Publications

Peer-reviewed papers and preprints from the Davies Cancer Lab.

2026

Preprint

A Compact, Standalone & Battery-Powered 3D Organoid-on-Chip System with Programmable Flow Control

Vaibhav Murthy Raviraj ThakurSamuel Olson Emma Wolcott Darya Budkina Francis Anderson Ting Zheng Austin Wright Jeremy Copperman Luiz BertassoniEllen Langer Alexander E. Davies

Organoids-on-chip combine the 3D complex microenvironment and cellular composition of organoids with microfluidic flow, increasing nutrient-waste exchange and mimicking the contributions of in vivo interstitial and vascular flow. However, the widespread adoption of organoid-on-chip platforms is limited by the lack of incubator-friendly flow control systems. Existing approaches often rely on commercially available syringe or peristaltic pumps, but these are bulky, lack scalability, and present a significant barrier for clinical translation. To circumvent these issues, we present the Compact Active Perfusion Standalone Organoid-on-Chip (CAPS-OC) platform, a fully integrated and battery-powered microfluidic system capable of culturing organoids in active media flow. To achieve this, we introduce a novel low-power mechanism of pressure pulse generation using an off-the-shelf compact rotary actuator (CRA), and package it into a compact electromechanical assembly. This assembly provides timed pneumatic inputs to achieve programmable control of membrane-based peristaltic pumps, with ∼100 µL/hr dynamic range achieved on a custom microfluidic organoid chip. We biologically validated this system by culturing pancreatic cancer organoids derived from a KrasLSL-G12D/+; Trp53LSL-R172H/WT; Pdx1-Cre (KPC) genetically engineered mouse model. We found that our chip enhances proliferation and helps sustain a population of larger (>150 µm) organoids compared to standard dome based static culture. Additionally, through immunostaining, we observe that KPC organoids cultured in the chip show more aggressive PDAC phenotype with reduced nuclear expression of GATA6, whereas organoids in static culture retain less aggressive classical- like subtype. Finally, testing of a RAS inhibitor drug, daraxonrasib, on the KPC organoids on chip showed size-based sensitivity elucidating the impact of active perfusion on the drug diffusion kinetics. Altogether, we establish CAPS-OC as a valuable tool for the bioengineering community and for clinically translating organoid model systems.

MMIST: Molecular and Morphodynamics-Integrated Single-cell Trajectories

Single-cell morphodynamical trajectories enable prediction of gene expression accompanying cell state change

Jeremy Copperman Ian McLeanSean GrossJalim Singh Vaibhav Murthy Young Hwan Chang Alexander Davies Daniel ZuckermanLaura Heiser

Cell Systems

Here, we develop MMIST, molecular and morphodynamics-integrated single-cell trajectories. This analysis predicts expression of thousands of RNA transcripts through extracellular signal-induced epithelial-mesenchymal transition (EMT) and mesenchymal-epithelial transition (MET) with near-continuous time resolution. The MMIST framework leverages true single-cell dynamical behavior to generate molecular-level omic inferences and is broadly applicable across biological domains, imaging approaches, and molecular snapshot data.

2025

Graphical abstract for Serial Imaging of Tumor and microEnvironment (SITE) platform for live-cell ex vivo modeling of primary and metastatic cancer dynamics
Preprint

Serial Imaging of Tumor and microEnvironment (SITE) platform for live-cell ex vivo modeling of primary and metastatic cancer dynamics

Vaibhav Murthy Rawan Makkawi Francis Anderson Carol Halsey Elise Manalo-HallSanjay SrikanthGabriella TangkilisanTing ZhengJames McGannMark R. Birtwistle Jeremy Copperman Alexander E. Davies

Understanding cancer onset and progression is extremely challenging, in part due to experimental limitations in measuring and interpreting key signaling and tumor-host interactions that determine cancer behavior over time, across cell and tissue scales. Here we developed SITE (Serial Imaging of Tumor and microEnvironment), a spatially and temporally integrated platform combining ex vivo culture, biosensors, live imaging, and computation. Applied to modeling primary and lung metastatic breast cancer, SITE revealed tissue-specific tumor–host interactions and ERK signaling patterns linked to distinct single-cell behaviors. We found that multicellular niche formation involved active protrusion and cell–cell contact driven by both cancer and host cells. Mathematical modeling showed ERK signaling was co-influenced by neighboring cancer and host cells. Paracrine signaling among cancer cells increased signaling in a cluster-size–dependent manner, while disruption of cancer–cancer signaling loops amplified tissue-specific differences in tumor architecture. Applied specifically to breast cancer, we demonstrated the utility of the SITE platform, enabling quantitative exploration of ex vivo signaling and tumor-host interaction dynamics.

2024

FKMD diagram

Featurizing Koopman mode decomposition for robust forecasting

David Aristoff Jeremy Copperman Nathan Mankovich Alexander Davies

The Journal of Chemical Physics

This article introduces an advanced Koopman mode decomposition (KMD) technique—coined Featurized Koopman Mode Decomposition (FKMD)—that uses delay embedding and a learned Mahalanobis distance to enhance analysis and prediction of high-dimensional dynamical systems. We show that FKMD improves predictions for a high-dimensional linear oscillator, a high-dimensional Lorenz attractor that is partially observed, and a cell signaling problem from cancer research.

2023

Graphical abstract for Host-derived growth factors drive ERK phosphorylation and MCL1 expression to promote osteosarcoma cell survival during metastatic lung colonization

Host-derived growth factors drive ERK phosphorylation and MCL1 expression to promote osteosarcoma cell survival during metastatic lung colonization

Camille A. McAloney Rawan Makkawi Yogesh BudhathokiMatthew V. Cannon Amy C. GrossEmily M. FranzMaren CamTatyana A. VetterRebekka Duhen Alexander E. Davies Ryan D. Roberts

Cellular Oncology

For patients with osteosarcoma, disease-related mortality most often results from lung metastasis—a phenomenon shared with many solid tumors. While established metastatic lesions behave aggressively, very few of the tumor cells that reach the lung will survive. By identifying mechanisms that facilitate survival of disseminated tumor cells, we can develop therapeutic strategies that prevent and treat metastasis. Here, we analyzed single cell RNA-sequencing data from murine metastasis-bearing lungs to interrogate changes in both host and tumor cells during colonization. We used these data to elucidate pathways that become activated in cells that survive dissemination and identify candidate host-derived signals that drive activation. We validated these findings through live cell reporter systems, immunocytochemistry, and fluorescent immunohistochemistry. We then validated the functional relevance of key candidates using pharmacologic inhibition in models of metastatic osteosarcoma. We show that niche-derived growth factors drive MAPK activity and MCL1 expression in osteosarcoma, promoting metastatic colonization. Although later metastases produce less MCL1, they remain dependent on it. Furthermore, combining MCL1 inhibition with chemotherapy both prevented colonization and eliminated established metastases in murine models of osteosarcoma. Taken together, these data show that MCL1 is a promising target for clinical trials in both human and canine patients.