Article
Cell Biology
Ching-Yun Kung, Wen-Liang Fang, Yi-Ping Hung, Kuo-Hung Huang, Ming -Huang Chen, Yee Chao, Shih-Chieh Lin, Anna Fen-Yau Li, Su -Shun Lo, Chew-Wun Wu
Summary: Compared to earlier stages, stage IV gastric cancer patients showed significantly higher levels of cell-free DNA (cfDNA). This study analyzed cfDNA and tumor DNA using next-generation sequencing (NGS) and found different mutation patterns between the two. The most commonly mutated genes in tumor samples were TP53, ARID1A, KMT2C, and KMT2D, while in cfDNA samples, FAT4 and MACF1 were the most commonly mutated genes. The concordance of mutation patterns between cfDNA and tumor DNA was 42.0%. The study suggests that monitoring cfDNA mutation patterns could be useful in the treatment of stage IV gastric cancer.
Article
Oncology
Martin Metzenmacher, Balazs Hegedus, Jan Forster, Alexander Schramm, Peter A. A. Horn, Christoph A. A. Klein, Nicola Bielefeld, Till Ploenes, Clemens Aigner, Dirk Theegarten, Hans-Ulrich Schildhaus, Jens T. T. Siveke, Martin Schuler, Smiths S. S. Lueong
Summary: In this study, we analyzed plasma and tumor samples from lung cancer patients using next-generation sequencing, radiological imaging, and droplet digital polymerase chain reaction (ddPCR) mutation and methylation assays. The results showed a 62% concordance between tumor-reported and circulating-free DNA (cfDNA) sequencing in baseline liquid and tissue biopsies from stage IV patients. Interestingly, ctDNA sequencing allowed for the identification of resistance-mediating p.T790M mutations in baseline plasma samples for which no such mutation was observed in the corresponding tissue. Serial ctDNA mutation analysis revealed a general decrease in ctDNA loads between baseline and first reassessment. Additionally, ctDNA methylation assay showed a high area under the curve (AUC) in early and late stage cases. The decrease in ctDNA and (meth)cfDNA between baseline and first reassessment was reflected by a decrease in CT-derive tumor surface area, irrespective of tumor mutational status.
TRANSLATIONAL ONCOLOGY
(2022)
Article
Oncology
Yiting Dong, Yixiang Zhu, Minglei Zhuo, Xiaomin Chen, Yinpeng Xie, Jianchun Duan, Hua Bai, Shiguang Hao, Zicheng Yu, Yuting Yi, Yanfang Guan, Jie Yuan, Xuefeng Xia, Xin Yi, Jie Wang, Zhijie Wang
Summary: Recent studies have shown the unstable prediction ability of blood-based tumor mutational burden (bTMB) in predicting the response to immune checkpoint inhibitors in non-small cell lung cancer patients. This study developed a novel approach, MSAF-adjusted bTMB (Ma-bTMB), to better select beneficiaries of immune checkpoint inhibitors based on the integration of maximum somatic allele frequency (MSAF). The results demonstrated that Ma-bTMB effectively identified beneficiaries of immune checkpoint inhibitors in patients with advanced NSCLC.
Article
Oncology
Yuan-Tzu Lan, Shih-Ching Chang, Pei-Ching Lin, Chien-Hsing Lin, Wen-Yi Liang, Wei-Shone Chen, Jeng-Kai Jiang, Shung-Haur Yang, Jen-Kou Lin
Summary: Through NGS analysis of 95 metastatic CRC patients, a high concordance (91%) of mutation patterns in 10 genes between cfDNA and tumor samples was observed. The KRAS mutation status in cfDNA showed a sensitivity of 88.2% and specificity of 100% for predicting KRAS mutation in tumor tissue. Right-sided CRCs were more likely to develop peritoneal metastases, while left-sided tumors were more likely to have lung metastases.
