Article
Medical Laboratory Technology
Kaixiang Zhou, Yang Liu, Qing Yuan, Dong Lai, Shanshan Guo, Zhenni Wang, Liping Su, Huanqin Zhang, Xiangxu Wang, Wenjie Guo, Xiaoying Ji, Xiwen Gu, Qichao Huang, Xu Guo, Jinliang Xing
Summary: In this study, the researchers comprehensively analyzed the fragmentomic and mutational characteristics of cell-free mitochondrial DNA (cf-mtDNA) in urine and plasma samples. They found that urine cf-mtDNA exhibited increased copy numbers and wider spread in fragment size distributions compared to plasma cf-mtDNA. The results also showed that urine cf-mtDNA originated predominantly from local shedding and transrenal excretion. Furthermore, an enhanced fragmentation and mutation profiles of urine cf-mtDNA were observed in renal cell carcinoma (RCC) and colorectal cancer (CRC) patients, which could potentially be used for cancer diagnosis.
CLINICAL CHEMISTRY
(2022)
Article
Medicine, Research & Experimental
Ymke van Der Pol, Normastuti Adhini Tantyo, Nils Evander, Anouk E. Hentschel, Birgit M. M. Wever, Jip Ramaker, Sanne Bootsma, Marieke F. Fransen, Kristiaan J. Lenos, Louis Vermeulen, Famke L. Schneiders, Idris Bahce, Jakko A. Nieuwenhuijzen, Renske D. M. Steenbergen, D. Michiel Pegtel, Norbert Moldovan, Florent Mouliere
Summary: This study demonstrates the use of Oxford Nanopore Technologies (ONT) sequencing to obtain genomic and fragmentomic data from liquid biopsies. The results show that copy number aberrations and cfDNA fragmentation patterns can be determined in less than 24 hours. Furthermore, ONT sequencing allows analysis of previously understudied cfDNA populations.
EMBO MOLECULAR MEDICINE
(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
Szilvia Lilla Csoma, Judit Bedekovics, Gergo Veres, Anita arokszallasi, Csilla Andras, Gabor Mehes, Attila Mokanszki
Summary: In the era of personalized oncology, next-generation sequencing plays a crucial role in identifying genetic aberrations in biliary tract cancers. Our study demonstrates that liquid biopsy of peripheral blood can effectively monitor the molecular genetic profile and chemotherapy response in BTCs, providing a minimally invasive testing approach for precision oncology treatment.
Article
Oncology
Ariana Rostami, Scott Bratman, Kathy Han
Summary: Liquid biopsy approaches for detecting viral DNA play a crucial role in diagnosing virally-associated cancers. The CaptHPV method based on next-generation sequencing is discussed for its potential in detecting plasma HPV DNA in HPV-associated cancers and its potential clinical utility.
CLINICAL CANCER RESEARCH
(2021)
Article
Medicine, Research & Experimental
Florent Mouliere, Christopher G. Smith, Katrin Heider, Jing Su, Ymke van der Pol, Mareike Thompson, James Morris, Jonathan C. M. Wan, Dineika Chandrananda, James Hadfield, Marta Grzelak, Irena Hudecova, Dominique-Laurent Couturier, Wendy Cooper, Hui Zhao, Davina Gale, Matthew Eldridge, Colin Watts, Kevin Brindle, Nitzan Rosenfeld, Richard Mair
Summary: The study focused on detecting glioma-derived cell-free DNA (cfDNA) in body fluids and found that tumor-derived DNA could be identified in the majority of CSF, plasma, and urine samples with different tumor fractions. They also discovered a significant difference in cfDNA fragment sizes between glioma patients and individuals with non-malignant brain disorders or healthy individuals, which could potentially aid in non-invasive cancer detection using machine learning models.
