Study hints at a mechanism behind aggressive melanoma

A mutation in a gene involved in chromatin remodeling is associated with aggressive melanoma, according to a new study that combined in vitro and animal model data.

The gene, ARID2, is a part of the switch/sucrose nonfermentable (SWI/SNF) complex, which maneuvers cellular structures called nucleosomes to make cellular DNA accessible. About 20% of human cancers have a mutation within the SWI/SNF complex.

In the new study, published in Cell Reports, researchers reported that the ARID2 subunit was mutated in about 13% of melanoma patients identified through the Cancer Genome Atlas.

ARID2 mutations have been found in early melanoma lesions, which the authors suggested may play a role in early cancer cell dissemination. Other studies have shown SWI/SNF mutations, including ARID2 mutations, in melanoma metastases, especially the brain.

The researchers also found an up-regulation of synaptic pathways in melanoma cells as well as the Cancer Genome Atlas, which also suggests a potential role of ARID2 loss in metastasis or targeting the brain, since synaptic activation in cancer cells has been shown elsewhere to influence cell migration and survival in the brain.

“We look forward to future studies that investigate the role of the PBAF complex ... in order to better tailor treatments for melanoma patients,” wrote the study authors, who were led by Emily Bernstein, PhD, a professor in oncological sciences with the Icahn School of Medicine at Mount Sinai, New York.

The SWI/SNF complex includes a subcomplex that targets specific DNA sequences or chromatin reader domains. There are multiple versions of the targeting subcomplex, but two of the most frequently occurring are BAF and PBAF. The most commonly mutated subunit in melanoma is ARID2, which is part of PBAF, and contains an AT-rich region responsible for non–sequence-specific DNA interactions. There is evidence that it plays a role in tumor suppression. In mouse tumors, depletion of ARID2 is associated with increased sensitivity to immune checkpoint inhibition and destruction by T cells.

To better understand the role of ARID2 in tumor suppression, the researchers used CRISPR-Cas9 to create ARID2 deficiency in a known human metastatic melanoma cell line. They found there was reduced chromatin accessibility and accompanying gene expression among some PBAF and shared BAF-PBAF–occupied regions. There was also increased chromatin accessibility and gene expression in BAF-occupied regions, and these changes were associated with tumor aggression. In mice, they led to metastasis of distal organs.

This mechanism appears to be conserved between different melanoma cell lines, but deregulated transcriptional targets were different depending on the dominant transcription factors in the cell line. That suggests that the effect of ARID2 mutation or loss may be different depending on the stage of melanoma progression or level of invasiveness. “As melanoma comprises transcriptionally distinct, heterogeneous cell populations, we envision future studies utilizing single-cell methodologies to better understand the nuanced effects of ARID2 loss within subpopulations of cells in human melanoma tumors,” the authors wrote.

The study is limited by the fact that not all ARID2 mutations lead to complete loss of protein, and may lead instead to aberrant complexes.

The study was funded by the National Institutes of Health.

A mutation in a gene involved in chromatin remodeling is associated with aggressive melanoma, according to a new study that combined in vitro and animal model data.

The gene, ARID2, is a part of the switch/sucrose nonfermentable (SWI/SNF) complex, which maneuvers cellular structures called nucleosomes to make cellular DNA accessible. About 20% of human cancers have a mutation within the SWI/SNF complex.

In the new study, published in Cell Reports, researchers reported that the ARID2 subunit was mutated in about 13% of melanoma patients identified through the Cancer Genome Atlas.

ARID2 mutations have been found in early melanoma lesions, which the authors suggested may play a role in early cancer cell dissemination. Other studies have shown SWI/SNF mutations, including ARID2 mutations, in melanoma metastases, especially the brain.

The researchers also found an up-regulation of synaptic pathways in melanoma cells as well as the Cancer Genome Atlas, which also suggests a potential role of ARID2 loss in metastasis or targeting the brain, since synaptic activation in cancer cells has been shown elsewhere to influence cell migration and survival in the brain.

“We look forward to future studies that investigate the role of the PBAF complex ... in order to better tailor treatments for melanoma patients,” wrote the study authors, who were led by Emily Bernstein, PhD, a professor in oncological sciences with the Icahn School of Medicine at Mount Sinai, New York.