AMERICAN JOURNAL OF CANCER RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Florian Richter, Clara Henssen, Tim Alexander Steiert, Tobias Meissner, Anne-Sophie Mehdorn, Christoph Roecken, Andre Franke, Jan-Hendrik Egberts, Thomas Becker, Susanne Sebens, Michael Forster
Summary: Esophageal cancer (EC) has a high mortality rate, and optimizing therapies and dynamically adapting to individuals is crucial. Liquid biopsy is an increasingly important method for residual disease monitoring, but conflicting detection rates and varying levels of circulating tumor DNA (ctDNA) have been observed in previous studies. This study aims to resolve this discrepancy and found that ctDNA in blood can be used for therapy monitoring of EC patients. A combination of solid and liquid samples should be used to guide individualized EC therapy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
H. C. Pommergaard, C. W. Yde, L. B. Ahlborn, C. L. Andersen, T. Henriksen, J. P. Hasselby, A. A. Rostved, C. L. Sorensen, K. S. Rohrberg, F. C. Nielsen, A. Rasmussen
Summary: Mutational analysis of circulating tumor DNA (ctDNA) showed limited reliability in early detection of recurrence after resection for hepatocellular carcinoma (HCC) in patients with resectable HCC, but was reliably detected in patients with advanced HCC.
MOLECULAR BIOLOGY REPORTS
(2022)
Article
Gastroenterology & Hepatology
L. Sivapalan, H. M. Kocher, H. Ross-Adams, C. Chelala
Summary: PDAC is expected to become the second leading cause of cancer-related mortality in the next decade, with limited treatment options and poor long-term prognosis. Liquid biopsies, particularly ctDNA analyses, are increasingly being studied as a promising avenue for enhancing the characterization of PDAC tumor genomes, potentially leading to new therapeutic targets and improved treatment stratification. Challenges in terms of technical, analytical and biological aspects need to be addressed for the full realization of the potential of liquid biopsies in PDAC management.
Article
Cell Biology
Benedict Herhaus, Elmo Neuberger, Ema Juskeviciute, Perikles Simon, Katja Petrowski
Summary: This study investigated the effects of acute stress on the dynamics of circulating cell-free DNA (cfDNA). The results showed that a brief psychological stressor was sufficient to rapidly increase cfDNA levels, with a stronger association observed in individuals with higher basal cfDNA levels. This rapid regulation of cfDNA may be attributed to the transient activation of immune cells caused by neuroendocrine-immune activation. Further research is needed to evaluate the reliability of cfDNA as a marker of neuroendocrine-immune activation.
Article
Agriculture, Multidisciplinary
Inci Sahin Negis, Cengiz Ikten, Levent Unlu
Summary: Next-generation sequencing combined with bioinformatic analysis is an effective method for SNP discovery in genomes. In this study, a genomic DNA library prepared from Frankliniella occidentalis adults collected from multiple locations in Turkey was sequenced using the NGS-seq technology. Bioinformatic analysis identified 61 SNPs, with 46 in protein-coding genes and 15 in tRNA regions.
JOURNAL OF PLANT DISEASES AND PROTECTION
(2023)
Article
Oncology
Maria Gabriela O. Fernandes, Natalia Cruz-Martins, Conceicao Souto Moura, Susana Guimaraes, Joana Pereira Reis, Ana Justino, Maria Joao Pina, Adriana Magalhaes, Henrique Queiroga, Jose Carlos Machado, Venceslau Hespanhol, Jose Luis Costa
Summary: Plasma ctDNA testing showed high accuracy and clinical relevance in newly diagnosed advanced NSCLC patients, highlighting its potential as a valuable tool for mutation detection in clinical practice.
Article
Oncology
Aliki Ntzifa, Athanasios Kotsakis, Vassilis Georgoulias, Evi Lianidou
Summary: Liquid biopsy, particularly using crystal dPCR technology, is crucial for accurate detection of genomic alterations in NSCLC patients. Analysis of EGFR mutations in ctDNA and CTCs reveals clinical utility and high sensitivity, highlighting the importance of accurate molecular analysis in cancer management.
