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Targeted Anticancer Therapies and Precision Medicine in Cancer: A PLOS Cross-Journal Call for Papers

PLOS ONE Guest Editors –

Andrew Cherniack

Anette Duensing

Steven Gray

Sunil Krishnan

Chandan Kumar-Sinha

Gayle Woloschak

PLOS Computational Biology Guest Editors –

 
 

Aaron Goldman

Feixiong Cheng

Anna Panchenko

Benjamin Ribba

Igor Berezovsky

– Call for papers for a PLOS Collection –

 

According to the World Health Organization, an estimated 9.6 million people died from cancer in 2018, making cancer the second-leading cause of death worldwide (https://doi.org/10.3322/caac.21492). Although advances in cancer research over the past decades have shed light on how normal cells undergo oncogenic transformation and have spurred the development of targeted therapeutics, there is clearly still an unmet need to improve cancer detection and bring new treatment options to patients.

 

To address this, PLOS ONE and PLOS Computational Biology are launching a call for papers describing targeted therapies and precision medicine in cancer. Manuscripts submitted to this call and accepted for publication will be published in a dedicated Collection curated by a panel of Guest Editors.

 

The scope of this call for papers encompasses four areas:

 

​1) Identification and classification of driver genes and somatic alterations

 

Precision medicine approaches aimed at specifically eliminating cells harboring mutant genes hold great therapeutic promise. Therefore, identifying driver genes is critically important for the development of successful anti-cancer therapies. Furthermore, cancer genomics studies over the last decade have defined numerous somatic aberrations in driver genes, but functional characterization of these represents a major bottleneck in translating cancer genomics findings into precision therapy approaches. Studies have also identified a number of pathogenic germline variants in non-familial cancers, the functional characterization of which might help identify novel therapeutic avenues for intervention.

 

We encourage the submission of manuscripts that describe research in these areas, including:

 

  • The identification or classification of driver genes
  • Algorithms for predicting driver genes
  • Functional characterization of variants of unknown significance

Methodological papers describing new sequencing approaches or applications will also be considered.

 

​2) Target and drug discovery 

 

Targeting oncogenic kinases has been a major focus of cancer therapeutic drug development. However, drugs targeting other classes of proteins, such as proteasome inhibitors or HDAC inhibitors, have also shown clinical promise for treating certain cancers. In addition, there is increasing evidence of ‘undruggable’ genomic drivers, such as alterations in epigenetic modifiers or genes involved in cellular metabolism. We welcome manuscripts reporting research in all areas of target and drug discovery, including:

 

  • Computational, chemoinformatic and/or machine learning approaches to finding ‘druggable’ targets as well as identifying novel compounds
  • New approaches to target ‘undruggable’ cancer drivers
  • Small molecule or peptide screens
  • Research into the targets and mechanism of action of anti-cancer drugs
  • The activity of new anti-cancer therapeutics
  • Design of novel target inactivation methods (PROTACs, targeting protein-protein interactions, antibody-drug conjugates, nanoparticles, etc.)
  • Repurposing of existing drugs for new indications

 

We will also consider submissions reporting the development or use of experimental models to test precision medicine approaches, including organoid culture or ex vivo culture, genetically engineered mouse models, CRISPR screens and other approaches.

 

​3) Mechanisms of drug resistance

 

The approval of tamoxifen for treating ER-positive breast cancer nearly 50 years ago ushered in a new era of precision medicine. Dozens of selective inhibitors have since been approved for the treatment of many different forms of cancer and have shown astonishing clinical effects. Unfortunately, a large proportion of tumor cells rapidly acquire resistance to these therapies, limiting the effectiveness of the treatments and gradually decreasing patients’ therapeutic options. As part of this call for papers, we are soliciting manuscripts reporting research into the mechanisms of drug resistance and potential strategies for circumventing drug resistance.

 

​4) Early detection and screening 

 

The advances in cancer research and therapies mean that many people who develop cancer can now be completely cured. However, a patient’s prognosis often depends on the stage at which a tumor is detected. Therefore, early detection is an important strategy to limit cancer deaths worldwide, to decrease treatment costs and increase quality of life. We encourage submission of manuscripts describing strategies to detect cancer at its earliest stages, from identifying circulating biomarkers to developing imaging technologies. We also welcome submissions on monitoring the response to therapy through sensitive, non-invasive detection of cancer cells or cell-free DNA/RNA in patient samples, as well as submissions that bring a methodological focus to detection and screening.

