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Undergraduate research experiences.
Scholar-in-residence positions for HBCU faculty.
Video tutorial series for clinicians and clinical scientists.

Outreach Core

3 activities

Goal: To increase the visibility and training of the field of System Cancer Biology to groups outside of UVA

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Program I. Two Undergrad Research Experiences per summer in SASCO labs

Summer 2023

•Project 1: Sam Pressman (Stony Brook), SURP

• Project 2: Leanne Maharaj (UVA), SRIP

• Project 3: Mariah Snelson (Johns Hopkins), REU

Video tutorial series for clinicians and clinical scientists.
Scholar-in-residence position

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Quantitative analysis of CPC recruitment during chromosome missegregation

Project 1

Samuel Presman, Stonybrook

SURP student

Mentor-Catalina Alvarez,

PIs-Todd Stukenberg, Kevin Janes

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A new pipeline obtains quantitative data more efficiently

36 species

51 timepoints

1,836 CSV files

vcell_plots()

The first part of my contribution was to add line graphs to allow for quantitative analysis of the data obtained from Vcell. Originally, the concentration values were manually pulled from the heatmaps by Catalina. The line plots significantly reduced the amount of time needed to analyze the spatial and temporal dynamics of the model. So now, with the click of a button, we can get in seconds what took minutes of manual work. Another new addition was the R function save_plots(), which automatically structures the outputs into a more accessible format. So essentially, am analysis of three different simulations, which would have taken probably in the range of 20 to 30 minutes, can now be done in a couple of seconds. This obviously saves a lot of time and opens us up to the opportunity of analyzing many more simulations in a day.

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The Metabolic Effects of KRAS Mutation in Colorectal Cancer

Project 2:

Leanne Maharaj (UVA)

SRIP student

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RIPTiDe integrates transcriptomic data with a model to reveal metabolic differences between wildtype and mutated KRAS samples

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Data collection techniques and image analysis for the study of glioblastoma multiforme and pancreatic ductal adenocarcinoma progression

Project 3: Mariah Snelson

(Johns Hopkins)

P.I. Dr. Matthew Lazzara

Mentors: Sarah Buchanan, Michelle Barbeau

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Chemo-induced Senescence in Pancreatic Ductal Adenocarcinoma

Aim: Develop an image analysis pipeline for banked images to study senescent cells in chemotherapy treated and untreated conditions

4 Lim, Biochemical and Biophysical Research Communications, 2006

5 Netterfield et al., bioRxiv (Michael Yaffe’s lab)

Normal cells

Senescent cell

Enlarged, flattened morphology

Senescent cell

Multinucleated

Senescent cell morphology: enlarged, multinucleated, irregularly shaped⁴
Chemotherapeutic drugs shown to drive DNA damage-induced senescence⁵

Hoechst and e-cadherin stained images illustrating various phenotypes

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Program 2. Scholar-in-residence positions for HBCU faculty.�

The UVA Cancer Center (Amy Bouton) has developed a highly innovative program to provide cancer research experiences to the faculty of HBCUs.

HBCU Faculty spend summers immersed in laboratories at UVA with the goals of employing new techniques in their own research and incorporating state-of-the-art technologies in their curricula.

STRIVE (Short-Term Research Initiative for Visiting Educators)

Dr. Dumas and 4 of his students from Hampton University

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Program 2. Scholar-in-residence positions for HBCU faculty.�

Cimona Hinton (Clark Atlanta U)

Kevin Janes/Lixin Wang (Project 1)

•Cimona has had regular meetings and attended the Janes Lab group meetings.

She visited in July:

•worked with Kevin and Lixin to initiate project will be completed by her PhD student that will visit soon

•multiple meetings with Dina Halme to learn the ropes of organizing a cancer center

•multiple meetings with Sara Groves and Todd Stukenberg to act as a consultant for outreach project 3

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Program 3. Video tutorial series for clinicians and clinical scientists.�

There is a need to prepare MD/Clinicians for the revolution of Systems Cancer Biology

The hope is that educating clinicians about systems approaches will make them better collaborators and enable more efficient translation to the bedside of systems findings.

(NIH Website)

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Program 3. Video tutorial series for clinicians and clinical scientists.�

Develop short video tutorials to introduce clinicians and clinical scientists to the power of systems approaches and provide tools to allow them to be conversant with experts in systems biology.

(NIH Website)

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Program 3. Video tutorial series for clinicians and clinical scientists.�

Three ~25-minute video tutorials

1) Why use systems approaches?

2) Basic concepts of systems biology

3) Introduction to computer programs used by system cancer biologists

RFA mechanism 1/yr

Year 1-produce 1^st video

$12,000 for salary + fringe

$2,500 for Supplies

$3,000 for Clinician consultant fees.

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Program 3. Video tutorial series for clinicians and clinical scientists.�

Education Scholar: Sarah Grove

Started July 1
Multiple meetings with Todd Stukenberg to brainstorm and outline first video
Met with BJ Purrow (MD/PhD Project 3) to discuss challenges/goals of working with MDS

Established collaborations with Cimona Hinton to provide feedback for each of the stages of the video