Article
Biotechnology & Applied Microbiology
Jinghua Sun, Ge Sun, KeMou Lu, Lingling Xu, XiaoNa Qu, Ye Cheng, Evenki Pan, Peng Yang, Tingting Wu, Yang Zhang, HongMei He
Summary: This study investigated a case of lung adenocarcinoma (LADC) with EGFR mutations who underwent sequential EGFR TKI treatment. Dynamic changes in tumor heterogeneity were observed in the different lesions of the patient's CT images. Analysis of ctDNA using targeted next generation sequencing (NGS) revealed dynamic changes in mutational profiles between the primary and metastatic tumors, providing insights into tumor evolution for guiding treatment decision-making.
ONCOTARGETS AND THERAPY
(2022)
Article
Oncology
Ana Barbosa, Pedro Pinto, Ana Peixoto, Joana Guerra, Manuela Pinheiro, Catarina Santos, Carla Pinto, Carla Escudeiro, Carla Bartosch, Rui Santos, Andreia Brandao, Joao Silva, Manuel R. Teixeira
Summary: Genetic testing for somatic alterations in ovarian cancer patients can be effectively done through ctDNA analysis, with potential implications for targeted therapy. This study highlights the importance of using NGS-based ctDNA testing to stratify patients and predict treatment outcomes.
FRONTIERS IN ONCOLOGY
(2021)
Article
Oncology
Katherine Clifton, Jingqin Luo, Yu Tao, Jennifer Saam, Thereasa Rich, Anna Roshal, Ashley Frith, Caron Rigden, Foluso Ademuyiwa, Katherine Weilbaecher, Leonel Hernandez-Aya, Lindsay L. Peterson, Nusayba Bagegni, Rama Suresh, Ron Bose, Mateusz Opyrchal, Tanya M. Wildes, Cynthia Ma
Summary: This study aimed to assess mutation profiles in older adult breast cancer patients using a ctDNA assay, and found more frequent ATM, BRAF, and PIK3CA mutations in older patients. Results also showed that ctDNA testing influenced treatment management in a portion of patients from a single institution.
BREAST CANCER RESEARCH AND TREATMENT
(2021)
Article
Microbiology
Valerio Vitali, Rebecca Rothering, Francesco Catania
Summary: This research investigates the biomedical and evolutionary significance of amitosis, focusing on the suitability of single-cell whole-genome sequencing in studying the consequences of amitosis in Paramecium tetraurelia. The study reveals that somatic assortment levels in P. tetraurelia suggest that IES retention levels are largely established during macronuclear development and remain stable during vegetative growth.
Article
Medical Laboratory Technology
Jared C. Nesvet, Katie A. Antilla, Danielle S. Pancirer, Alexander X. Lozano, Jordan S. Preiss, Weijie Ma, Aihua Fu, Seung-Min Park, Sanjiv S. Gambhir, Alice C. Fan, Joel W. Neal, Sukhmani K. Padda, Millie Das, Tianhong Li, Heather A. Wakelee, Shan X. Wang
Summary: The GMR assay demonstrated high diagnostic sensitivity and specificity in detecting EGFR mutations and monitoring treatment response noninvasively. After 2 weeks of therapy, predicted responders showed a higher rate of disappearance of ctDNA by GMR compared to predicted nonresponders, with 100% concordance with radiographic response.
CLINICAL CHEMISTRY
(2021)
Article
Oncology
Zachary R. Chalmers, Michael C. Burns, Ericka M. Ebot, Garrett M. Frampton, Jeffrey S. Ross, Maha H. A. Hussain, Sarki A. Abdulkadir
Summary: In summary, early-onset prostate cancer patients with clinically advanced and metastatic disease display distinct molecular alterations compared to older patients, with increased frequency of TMPRSS2-ERG fusions and fewer AR, SPOP, and ASXL1 alterations.
PROSTATE CANCER AND PROSTATIC DISEASES
(2021)
Review
Oncology
Weijie Ma, Brian Pham, Tianhong Li
Summary: Immune checkpoint inhibitors have shown significant efficacy in treating various cancer types, but only a small percentage of patients benefit from them. Advances in precision immuno-oncology are focused on personalized therapies based on genomic alterations and biomarkers.
