keyword
https://read.qxmd.com/read/38484302/external-quality-assessment-on-molecular-tumor-profiling-with-circulating-tumor-dna-based-methodologies-routinely-used-in-clinical-pathology-within-the-coin-consortium
#21
JOURNAL ARTICLE
Paul van der Leest, Pim Rozendal, John Hinrichs, Carel J M van Noesel, Karen Zwaenepoel, Birgit Deiman, Cornelis J J Huijsmans, Ronald van Eijk, Ernst Jan M Speel, Rick J van Haastert, Marjolijn J L Ligtenberg, Ron H N van Schaik, Maurice P H M Jansen, Hendrikus J Dubbink, Wendy W de Leng, Mathie P G Leers, Menno Tamminga, Daan van den Broek, LĂ©on C van Kempen, Ed Schuuring
BACKGROUND: Identification of tumor-derived variants in circulating tumor DNA (ctDNA) has potential as a sensitive and reliable surrogate for tumor tissue-based routine diagnostic testing. However, variations in pre(analytical) procedures affect the efficiency of ctDNA recovery. Here, an external quality assessment (EQA) was performed to determine the performance of ctDNA mutation detection work flows that are used in current diagnostic settings across laboratories within the Dutch COIN consortium (ctDNA on the road to implementation in The Netherlands)...
March 14, 2024: Clinical Chemistry
https://read.qxmd.com/read/38484152/analytical-validation-of-next-personal%C3%A2-an-ultra-sensitive-personalized-circulating-tumor-dna-assay
#22
JOURNAL ARTICLE
Josette Northcott, Gabor Bartha, Jason Harris, Conan Li, Fabio C P Navarro, Rachel Marty Pyke, Manqing Hong, Qi Zhang, Shuyuan Ma, Tina X Chen, Janet Lai, Nitin Udar, Juan-Sebastian Saldivar, Erin Ayash, Joshua Anderson, Jiang Li, Tiange Cui, Tu Le, Ruthie Chow, Randy Jerel Velasco, Chris Mallo, Rose Santiago, Robert C Bruce, Laurie J Goodman, Yi Chen, Dan Norton, Richard O Chen, John M Lyle
We describe the analytical validation of NeXT Personal® , an ultra-sensitive, tumor-informed circulating tumor DNA (ctDNA) assay for detecting residual disease, monitoring therapy response, and detecting recurrence in patients diagnosed with solid tumor cancers. NeXT Personal uses whole genome sequencing of tumor and matched normal samples combined with advanced analytics to accurately identify up to ~1,800 somatic variants specific to the patient's tumor. A personalized panel is created, targeting these variants and then used to sequence cell-free DNA extracted from patient plasma samples for ultra-sensitive detection of ctDNA...
March 14, 2024: Oncotarget
https://read.qxmd.com/read/38480816/impact-of-lkb1-status-on-radiation-outcome-in-patients-with-stage-iii-non-small-cell-lung-cancer
#23
JOURNAL ARTICLE
Piyada Sitthideatphaiboon, Chonnipa Nantavithya, Poonchavist Chantranuwat, Chanida Vinayanuwattikun, Virote Sriuranpong
Preclinical studies suggest that loss of LKB1 expression renders cancer cells less responsive to radiation partly through NRF2-mediated upregulation of antioxidant enzymes protecting against radiation-induced DNA damage. Here we investigated the association of an alteration in this pathway with radio-resistance in lung cancer patients. Patients with locally advanced non-small cell lung cancer (LA-NSCLC) who were treated with chemoradiotherapy (CRT) and analyzed for LKB1 expression using semiquantitative immunohistochemistry...
March 14, 2024: Scientific Reports
https://read.qxmd.com/read/38478957/chromatin-and-nucleosome-associated-features-in-liquid-biopsy-implications-for-cancer-biomarker-discovery
#24
JOURNAL ARTICLE
Lucas Penny, Sasha Main, Steven De Michino, Scott Bratman
Cell-free DNA (cfDNA) from the bloodstream has been studied for cancer biomarker discovery, and chromatin-derived epigenetic features have come into the spotlight for their potential to expand clinical applications. Methylation, fragmentation, and nucleosome positioning patterns of cfDNA have previously been shown to reveal epigenomic and inferred transcriptomic information. More recently, histone modifications have emerged as a tool to further identify tumor-specific chromatin variants in plasma. A number of sequencing methods have been developed to analyze these epigenetic markers, offering new insights into tumor biology...