EMBO MOLECULAR MEDICINE
(2021)
Article
Microbiology
Martin Hoenigl, Matthias Egger, Jessica Price, Robert Krause, Juergen Prattes, P. Lewis White
Summary: Timely diagnosis remains an unmet need in non-neutropenic patients at risk for aspergillosis, including those with COVID-19-associated pulmonary aspergillosis (CAPA). Currently available mycological tests show limited sensitivity when testing blood specimens. Metagenomic next-generation sequencing (mNGS) to detect microbial cell-free DNA (mcfDNA) in plasma might overcome some of the limitations of conventional diagnostics.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Article
Biophysics
Lin Wang, Yu Zhuang, Yue Yu, Zhiwei Guo, Qiaomei Guo, Lihua Qiao, Xueqing Wang, Xiaohui Liang, Pengpeng Zhang, Qifan Li, Chenjun Huang, Rong Cong, Yinghui Li, Bin Che, Huihui Xiong, Guomin Lin, Mingming Rao, Rongjun Hu, Wei Wang, Guohua Yang, Jiatao Lou
Summary: We developed the OPERA system to detect mutations with low variant allelic frequency (VAF) in short DNA fragments. OPERA can detect mutations as low as 0.0025% VAF, while CAPP-Seq can only detect mutations >0.03% VAF. OPERA has high sensitivity in detecting mutations in synthetic fragments and plasma samples from lung cancer patients.
BIOSENSORS & BIOELECTRONICS
(2023)
Review
Oncology
Paul Hofman
Summary: Liquid biopsy (LB) has become the only option to detect molecular targets for first-line treatment in treatment-naive NSCLC patients. Despite not being commonly used in diagnosis currently, Next-Generation Sequencing (NGS) shows the most promise for assessing genetic abnormalities.
Article
Oncology
Minsuk Kwon, Bo Mi Ku, Steve Olsen, Sehhoon Park, Martina Lefterova, Justin Odegaard, Hyun-Ae Jung, Jong-Mu Sun, Se-Hoon Lee, Jin Seok Ahn, Keunchil Park, Myung-Ju Ahn
Summary: This study found that cell-free plasma DNA (cfDNA) next-generation sequencing (NGS) could detect ALK fusions and resistance mutations and predict the response and resistance to tyrosine kinase inhibitor (TKI) therapy in patients with ALK-rearranged non-small cell lung cancer (ALK+ NSCLC). Furthermore, the absence of ctDNA at baseline and clearance of ctDNA at 2 months were associated with longer progression-free survival and overall survival. Patients with co-occurring TP53 alterations and ALK fusions at baseline showed shorter progression-free survival.
Article
Genetics & Heredity
Dana W. Y. Tsui, Michael L. Cheng, Maha Shady, Julie L. Yang, Dennis Stephens, Helen Won, Preethi Srinivasan, Kety Huberman, Fanli Meng, Xiaohong Jing, Juber Patel, Maysun Hasan, Ian Johnson, Erika Gedvilaite, Brian Houck-Loomis, Nicholas D. Socci, S. Duygu Selcuklu, Venkatraman E. Seshan, Hongxin Zhang, Debyani Chakravarty, Ahmet Zehir, Ryma Benayed, Maria Arcila, Marc Ladanyi, Samuel A. Funt, Darren R. Feldman, Bob T. Li, Pedram Razavi, Jonathan Rosenberg, Dean Bajorin, Gopa Iyer, Wassim Abida, Howard I. Scher, Dana Rathkopf, Agnes Viale, Michael F. Berger, David B. Solit
Summary: This study found that cfDNA tumor fraction can help interpret negative cfDNA results and guide the selection of subsequent sequencing platforms most likely to identify clinically-relevant genomic alterations through analysis of plasma samples from 118 metastatic cancer patients.
Article
Oncology
Melanie Pages, Denisse Rotem, Gregory Gydush, Sarah Reed, Justin Rhoades, Gavin Ha, Christopher Lo, Mark Fleharty, Madeleine Duran, Robert Jones, Sarah Becker, Michaela Haller, Claire E. Sinai, Liliana Goumnerova, Todd R. Golub, J. Christopher Love, Keith L. Ligon, Karen D. Wright, Viktor A. Adalsteinsson, Rameen Beroukhim, Pratiti Bandopadhayay
Summary: The study systematically evaluated the feasibility of profiling pediatric brain tumors using ctDNA obtained from plasma, CSF, and urine. Results showed that most samples had very low levels of somatic mutations, posing a challenge for detection using whole-genome or targeted sequencing methods. Substantial challenges remain in genetically characterizing pediatric brain tumors from liquid biopsies.