CLINICAL & EXPERIMENTAL METASTASIS
(2022)
Article
Oncology
Richard S. P. Huang, Karthikeyan Murugesan, Meagan Montesion, Dean C. Pavlick, Douglas A. Mata, Matthew C. Hiemenz, Brennan Decker, Garrett Frampton, Lee A. Albacker, Jeffrey S. Ross
Summary: The study analyzed a large cohort of solid tumor cases to investigate CD274 copy-number changes and their correlation with PD-L1 protein expression. The prevalence of CD274 copy-number changes varied across different tumor types and was found to be significantly associated with PD-L1 positivity in certain tumor types, indicating its potential as a biomarker for immune checkpoint inhibitor therapy.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2021)
Article
Oncology
Weijie Ma, Jie Zeng, Shuai Chen, Yue Lyu, Kyra A. Toomey, Chinh T. Phan, Ken Y. Yoneda, Tianhong Li
Summary: This study is the first to show that TKIs can have various effects on blood immune cells, which may affect their response to ICIs. Further validation of the blood biomarker and in vitro assay is warranted.
BIOMARKER RESEARCH
(2021)
Article
Multidisciplinary Sciences
Coren A. Milbury, James Creeden, Wai-Ki Yip, David L. Smith, Varun Pattani, Kristi Maxwell, Bethany Sawchyn, Ole Gjoerup, Wei Meng, Joel Skoletsky, Alvin D. Concepcion, Yanhua Tang, Xiaobo Bai, Ninad Dewal, Pei Ma, Shannon T. Bailey, James Thornton, Dean C. Pavlick, Garrett M. Frampton, Daniel Lieber, Jared White, Christine Burns, Christine Vietz
Summary: FoundationOne (R) CDx is an FDA-approved companion diagnostic test that utilizes comprehensive genomic profiling technology to analyze 324 cancer genes in solid tumors. It accurately identifies patients who may benefit from specific drug therapies and helps improve treatment outcomes for cancer patients.
Article
Multidisciplinary Sciences
Ilya G. Serebriiskii, Valery Pavlov, Rossella Tricarico, Grigorii Andrianov, Emmanuelle Nicolas, Mitchell Parker, Justin Newberg, Garrett Frampton, Joshua E. Meyer, Erica A. Golemis
Summary: Loss or dysfunction of the PTEN tumor suppressor gene can activate pro-tumorigenic signaling pathways. In this study, the authors analyze sequencing data from a large cohort of colorectal cancer patients with PTEN mutations and identify distinct patterns of associations with genomic and clinical features.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Radwa Sharaf, Meagan Montesion, Julia F. Hopkins, Jiarong Song, Garrett M. Frampton, Lee A. Albacker
Summary: This study highlights the importance of RAD21 and HGF in telomere lengthening, supporting unlimited replication in tumors. These findings open avenues for work aimed at targeting this crucial pathway in tumorigenesis.
Article
Oncology
Richard Benjamin Young, Hemali Panchal, Weijie Ma, Shuai Chen, Aaron Steele, Andrea Iannucci, Tianhong Li
Summary: This study analyzed the clinical outcomes and predictive factors of hospitalized cancer patients receiving ICI therapy. Results showed that these patients had poor survival outcomes with high inpatient mortality and 90-day mortality rates. Having >= 3 comorbidities, pre-treatment absolute lymphocyte counts <600 cells/mu L, and pre-treatment derived neutrophil to lymphocyte ratio (dNLR) >4 were associated with poor survival outcomes.
FRONTIERS IN ONCOLOGY
(2022)
Article
Oncology
Weijie Ma, Jie Zeng, Dennis J. Montoya, Kyra Toomey, Chihong Zhou, Shuai Chen, Dingning Liu, Michael Babich, James A. Radosevich, Tianhong Li
Summary: Adenocarcinomas account for nearly 40% of all cancer types and are responsible for over 70% of cancer-related deaths. Labyrinthin (LAB) is a new cancer neoantigen expressed on the surface of adenocarcinoma cells in various cancer types. This study developed an immunohistochemistry assay to detect LAB expression in non-small-cell lung cancer (NSCLC) and investigated its clinical significance. Further research is needed to confirm LAB expression as a biomarker for selecting patients for LAB-targeted cancer therapy.
