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Cancers
Special Issues
Genetic, Epigenetic, and Epitranscriptomic Changes in Lung Cancer
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Genetic, Epigenetic, and Epitranscriptomic Changes in Lung Cancer

A special issue of Cancers (ISSN 2072-6694). This special issue belongs to the section "Cancer Pathophysiology".

Deadline for manuscript submissions: 15 August 2024 | Viewed by 2419

Special Issue Editors

Dr. Giovanni Nigita

E-Mail Website
Guest Editor
Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH 43210, USA
Interests: computational biology; ncRNAs; epitranscriptomics; noncoding RNA editing; cancer informatics
Special Issues, Collections and Topics in MDPI journals
Dr. Mario Acunzo

E-Mail Website
Guest Editor
Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA 23284, USA
Interests: ncRNAs; epitranscriptomics; lung cancer; circulating biomarkers
Special Issues, Collections and Topics in MDPI journals
Dr. Patrick Nana-Sinkam

E-Mail Website
Guest Editor
Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA 23284, USA
Interests: lung cancer screening; noncoding RNA; biomarkers; liquid biopsy; health disparities

Special Issue Information

Dear Colleagues,

Lung cancer remains the leading cause of cancer death worldwide. The World Health Organization (WHO) confirmed that lung cancer occurred in more than two million people in 2020. Lung cancer is mainly classified as non-small cell lung cancer (NSCLC), which represents approximately 85% of all lung cancers, and small cell lung cancer (SCLC), which represents about 15%. Despite advancements in diagnosing and treating lung cancer, patients continue to have a poor prognosis with an overall 5-year survival of ~18%. Despite numerous advances in early detection, targeted therapeutics, and immunotherapy, as well as the employment of new technologies such as next-generation sequencing and bioinformatics resources, the molecular drivers that lead to poor outcomes have yet to be fully understood.

The aim of this Special Issue is to present recent advances in the genomic characterization, epigenetics, and epitranscriptomics of lung cancer. These concepts will be presented in the context of databases and bioinformatics resources to study lung cancer, non-invasive lung cancer biomarkers, molecularly targeted therapies, and immunotherapy.

Dr. Giovanni Nigita
Dr. Mario Acunzo
Dr. Patrick Nana-Sinkam
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Cancers is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • non-small cell lung cancer
  • small cell lung cancer
  • biology and genomic characterization
  • epigenetics and epitranscritomics
  • databases and bioinformatics resources
  • target drugs
  • immunotherapy
  • diagnosis and prognosis
  • non-invasive biomarkers
  • translational research

Published Papers (2 papers)

