Instructions

Here you will find detailed instructions on how to structure your paper and what to include to fulfill our publication requirements. Below is the list of contents of our guidelines; you may obviously jump directly to the desired section by clicking on it, though we urge first-time Clinical Cancer Epigenetics authors to read our entire guidelines throughout as they often substantially differ from those of most journals.

For all manuscript types, please submit your manuscript and each Table separately as text files, if possible in a Word ‘.docx’ format. The preferred Figure file format is AI, PSD, SVG, TIFF, or RAW in RGB 8bit and 150-300 dpi resolution. Preferred graphic (charts) file format is SVG or EPS. Please write to us at manuscript@ces.b2sg.org if you need help formatting your figures or tables.

1. Manuscript types:
1.1. Research Articles
1.2. Cutting-edge Communications
1.3. Systematic Reviews & Metaanalyses
1.4. Reviews
1.5. Mini-reviews
1.6. New & Noteworthy
1.7. Editorials

2. Additional Information:
2.1. Copyrights
2.2. Editorial process
2.3. Language editing
2.4. Selection of Reviewers
2.5. Final assignment to a CES journal
2.6. Publication-associated fees
2.7. Open access

1.1. Research Articles: RA report novel, never published research, wherein data collectively present a relatively large and coherent picture of a well defined clinical application or outcome. With the exception of the Abstract (limited to 200 words), the length of the text and number of Figures, Tables and References are unlimited. That being said, please do keep in mind that a focused and succinctly formulated message has a much better chance of being read and remembered. As the late German composer Johannes Brahms reportedly once said: Es ist nicht schwer, zu komponieren. Aber es ist fabelhaft schwer, die überflüssigen Noten unter den Tisch fallen zu lassen (It is not hard to compose, but what is fabulously hard is to leave out -under the table- the superfluous notes). Similarly, too many Figures and Tables for too little text would throw off the layout and esthetics of the paper, rendering it cumbersome to read. Keeping these considerations in mind would also go a long way to supporting the FAIR Act to authors, reviewers, and readers alike.

Manuscripts in this category should include the following:

1.1.1. Cover Page: This is the first page(s) of the manuscript; it should include:

• Article type: please state here the type of manuscript you are submitting (e.g. Research Article, Review, etc…).
• Title: states the main finding of the study; active voice preferred. Maximum 175 characters including spaces, though the shorter the better.
• Running title: title is reduced here to a news headline; passive voice is acceptable. Maximum 65 characters including spaces.
• Authors: list all authors with first (given) name first, followed by middle initial or initials, followed by last name (surname), and finally a number in superscript referring to the affiliation; e.g. Jane M. Smith¹ and John M.C. Smith². Authors with multiple affiliations should indicate that fact with multiple numbers in superscript; e.g. John M.C. Smith^1,2 or Jane M. Smith^1-3.
• Affiliation & contact information: preceded by the number in superscript (with no space), please list here for each author in this order: research institution or hospital, department, when applicable laboratory name or division, street and street number, Zip or city code or equivalent, professional Email address or addresses, and professional telephone number or numbers.
• Corresponding author or authors: a maximum of two corresponding authors is allowed. Corresponding author(s) should be marked by an asterisk; e.g. Jane M. Smith^1*. Traditionally, these are either the last, first, or before the last authors. Corresponding author(s) need not enter here again their affiliation or contact info.
• Conflict of interest: authors state here whether they have any conflict of interest that pertains to the study. The corresponding author is also required to fill and sign on behalf of all authors the Conflict of Interest Statement form which will be emailed to the corresponding author(s). Though the corresponding author(s) is required to clear the Conflict of Interest Statement check list with all co-authors, only the corresponding author(s) signature(s) is/are required.
• Number of Figures, Tables, and Videos: here should be listed the number of figures, tables, and video, both regular and supplemental, that are associated to the manuscript. This is to allow us to double-check that no data were inadvertently left out of the submission.
  

