisms, aiding in #personalizedmedicine approaches. Our latest use case demonstrates how g.nome® simplifies complex #omics analysis, enabling researchers and clinicians to effortlessly conduct differential gene expression studies. By leveraging publicly available #RNAseq datasets from the Sequence Read Archive (SRA), we uncover novel genetic insights, driving future CRC research and therapeutic strategies. See how we identified potential biomarkers for early detection and prognosis of CRC, spotlighting key genes like KRT23 and ETV4. Our streamlined approach reduces technical barriers, allowing you to quickly derive meaningful insights from complex data. Read the full use case: https://lnkd.in/gkd6tRKT

In a groundbreaking study published in Springer Nature Group's Nature Cell Biology, researchers from the Mass General Cancer Center have identified a gene that plays a pivotal role in the spread of cancer cells throughout the body. This gene, known as Gstt1, is crucial for metastatic cancer cells to modify their environment and thrive in new locations. 🧬 The study reveals that Gstt1 encodes an enzyme part of a superfamily that protects cells from toxins. More importantly, it allows cancer cells to alter and secrete fibronectin, a protein essential for cell attachment to the extracellular matrix. 🎯 Silencing the Gstt1 gene in lab models prevented metastatic growth, offering a beacon of hope for new treatment strategies, particularly for pancreatic cancer patients who often face a diagnosis at the metastatic stage. 💡 This discovery is not just a scientific triumph but a potential lifesaver. It underscores the importance of persistent research and innovation in the battle against cancer. 🤝 Join us in applauding the Mass General Cancer Center team for their dedication and breakthrough that may pave the way for novel therapeutic avenues targeting metastatic cancer, which is responsible for 90% of cancer-related deaths. cc: Dr. Jessica Lin, Dr. Justin Gainor #CancerResearch #Metastasis #Genetics #Innovation #Healthcare #ScienceNews https://lnkd.in/dH5yBKrM

ANGLE PLC (AIM:AGL, OTCQX:ANPCY), the #LiquidBiopsy specialist, said researchers at The University of New Mexico used the company's #Parsortix system to yeiled a potential breakthrough in the understanding of the progression of #MelanomaBrainMetastasis. The study focused on the gene expression profile of #CirculatingTumourCells (CTCs), which are pivotal in the development and progression of this form of #cancer. The research used the Parsortix system for harvesting #CTCs, which allowed for an in-depth analysis of their gene expression. This approach has shed light on the potential of using CTC profiling to prescribe more targeted treatments for #melanoma, particularly in cases where the cancer has metastasized to the brain. More at #Proactive #ProactiveInvestors #AIM #OTCQX #AGL #ANPCY #ANGLE #ANGLEplc http://ow.ly/5pbA1055gM4

Next-generation sequencing technology will dominate the market during the forecast period, as technologies continue to advance including the ability of NGS testing to identify genetic changes in extremely low quantities. NGS’s excellent sensitivity and specificity help identify mutations and other genomic changes associated with cancer with accuracy and makes it possible to analyze multiple genes and genomic areas at once. This allows the tests to provide comprehensive genomic profiling, which offers a more thorough knowledge of the genetic makeup of cancers. #ngs #liquidbiopsy #mrdtesting #mrd

TP53 OncoKitDx – Precision Oncogenetic Diagnostics  In line with our ongoing dedication to healthcare innovation, Goffin Molecular Technologies is pleased to highlight the TP53 OncoKitDx. This specialised diagnostic tool is carefully designed to detect mutations in the TP53 gene, a critical factor in the development and progression of cancer, particularly in conditions such as chronic lymphocytic leukaemia and Li-Fraumeni syndrome.    TP53 OncoKitDx Highlights:  ✅ Comprehensive Mutation Profiling: Detects point mutations, insertions, deletions, and more in TP53 gene regions, offering a complete genetic overview.    ✅ Versatile Mutation Analysis: Identifies both inherited and acquired TP53 mutations, catering to diverse clinical needs.  ✅ Technological Excellence: Integrates multiplex PCR with Next-Generation Sequencing for in-depth, precise analysis.  ✅ Precision Focus: Designed for accuracy, the kit is indispensable in cancer genetics.    Also Featuring:   🟢Hereditary OncoKitDx: For genetic predisposition analysis.  🟢Action ST OncoKit: Specialized in solid tumor mutation detection.  🟢Haematology OncoKitDx: Focused on hematologic malignancies.  🟢BRCA Plus OncoKitDx: For BRCA gene mutation analysis. 📧 Learn more about the TP53 OncoKitDx and our range of diagnostics by reaching out to us at info@goffinmt.com or contact our dedicated 'Health In Code' representative at weronika@goffinmt.com. #TP53OncoKitDx #CancerDiagnostics #PrecisionMedicine #GoffinMolecularTechnologies #OncologyResearch 