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Research

21 pages, 3137 KiB  
Article
Evaluation of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration (EBUS-TBNA) Samples from Advanced Non-Small Cell Lung Cancer for Whole Genome, Whole Exome and Comprehensive Panel Sequencing
by David Fielding, Vanessa Lakis, Andrew J. Dalley, Haarika Chittoory, Felicity Newell, Lambros T. Koufariotis, Ann-Marie Patch, Stephen Kazakoff, Farzad Bashirzadeh, Jung Hwa Son, Kimberley Ryan, Daniel Steinfort, Jonathan P. Williamson, Michael Bint, Carl Pahoff, Phan Tien Nguyen, Scott Twaddell, David Arnold, Christopher Grainge, Andrew Pattison, David Fairbairn, Shailendra Gune, Jemma Christie, Oliver Holmes, Conrad Leonard, Scott Wood, John V. Pearson, Sunil R. Lakhani, Nicola Waddell, Peter T. Simpson and Katia Nonesadd Show full author list remove Hide full author list
Cancers 2024, 16(4), 785; https://doi.org/10.3390/cancers16040785 - 15 Feb 2024
Viewed by 988
Abstract
Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is often the only source of tumor tissue from patients with advanced, inoperable lung cancer. EBUS-TBNA aspirates are used for the diagnosis, staging, and genomic testing to inform therapy options. Here we extracted DNA and RNA from [...] Read more.
Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is often the only source of tumor tissue from patients with advanced, inoperable lung cancer. EBUS-TBNA aspirates are used for the diagnosis, staging, and genomic testing to inform therapy options. Here we extracted DNA and RNA from 220 EBUS-TBNA aspirates to evaluate their suitability for whole genome (WGS), whole exome (WES), and comprehensive panel sequencing. For a subset of 40 cases, the same nucleic acid extraction was sequenced using WGS, WES, and the TruSight Oncology 500 assay. Genomic features were compared between sequencing platforms and compared with those reported by clinical testing. A total of 204 aspirates (92.7%) had sufficient DNA (100 ng) for comprehensive panel sequencing, and 109 aspirates (49.5%) had sufficient material for WGS. Comprehensive sequencing platforms detected all seven clinically reported tier 1 actionable mutations, an additional three (7%) tier 1 mutations, six (15%) tier 2–3 mutations, and biomarkers of potential immunotherapy benefit (tumor mutation burden and microsatellite instability). As expected, WGS was more suited for the detection and discovery of emerging novel biomarkers of treatment response. WGS could be performed in half of all EBUS-TBNA aspirates, which points to the enormous potential of EBUS-TBNA as source material for large, well-curated discovery-based studies for novel and more effective predictors of treatment response. Comprehensive panel sequencing is possible in the vast majority of fresh EBUS-TBNA aspirates and enhances the detection of actionable mutations over current clinical testing. Full article
(This article belongs to the Special Issue Genetic, Epigenetic, and Epitranscriptomic Changes in Lung Cancer)
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11 pages, 846 KiB  
Article
Clinical Characteristics, Response to Platinum-Based Chemotherapy and Poly (Adenosine Phosphate-Ribose) Polymerase Inhibitors in Advanced Lung Cancer Patients Harboring BRCA Mutations
by Johnathan Arnon, Michael Tabi, Yakir Rottenberg, Aviad Zick, Philip Blumenfeld, Tamar Hamburger, Eli Pikarsky, Eti Avraham, Leeby Levine, Aron Popovtzer, Tamar Yablonski-Peretz, Luna Kadouri and Hovav Nechushtan
Cancers 2023, 15(19), 4733; https://doi.org/10.3390/cancers15194733 - 26 Sep 2023
Cited by 1 | Viewed by 969
Abstract
The oncogenic role and clinical relevance of BRCA mutations in NSCLC remain unclear. We aim to evaluate the characteristics and clinical outcomes of patients with NSCLC harboring BRCA mutations treated at Hadassah Medical Center (HMC). We retrospectively assessed all patients with advanced NSCLC [...] Read more.
The oncogenic role and clinical relevance of BRCA mutations in NSCLC remain unclear. We aim to evaluate the characteristics and clinical outcomes of patients with NSCLC harboring BRCA mutations treated at Hadassah Medical Center (HMC). We retrospectively assessed all patients with advanced NSCLC who underwent next-generation sequencing (NGS) and were found to have pathogenic somatic BRCA mutations (p-BRCA). We compared clinical outcomes in NSCLC patients with wild-type BRCA (wt-BRCA) matched by age, stage, gender, smoking, PDL-1 and driver mutations. Between 2015 and 2022, we evaluated 598 patients with advanced NSCLC using NGS and found 26 patients with p-BRCA, of whom 17 (65.4%) were carriers of germline BRCA variants and represented 1% of all BRCA carriers HMC. The median age of diagnosis was 67 years old (40–78), 13 patients (50%) had a history of smoking and 9 patients (34.6%) had additional driver mutations (EGFR, ALK, BRAF, MET or ERBB2). Objective response rate and median progression-free survival (PFS) for first-line platinum-based chemotherapy in the p-BRCA group compared to wt-BRCA controls were 72.2% and 16 months (CI 95%, 5–22), compared to 47.4% and 7 months (CI 95%, 5–9), respectively, and HR for PFS was 0.41 (CI 95%, 0.17–0.97). Six patients in the p-BRCA group were treated with advanced-line poly (adenosine-phosphate-ribose) polymerase inhibitors (PARPi), with a durable response observed in four patients (66%). In this cohort, patients with NSCLC harboring p-BRCA exhibit high-sensitivity PARPi and a prolonged response to platinum, suggesting some oncogenic role for BRCA mutations in NSCLC. The results support further prospective trials of the treatment of NSCLC harboring p-BRCA with PARPi. Full article
(This article belongs to the Special Issue Genetic, Epigenetic, and Epitranscriptomic Changes in Lung Cancer)
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