Topic outline

  • General

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  • Course Information

    Course title: Cancer biology core class for Bridge postbac scholars

    Instructor: Pablo Sánchez Vela, MD; sanchezp@mskcc.org

    Grading policy: This class is a not for grade class, but scholars will be evaluated with a grade to get a sense of how they performed in this class

    Duration: 5 in-person sessions plus recorded lectures

    Audience: Bridge postbac scholars


    Course topics and learning objectives

    The Cancer Biology course will teach scholars how to think about cancer as a disease and as a biological problem. This course leverages the world-class research and clinical expertise at Memorial Sloan Kettering Cancer Center (MSK). This course will feature five in-person sessions as well as several recorded lectures that Bridge scholars are required to view on their own time and ahead of the first lecture.

    This course will:

    • Provide a review of advanced concepts in cancer biology
    • Expose scholars to techniques and experimental design applied to basic-translational cancer research
    • Potentiate the ability to perform critic analysis of basic-translational research
    • Strengthen capacities to develop a research project


    Scientific topics covered in the recorded lectures will include:  

    • Cancer as a disease
    • Genetic and epigenetic mechanisms
    • Computational biology and oncology
    • Cancer signaling
    • Cancer metabolism
    • Metastasis
    • Tumor modeling and heterogeneity
    • Cancer types and microenvironments

    The structure of the program will be:
    • Session 1: Intro to Cancer Biology
    • Session 2: Guided Paper Discussion
    • Session 3: Guided Paper Discussion
    • Session 4: Guided Paper Discussion
    • Session 5: Group activity Practice
    • Recoded GSK Lectures
    • Take home group activity (1st Submission)
    • Take home group activity (Feedback)
    • Take home group activity (Oral presentation)

    How students will be evaluated

    Take Home assignment (67%):
    A two parts activity that will be required to be submitted by TDA.

    Class Participation and Attendance (33%):
    All scholars are expected to attend all sessions. A scholar must notify the Bridge team and instructor prior to class if they will absent. This notice should be sent by email.

    Recommended Textbook:

    The Biology of Cancer Third Edition.

    • Author :  Robert A. Weinberg
    • Publisher ‏ : ‎ W. W. Norton & Company
    • Edition : Third edition (July 1, 2023)
    • Language ‏ : ‎ English
    • Paperback ‏ : ‎ 984 pages
    • ISBN-10 ‏ : ‎ 0393887650
    • ISBN-13 ‏ : ‎ 978-0393887655

  • Session 1: Intro to Cancer Bio Lecture (Wednesday, August 6, 2025)

    In this first 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.

    To help to introduce the topic of the History of Cancer Biology, Oncogenes and Tumor Suppressors, we are providing a series of recorded lectures from GSK. These lectures should be watched before the class. If you have any questions from these lectures, please, bring them to the in person class.

  • Session 2: Guided Paper Discussion (Wednesday, August 13, 2025)

    Paper discussions will include description of figure panels included in the article by the students, 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.

    We will discuss the following paper: 
    Bolton KL, Ptashkin RN, Gao T, Braunstein L, Devlin SM, Kelly D, Patel M, Berthon A, Syed A, Yabe M, Coombs CC, Caltabellotta NM, Walsh M, Offit K, Stadler Z, Mandelker D, Schulman J, Patel A, Philip J, Bernard E, Gundem G, Ossa JEA, Levine M, Martinez JSM, Farnoud N, Glodzik D, Li S, Robson ME, Lee C, Pharoah PDP, Stopsack KH, Spitzer B, Mantha S, Fagin J, Boucai L, Gibson CJ, Ebert BL, Young AL, Druley T, Takahashi K, Gillis N, Ball M, Padron E, Hyman DM, Baselga J, Norton L, Gardos S, Klimek VM, Scher H, Bajorin D, Paraiso E, Benayed R, Arcila ME, Ladanyi M, Solit DB, Berger MF, Tallman M, Garcia-Closas M, Chatterjee N, Diaz LA Jr, Levine RL, Morton LM, Zehir A, Papaemmanuil E. Cancer therapy shapes the fitness landscape of clonal hematopoiesis. Nat Genet. 2020 Nov;52(11):1219-1226. doi: 10.1038/s41588-020-00710-0. Epub 2020 Oct 26. PMID: 33106634; PMCID: PMC7891089.



    Additionally, to help to introduce the topic of Precision Medicine (Cancer Genomics and Lung Cancer) , Breast Cancer, and Cancer Metastasis we are providing a series of recorded lectures from GSK. These lectures should be watched before the class. If you have any questions from these lectures, please, bring them to the in person class.