1.1.2. Abstract: should not be structured but must include, in this order: an introduction delineating current knowledge relevant to the topic at hand, the void in knowledge that is addressed in the paper, how was the problematic addressed including any novel methodologies, followed by the most important findings and conclusions. Maximal length is 200 words, and references are not permitted. Recurrent technical terms should be spelled only once, followed by an abbreviation in brackets, and referred to thereafter only in the abbreviated form. Common-knowledge abbreviations should not be defined (e.g. DNA, RNA, miRNA, lncRNA) and presented only in the abbreviated form. Abbreviations are allowed only for recurrent terminologies, except for abbreviations that can help indexation of the paper and in literature search. For example, both gastroesophageal reflux disease and its GERD abbreviation, or histone deacetylase and the HDAC abbreviation should be mentioned, even if they are mentioned only once in the Abstract.

1.1.3. Main Implications: this section should highlight in one or two brief sentences the main immediate and future implications of the findings to the field(s). This section should not restate the conclusions as stated in the Abstract or in the “Conclusions” section of the manuscript.

1.1.4. Introduction: this section is used to set the stage for the study by introducing both the topic in general and the problem at hand. The authors should clearly delineate here the state of affairs for the problem in question (identify the most recent developments and the most pressing unresolved questions). The authors should also use the Introduction section to present the rationale of the study: what inspired them to doing the study, what strategies they employed to tackle unanswered questions, and why is the current study relevant to epigenetics and cancer. The Introduction, however, should not be used to extensively review or discuss the field.

1.1.5. Materials & Methods:

General considerations: Following the stipulations of our publisher, the B² Scientific Group, we do our utmost to provide our readers with a Materials & Methods section that is as detailed as possible as to promote transparency and significantly improve reproducibility. It should be noted, therefore, that we put much more emphasis on the M&M section than most (if not all) journals, and authors are strongly urged to pay particular attention to this section. The M&M section should be broken down into paragraphs with numbered headers defining the section being covered. Examples of headers include Animal experiments, Assays (e.g. FACS, GWAS, PCR, etc…), Biological & chemical reagents, Bioinformatics & Omics analyses, Biomarker study design, Biophysical methods, Cell lines & cell culture, Clinical assessments & procedures, Clinical trial phase I/II/III/IV design, Gene nomenclature, Histopathology & Immunohistochemistry, Patients & cohorts, Pharmacokinetics, Statistical analyses, Surgical procedures, Toxicity studies, and Treatment protocols.

Reagent guidelines: All reagents must be accompanied with the manufacturer’s name, catalog number, and lot number. For non-commercial reagents, references of published articles in which reagents’ synthesis or production and characterization are well described should be cited. In case none exists, a detailed description of the reagent (synthesis, production, purification, purity, stereoisomer composition, characterization, specificity, etc…) should be included either in the M&M or Results section, as deemed appropriate by the authors. In case 10 or more reagents are reported, please list in a Table the manufacturer’s name, catalog number, lot number, and any other salient reagent’s characteristics or information (e.g. nature of solvent, solute’s concentration of stock solution, storage temperature, etc…). In this case, it is not necessary to refer to this Table in the Results section.

Cell line authentication guidelines: The source of cell lines, commercial or otherwise, needs to be disclosed. Authors also need to separately provide certificates of authentication for all cell lines used, and certificates may not be older than six months at the date of the last experiment. Following ATCC ASN-0002-2011 guidelines, short tandem repeat (STR) cell line profiling is the preferred cell line authentication method by all B²SG journals. For human cells, this consists of profiling the gender discriminant AMELX gene and the eight highly polymorphic markers CSF1PO, D5S818, D13S317, D7S820, D16S539, TH01, TPOX, and vWA. Example of companies that provide cell authentication services may be found here. You may also check here whether your cell line is listed by the International Cell Line Authentication Committee among the nearly 500 cell lines whose identity was found to be false. For example, the MDA-MB-435 cell line, which at the time of this writing was published in more than 700 articles as an in vitro model for breast carcinoma, is in fact a melanoma cell line.