March 13, 2024: Biochemistry and Cell Biology
https://read.qxmd.com/read/38478628/genome-wide-repeat-landscapes-in-cancer-and-cell-free-dna
#25
JOURNAL ARTICLE
Akshaya V Annapragada, Noushin Niknafs, James R White, Daniel C Bruhm, Christopher Cherry, Jamie E Medina, Vilmos Adleff, Carolyn Hruban, Dimitrios Mathios, Zachariah H Foda, Jillian Phallen, Robert B Scharpf, Victor E Velculescu
Genetic changes in repetitive sequences are a hallmark of cancer and other diseases, but characterizing these has been challenging using standard sequencing approaches. We developed a de novo kmer finding approach, called ARTEMIS (Analysis of RepeaT EleMents in dISease), to identify repeat elements from whole-genome sequencing. Using this method, we analyzed 1.2 billion kmers in 2837 tissue and plasma samples from 1975 patients, including those with lung, breast, colorectal, ovarian, liver, gastric, head and neck, bladder, cervical, thyroid, or prostate cancer...
March 13, 2024: Science Translational Medicine
https://read.qxmd.com/read/38477342/an-autocatalytic-crispr-cas-amplification-effect-propelled-by-the-lna-modified-split-activators-for-dna-sensing
#26
JOURNAL ARTICLE
Ke Sun, Lei Pu, Chuan Chen, Mutian Chen, Kaiju Li, Xinqiong Li, Huanqing Li, Jia Geng
CRISPR-Cas systems with dual functions offer precise sequence-based recognition and efficient catalytic cleavage of nucleic acids, making them highly promising in biosensing and diagnostic technologies. However, current methods encounter challenges of complexity, low turnover efficiency, and the necessity for sophisticated probe design. To better integrate the dual functions of Cas proteins, we proposed a novel approach called CRISPR-Cas Autocatalysis Amplification driven by LNA-modified Split Activators (CALSA) for the highly efficient detection of single-stranded DNA (ssDNA) and genomic DNA...
March 13, 2024: Nucleic Acids Research
https://read.qxmd.com/read/38476004/high-efficiency-egfr-genotyping-using-cell-free-dna-in-bronchial-washing-fluid
#27
JOURNAL ARTICLE
Yoshihiko Murata, Yumi Nakajima, Yukio Sato, Nobuyuki Hizawa, Daichi Yamakawa, Daisuke Matsubara, Masayuki Noguchi, Yuko Minami
BACKGROUND: EGFR mutation testing is required for treatment of lung adenocarcinoma using epidermal growth factor receptor-tyrosine kinase inhibitor. However, the amounts of tumor tissue or tumor cells obtained by bronchoscopy are often insufficient. Bronchial washing fluid, obtained by lavage with saline after tumor biopsy or brushing, and the supernatant of bronchial washing fluid are thought to contain cell-free DNA that would be potentially applicable for EGFR testing. METHODS: From among patients with suspected adenocarcinoma or non-small cell lung carcinoma diagnosed from biopsy or surgical specimens at the University of Tsukuba Hospital between 2015 and 2019, cell-free DNAs from 80 specimens of supernatant of bronchial washing fluid (50 with EGFR mutation and 30 with wild type EGFR) and 8 blood serum samples were examined for EGFR mutation using droplet digital PCR...
March 12, 2024: Japanese Journal of Clinical Oncology
https://read.qxmd.com/read/38474101/prognostic-value-of-circulating-cell-free-dna-concentration-and-neutrophil-to-lymphocyte-ratio-in-patients-with-pancreatic-ductal-adenocarcinoma-a-prospective-cohort-study
#28
JOURNAL ARTICLE
Bianca Varzaru, Razvan Andrei Iacob, Stefania Bunduc, Ioana Manea, Andrei Sorop, Andreea Spiridon, Raluca Chelaru, Adina Croitoru, Mihaela Topala, Gabriel Becheanu, Mona Dumbrava, Simona Dima, Irinel Popescu, Cristian Gheorghe
Circulating cell-free DNA (ccfDNA) quantity correlates with the clinical characteristics and prognosis of various cancer types. We investigated whether ccfDNA levels and the neutrophil-to-lymphocyte ratio (NLR) have prognostic value in patients with pancreatic ductal adenocarcinoma (PDAC). Peripheral blood was collected from 82 patients with PDAC prior to any diagnostic procedure or the administration of chemotherapy. Plasma DNA was isolated, and ccfDNA concentration and NLR were determined. We found that ccfDNA levels were correlated with age and tumor burden...
