Literature DB >> 29601337

Future of Liquid Biopsies With Growing Technological and Bioinformatics Studies: Opportunities and Challenges in Discovering Tumor Heterogeneity With Single-Cell Level Analysis.

Naveen Ramalingam, Stefanie S Jeffrey.   

Abstract

Liquid biopsy provides minimally invasive and readily obtainable access to tumor-associated biological material in blood or other body fluids. These samples provide important insights into cancer biology, such as primary tumor heterogeneity; real-time tumor evolution; response to therapy, including immunotherapy; and mechanisms of cancer metastasis. Initial biological materials studied were circulating tumor cells and circulating nucleic acids, including circulating tumor DNA and microRNAs; more recently, studies have expanded to investigate extracellular vesicles, such as exosomes, microvesicles, and large oncosomes; tumor-derived circulating endothelial cells; and tumor-educated platelets. Even with an ongoing ambitious investment effort to develop liquid biopsy as an early cancer detection test in asymptomatic individuals, current challenges remain regarding how to access and analyze rare cells and tumor-derived nucleic acids in cancer patients. Technologies and associated bioinformatics tools are continuously evolving to capture these rare materials in an unbiased manner and to analyze them with high confidence. After first presenting recent applications of liquid biopsy, this review discusses aspects affecting the field, including tumor heterogeneity, single-cell analyses, and associated computational tools that will shape the future of liquid biopsy, with resultant opportunities and challenges.

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Year:  2018        PMID: 29601337      PMCID: PMC5880298          DOI: 10.1097/PPO.0000000000000308

Source DB:  PubMed          Journal:  Cancer J        ISSN: 1528-9117            Impact factor:   3.360


  72 in total

1.  Prospective Validation of Rapid Plasma Genotyping for the Detection of EGFR and KRAS Mutations in Advanced Lung Cancer.

Authors:  Adrian G Sacher; Cloud Paweletz; Suzanne E Dahlberg; Ryan S Alden; Allison O'Connell; Nora Feeney; Stacy L Mach; Pasi A Jänne; Geoffrey R Oxnard
Journal:  JAMA Oncol       Date:  2016-08-01       Impact factor: 31.777

2.  Distinctive gene expression patterns in human mammary epithelial cells and breast cancers.

Authors:  C M Perou; S S Jeffrey; M van de Rijn; C A Rees; M B Eisen; D T Ross; A Pergamenschikov; C F Williams; S X Zhu; J C Lee; D Lashkari; D Shalon; P O Brown; D Botstein
Journal:  Proc Natl Acad Sci U S A       Date:  1999-08-03       Impact factor: 11.205

Review 3.  Circulating tumour cells in cancer patients: challenges and perspectives.

Authors:  Klaus Pantel; Catherine Alix-Panabières
Journal:  Trends Mol Med       Date:  2010-07-29       Impact factor: 11.951

4.  Building trans-omics evidence: using imaging and 'omics' to characterize cancer profiles.

Authors:  Arunima Srivastava; Chaitanya Kulkarni; Parag Mallick; Kun Huang; Raghu Machiraju
Journal:  Pac Symp Biocomput       Date:  2018

5.  Detection of circulating tumor DNA in early- and late-stage human malignancies.

Authors:  Chetan Bettegowda; Mark Sausen; Rebecca J Leary; Isaac Kinde; Yuxuan Wang; Nishant Agrawal; Bjarne R Bartlett; Hao Wang; Brandon Luber; Rhoda M Alani; Emmanuel S Antonarakis; Nilofer S Azad; Alberto Bardelli; Henry Brem; John L Cameron; Clarence C Lee; Leslie A Fecher; Gary L Gallia; Peter Gibbs; Dung Le; Robert L Giuntoli; Michael Goggins; Michael D Hogarty; Matthias Holdhoff; Seung-Mo Hong; Yuchen Jiao; Hartmut H Juhl; Jenny J Kim; Giulia Siravegna; Daniel A Laheru; Calogero Lauricella; Michael Lim; Evan J Lipson; Suely Kazue Nagahashi Marie; George J Netto; Kelly S Oliner; Alessandro Olivi; Louise Olsson; Gregory J Riggins; Andrea Sartore-Bianchi; Kerstin Schmidt; le-Ming Shih; Sueli Mieko Oba-Shinjo; Salvatore Siena; Dan Theodorescu; Jeanne Tie; Timothy T Harkins; Silvio Veronese; Tian-Li Wang; Jon D Weingart; Christopher L Wolfgang; Laura D Wood; Dongmei Xing; Ralph H Hruban; Jian Wu; Peter J Allen; C Max Schmidt; Michael A Choti; Victor E Velculescu; Kenneth W Kinzler; Bert Vogelstein; Nickolas Papadopoulos; Luis A Diaz
Journal:  Sci Transl Med       Date:  2014-02-19       Impact factor: 17.956