Review
Oncology
Luis A. Godoy, Joy Chen, Weijie Ma, Jag Lally, Kyra A. Toomey, Prabhu Rajappa, Roya Sheridan, Shirish Mahajan, Nicholas Stollenwerk, Chinh T. Phan, Danny Cheng, Robert J. Knebel, Tianhong Li
Summary: In the past decade, targeted therapy for oncogene-driven NSCLC and immune checkpoint inhibitors for non-oncogene-driven NSCLC have significantly improved the survival and quality of life for patients with unresectable NSCLC. These biomarker-guided neoadjuvant therapies are also being used in patients with early-stage NSCLC, with the approval of neoadjuvant nivolumab and chemotherapy for stage IB-IIIA NSCLC. Ongoing trials are evaluating the efficacy of neoadjuvant immune checkpoint inhibitor combinations and neoadjuvant molecular targeted therapies for NSCLC.
BIOMARKER RESEARCH
(2023)
Article
Immunology
Weijie Ma, Sixi Wei, Siqi Long, Eddie C. Tian, Bridget Mclaughlin, Maria Jaimes, Dennis J. Montoya, Varun R. Viswanath, Jeremy Chien, Qianjun Zhang, Jonathan E. Van Dyke, Shuai Chen, Tianhong Li
Summary: The use of multicolor spectrum flow cytometry helps identify potential blood immune biomarkers for immune checkpoint inhibitor (ICI) treatment in non-small-cell lung cancer (NSCLC) patients. The frequency of CD4+ central memory cells and CD4-CD8- double-negative (DN) T cells before treatment is associated with progression-free survival (PFS). ICIs significantly change the frequency of cytotoxic CD8+PD1+ T cells, DN T cells, CD16+CD56dim and CD16+CD56- natural killer (NK) cells, and CD14+HLDRhigh and CD11c+HLADR + monocytes. An increase in the frequency of CD16+CD56dim NK cells and CD14+HLADRhigh monocytes after treatment is associated with a longer PFS.
FRONTIERS IN IMMUNOLOGY
(2023)
Review
Surgery
Quan Wu, Weijie Ma, Qianqian Wang, Yaqi Liu, Yaokai Xu
Summary: This meta-analysis compares the clinical outcomes of Hybrid Hernia Repair (HHR) and Laparoscopic Hernia Repair (LHR) in the management of Incisional Ventral Hernias (IVH). The analysis showed that HHR did not demonstrate a clear advantage over LHR in reducing surgical complications, except for a lower incidence of postoperative seroma. Further research is needed to determine the optimal surgical approach for IVH.
Article
Oncology
Liangliang Zhang, Omar Hamdani, Ole Gjoerup, Cheryl Cho-Phan, Jeremy Snider, Emily Castellanos, Halla Nimeiri, Garrett Frampton, Jeffrey M. Venstrom, Geoffrey Oxnard, Samuel J. Klempner, Alexa B. Schrock
Summary: This study aimed to explore the characteristics of HER2 amplification in gastroesophageal adenocarcinoma (GEA) patients and investigate its association with the efficacy of trastuzumab. The results showed that the copy number of ERBB2 in HER2-amplified patients could predict progression-free survival in trastuzumab-treated patients. This study contributes to a better understanding of the importance of HER2 amplification in the treatment of GEA.
JCO PRECISION ONCOLOGY
(2022)
Article
Biochemical Research Methods
Jian Carrot-Zhang, Seunghun Han, Wanding Zhou, Jeffrey S. Damrauer, Anab Kemal, Rameen Canc Genome Atlas Anal Network, Andrew D. Cherniack, Rameen Beroukhim
Summary: This protocol presents a method to identify local ancestry and detect associated molecular changes in admixed populations, utilizing data from the Cancer Genome Atlas. It can be applied to examine germline contributions to cancer in patients with mixed ancestries. For more detailed information, refer to Carrot-Zhang et al. (2020).