March 1, 2024: International Journal of Molecular Sciences
https://read.qxmd.com/read/38473369/liquid-biopsy-for-glioma-using-cell-free-dna-in-cerebrospinal-fluid
#29
REVIEW
Ryosuke Otsuji, Yutaka Fujioka, Nobuhiro Hata, Daisuke Kuga, Ryusuke Hatae, Yuhei Sangatsuda, Akira Nakamizo, Masahiro Mizoguchi, Koji Yoshimoto
Glioma is one of the most common primary central nervous system (CNS) tumors, and its molecular diagnosis is crucial. However, surgical resection or biopsy is risky when the tumor is located deep in the brain or brainstem. In such cases, a minimally invasive approach to liquid biopsy is beneficial. Cell-free DNA (cfDNA), which directly reflects tumor-specific genetic changes, has attracted attention as a target for liquid biopsy, and blood-based cfDNA monitoring has been demonstrated for other extra-cranial cancers...
February 29, 2024: Cancers
https://read.qxmd.com/read/38473290/circulating-tumor-dna-profiling-in-liver-transplant-for-hepatocellular-carcinoma-cholangiocarcinoma-and-colorectal-liver-metastases-a-programmatic-proof-of-concept
#30
JOURNAL ARTICLE
Hanna Hong, Chase J Wehrle, Mingyi Zhang, Sami Fares, Henry Stitzel, David Garib, Bassam Estfan, Suneel Kamath, Smitha Krishnamurthi, Wen Wee Ma, Teodora Kuzmanovic, Elizabeth Azzato, Emrullah Yilmaz, Jamak Modaresi Esfeh, Maureen Whitsett Linganna, Mazhar Khalil, Alejandro Pita, Andrea Schlegel, Jaekeun Kim, R Matthew Walsh, Charles Miller, Koji Hashimoto, David Choon Hyuck Kwon, Federico Aucejo
INTRODUCTION: Circulating tumor DNA (ctDNA) is emerging as a promising, non-invasive diagnostic and surveillance biomarker in solid organ malignancy. However, its utility before and after liver transplant (LT) for patients with primary and secondary liver cancers is still underexplored. METHODS: Patients undergoing LT for hepatocellular carcinoma (HCC), cholangiocarcinoma (CCA), and colorectal liver metastases (CRLM) with ctDNA testing were included. CtDNA testing was conducted pre-transplant, post-transplant, or both (sequential) from 11/2019 to 09/2023 using Guardant360, Guardant Reveal, and Guardant360 CDx...
February 25, 2024: Cancers
https://read.qxmd.com/read/38473224/integrating-artificial-intelligence-for-advancing-multiple-cancer-early-detection-via-serum-biomarkers-a-narrative-review
#31
REVIEW
Hsin-Yao Wang, Wan-Ying Lin, Chenfei Zhou, Zih-Ang Yang, Sriram Kalpana, Michael S Lebowitz
The concept and policies of multicancer early detection (MCED) have gained significant attention from governments worldwide in recent years. In the era of burgeoning artificial intelligence (AI) technology, the integration of MCED with AI has become a prevailing trend, giving rise to a plethora of MCED AI products. However, due to the heterogeneity of both the detection targets and the AI technologies, the overall diversity of MCED AI products remains considerable. The types of detection targets encompass protein biomarkers, cell-free DNA, or combinations of these biomarkers...
February 21, 2024: Cancers
https://read.qxmd.com/read/38472567/circulating-tumor-dna-ctdna-and-its-role-in-gynecologic-malignancies
#32
REVIEW
Tali Pomerantz, Rebecca Brooks
Circulating tumor DNA (ctDNA) refers to small fragments of DNA released into the bloodstream by cancer cells. It is obtained through "liquid biopsy;" which most commonly refers to plasma or blood samples, but can be obtained from a number of bodily fluids including ascitic fluid, saliva, and even urine and stool. ctDNA is detected via polymerase chain reaction (PCR) or next-generation sequencing (NGS). The DNA from these samples is analyzed for the detection of point mutations, copy-number alterations, gene fusion, and DNA methylation...
