This week in MathOnco 269

Allelic frequency, adaptive therapy, mixed effect modeling, birth-death processes

Jeffrey West

Ryan Schenck

Maximilian Strobl

, and 2 others

Sep 21, 2023

`> mathematical-oncology.org`

`From the editor:`

This week we have articles on allelic frequency, adaptive therapy, mixed effect modeling, birth-death processes and more.

Thanks,

Jeffrey West jeffrey.west@moffitt.org

PS. Don’t forget to check apply for the IMO Workshop!

Variant of allele frequency: a decision-making tool in precision oncology?
Luca Boscolo Bielo, Dario Trapani, Matteo Repetto, Antonio Marra, Vivek Subbiah, Giuseppe Curigliano
Stochastic competitive release and adaptive chemotherapy
J. Park and P. K. Newton
Mixed effects modeling of radiotherapy in combination with immune checkpoint blockade or inhibitors of the DNA damage response pathway
David Hodson, Hitesh Mistry, Sofia Guzzetti, Michael Davies, Anna Staniszewska, Paul Farrington, Elaine Cadogan, James Yates, Leon Aarons, Kayode Ogungbenro

The tidyomics ecosystem: Enhancing omic data analyses
William J Hutchison, Timothy J Keyes, Helena L Crowell, Charlotte Soneson, …Kara L Davis, Anthony T Papenfuss, Michael I Love, Stefano Mangiola
A clinicogenomic model including GARD predicts outcome for radiation treated patients with HPV+ oropharyngeal squamous cell carcinoma
Emily Ho, Loris DeCecco, Stefano Cavalieri, Geoff Sedor, …, Jimmy Caudell, Michael W Kattan, Lisa Licitra, Javier Torres-Roca, Jacob G Scott
Single-cell mutational burden distributions in birth-death processes
Christo Morison, Dudley Stark, Weini Huang
A hematopoietic stem cell subset that retains memory of prior inflammatory stress accumulates in aging and clonal hematopoiesis
Andy G.X. Zeng, Murtaza S. Nagree, Niels Asger Jakobsen, Sayyam Shah, …, Steven Z. Josefowicz, Paresh Vyas, John E. Dick, Stephanie Z. Xie
Digitize your Biology! Modeling multicellular systems through interpretable cell behavior
Jeanette A.I. Johnson, Genevieve L Stein-O'Brien, Max Booth, Randy Heiland, …, Joe Gray, Laura M. Heiser, Elana J. Fertig, Paul Macklin

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: Evolvability of cancer-associated genes under APOBEC3A/B selection (BioRxiv)

Artist: Joon-Hyun Song, Mehdi Damaghi (@mehdiDamaghi)

Caption: Cytidine deaminases such as AID and APOBECs can inadvertently increase the heterogeneity of viral genomes while fulfilling their roles in mutating defective viral genomes. Decades of research on mutational signatures in cancer have unveiled a significant number of mutations induced by APOBEC activity. This prompts questions about the role of APOBEC in cancer evolution. Does APOBEC aid or hinder the evolution of cancer? How does the human genome itself respond to potential damage caused by APOBEC-induced mutations? Our research suggests that APOBEC may evolve to produce mutation motifs that are less harmful to our genome. Furthermore, our clonal expansion simulations indicate that APOBEC activity might ultimately increase the heterogeneity of the cancer population. Read the pre-print here.

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