 

Articles must be submitted by 21 June 2019. Accepted submissions will be published in a Targeted Anticancer Therapies and Precision Medicine in Cancer Collection in November 2019.

 
 

Meet the Editors

Andrew Cherniack

Guest Editor, PLOS ONE

Andrew Cherniack is a group leader in the Cancer Program at the Broad Institute of MIT and Harvard as a member of the Meyerson Lab. He led the Broad Institute’s effort to analyze somatic DNA copy number alterations for The Cancer Genome Atlas (TCGA) and is now co-principal investigator of the Broad Institute’s copy number Genome Data Analysis Center for the National Cancer Institute’s Genomic Data Analysis Network (GDAN). He also leads the oncoming effort to identify new cancer therapeutic targets for the partnership with Bayer. Prior to joining the Broad Institute in 2010, Dr. Cherniack worked in both academia and industry, with a 9-year tenure at the Abbott Bioresearch Center following a similar time period in the Program in Molecular Medicine at UMass Medical School, where he was a postdoctoral researcher and a research assistant professor. Dr. Cherniack holds a Ph.D. in molecular genetics from Ohio State University and a B.A. in biology from the University of Pennsylvania.

 

Anette Duensing

Guest Editor, PLOS ONE

Anette Duensing is an Assistant Professor of Pathology at the University of Pittsburgh School of Medicine and Member of the Cancer Therapeutics Program at the University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center. Dr. Duensing’s research focuses on bone and soft tissue sarcomas with the goal of identifying novel therapeutic approaches that target the underlying molecular biology of these malignancies. Her special interest and expertise are in gastrointestinal stromal tumors (GISTs), a sarcoma characterized by mutations in the KIT or PDGFRA receptor tyrosine kinases and the first solid tumor entity that was successfully treated with small molecule kinase inhibitors. Dr. Duensing holds an M.D. degree from the University of Hannover School of Medicine, Germany, and was a research scholar of the Dr. Mildred Scheel Stiftung für Krebsforschung (German Cancer Aid/Deutsche Krebshilfe) at Brigham and Women's Hospital, Harvard Medical School. She is the recipient of an AACR Scholar-in-Training Award (AACR-AstraZeneca), a Young Investigator Award from The Liddy Shriver Sarcoma Initiative, a UPCI Junior Scholar Award, a Jeroen Pit Science Award, a Research Award from the GIST Group Switzerland and was named Hillman Fellow for Innovative Cancer Research. Dr. Duensing is co-founder and leader of the Pittsburgh Sarcoma Research Collaborative (PSaRC), a highly translational, interdisciplinary sarcoma research program. She is also affiliated with the Department of Urology at the University of Heidelberg, Germany. Dr. Duensing is an Academic Editor for PLOS ONE and author of nearly 70 original articles, reviews and book chapters.

 

Steven G. Gray

Guest Editor, PLOS ONE

Steven Gray graduated from Trinity College Dublin in 1992. He joined the laboratory of Tomas J. Ekström at the Karolinska Institute (Sweden) in 1996 and received his PhD in 2000. He moved to the Van Andel Research Institute in Michigan, USA where he continued his studies on the therapeutic potential of histone deacetylase inhibitors in the treatment of cancer. He also spent time as a visiting fellow at Harvard Medical School, Boston working on epigenetic therapies for neurodegenerative disease. Returning to Europe, Dr. Gray spent some time at the German Cancer Research Centre (DKFZ - Heidelberg), and subsequently moved to Copenhagen to work for Novo Nordisk as part of the research team of Prof Pierre De Meyts at the Hagedorn Research Institute working on epigenetic mechanisms underpinning diabetes pathogenesis. Dr. Gray is currently a senior clinical scientist at St James's Hospital at the Thoracic Oncology Research Group at St. James's Hospital. He holds adjunct positions at both Trinity College Dublin (senior clinical lecturer with the Dept. of Clinical Medicine), and at Technical University Dublin (adjunct senior lecturer, School of Biology - DIT). Dr. Gray has published over 100 peer-reviewed articles, 15 book chapters and has edited 1 book. Research in Dr Gray’s laboratory focuses on Receptor Tyrosine Kinases as potential therapeutic targets for the treatment of mesothelioma; epigenetic mechanisms underpinning drug resistance in lung cancer; targeting epigenetic readers, writers and erasers for the treatment of mesothelioma and thoracic malignancy; circulating tumour cells; and non-coding RNA repertoires in mesothelioma and thoracic malignancy.

