This week in MathOnco 237

Spatial genetics, whole body immune visualization, evolutionary bioreactors, and multicellular communication

“This week in Mathematical Oncology” — Dec. 15, 2022

> mathematical-oncology.org

From the editor:

Today we feature articles on spatial genetics, whole body immune visualization, evolutionary bioreactors, and multicellular communication.

This will be the last #MathOnco newsletter of the year. Merry Christmas, happy new year, see you in 2023!

Thanks,

Jeffrey West
jeffrey.west@moffitt.org

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“Efficiency is doing things right; effectiveness is doing the right things.”
— P. Drucker

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1. Spatial biology of cancer evolution
   Zaira Seferbekova, Artem Lomakin, Lucy R. Yates, Moritz Gerstung

2. Reimagining Cancer Staging in the Era of Evolutionary Oncology
   Kedar S. Kirtane, Mohammed U. Zahid, Heiko Enderling, Louis B. Harrison

3. Whole-body CD8+ T cell visualization before and during cancer immunotherapy: a phase 1/2 trial
   Laura Kist de Ruijter, Pim P. van de Donk, Jahlisa S. Hooiveld-Noeken, Danique Giesen, …, Simon P. Williams, Alexander Ungewickell, Derk J. A. de Groot, Elisabeth G. E. de Vries

4. Science Forum: A low-cost, open-source evolutionary bioreactor and its educational use
   Vishhvaan Gopalakrishnan, Dena Crozier, Kyle J Card, Lacy D Chick, …, Daniel Nichol, Soumyajit Mandal, Robert A Bonomo, Jacob G Scott

5. An untrained deep learning method for reconstructing dynamic MR images from accelerated model-based data
   Kalina P. Slavkova, Julie C. DiCarlo, Viraj Wadhwa, Sidharth Kumar, Chengyue Wu, John Virostko, Thomas E. Yankeelov, Jonathan I. Tamir

6. Back to basic: Trials and tribulations of alkalizing agents in cancer
   Robert J. Gillies, Arig Ibrahim-Hashim, Bryce Ordway, Robert A. Gatenby

7. Growth dynamics of brain metastases differentiate radiation necrosis from recurrence
   Beatriz Ocaña-Tienda, Julián Pérez-Beteta, David Molina-García, Beatriz Asenjo,…, Manuel Llorente, Natalia Carballo, Estanislao Arana, Víctor M Pérez-García

1. Identifying mechanisms driving the early response of triple negative breast cancer patients to neoadjuvant chemotherapy using a mechanistic model integrating in vitro and in vivo imaging data
   Guillermo Lorenzo, Angela M. Jarrett, Christian T. Meyer, Vito Quaranta, Darren R. Tyson, Thomas E. Yankeelov

2. A novel model of multicellular communication through extracellular matrix microstructure
   John Metzcar, Ben S. Duggan, Brandon Fischer, Matthew Murphy, Paul Macklin

3. Competition between chemoattractants causes unexpected complexity and can explain negative chemotaxis
   Adam Dowdell, Peggy Paschke, Peter Thomason, Luke Tweedy, Robert H. Insall

4. Emergent dynamics of underlying regulatory network links EMT and androgen receptor-dependent resistance in prostate cancer
   Rashi Jindal, Abheepsa Nanda, Maalavika Pillai, Kathryn E Ware, Divyoj Singh, Manas Sehgal, Andrew J. Armstrong, Jason A Somarelli, Mohit Kumar Jolly

1. gptchatteR
   Github.com
   isinaltinkaya: “An experimental and unofficial wrapper for interacting with OpenAI GPT models in R. gptchatteR uses the openai library to handle the OpenAI API endpoints.”

The newsletter now has a dedicated homepage where we post the cover artwork for each issue. We encourage submissions that coincide with the release of a recent paper from your group. This week’s artwork:

Based on the paper: “Investigating Two Modes of Cancer-Associated Antigen Heterogeneity in an Agent-Based Model of Chimeric Antigen Receptor T-Cell Therapy” in cells

Artists: Tina Giorgadze & Kerri-Ann Norton

Caption: "The tumor microenvironment is a complex system involving cross-talk between tumor cells, immune cells and stromal cells in the microenvironment. One of the most studied cross-talks is between tumor cells and endothelial cells that make up the tumor vasculature. Tumor cells that are too distant from the surrounding vasculature become hypoxic, due to low oxygen, and release vascular endothelial growth factor, which in turn signals mature vasculature to sprout and promote angiogenesis towards to the hypoxic region of the tumor. Here we show an in silico model of a developing tumor, indicating the hypoxic tumor cells in purple and the developing vasculature as a red “skeleton”. This hypoxic tumor region would be less susceptible to treatment due to its distance from the mature vessels and being in a hypoxic microenvironment."

Visit the mathematical oncology page to view jobs, meetings, and special issues. We will post new additions here, but the full list can found at mathematical-oncology.org.

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2. Conferences / Meetings

3. Special issues

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