2024 Cancer Biology Core Class
Topic outline
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Introduction to course and basic techniques applied in basic cancer research
In this session, the structure, aims and evaluation system for the course will be presented. Additionally, an overview of techniques used in basic cancer research will be provided, and general principles of experimental design will be discussed.
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Guided paper discussions.
Selected papers will include both preclinical (in vitro mechanistic data, in vivo treatment, patient-derived xenografts, etc) and clinical data.
Paper discussions will include description of figure panels included in the article by the scholars, who will be called by the class lead to provide context, describe the results in each figure, discuss the interpretation and implications of the results, suggest additional experiments or controls that would expand the implications of the results, and criticize the methodology, presentation and description of the results in the paper. The main goal of this activity is to “act as peer-reviewers” and train critical thinking.
The paper to be discussed in Session 2 is:
- Comprehensive molecular characterization of lung tumors implicates AKT and MYC signaling in adenocarcinoma to squamous cell transdifferentiation (Quintanal-Villalonga et al., Journal of Hematology and Oncology 2021, PMID: 34656143)
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Guided paper discussions.
Selected papers will include both preclinical (in vitro mechanistic data, in vivo treatment, patient-derived xenografts, etc) and clinical data.
Paper discussions will include description of figure panels included in the article by the scholars, who will be called by the class lead to provide context, describe the results in each figure, discuss the interpretation and implications of the results, suggest additional experiments or controls that would expand the implications of the results, and criticize the methodology, presentation and description of the results in the paper. The main goal of this activity is to “act as peer-reviewers” and train critical thinking.
The paper to be discussed in Session 3 is:
Inhibition of Karyopherin β1-Mediated Nuclear Import Disrupts Oncogenic Lineage-Defining Transcription Factor Activity in Small Cell Lung Cancer (Kelenis et al., Cancer Research 2022, PMID: 35748745)
*A pre-publication version prior to peer-review will be provided.
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Guided paper discussions.
Selected papers will include both preclinical (in vitro mechanistic data, in vivo treatment, patient-derived xenografts, etc) and clinical data.
Paper discussions will include description of figure panels included in the article by the scholars, who will be called by the class lead to provide context, describe the results in each figure, discuss the interpretation and implications of the results, suggest additional experiments or controls that would expand the implications of the results, and criticize the methodology, presentation and description of the results in the paper. The main goal of this activity is to “act as peer-reviewers” and train critical thinking.
The paper to be discussed in Session 4 is:
MYC Drives Progression of Small Cell Lung Cancer to a Variant Neuroendocrine Subtype with Vulnerability to Aurora Kinase Inhibition (Mollaoglu et al., Cancer Cell 2017, PMID: 28089889)
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Guided live research activity.
In this activity, scholars will be divided into two groups. A translational research project with preliminary data, common for both teams, will be shared with the scholars at the beginning of the session. As an example, the project could be "Study of the role of X gene in Y cancer type, and therapeutic implications".
The scholars will have time to design which next experiments they would like to conduct, and in 10-minute shifts, the class instructor will be visiting each of the teams providing the results for those experiments in real time (i.e., drawing plots, western blots, etc. on the white board). During the 10 minutes the class instructor is providing results for one team, the other team will have time to design a new set of experiments for their next shift. After 4-5 shifts, the scholars will be given time to structure their results into a consistent story, and then each team will present their "paper" to the other team. During that presentation the whole class will be discussing the approaches taken, missing experiments or controls that might be important for their story to be consistent, etc.
The main goal of this session is that the scholars get familiarized with experimental design and interpretation of results to answer a specific scientific question, in a guided environment.
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Mandatory lectures for the course:
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Recommended for review lectures:
The below two lectures are a supplementary material for the course. They are not mandatory, but strongly recommend as they are very important disciplines in cancer research currently.
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Take Home Assignments (67%).
Similar to the guided live research session, the scholars will be assigned a translational research project with preliminary data, in groups of 2-3 people, as an assignment. The scholars will have to design a small project (2 pages) addressing the scientific question posed (i.e. a light version of the research strategy section of a grant).
The project will have the following structure:
a. Background: A brief background (one paragraph, less than half a page) will be provided on the topic related to the research question, elaborating on the clinical and biological context to justify the experimental approaches suggested (i.e. “Gene X is overexpressed in different tumor types and has been associated to worse overall survival in patients. Even if gene X is overexpressed in a subset of lung tumors, to date the role of gene X has not been studied in the context of lung cancer”).
b. Hypothesis: A small paragraph (3-4 sentences) stating the overarching hypothesis defining the project (i.e., “We hypothesize that gene X may have an oncogenic role in a subset of patients with lung cancer in whose tumors gene X is overexpressed”).
c. Experimental approach: State the specific aims of the proposal, with a relatively detailed description of the experimental methodology proposed to approach each of the specific aims. Imagine any resource you may need (in vitro or in vivo model, clinical cohort, clinical tissue,…) is available for you to leverage, but make sure to describe the model with detail. Please justify why and how you are going to do what (i.e. “To study the role of X gene in two lung cancer cell lines, we will leverage CRISPR-Cas9 technology and overexpression viral vectors to generate isogenic cell lines with differential X gene expression, and we will perform tumorigencity surrogate assays (proliferation and soft agar”).
d. Potential pitfalls and alternative approaches: One short paragraph describing potential limitations or biases of the methods described, and proposing alternative approaches to perform the specific aims, particularly in the case where the previously described methods may be technically challenging (i.e., “If gene X knock out by CRISPR-Cas9 is not possible, as gene X might be essential and complete abrogation of its expression might be toxic, we will use siRNA technology as an alternative, to downregulate gene X expression”). This section can also be integrated in (c).
This activity will be divided in two parts:
- The project will be submitted (Deadline: September 13, 2023), and feedback will be provided by September 27, 2023, the latest.
- The scholars will have the chance to resubmit after addressing the comments provided (Deadline: October 11, 2023). This will make the activity a learning experience, rather than just an evaluation.
Although this is a non-for grade class, the project will be evaluated for the scholars to calibrate how well poised they are for graduate course. As a reference, a letter grade with a minimum of a B is would had been needed to pass the course, if it was for grade.
The main goals of this activity are that (1) the scholars face the blank page and individually perform the creative activity of designing a project on their own, and that (2) they hopefully learn from the feedback provided.
- The project will be submitted (Deadline: September 13, 2023), and feedback will be provided by September 27, 2023, the latest.
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View Make a submission
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View Make a submission
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