LongSom: a #bioinformatics workflow for detecting de novo SNVs, CNAs, #cancer gene fusions to reconstruct tumor clonal heterogeneity. Shows that with PacBio long-read single-cell RNA-Seq you can reconstruct clones and find clinically relevant SNVs in each clone. https://lnkd.in/g4ipiAUY Nice work by the same group that produced this ovarian cancer publication using concatenation-based approach (which is essentially a precursor to the MAS-Seq/Kinnex single-cell RNA kit) for throughput increase. They applied LongSom to the same dataset. https://lnkd.in/gXxrHvxX

Researchers have adapted CRISPR-Cas9 technology to target somatic mutations that generate motifs adjacent to protospacers (PAMs) in pancreatic cancer genomes. The researchers developed a bioinformatics pipeline called PAMfinder to identify these mutations in the cancer genome. By designing sgRNAs to target these novel PAMs, CRISPR-Cas9 can selectively introduce DSBs into cancer cells, destroying them while sparing normal cells. This method exploits the high mutational load of cancer cells, particularly in non-coding regions, to create a wide range of specific targets for CRISPR-mediated cell killing. Functional assays in three pancreatic cancer cell lines demonstrated 69-99% selective cell death using 4-9 sgRNAs designed to target PAM sequences. In addition, the absence of off-target effects confirmed the strategy's efficacy, demonstrating high specificity and a substantial reduction in cancer cell viability. 

Interesting tumor microenvironment study detailing the use of EcoTyper, a digital cytometry framework, to characterize the cell states and multicellular communities in Soft Tissue Sarcoma (STS) clinical specimens. EcoTyper is a machine learning based framework that allows for the identification of cell-type-specific gene expression from bulk tissue transcriptomes and the discovery of novel multicellular communities or 'ecotypes' in the tumor microenvironment. In the study, the authors identified 23 distinct cell states across malignant, immune, and stromal cells from the soft tissue sarcoma (STS) patient cohorts. Their analysis also identified strong correlations between sarcoma ecosystems and genomic alterations, like SNV/indels and CNAs in SE3 sarcomas and APOBEC mutagenesis in SE2 sarcomas, a genetic alteration which is known to impact immune infiltration and patient survival. The study's results also identified opportunities for personalized immunotherapy in STS, revealing three sarcoma ecotypes that predict responses to immune-checkpoint inhibition (ICI) and prognosis. Paper and research by @Ajay Subramanian and larger team. Link to full publication: Sarcoma microenvironment cell states and ecosystems are associated with prognosis and predict response to immunotherapy. https://lnkd.in/ew29YP-5

Researchers have adapted CRISPR-Cas9 technology to target somatic mutations that generate motifs adjacent to protospacers (PAMs) in pancreatic cancer genomes. The researchers developed a bioinformatics pipeline called PAMfinder to identify these mutations in the cancer genome. By designing sgRNAs to target these novel PAMs, CRISPR-Cas9 can selectively introduce DSBs into cancer cells, destroying them while sparing normal cells. This method exploits the high mutational load of cancer cells, particularly in non-coding regions, to create a wide range of specific targets for CRISPR-mediated cell killing. Functional assays in three pancreatic cancer cell lines demonstrated 69-99% selective cell death using 4-9 sgRNAs designed to target PAM sequences. In addition, the absence of off-target effects confirmed the strategy's efficacy, demonstrating high specificity and a substantial reduction in cancer cell viability.