6.  Exosomes: secreted vesicles and intercellular communications.

Authors:  Clotilde Théry
Journal:  F1000 Biol Rep       Date:  2011-07-01

7.  Tumor-derived microvesicles mediate human breast cancer invasion through differentially glycosylated EMMPRIN.

Authors:  Kerstin Menck; Christian Scharf; Annalen Bleckmann; Lydia Dyck; Ulrike Rost; Dirk Wenzel; Vishnu M Dhople; Laila Siam; Tobias Pukrop; Claudia Binder; Florian Klemm
Journal:  J Mol Cell Biol       Date:  2014-12-11       Impact factor: 6.216

8.  Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer.

Authors:  Jens G Lohr; Viktor A Adalsteinsson; Kristian Cibulskis; Atish D Choudhury; Mara Rosenberg; Peter Cruz-Gordillo; Joshua M Francis; Cheng-Zhong Zhang; Alex K Shalek; Rahul Satija; John J Trombetta; Diana Lu; Naren Tallapragada; Narmin Tahirova; Sora Kim; Brendan Blumenstiel; Carrie Sougnez; Alarice Lowe; Bang Wong; Daniel Auclair; Eliezer M Van Allen; Mari Nakabayashi; Rosina T Lis; Gwo-Shu M Lee; Tiantian Li; Matthew S Chabot; Amy Ly; Mary-Ellen Taplin; Thomas E Clancy; Massimo Loda; Aviv Regev; Matthew Meyerson; William C Hahn; Philip W Kantoff; Todd R Golub; Gad Getz; Jesse S Boehm; J Christopher Love
Journal:  Nat Biotechnol       Date:  2014-04-20       Impact factor: 54.908

9.  RNA-Seq of single prostate CTCs implicates noncanonical Wnt signaling in antiandrogen resistance.

Authors:  David T Miyamoto; Yu Zheng; Ben S Wittner; Richard J Lee; Huili Zhu; Katherine T Broderick; Rushil Desai; Douglas B Fox; Brian W Brannigan; Julie Trautwein; Kshitij S Arora; Niyati Desai; Douglas M Dahl; Lecia V Sequist; Matthew R Smith; Ravi Kapur; Chin-Lee Wu; Toshi Shioda; Sridhar Ramaswamy; David T Ting; Mehmet Toner; Shyamala Maheswaran; Daniel A Haber
Journal:  Science       Date:  2015-09-18       Impact factor: 47.728

10.  Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors.

Authors:  Viktor A Adalsteinsson; Gavin Ha; Samuel S Freeman; Atish D Choudhury; Daniel G Stover; Heather A Parsons; Gregory Gydush; Sarah C Reed; Denisse Rotem; Justin Rhoades; Denis Loginov; Dimitri Livitz; Daniel Rosebrock; Ignaty Leshchiner; Jaegil Kim; Chip Stewart; Mara Rosenberg; Joshua M Francis; Cheng-Zhong Zhang; Ofir Cohen; Coyin Oh; Huiming Ding; Paz Polak; Max Lloyd; Sairah Mahmud; Karla Helvie; Margaret S Merrill; Rebecca A Santiago; Edward P O'Connor; Seong H Jeong; Rachel Leeson; Rachel M Barry; Joseph F Kramkowski; Zhenwei Zhang; Laura Polacek; Jens G Lohr; Molly Schleicher; Emily Lipscomb; Andrea Saltzman; Nelly M Oliver; Lori Marini; Adrienne G Waks; Lauren C Harshman; Sara M Tolaney; Eliezer M Van Allen; Eric P Winer; Nancy U Lin; Mari Nakabayashi; Mary-Ellen Taplin; Cory M Johannessen; Levi A Garraway; Todd R Golub; Jesse S Boehm; Nikhil Wagle; Gad Getz; J Christopher Love; Matthew Meyerson
Journal:  Nat Commun       Date:  2017-11-06       Impact factor: 14.919

