The Protein Behind Immunotherapy Resistance – ScienceDaily

Immunotherapy is an advanced approach to treating cancer by turning the patient’s immune system against the tumor. Our increasing knowledge of the mechanisms by which the body regulates immune responses has transformed our fight against cancer.

But despite success rates, immunotherapy has repeatedly encountered a difficult snag: Cancer cells often evade the “radar” of immune cells seeking to destroy them. This, in turn, leads to treatment resistance, which in many cases may benefit from a deeper understanding of the mechanisms that can help circumvent it.

A new study led by scientists at EPFL has now revealed a protein that plays a key role in helping tumors avoid destruction by the immune system. This protein, called the fragile X mental retardation protein (FMRP), regulates a network of genes and cells in the tumor microenvironment that contribute to its ability to “hide” from immune cells. Normally, FMRP is involved in the regulation of protein translation and mRNA stability in neurons. But researchers have found that it is aberrantly regulated in multiple forms of cancer.

The study published in Sciences, led by researchers in the Douglas Hanahan group at the Swiss Institute for Experimental Cancer Research (ISREC) and the Lausanne branch of the Ludwig Institute for Cancer Research, together with colleagues from Lausanne University Hospital (CHUV) and other Swiss institutions. The discovery also gave rise to an EPFL subsidiary, Opna Bio, whose staff was also involved in the search.

But why FMRP? The idea came from previous studies that showed that cancer cells that naturally overexpress FMRP are invasive and metastatic. Other studies show that, by contrast, if FMRP fails to be expressed in developing neurons, it can lead to cognitive defects (hence the “mental retardation” part of the protein’s name).

With this evidence in mind, the researchers set out to investigate FMRP expression in human tumours. They then evaluated its tumor-promoting functions in mouse models of cancer, and finally examined its association with the prognosis of human cancer patients.

The study included several steps to collect data. First, the scientists performed FMRP immunoprecipitation on tissues taken from human tumors. The results of the majority of tumors were positive, whereas the corresponding normal tissue was not. This means that FMRP is specifically and highly expressed in tumor cells.

The team then turned to the main part of their research, which was to determine the functional significance of FMRP in those tumors — they express the protein, but what does it do?

FMRP is involved in the immune system

To explore this, scientists have developed lines of what are called “knockout” cancer cells. Genetically engineer cells or organisms to lose – “knock out” – a particular gene in order to find clues about its function. Essentially, whatever change occurs in the disassembled cells compared to the cells that still carry the gene – called “wild type” – can generally be traced back to the missing gene.

In this case, the scientists used the popular CRISPR-Cas9 gene-editing technology to knock out a gene (named FMR1) that produces FMRP in mouse cancer cells originating from the pancreas, colon, breast, and cutaneous melanocytes. They then compared the cancer cells that had been knocked out with FMRP to cancer cells that still had the FMR1 gene and therefore expressed the FMRP protein.

Researchers have evaluated the survival rates between mice with tumors containing FMRP tumor cells and those with FMRP wild type cells, for the first time in mice whose immune systems have been compromised. Comparison revealed similar survival rates. In marked contrast, when they compared the knockout tumors with wild-type tumors growing in mice with properly functioning immune systems, they found that the tumors without FMRP grew more slowly, and the animals lived longer.

What this part of the study showed is that FMRP is not involved in stimulating tumor growth per se, but rather that it implicates the adaptive immune system (the part of our immune system that we “train” with vaccines).

This was further confirmed by the observation that the wild-type tumors had very few infiltrating T lymphocytes, whereas the knockout tumors were highly inflammatory. Depletion of T cells from FMRP tumors caused them to start growing more quickly and reduced survival rates in mice, implying that FMRP is somehow involved in tumors that evade the immune system.

How FMRP-expressing tumors defend against immune cells

The team continued with the molecular genotyping of both tumors subject to remission and wild-type tumors. This revealed significant differences in gene transcription across the entire genome, indicating that FMRP interacts with multiple genes. In addition, tumors showed marked differences in the abundance of tumor cells, macrophages, and T cells, suggesting a role for FMRP in modulating components of the immune system.

The next phase of the study looked at the production of specific factors involved in characteristic immune responses – evasion versus attack. Tumors that express FMRP have been found to produce interleukin-33, a protein that stimulates the production of regulatory T cells, a specialized subpopulation of T cells that suppress immune responses. They also produce protein S, a glycoprotein known to promote tumor growth. Finally, tumors produce exosomes — cellular organelles that have been shown to trigger the production of a type of macrophage cell that normally aids in wound healing and tissue repair. Collectively, all three factors are immunosuppressive and contribute to the tumor barrier against T lymphocyte attacks.

In contrast, FMRP-knockout tumor cells actually reduced all three factors (interleukin-33, S protein, and exosomes) while upregulating a different chemical called “CC motif chemokine ligand 7” (CCL7), which helps recruit and activate T cells. . This process is further supported by the stimulation of immunogenic (not immunosuppressive) macrophages. These cells produce three other inflammatory proteins that work together with CCL7 in recruiting T cells.

Predicting outcomes of immunotherapy in human patients

In the clinical context, the question is whether FMRP levels can help shape a prognosis for patients undergoing immunotherapy. Unexpectedly, both mRNA of the FMR1 gene and FMRP protein levels were insufficient to predict outcome in cohorts of cancer patients.

To address this, the researchers built on the fact that FMRP, in the cell, up and down modulates mRNA stability by directly binding it. This means that FMRP may alter the levels of RNA that can be captured in transcriptome data sets, which can be collected to identify a ‘signature of a gene’ to help track its functional activity. This approach worked, allowing the scientists to track a genetic fingerprint of the cancer regulatory activity of FMRP in a network of 156 genes.

The FMRP cancer network activity signature has been shown to be predictive of poor survival across several human cancers, consistent with the immunosuppressive effects of FMRP, and, in some patients, has been linked to poor response to immunotherapies.

The work shows that FMRP regulates a network of genes and cells in the tumor microenvironment, all of which help tumors avoid immune system destruction.

Douglas Hanahan says, “Having studied the complex cellular structure of solid tumors for decades, I am personally amazed at our finding that a selected neuronal regulatory protein – FMRP – can orchestrate the formation of a multifaceted protective barrier against attack by the immune system that thus limits the benefit of immunotherapies.” , thus presenting FMRP as a novel therapeutic target for cancer.”

Other contributors

  • Opna Bio SA
  • Agora Cancer Research Center
  • Swiss Institute for Bioinformatics (SIB)
  • Bern University
  • EPFL Institute of Bioengineering
  • University of Lausanne (UNIL)
  • National Children’s Health Center (Beijing)
  • Swiss Cancer Center Lehmann (SCCL)

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