 

Sunil Krishnan

Guest Editor, PLOS ONE

Sunil Krishnan is the Director of the Center for Radiation Oncology Research and the John E. and Dorothy J. Harris Professor of Gastrointestinal Cancer in the department of Radiation Oncology at MD Anderson Cancer Center. He received his medical degree from Christian Medical College, Vellore, India and completed a radiation oncology residency at Mayo Clinic, Rochester, Minnesota. In the clinic, he treats patients with hepatobiliary, pancreatic and rectal tumors with radiation therapy. His laboratory has developed new strategies and tools to define the roles and mechanisms of radiation sensitization with gold nanoparticles, chemotherapeutics, biologics and botanicals. Dr. Krishnan serves as the co-chair of the gastrointestinal scientific program committee of ASTRO, co-chair of the gastrointestinal translational research program of RTOG, consultant to the IAEA for rectal and liver cancers, chair of the NCI pancreatic cancer radiotherapy working group, and Fellow of the American College of Physicians. He has co-authored over 200 peer-reviewed scientific publications, co-authored 17 book chapters, and co-edited 3 books.

 

Chandan Kumar-Sinha

Guest Editor, PLOS ONE

Chandan Kumar-Sinha is a Research Assistant Professor in the Department of Pathology at the University of Michigan. He obtained Bachelor's degree in Zoology from Delhi University, Master's in Biotechnology from Madurai Kamraj University, and PhD in Plant Molecular Biology from Indian Institute of Science. He completed a Postdoctoral Fellowship at the Department of Pathology, University of Michigan, where he worked on genomic profiling of cancers. Thereafter, he joined the Advanced Center for Treatment, Research and Education in Cancer in India as a faculty member. After establishing a cancer genomics group there, he moved back to the University of Michigan to pursue translational cancer research. Dr. Kumar-Sinha’s current research involves integrative clinical sequencing using high-throughput genome and transcriptome analyses to inform precision oncology. He has authored 50 peer-reviewed publications, one book chapter, and is named co-inventor on a patent.

 

Gayle E. Woloschak

Guest Editor, PLOS ONE

Gayle Woloschak is Professor of Radiation Oncology, Radiology, and Cell and Molecular Biology in the Feinberg School of Medicine, Northwestern University.  Dr. Woloschak received her Ph.D. in Medical Sciences from the University of Toledo (Medical College of Ohio). She did her postdoctoral training at the Mayo Clinic, and then moved to Argonne National Laboratory until 2001. Her scientific interests are predominantly in the areas of molecular biology, radiation biology, and nanotechnology studies, and she has authored over 200 papers. She is a member of the National Council on Radiation Protection, the International Commission on Radiation Protection and numerous other committees and also serves on the US delegation to the United National Scientific Committee on the Effects of Atomic Radiation.

 

Aaron Goldman

Guest Editor, PLOS Computational Biology

Aaron Goldman is a faculty member in the Department of Medicine at Harvard Medical School as well as leading the research efforts at a biotechnology start-up company, Mitra Biotech, which focuses on personalized cancer medicine. The goal of their research is to interrogate and interpret how the diversity of cells within a tumor (stroma, immune cells, tumor cells) contribute to drug response and resistance. They leverage a number of tools to achieve this goal including ex-vivo human tumor models, computational biology, mathematical models and nanotechnology, which inspire novel therapeutic approaches for cancer.

 
 

Feixiong Cheng

Guest Editor, PLOS Computational Biology

Feixiong Cheng, PhD, is the Assistant Professor of the Department of Molecular Medicine at the Cleveland Clinic Lerner College of Medicine (CCLCM) of Case Western Reserve University, an Assistant Staff of the Genomic Medicine Institute of the Cleveland Clinic Foundation, and a full faculty member of Case Comprehensive Cancer Center at the Case Western Reserve University School of Medicine.
Dr. Cheng is recognized a leading computational systems biologist by training, with expertise in analyzing, visualizing, and mining data from real world (e.g., electronic health records and health care claims) and experiments that profile the molecular states of human cells and tissues by interactomics, genomics, transcriptomics, proteomics, radiomics, and metabolomics for drug discovery and patient care. The primary goal of his lab is to combine tools from multi-omics, network medicine, bioinformatics, computational biology, chemical biology, and experimental pharmacology and systems biology assays (e.g., single cell sequencing), to address the challenging questions toward understanding of multiple complex diseases (e.g., cancer, cardio-oncology, and pulmonary vascular disease), which could have a major impact in identifying novel real-world data-driven diagnostic biomarkers and therapeutic targets for precision medicine. Dr. Cheng has over 10 years of systems biology, pharmacogenomics, drug discovery and development, computational biology, and bioinformatics research experiences, and has authored over 100 papers and several U.S. patents. Dr. Cheng has received several awards, including NIH Pathway to Independence Award (K99/R00) and 2015 Vanderbilt Postdoc of the Year Honorable mention.