Review
Biochemistry & Molecular Biology
Simita Gaglani, Edgar Gonzalez-Kozlova, Dara J. Lundon, Ashutosh K. Tewari, Navneet Dogra, Natasha Kyprianou
Summary: Extracellular vesicles (EVs) play a crucial role in non-invasive liquid biopsy for cancer detection, with exosomes having significant diagnostic value in prostate cancer and potential therapeutic applications.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Oncology
Sehhoon Park, Steve Olsen, Bo Mi Ku, Min-Sang Lee, Hyun-Ae Jung, Jong-Mu Sun, Se-Hoon Lee, Jin Seok Ahn, Keunchil Park, Yoon-La Choi, Myung-Ju Ahn
Summary: This study analyzed the concordance of actionable genomic alterations in non-small cell lung cancer patients detected through circulating tumor DNA (ctDNA) and tissue sequencing. The results showed that ctDNA testing can identify additional actionable genomic alterations beyond tissue testing.
Review
Genetics & Heredity
Sarah M. Dermody, Chandan Bhambhani, Paul L. Swiecicki, J. Chad Brenner, Muneesh Tewari
Summary: Liquid biopsy is a promising method for cancer detection, using bodily fluids such as urine to detect cancer biomarkers. Trans-renal ctDNA (TR-ctDNA) in urine has shown potential as a cancer biomarker approach.
FRONTIERS IN GENETICS
(2022)
Article
Multidisciplinary Sciences
Rebecca A. Luchtel, Tushar Bhagat, Kith Pradhan, William R. Jacobs, Mark Levine, Amit Verma, Niraj Shenoy
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Oncology
Meijun Du, Yijun Tian, Winston Tan, Liewei Wang, Liguo Wang, Deepak Kilari, Chiang-Ching Huang, Liang Wang, Manish Kohli
PROSTATE CANCER AND PROSTATIC DISEASES
(2020)
Article
Medicine, General & Internal
Niraj Shenoy, Rebecca Luchtel, Perminder Gulani
Article
Oncology
Niraj Shenoy
Review
Urology & Nephrology
Xiaoyang Wang, Robert Lopez, Rebecca A. Luchtel, Sassan Hafizi, Benjamin Gartrell, Niraj Shenoy
Summary: This article reviews the advancements in targeted therapies and immune checkpoint inhibitors in the treatment landscape of Renal Cell Carcinoma (RCC) over the last decade, emphasizing the importance of understanding the mechanisms adopted by RCC cells to evade immune killing and exploring current clinical trials and future directions in the field.
KIDNEY INTERNATIONAL
(2021)
Article
Multidisciplinary Sciences
Niraj Shenoy
SCIENTIFIC REPORTS
(2020)
Review
Oncology
Ruchika Bhawal, Ann L. Oberg, Sheng Zhang, Manish Kohli
Article
Oncology
Manish Kohli, Winston Tan, Berengere Vire, Pierre Liaud, Melina Blairvacq, Frederic Berthier, Daniel Rouison, George Garnier, Lea Payen, Thierry Cousin, Dominique Joubert, Alexandre Prieur
Summary: Metastatic renal cell carcinoma (mRCC) is a significant portion of newly diagnosed kidney cancers, and better understanding of disease progression has led to the identification of hPG80 as a potential prognostic marker, which may improve current clinical prognostic models for mRCC patients.
Article
Oncology
Arturo Araujo, Leah M. Cook, Jeremy S. Frieling, Winston Tan, John A. Copland, Manish Kohli, Shilpa Gupta, Jasreman Dhillon, Julio Pow-Sang, Conor C. Lynch, David Basanta
Summary: By utilizing a first-principles approach and mathematical modeling, this study demonstrates the potential for optimizing standard-of-care therapies for bone metastatic prostate cancer patients to delay the emergence of resistant disease. The results suggest that routine measurements and patient-specific predictions can lead to improvements in treatment outcomes and overall patient survival.