March 12, 2024: Current Treatment Options in Oncology
https://read.qxmd.com/read/38472095/evaluation-of-the-cytotoxic-activity-of-sorafenib-loaded-camel-milk-casein-nanoparticles-against-hepatocarcinoma-cells
#33
JOURNAL ARTICLE
Aastha Mittal, Neelam Mahala, Nikhil Hanamant Dhanawade, Sunil Kumar Dubey, Uma S Dubey
Sorafenib, a multikinase inhibitor is used to treat hepatocellular and renal carcinoma. However, a low solubility impedes its bioavailability and thus, effectiveness. This study aims to enhance its effectiveness by using novel camel milk casein nanoparticles as a delivery system. This study evaluates the cytotoxicity of sorafenib encapsulated in camel milk casein nanoparticles against human hepatocarcinoma cells (HepG2 cells) in vitro. Optimal drug loaded nanoparticles were stable for 1 month, had encapsulation efficiency of 96%, exhibited a particle size of 230 nm, zeta potential of -14...
March 2024: Biotechnology Journal
https://read.qxmd.com/read/38471640/ph-sensitive-cationic-nanoparticles-for-endosomal-cell-free-dna-scavenging-against-acute-inflammation
#34
JOURNAL ARTICLE
Yilin Feng, Cong Wei, Yanrong Gu, Hong Zhang, Lixin Liu, Tianyu Zhao, Yongming Chen
Cell-free DNA (cfDNA) released from dead cells could be a player in some autoimmune disorders by activating Toll-like receptor 9 (TLR9) and inducing proinflammatory cytokines. Cationic nanoparticles (cNPs) address cfDNA clearance, yet challenges persist, including toxicity, low specificity and ineffectiveness against endocytosed cfDNA. This study introduced pH-sensitive cNPs, reducing off-target effects and binding cfDNA at inflammatory sites. This unique approach inhibits the TLR9 pathway, offering a novel strategy for inflammation modulation...
March 10, 2024: Journal of Controlled Release
https://read.qxmd.com/read/38470545/cell-free-dna-concentration-as-a-biomarker-of-response-and-recurrence-in-her2-negative-breast-cancer-receiving-neoadjuvant-chemotherapy
#35
JOURNAL ARTICLE
Mark Jesus M Magbanua, Ziad Ahmed, Rosalyn W Sayaman, Lamorna Brown Swigart, Gillian L Hirst, Christina Yau, Denise M Wolf, Wen Li, Amy L Delson, Jane Perlmutter, Paula Pohlmann, W Fraser Symmans, Douglas Yee, Nola M Hylton, Laura J Esserman, Angela M DeMichele, Hope S Rugo, Laura J van 't Veer
PURPOSE: We previously demonstrated the clinical significance of circulating tumor DNA (ctDNA) in patients with HER2-negative breast cancer receiving neoadjuvant chemotherapy (NAC). Here, we compared its predictive and prognostic value with cell-free DNA (cfDNA) concentration measured in the same samples from the same patients. EXPERIMENTAL DESIGN: 145 hormone receptor (HR)-positive/HER2-negative and 138 triple-negative breast cancer (TNBC) patients with ctDNA data from a previous study were included in the analysis...
March 12, 2024: Clinical Cancer Research
https://read.qxmd.com/read/38467532/prognostic-nutrition-index-as-a-predictive-factor-for-overall-survival-in-trabectedin-treated-advanced-soft-tissue-sarcoma
#36
JOURNAL ARTICLE
Hideaki Sabe, Satoshi Takenaka, Shigeki Kakunaga, Hironari Tamiya, Toru Wakamatsu, Sho Nakai, Haruna Takami, Yoshiki Yamada, Seiji Okada
BACKGROUND: Trabectedin binds covalently to the DNA minor groove and causes DNA to bend toward the main groove, then trabectedin regulates the transcription of the involved genes in cell proliferation or acts on the mononuclear phagocyte system in tumors, which contributes to its antitumor effects. Several clinical trials confirmed the efficacy of trabectedin for patients with advanced soft tissue sarcoma (STS) although clinically useful biomarkers remained unidentified. This study aimed to identify prognostic factors of trabectedin treatment, especially focusing on the systemic inflammatory, immune response, and nutritional status...