Gene Nomenclature guidelines: Authors are free to use whichever gene nomenclature they wish. To avoid gene symbol or species ambiguity, however, papers should alphabetically list in this section the symbols of all genes experimentally manipulated or modulated, along with their unique NCBI identification number (Reference: Gene 491: 103-109, 2012). In case 10 or more genes are reported, list all genes and NCBI gene IDs in a Table. It is not necessary to refer to this Table in the Results section. The Gene Nomenclature guidelines apply only to genes actively investigated in the study and do not concern genes that are merely mentioned in the paper, nor do they apply to the large number of genes uncovered in bioinformatic and OMIC analyses.

EXACT guidelines: In accordance with the B² Scientific Group EXACT guidelines, it is the Cancer Epigenetics Society policy to make protocols, data, and reagents as accessible and transparent as possible to speed up knowledge and technology exchange, and to improve reproducibility and clinical applicability of cancer-related findings. Authors publishing with us do so with the tacit agreement that they are willing to make non-commercially available reagents (such as antibodies, cell lines, plasmids, etc…) immediately available to academic and other nonprofit organizations. The sharing of reagents with commercial entities, however, is done at the sole discretion of the authors, and authors are released from any material sharing obligation should the reagent already be deposited in an active public or commercial repository (e.g. ATCC for cell lines, Jackson laboratory for mouse strains, or Bloomington Drosophila Stock Center at Indiana University for fly stocks). At any rate, the scientist requesting the reagent shall incur any reasonable shipping, packaging and customs-related costs, and must comply with a reasonably drafted Material Transfer Agreement. Any unpublished DNA and protein-related findings (e.g. new genes or proteins, new crystallographic structures, new genomic, proteomic, or epigenomic data) must be deposited in appropriate public repositories, and accession numbers included in the final version of the manuscript, before accepted articles are published. So while submission is not contingent upon deposit of data in public repositories, publication is. We do not recommend any particular repositories to which data must be contributed to, as long as it these are accessible with no restriction and at no cost to the public. Finally, EXACT guidelines stipulate that the M&M section describes experiments in enough details to allow experienced investigators to easily recapitulate the experiments and results. These for example include minute details such as the amount of DNA and cycling conditions used in PCR reactions or the amount of RNA used in reverse transcription reactions, the number, intensity and duration of sonication cycles in chromatin preparations, which cell line passages were used, and how were cells passaged (e.g. trypsinized or mechanically detached), etc… For the current list of required technical details to be provided, please check the EXACT guidelines & Form, v0.1, valid for submissions made on or before September 1st, 2016. An updated version of the EXACT guidelines Form will be made available here for submissions made after September 1st, 2016.

International Committee of Medical Journal Editors (ICMJE) guidelines: There currently are six ICMJE-approved registries for clinical trials and Clinical Cancer Epigenetics requires that any clinical trial submitted for publication be recorded at one of the six registries prior to publication. These are the Australian New Zealand Clinical Trials Registry (ANZCTR), EU Clinical Trials Register/EudraCT database (EudraCT), the International Standard Randomised Controlled Trial Number (ISRCTN) registry, Japan’s University hospital Medical Information Network Clinical Trials Registry (UMIN-CTR), Netherlands Trial Register (NTR), and the National Institutes of Health (NIH) Clinical Trials registry (ClinicalTrials.gov). All submitted manuscripts are required to include clinical trial registration numbers.

Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines: Clinical Cancer Epigenetics requires a completed PRISMA checklist and flow diagram as a condition of submission when reporting findings from systematic reviews and metaanalyses. Templates for these can be found here at the PRISMA website which also describes several PRISMA checklist extensions for different designs and types of data beyond conventional systematic reviews evaluating randomized trials. At minimum, the submitted manuscript should report the content addressed by each item of the checklist.

1.1.6. Results & Discussion: this section should be broken down into paragraphs with headers summarizing the main findings. Each Result should be immediately discussed (there are no separate Results and Discussion sections), leading to a general discussion at the end of the Results & Discussion section. Any speculative analysis also belongs to this section: contrary to most journals, not only do we allow, we in fact encourage hypothetical assertions as long as they are supported by solid rationale and reasoning and are clearly marked as conjectures and written in the conditional tense. These are meant to stimulate ‘soft’ lines of thinking and inquiries outside of the comfort zone and safety net provided by hard data. These, however, should not be included in the Abstract and do not need to be discussed in the section below.