Article
Oncology
Rachel L. Dittmar, Suyu Liu, Mei Chee Tai, Kimal Rajapakshe, Ying Huang, Gary Longton, Christine DeCapite, Mark W. Hurd, Pamela L. Paris, Kimberly S. Kirkwood, Cristian Coarfa, Anirban Maitra, Randall E. Brand, Ann M. Killary, Subrata Sen
Summary: The study identified miR-34a-5p, miR-130a-3p, and miR-222-3p as significantly differentially abundant in plasma from stage II PDAC cases, and when combined with CA19-9, improved the diagnostic accuracy for PDAC. Further analysis of larger cohorts is needed to develop an effective early detection biomarker assay for clinical settings.
CANCER PREVENTION RESEARCH
(2021)
Article
Oncology
Hui-Ming Lin, Kevin Huynh, Manish Kohli, Winston Tan, Arun A. Azad, Nicole Yeung, Kate L. Mahon, Blossom Mak, Peter D. Sutherland, Andrew Shepherd, Natalie Mellett, Maria Docanto, Corey Giles, Margaret M. Centenera, Lisa M. Butler, Peter J. Meikle, Lisa G. Horvath
Summary: Elevated circulating ceramide species are associated with poorer clinical outcomes in prostate cancer patients, and these circulating lipid profiles could be used to predict therapeutic efficacy at different stages of PC.
PROSTATE CANCER AND PROSTATIC DISEASES
(2021)
Article
Multidisciplinary Sciences
Ritesh K. Aggarwal, Rebecca A. Luchtel, Venkata Machha, Alexander Tischer, Yiyu Zou, Kith Pradhan, Nadia Ashai, Nandini Ramachandra, Joseph M. Albanese, Jung-in Yang, Xiaoyang Wang, Srinivas Aluri, Shanisha Gordon, Ahmed Aboumohamed, Benjamin A. Gartrell, Sassan Hafizi, James Pullman, Niraj Shenoy
Summary: Reduced succinate dehydrogenase (SDH) activity leading to oncogenic succinate accumulation is a common feature in clear cell renal cell carcinoma (ccRCC), with significant adverse impact on patient survival. This study highlights the importance of SDH deficiency in ccRCC pathogenesis and progression.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Oncology
Umang Swami, Jennifer Anne Sinnott, Benjamin Haaland, Nicolas Sayegh, Taylor Ryan McFarland, Nishita Tripathi, Benjamin L. Maughan, Nityam Rathi, Deepika Sirohi, Roberto Nussenzveig, Manish Kohli, Sumanta K. Pal, Neeraj Agarwal
Summary: The study reveals that most patients with metastatic prostate cancer receive only androgen deprivation therapy as upfront treatment, and in those treated with a novel hormonal therapy, receiving an alternate novel hormonal therapy as the next treatment is associated with improved overall survival compared to docetaxel, though limitations include the retrospective design of the study.
Article
Multidisciplinary Sciences
Winston Tan, Tiantian Zheng, Amy Wang, Joanna Roacho, Seng Thao, Pan Du, Shidong Jia, Jianjun Yu, Bonnie L. King, Manish Kohli
Summary: Docetaxel chemotherapy is a standard treatment for mCRPC patients, but the genomic perturbations underlying resistance have not been fully characterized. The study found that RB1, TP53, and PTEN gene alterations were relatively modest during chemotherapy, potentially indicating the persistence of a clonal signature associated with treatment-induced lineage plasticity.
SCIENTIFIC REPORTS
(2022)
Article
Oncology
Jinyong Huang, Meijun Du, Alex Soupir, Liewei Wang, Winston Tan, Krishna R. Kalari, Deepak Kilari, Jong Park, Chiang-Ching Huang, Manish Kohli, Liang Wang
Summary: A multi-gene copy number alteration-based risk score derived from plasma cfDNA can predict clinical outcomes in metastatic castrate resistant prostate cancer patients, including survival and treatment response.