The SWI/SNF complex includes a subcomplex that targets specific DNA sequences or chromatin reader domains. There are multiple versions of the targeting subcomplex, but two of the most frequently occurring are BAF and PBAF. The most commonly mutated subunit in melanoma is ARID2, which is part of PBAF, and contains an AT-rich region responsible for non–sequence-specific DNA interactions. There is evidence that it plays a role in tumor suppression. In mouse tumors, depletion of ARID2 is associated with increased sensitivity to immune checkpoint inhibition and destruction by T cells.

To better understand the role of ARID2 in tumor suppression, the researchers used CRISPR-Cas9 to create ARID2 deficiency in a known human metastatic melanoma cell line. They found there was reduced chromatin accessibility and accompanying gene expression among some PBAF and shared BAF-PBAF–occupied regions. There was also increased chromatin accessibility and gene expression in BAF-occupied regions, and these changes were associated with tumor aggression. In mice, they led to metastasis of distal organs.

This mechanism appears to be conserved between different melanoma cell lines, but deregulated transcriptional targets were different depending on the dominant transcription factors in the cell line. That suggests that the effect of ARID2 mutation or loss may be different depending on the stage of melanoma progression or level of invasiveness. “As melanoma comprises transcriptionally distinct, heterogeneous cell populations, we envision future studies utilizing single-cell methodologies to better understand the nuanced effects of ARID2 loss within subpopulations of cells in human melanoma tumors,” the authors wrote.

The study is limited by the fact that not all ARID2 mutations lead to complete loss of protein, and may lead instead to aberrant complexes.

The study was funded by the National Institutes of Health.

A mutation in a gene involved in chromatin remodeling is associated with aggressive melanoma, according to a new study that combined in vitro and animal model data.

The gene, ARID2, is a part of the switch/sucrose nonfermentable (SWI/SNF) complex, which maneuvers cellular structures called nucleosomes to make cellular DNA accessible. About 20% of human cancers have a mutation within the SWI/SNF complex.

In the new study, published in Cell Reports, researchers reported that the ARID2 subunit was mutated in about 13% of melanoma patients identified through the Cancer Genome Atlas.

ARID2 mutations have been found in early melanoma lesions, which the authors suggested may play a role in early cancer cell dissemination. Other studies have shown SWI/SNF mutations, including ARID2 mutations, in melanoma metastases, especially the brain.

The researchers also found an up-regulation of synaptic pathways in melanoma cells as well as the Cancer Genome Atlas, which also suggests a potential role of ARID2 loss in metastasis or targeting the brain, since synaptic activation in cancer cells has been shown elsewhere to influence cell migration and survival in the brain.

“We look forward to future studies that investigate the role of the PBAF complex ... in order to better tailor treatments for melanoma patients,” wrote the study authors, who were led by Emily Bernstein, PhD, a professor in oncological sciences with the Icahn School of Medicine at Mount Sinai, New York.

The SWI/SNF complex includes a subcomplex that targets specific DNA sequences or chromatin reader domains. There are multiple versions of the targeting subcomplex, but two of the most frequently occurring are BAF and PBAF. The most commonly mutated subunit in melanoma is ARID2, which is part of PBAF, and contains an AT-rich region responsible for non–sequence-specific DNA interactions. There is evidence that it plays a role in tumor suppression. In mouse tumors, depletion of ARID2 is associated with increased sensitivity to immune checkpoint inhibition and destruction by T cells.

To better understand the role of ARID2 in tumor suppression, the researchers used CRISPR-Cas9 to create ARID2 deficiency in a known human metastatic melanoma cell line. They found there was reduced chromatin accessibility and accompanying gene expression among some PBAF and shared BAF-PBAF–occupied regions. There was also increased chromatin accessibility and gene expression in BAF-occupied regions, and these changes were associated with tumor aggression. In mice, they led to metastasis of distal organs.

This mechanism appears to be conserved between different melanoma cell lines, but deregulated transcriptional targets were different depending on the dominant transcription factors in the cell line. That suggests that the effect of ARID2 mutation or loss may be different depending on the stage of melanoma progression or level of invasiveness. “As melanoma comprises transcriptionally distinct, heterogeneous cell populations, we envision future studies utilizing single-cell methodologies to better understand the nuanced effects of ARID2 loss within subpopulations of cells in human melanoma tumors,” the authors wrote.

The study is limited by the fact that not all ARID2 mutations lead to complete loss of protein, and may lead instead to aberrant complexes.

The study was funded by the National Institutes of Health.