Genetic Profiling Suggests Rationale for Limited Response to Immunotherapy in Osteosarcoma

Andy Futreal, PhD

Andy Futreal, PhD

Treatment with immune checkpoint inhibitors appears to elicit limited clinical activity in patients with osteosarcoma. In a study, investigators at MD Anderson Cancer Center (MD Anderson) found that certain factors like poor infiltration of the tumor by immune cells, low activity from available T cells, a lack of immune-stimulating neoantigens, and multiple immune-suppressing pathways may interfere with response to immunotherapy in these patients, according to a press release from the organization.¹

Osteosarcoma samples from 48 patients with primary, relapsed, and metastatic disease were analyzed with whole genome, RNA, T-cell receptor (TCR) sequencing, immunohistochemistry, and reverse-phase protein array profiling (RPPA).²

The analysis showed no differences in primary, local recurrence, and lung metastasis specimens relating to mutational burden, predicted neoantigens, subclonal proportions, copy number alteration, or altered pathways. Overall, trends were similar to what was previously reported in the field. There were interesting trends observed in signature 8 specimens and those with high levels of genomic rearrangements, however.

Signature 8 specimens had a positive association with mutational burden, disease-free relapse status, and survival. In specimens that had a high level of genomic rearrangements, which were divided into two major groups (signatures 2 and 4), there was an association with chromothripsis in younger patients compared with older patients whose rearrangements were not clustered.

Another trend supports a prior finding that osteosarcoma cells may maintain viability of their unstable genome induced byTP53/RB1mutations through whole-genome doubling (WGD) or telomere lengthening.In the MD Anderson cohort, high copy number and rearrangement burden were associated with WGD and normalized telomere lengths (P<.001 and&nbsp;P<1e -4, respectively).²

In samples that were evaluated based on pathologic tumor response to neoadjuvant chemotherapy and histologic subtypes, favorable tumor necrosis was observed. Specifically, &ge;90% necrosis COSMIC 3 signature scores, telomere lengths, and Th2 T-cell scores were seen in these samples, suggesting that patients with osteosarcoma who have favorable necrosis may have fewer stable genomes and chronic activation of the immune response.

The mutational burden in these subjects was not associated with immune infiltrate levels, and less than 30% of expressed nonsynonymous changes assessed through RNA sequencing were predicted to be strong-binded neoantigens.

Most osteosarcoma samples were positive for T-cell infiltrate, but, the low productive clonality suggests that lack of T-cell diversity may also prevent an effective immune response. Analyses of immune infiltration scores and gene expression enrichment scores also showed that the majority of osteosarcoma specimens may not have sufficient immune infiltrate to achieve meaningful responses to immune checkpoint therapy alone and osteosarcoma have multiple immune-suppressive mechanisms that may affect response.

&ldquo;This study is important not only because it focuses on a rare cancer, but it sets the groundwork for understanding the multifaceted reasons this cancer doesn&rsquo;t respond to immunotherapy, despite having certain hallmarks that suggest it would,&rdquo; said corresponding author Andy Futreal, PhD, chair of Genomic Medicine at MD Anderson, in a statement. &ldquo;Understanding those reasons and beginning to pick them apart does begin to give us lines of sight on how to get around the tumor&rsquo;s methods of subverting the immune system.&rdquo;

The study cohort was compiled of patients with high-grade osteosarcoma who were low-risk and had adverse survival outcomes. Seventy-three percent of the patients had unfavorable responses to standard therapy and 67% were deceased. Whole genome sequencing was conducted first, and then data from those samples were integrated with transcriptome, TCR sequencing, RPPA, and immunostaining to provide full insight on the immunogenomic landscape of osteosarcoma. &nbsp;

&ldquo;By understanding the interplay between tumor genomics and the immune response, we are better equipped to identify osteosarcoma patients who are more likely to benefit from immunotherapy,&rdquo; said Andrew Livingston, MD, assistant professor of Sarcoma Medical Oncology and Pediatrics at MD Anderson in a statement. &ldquo;These findings lay the groundwork for novel clinical trials combining immunotherapy agents with targeted or cell-based therapies to improve outcomes for our patients.&rdquo;

References

1. Osteosarcoma profiling reveals why immunotherapy remains ineffective [news release]. Houston, TexasMD Anderson Cancer Center; February 21, 2020. https://bit.ly/2VcVN0i. Accessed February 21, 2020.
2. Wu CC, Ceird HC, Futreal PA, et al. Immuno-genomic landscape of osteosarcoma. Nat Commun. 2020;11, 1008. https://doi.org/10.1038/s41467-020-14646-w.