March 10, 2024: Journal of Orthopaedic Science: Official Journal of the Japanese Orthopaedic Association
https://read.qxmd.com/read/38466935/frameshift-mutations-in-peripheral-blood-as-a-biomarker-for-surveillance-of-lynch-syndrome
#37
JOURNAL ARTICLE
Yurong Song, Holli Loomans-Kropp, Ryan N Baugher, Brandon Somerville, Shaneen S Baxter, Travis D Kerr, Teri M Plona, Stephanie D Mellott, Todd B Young, Heidi E Lawhorn, Lei Wei, Qiang Hu, Song Liu, Alan Hutson, Ligia Pinto, John D Potter, Shizuko Sei, Ozkan Gelincik, Steven M Lipkin, Johannes Gebert, Matthias Kloor, Robert H Shoemaker
BACKGROUND: Lynch syndrome (LS) is a hereditary cancer predisposition syndrome caused by germline mutations in DNA mismatch repair (MMR) genes, which lead to high microsatellite instability (MSI-H) and frameshift mutations (FSMs) at coding mononucleotide repeats (cMNRs) in the genome. Recurrent FSMs in these regions are thought to play a central role in the increased risk of various cancers. However, there are no biomarkers currently available for the surveillance of MSI-H-associated cancers...
March 11, 2024: Journal of the National Cancer Institute
https://read.qxmd.com/read/38466144/targeted-delivery-of-catalase-and-photosensitizer-ce6-by-a-tumor-specific-aptamer-is-effective-against-bladder-cancer-in-vivo
#38
JOURNAL ARTICLE
Yang Zhang, Ru Jia, Xiaoyi Wang, Yixuan Zhang, Jinhui Wu, Quansheng Yu, Qiang Lv, Chao Yan, Pengchao Li
Photodynamic therapy (PDT) is often applied in a clinical setting to treat bladder cancer. However, current photosensitizers report drawbacks such as low efficacy, low selectivity, and numerous side effects, which have limited the clinical values of PDT for bladder cancer. Previously, we developed the first bladder cancer-specific aptamer that can selectively bind to and be internalized by bladder tumor cells versus normal uroepithelium cells. Here, we use an aptamer-based drug delivery system to deliver photosensitizer chlorine e6 (Ce6) into bladder tumor cells...
March 11, 2024: Molecular Pharmaceutics
https://read.qxmd.com/read/38464122/machine-learning-identifies-cell-free-dna-5-hydroxymethylation-biomarkers-that-detect-occult-colorectal-cancer-in-plco-screening-trial-subjects
#39
Diana C West-Szymanski, Zhou Zhang, Xiao-Long Cui, Krissana Kowitwanich, Lu Gao, Zifeng Deng, Urszula Dougherty, Craig Williams, Shannon Merkle, Matthew Moore, Chuan He, Marc Bissonnette, Wei Zhang
BACKGROUND: Colorectal cancer (CRC) is a leading cause of cancer-related mortality, and CRC detection through screening improves survival rates. A promising avenue to improve patient screening compliance is the development of minimally-invasive liquid biopsy assays that target CRC biomarkers on circulating cell-free DNA (cfDNA) in peripheral plasma. In this report, we identify cfDNA biomarker candidate genes bearing the epigenetic mark 5-hydroxymethylcytosine (5hmC) that diagnose occult CRC up to 36 months prior to clinical diagnosis using the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial samples...
February 26, 2024: bioRxiv
https://read.qxmd.com/read/38462745/unlocking-the-potential-of-tumor-derived-dna-in-urine-for-cancer-detection-methodological-challenges-and-opportunities
#40
REVIEW
Birgit M M Wever, Renske D M Steenbergen
High cancer mortality rates and the rising cancer burden worldwide drive the development of innovative methods in order to advance cancer diagnostics. Urine contains a viable source of tumor material and allows for self-collection from home. Biomarker testing in this liquid biopsy represents a novel approach that is convenient for patients and can be effective in detecting cancer at a curable stage. Here, we set out to provide a detailed overview of the rationale behind urine-based cancer detection, with a focus on non-urological cancers, and its potential for cancer diagnostics...
March 10, 2024: Molecular Oncology
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