  • Session 3: Guided Paper Discussion (Wednesday, August 20, 2025)

    Paper discussions will include description of figure panels included in the article by the students, 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.

    We will discuss the following paper: 

    Chia SB, Johnson BJ, Hu J, Valença-Pereira F, Chadeau-Hyam M, Guntoro F, Montgomery H, Boorgula MP, Sreekanth V, Goodspeed A, Davenport B, De Dominici M, Zaberezhnyy V, Schleicher WE, Gao D, Cadar AN, Petriz-Otaño L, Papanicolaou M, Beheshti A, Baylin SB, Guarnieri JW, Wallace DC, Costello JC, Bartley JM, Morrison TE, Vermeulen R, Aguirre-Ghiso JA, Rincon M, DeGregori J. Respiratory viral infections awaken metastatic breast cancer cells in lungs. Nature. 2025 Sep;645(8080):496-506. doi: 10.1038/s41586-025-09332-0. Epub 2025 Jul 30. PMID: 40739350; PMCID: PMC12422975.

    To help to introduce the topic of Cancer Evolution, Tumor Microenvironment (and Pancreatic Cancer), we are providing a series of recorded lectures from GSK. These lectures should be watched before the class. If you have any questions from these lectures, please, bring them to the in person class.

  • Session 4: Wednesday, August 27, 2025

    Paper discussions will include description of figure panels included in the article by the students, 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.

    We will discuss the following paper:
    Barriga FM, Tsanov KM, Ho YJ, Sohail N, Zhang A, Baslan T, Wuest AN, Del Priore I, Meškauskaitė B, Livshits G, Alonso-Curbelo D, Simon J, Chaves-Perez A, Bar-Sagi D, Iacobuzio-Donahue CA, Notta F, Chaligne R, Sharma R, Pe'er D, Lowe SW. MACHETE identifies interferon-encompassing chromosome 9p21.3 deletions as mediators of immune evasion and metastasis. Nat Cancer. 2022 Nov;3(11):1367-1385. doi: 10.1038/s43018-022-00443-5. Epub 2022 Nov 7. PMID: 36344707; PMCID: PMC9701143.

    The uploaded lectures should be watched before the class. If you have any questions from these lectures, please, bring them to the in person class.

  • Session 5: Group activity (Wednesday, September 3, 2025)

    In this activity, students will be divided into two groups. A translational research project with preliminary data, common for both teams, will be shared with the students 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 students will have time to design which next experiments they would like to conduct, and in 10-minute shifts, the class lead 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 lead 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 students 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 students get a taste of how to design experiments and interpret results to answer a specific scientific question, in a guided environment. 


    The paper provides a guide on how to think about experimental design.

  • Recorded lectures

    Scholars will be required to watched 4 recorded basic and translational science lectures from scientists in Sloan Kettering Institute and Human Oncology and Pathogenesis Program. These lectures will be viewed on their own time ahead of the first class and will help prime discussions at the in-person sessions. These sessions will be posted on Moodle every week. A list of lecture topics will be provided the first week of class.

    • CRISPR and single-cell functional genomics
    • Cancer Metabolism
    • Central Nervous System function and metastasis
    • Immune Oncology


  • Take Home Translational Research Activity

    Similar to the guided live research session, the students will be assigned a translational research project with preliminary data, but this time individually, as an assignment. The students will have to design a small project (2-3 pages, Arial 12, small margins) 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).

    e.     Impact: One to two short phrases describing the potential implications (significance) of the study (i.e., “Understanding the role of gene X in lung cancer will help to inform rational therapeutic strategies with patients in which gene X is overexpressed”).


    This activity will be divided in two parts:

    a.   Thursday, September 25th, 2025; 23:59 PM.
    --- The project, the groups assignments, and the date of the presentation will be shared with the students.

    b.   Monday, October 27th, 2025; 23:59 PM.
    --- The students will need to upload their preliminary presentations.

    c.  November 3rd, 2025; 23:59 PM.
    --- Feedback will be provided.
    --- Students are expected to incorporate this feedback.

    d. TBD (1st half of December 2025). 
    --- The students will have the opportunity to defend their project in front of the rest of the class after addressing the comments provided. This will make the activity a learning experience, rather than just an evaluation.


    The project will be evaluated as a letter grade with a minimum of a B need to pass the course.

    The main goals of this activity are that (1) the students 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.

    Special attention should be given to the supportive material provided.