1.1.7. Reproducibility & Limitations Considerations: this section is meant to assist the reader to objectively and critically appraise the findings and conclusions, and to guide predictions on how likely are the data to be of general applicability should one conduct a related study with different cell lines, reagents, or patient cohorts. Accordingly, the authors should detail here any considerations that might limit the scope of the findings or prediction of reproducibility. These may include any number of technical considerations such as the number of cell lines used or their representativeness of the pathophysiological processes investigated: for example, studying mostly p53 mutant cell lines, because there are the only ones available, as a model system for a cancer that is mostly wild-type for p53 would require a call for caution in generalizing the conclusions of the study. Similarly, xenograft mouse models of tumors known to be highly dependent in patients on anatomical location or tumor microenvironment require a clear justification of the model and a statement to its limitations. In patient-centric studies, limitations may concern cohort size and statistical power, as well as any biases including those pertaining to gender, age, race, or geographical or socioeconomic background. Limitations may also concern cancers known to be genetically and/or epigenetically highly heterogeneous, which may render even large cohorts underpowered (whereby large cohorts are in fact heterogeneous collections of smaller -more- homogeneous cohorts; Reference: Cancer Inform. 14: 131-139, 2015). In studies using drugs (e.g. inhibitors) or miRNAs, (broad) target specificities need to be addressed here (e.g. use of FDA-approved MAO inhibitors to non-specifically inhibit LSD1/KDM1A). Studies that do not provide controls such as wobble mutants impervious to the tested miRNAs, or peptide-blocking antibodies to stringently verify antibody specificity, need to discuss these issues here too. Other inferences or assumptions (outside of hypotheses that are clearly stated as such) made by the authors that are backed only with little data should also be briefly discussed here. Finally, should the authors have received funding from the industry relevant to the study, the role of the funding industry in designing the study, analyzing and interpreting data (and particularly in censoring datapoints, experimental subsets, or patient groups), and/or supporting publication fees should be discussed here. In particular, the authors need to discuss how objectivity was maintained in spite of the commercial interests of the for-profit funding body.

1.1.8. Conclusions & Perspectives: this section should summarize the salient findings and their possible impact; it is limited to 150 words.

1.1.9. Author contributions: authors’ exact contribution should be listed here. There is no specific layout on how to present the contributions as these differ from one paper to another. This being said, this section should at the very least disclose the author or authors who first conceived the study (that first shining light bulb of an idea), those that designed it, those that initiated it, those that conducted the experiments or analyses, those who composed the graphics, illustrations, and/or Tables, and those who wrote the manuscript. If the illustrations were drawn by a non-scientific support staff not listed among the authors, these should be listed in the Acknowledgments section.

1.1.10. Patents & Awards: Any awards that pertain to this work should also be listed here including the name of the recipient or recipients (first name, middle name initial(s), last name), the award-giving organization, the date the award was given, and a link to the webpage disclosing the award. Similarly, any patents relevant to this submitted work should be listed here along with a link to the appropriate webpage or webpages.

1.1.11. Acknowledgments and/or Funding: here should be listed all people (full name, research institution, city, country) who contributed to the work and paper, but not sufficiently to be considered for authorship. These may include those who provided technical support, contributed previously published animal models, cell lines, or biological and chemical reagents, those who critically reviewed the paper or communicated unpublished results, as well as those who hosted research in their lab but had otherwise limited involvement in the study. Funding sources, grants, scholarships, Biotech or Pharmaceutical company-sponsored experiments or trials (including donation of drugs), etc… that pertain to the work should be cited here. In all cases, the grant, funding, or sponsoring entity should be named, and the grant or contract number should be cited. If this work (or parts of it) was previously presented at a scientific meeting, this should also be mentioned here (List of all authors: first name, middle name initial(s), last name); title of the presentation and abstract number; name, place, and date of the meeting; whether it was a talk or a poster).