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  16 in total

1.  11th International Symposium on Minimal Residual Cancer (ISMRC): 3-5 May 2018, Montpellier, France.

Authors:  Catherine Alix-Panabières; Klaus Pantel
Journal:  Clin Exp Metastasis       Date:  2018-07-06       Impact factor: 5.150

Review 2.  Liquid biopsy enters the clinic - implementation issues and future challenges.

Authors:  Michail Ignatiadis; George W Sledge; Stefanie S Jeffrey
Journal:  Nat Rev Clin Oncol       Date:  2021-01-20       Impact factor: 66.675

3.  LiqBioer: a manually curated database of cancer biomarkers in body fluid.

Authors:  Yiding Geng; Lu Jin; Guangjue Tang; Zhangxiang Zhao; Yunyan Gu; Dan Yang
Journal:  Database (Oxford)       Date:  2022-09-02       Impact factor: 4.462

Review 4.  When Tissue is an Issue the Liquid Biopsy is Nonissue: A Review.

Authors:  July Rodríguez; Jenny Avila; Christian Rolfo; Alejandro Ruíz-Patiño; Alessandro Russo; Luisa Ricaurte; Camila Ordóñez-Reyes; Oscar Arrieta; Zyanya Lucia Zatarain-Barrón; Gonzalo Recondo; Andrés F Cardona
Journal:  Oncol Ther       Date:  2021-03-10

Review 5.  Reducing Ovarian Cancer Mortality Through Early Detection: Approaches Using Circulating Biomarkers.

Authors:  Camille V Trinidad; Ashley L Tetlow; Leonidas E Bantis; Andrew K Godwin
Journal:  Cancer Prev Res (Phila)       Date:  2020-03

Review 6.  Single-Cell Analysis of Circulating Tumor Cells: How Far Have We Come in the -Omics Era?

Authors:  Elisabetta Rossi; Rita Zamarchi
Journal:  Front Genet       Date:  2019-10-17       Impact factor: 4.599

7.  Extracellular RNAs as potential biomarkers for cancer.

Authors:  Christine Happel; Aniruddha Ganguly; Danilo A Tagle
Journal:  J Cancer Metastasis Treat       Date:  2020-09-17

Review 8.  Tumor heterogeneity in muscle-invasive bladder cancer.

Authors:  Ho Won Kang; Wun-Jae Kim; Woonyoung Choi; Seok Joong Yun
Journal:  Transl Androl Urol       Date:  2020-12

9.  Analysis of Single Circulating Tumor Cells in Renal Cell Carcinoma Reveals Phenotypic Heterogeneity and Genomic Alterations Related to Progression.

Authors:  Vera Cappelletti; Elena Verzoni; Raffaele Ratta; Marta Vismara; Marco Silvestri; Rosanna Montone; Patrizia Miodini; Carolina Reduzzi; Melanie Claps; Pierangela Sepe; Maria Grazia Daidone; Giuseppe Procopio
Journal:  Int J Mol Sci       Date:  2020-02-21       Impact factor: 5.923

10.  The optimal sequence of bronchial brushing and washing for diagnosing peripheral lung cancer using non-guided flexible bronchoscopy.

Authors:  Jun Hyeok Lim; Min Jeong Kim; Sang-Hoon Jeon; Mi Hwa Park; Woo Youl Kim; Minkyung Lee; Jun Ho Kim; Jung Soo Kim; Young Sam Kim; Lucia Kim; Kyung-Hee Lee; Seung Min Kwak; Hyekyung Shin; Hae-Seong Nam
Journal:  Sci Rep       Date:  2020-01-23       Impact factor: 4.379

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