 

Anna Panchenko 

Guest Editor, PLOS Computational Biology

Anna Panchenko received her B.S. and Ph.D. from the Biophysics Department of Moscow State University in Russia, where she studied protein dynamics by Mossbauer spectroscopy. She was a post-doctoral fellow at the School of Chemical Science of the University of Illinois at Urbana-Champaign and later joined National Center for Biotechnology Information, NLM, NIH as an Intramural Research Fellow. Currently she is a Lead Scientist in the Computational Biology Branch at NCBI and she studies biomolecule interaction networks on both molecular and systems levels and how network perturbation can lead to diseases including cancer. Her goal is to find driving events, understand the molecular mechanisms of their action, link genotype with phenotype and decipher the relative roles of mutagenesis and selection in cancer progression. She is an author of several webservers and databases, and has authored more than ninety articles in scientific journals and one book on protein-protein interactions.

 

Benjamin Ribba 

Guest Editor, PLOS Computational Biology

Ben Ribba holds a master’s degree in applied mathematics and a PhD in biomathematics from the Department of Clinical Pharmacology of the University of Lyon, France. Among Dr. Ribba’s achievements is the application of a wide range of disease models for the understanding and analysis of tumor growth and response to drugs, leading to dose optimization. Dr. Ribba is author of more than 50 articles in peer-reviewed journals in the field of computational modeling in oncology. 
 
After eight years of academic research at Inria in France, Dr. Ribba joined Roche in 2015 in Basel, Switzerland. He is leading Translational Modeling and Simulation for early research and development. 

 

 

Igor Berezovsky 

Guest Editor, PLOS Computational Biology

Igor N. Berezovsky is a Principal Investigator at the Bioinformatics Institute of the Agency for Science, Technology, and research (BII/A*STAR, Singapore) and Adjunct Associate Professor at the Department of Biological Sciences in the Faculty of Science of the National University of Singapore (DBS/NUS). He has MSc in physics (1993) from Moscow Engineering Physics Institute and PhD in biophysics (1997) from Moscow Institute of Physics and Technology. After postdoctoral research at Weizmann Institute of Science (1999-2002) and Harvard University (2003-2006), Igor started his independent scientific career as a senior scientist/group leader at Bergen Center for Computational Science (2007), University of Bergen (Norway). He moved to Singapore and joined Bioinformatics Institute/A*STAR and DBS/NUS in 2014. Dr. Berezovsky gained recognition for the discovery of basic units of protein structure and function, closed loops and elementary functional loops, which provided a foundation for his works on the emergence and evolution of protein enzymatic function. He described a role of positive and negative design in protein stability and published a series of fundamental works on the physics and evolution of thermophilic adaptation and molecular mechanisms of adaptation to extreme environments. Currently, Dr. Berezovsky works on theoretical concepts of allostery with the goal to take protein activity under comprehensive allosteric control by different external perturbations and to advance computational design of allosteric drugs. Biophysics of chromatin and epigenetic regulation of the genome expression is a new area of Igor’s scientific interests.

 

 

Publishing Process

We aim to be as transparent as possible about our publishing and peer review processes. Papers submitted to PLOS ONE or PLOS Computational Biology and under consideration for the Targeted Anticancer Therapies and Precision Medicine in Cancer will be specially handled by hand-selected active researchers from our Editorial Boards working in anticancer therapy research.

Submission Instructions

Articles must be submitted by 21 June 2019. 

Are you ready to submit or want to learn more about how the submission process works? To make it as easy as possible for our communities, we have all of our submission instructions posted online. Click here for submission instructions for PLOS ONE and PLOS Computational Biology. If there are any details you can’t find, please email us at ONECalls@plos.org. In your email, please include the name of the journal that you are enquiring about.

When submitting to the Collection, select the Article Type “Research Article” and enter “Targeted Anticancer Therapies” in the Collections field in the Additional Information section of the submission form. Please also specify that you are submitting to the Collection “Targeted Anticancer Therapies and Precision Medicine in Cancer” in your cover letter.

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