1.1.12. Figure & Table Legend: Legends are included in the manuscript and not in the Figure or Table files. Legends must define all abbreviations (even if they are already defined in the main text) and contain enough information so that a Figure or Table may be read as a stand-alone element that can be understood independently of the text. Each Figure and Table requires a title (style: bold) that states the main finding or findings, whereas the rest of the legend is written in plain style. In case of multiple panels, the legend should be subdivided in subsections preceded by the letters identifying the Panels (A., B., C., etc…, style: bold). Graphics should have X and Y axes clearly defined in the Figure, not in the legend.

1.1.13. Figures, Tables, and Videos: each Figure, Table, or video should be submitted a separate file. There is no limit to the number of Figures, Tables, and videos that accompany the manuscripts. However, please do keep in mind that too many Figures and Tables for too little text will throw off the layout and esthetics of the paper, rendering it cumbersome to read. Figure and Tables should be numbered consecutively using Arabic numbers following the sequence in which they appear in the text. Number of panels should be kept to a reasonable number so that all panels are legible once in print. The maximum width for single column Figures and Tables is 8.2 cm or 3.25 inches, and for two-column Figures and Tables 16.9 cm or 6.75 inches. Maximum Figure and Table length is 24 cm or 9.25 inches. Preferred Figure file format is SVG, PSD, AI, TIFF, or RAW. Resolution should be set to a minimum of 150 dpi and a maximum of 300 dpi. PSD and TIFF files should be ‘flattened’ prior to submission to reduce size. Preferred graphic file format is SVG, EPS, or PDF. In the latter, and in case the graph was created in Excel, the chart and the plot areas (which usually are either white or transparent) should be deleted in Excel before saving the graph as a PDF. Tables are preferably generated in Word as Tables lacking vertical lines (with the possible exception of the first column). Each Table should be submitted separately as a Word file. Whenever possible, Tables should fit in a single page in the Portrait, not Landscape format. If absolutely necessary, a maximum of two pages are allowed per Table. Longer Tables should be included as Supplementary Tables (see below). Figures are abbreviated in the text as Fig. 1. Acceptable videos formats are MOV, MP4, MPG, AVI, WMV, either in 4:3 (minimum resolution: 512×384) or 16:9 aspect ratio (minimum resolution: 512×288), and should be no longer than 5 minutes. Please contact us at info@ces.b2sg.org, Subject line: Video requirements, if you wish to submit a different video format, aspect ratio, or length.

1.1.14. Supplementary Figures, Tables, and Videos: these follow the same guidelines as the regular files, with the following exceptions. First, the title and full legend of each Supplementary file should be including both in the Legend section of the main text and in the file itself. Second, Supplementary Tables can have up to 5 pages. Supplementary files are abbreviated in the text; e.g. SFig. 1 for Supplementary Figure 1, STable 1 for Supplementary Table 1, and SVideo 1 for Supplementary Video 1.

1.1.15. References: in accordance with the FAIR act, we strongly encourage, and whenever possible enforce, that original research papers that first reported a finding, whatever how long ago, are cited as a reference. Referring to reviews should be limited to a strict minimum (generally no more than 10% of all citations, and only reviews that either critically analyze an entire research sub-field, or that for example summarize current knowledge of a family of proteins will be accepted as references). To accommodate this policy, the number of references is unlimited for all manuscript types. For Endnote users, the B²SG Endnote style file may be downloaded here[19]. Citations in all B²SG journals are presented numerically in the order of their appearance in the paper and list the last name first, followed by the first (and middle) initial(s), followed by a comma. All authors should be listed in citations that include up to 5 authors. Those with more than 5 authors should list the first 2 authors, followed by an italicized “et al.,” followed by the last two authors. Below is an example of a citation with more than 5 authors:

Banaszynski LA, Wen D, et al., Zheng D, Allis CD. Hira-dependent histone H3.3 deposition facilitates PRC2 recruitment at developmental loci in ES cells. Cell 155: 107-120, 2013.