Research Highlights of 2024

December 16, 2024

As the year comes to a close, we reflect on the incredible strides made by IICD researchers in 2024. From innovative methodologies to state-of-the-art tools, these seven research highlights underscore IICD’s commitment to advancing cancer research. 

DIISCO is a machine learning method. Its input is cell-type proportions over time and gene expression of known receptor-ligand pairs. Its output is cell-type dynamics over time and networks characterizing the strength of cell-cell interactions and how they change over time. Image credit: Azizi Lab

DIISCO introduces a novel framework for studying the intricate dynamics of cell-to-cell interactions, providing unprecedented insight into how cells communicate.

"Our hope is that researchers will find DIISCO to be a valuable tool for characterizing temporal cell-cell interactions on their own datasets. As scRNA-seq becomes more widespread and cost-effective, building temporal datasets is becoming increasingly common, and DIISCO is well-suited to meet this growing demand. The method also has broad clinical applications, particularly in understanding dynamic cellular behavior over time," explained Cameron Park, PhD student in the Department of Biomedical Engineering and lead contributor to the study.

Read more about DIISCo

Visualization of in vivo CRISPRmap barcode detection on a xenograft tumor section, showing the guide distribution in the tumor microenvironment. Decoded CRISPR guide-identifying barcodes detected by CRISPRmap are shown as spots false-colored according to their guide identity.

CRISPRMap enables the high-resolution mapping of phenotypic changes in response to perturbations, revolutionizing our understanding of cellular behavior.

“Our lab has optimized CRISPRmap to be compatible with optical readout assays, allowing concurrent multiplexed profiling of proteins and mRNA species. Moreover, CRISPRmap is agnostic to the type of genetic perturbation, opening the way to explore targeted mutations, gene interference and activation, epigenetic modification, and CRISPR RNA editing,” explained Professor Jellert Gaublomme, the study's corresponding author.

Learn more about CRISPRMap.

Overview of the Starfysh Workflow

Starfysh is a breakthrough computational tool designed to analyze spatial heterogeneity in gene expression, shedding light on tumor biology.

“From constructing atlases of healthy and diseased tissues to guiding personalized cancer therapies, the potential applications of this computational tool are vast and promising,” explains Elham Azizi, Assistant Professor of Biomedical Engineering.

Discover Starfysh

llustration of a diPUFA phospholipid, a type of lipid with two polyunsaturated fatty acyl tails, breaking through a cell's outer lipid layer as the cell dies. New research has shown that diPUFA phospholipids are a key driver of a form of cell death known as ferroptosis. (Nicoletta Barolini)

Researchers uncover a rare fat molecule that plays a critical role in ferroptosis, offering potential new pathways for cancer therapies.

“The discovery that these diPUFA lipids are important drivers of ferroptosis deepens our understanding of this form of cell death, and these lipids’ role in controlling a cell’s homeostasis in general,” Brent Stockwell said.

Read the full study.

Cell observed microscopy technique

CellStitch leverages optimal transport to deliver accurate 3D segmentation of complex tissue samples, enhancing the precision of cancer research.

“Our method, CellStitch, bridges the gap between the well-studied 2D segmentation and the increasing demand for 3D cellular reconstruction. The method is especially applicable on anisotropic images, which is common in many shallow-depth 3D microscopic tissue images,” explains Yining Liu, a PhD student in computer science (co-advised by Andrew J. Blumberg and Itsik Pe’er) and one of the study co-authors.

Explore CellStitch.

Leica CM3050 S Research Cryostat

The introduction of a state-of-the-art cryostat has elevated the precision of tissue sectioning, supporting advanced histological studies.

The cryostat is crucial for projects that require detailed microscopic analysis of tissue structure and cellular composition.

Learn about the cryostat.

Confocal Microscope System

IICD now boasts a cutting-edge confocal microscope, enabling researchers to visualize cellular structures in unprecedented detail.

The Dragonfly’s spinning disk confocal imaging allows us to capture 3D images of thick and thin samples alike. Its speed allows for fast acquisition in screening efforts, and imaging of larger tissue sections,” said Jellert Gaublomme, IICD Associate Member who oversees the instrument.

Read about the new microscope.