Identify new types of cancer cells

Researchers at the Stanford Institute of Stem Cell Biology and Regenerative Medicine have designed a tool to examine how cells behave and interact in various environments in the body
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They use it to better understand how cancer develops and is treated

Dr.

Aaron Newman, assistant professor of biomedical data science and a member of the Institute, said: “Now we can study the building blocks of tissues—the way the entire cell ecosystem is built—not just the types of cells

The tool, called EcoTyper, combines new computer algorithms with algorithms previously developed by researchers to analyze cell types, how they line up with each other, and what RNA information the cells are generating
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Researchers can analyze the interactions of cells in a large number of large tissues, using computer analysis to determine the location of specific cell subtypes in the tissue and how they interact with neighboring cells

"EcoTyper is unique in that it can decode the cellular structure of tissues on a large scale in a high-definition and cost-effective manner," Newman said
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"This includes being able to analyze the types of tissue specimens stored after biopsy or clinical trials, otherwise it would be difficult and expensive to analyze with this method

Newman said that another advantage of EcoTyper is that researchers can use a large number of stored organizations and public databases to conduct virtual clinical trials.
They have analyzed thousands of cancer cases in a very cost-effective way
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A paper describing the tool was published in the September 30 issue of Cell
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Newman and Dr.

A companion article published in Cancer Cell on September 30 describes how to use EcoTyper to identify subtypes of lymphoma cells
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Newman and Ash Alizadeh, MD, professor of oncology, are the senior authors of this paper

"Ecological classification" of cancer cells and their neighbors

Although lung cancer looks very different from bladder cancer or other types of tumors under the microscope, EcoTyper allows researchers to find 10 different multicellular communities, called "ecotypes", which exist in more than a dozen different tumors Type in
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The researchers said they also found that the presence or absence of certain ecotypes in tumors is highly predictive of results, often indicating which treatments are most effective, even for different types of cancer

Luca said: "We have discovered an ecological type that can predict a good response to a specific immunotherapy
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" "In fact, it is even better than the other candidate biomarkers we tested, and even those specifically designed to predict response.

"EcoTyper can provide a platform for future treatments because you can better understand the bad cells in the tumor you want to attack," Gentles said
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This method of focusing on interacting cell populations in tumors is different from current methods, which usually target "driver mutations" or genes along specific pathways
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He added: "Many cancer therapies focus on specific cell types or genes, but there are always other cells that contribute to the cancer, or cells that don't have this genetic mutation
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" These are equally valuable therapeutic targets
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Talk about the most common blood cancer

Researchers in a paper published in the journal Cancer Cell tried to distinguish whether a certain type of lymphoma has two different subtypes, which is generally accepted in the field
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Using EcoTyper, they analyzed the microenvironment between and around diffuse large b-cell lymphoma cells
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By observing how cancerous cells and non-cancerous cells line up and interact, they can distinguish not only the two subtypes, but also the nine subtypes of this lymphoma
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Since the researchers are studying tissue samples from previous cases of lymphoma, they also have patient treatment records
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Steen said: "We have found that not only are there more subtypes of b-cell lymphoma than previously known, but we can also show that knowing which subtype people are enables us to better predict the possible progression of cancer.

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The researchers found positive results from a clinical trial of a lymphoma drug that seemed to have failed
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In fact, the researchers re-executed the clinical trial, this time using EcoTyper, and included their new understanding of how many types of b-cell lymphoma there are
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"What we see is that there is actually a specific subtype of lymphoma that responds to treatment," Alizadeh said
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"But in the initial trial, they were unable to identify these other subtypes, so in the negative results of all other lymphoma subtypes, this promising sign of efficacy was lost
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Alizadeh added: “The ability to find the right drugs and formulate effective cancer treatment plans based on specific cancer subtypes is the epitome of precise health and personalized medicine
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” “EcoTyper helps us do this
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”

Other co-authors of cell research at Stanford University include postdoctoral scholars Dr.
Magdalena Matusiak and Dr.
Almudena Espín-Pérez; former research assistant Amon Aziz; life science research professionals Sushama Varma and Chunfang Zhu, MD, PhD; official postdoctoral scholars Dr.
Joanna Przybyl; Maximilian Diehn, MD, Associate Professor of Radiation Oncology; Matt Van der Rein, MD, Professor of Pathology
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This Cell article research was funded by the Cancer Informatics Fund, the American Association for Cancer Research, the National Cancer Institute (authorized R01CA255450, R00CA187192, U54CA209971, U24CA224309, R01CA233975 and R01CA229529), Bakewell Foundation, SDW/DT and Shanahan Family Foundation , Support from the Stinehart-Reed Foundation
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The Virginia and DK Ludwig Cancer Research Fund, the Stanford Bio-x Interdisciplinary Initiative Seed Grant Program, and the Donald E and Delia B.
Baxter Foundation
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Other authors of cancer research include oncology lecturer Dr.
Mohammad Esfahani; Aziz; postdoctoral scholar Dr.
Brian sword; former postdoctoral scholar Dr.
Barzin Nabet; David Kurtz, MD, assistant professor of oncology; basic life research scientist Dr.
Zhilong Liu; life Scientific research professionals Farnaz Khameneh; Ranjana Advani, MD, professor of oncology; Yasodha Natkunam, MD, professor of pathology; and Diehn
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A researcher from the Cancer Institute of Oslo University Hospital also participated in the paper published in the journal Cancer Cell
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