Rapid and highly sensitive approach for multiplexed somatic fusion detection

Precision medicine in diagnosis, prognosis, and disease monitoring of bone and soft tissue sarcomas using liquid biopsy: a systematic review

INTRODUCTION

Liquid biopsy as a non-invasive method to investigate cancer biology and monitor residual disease has gained significance in clinical practice over the years. Whilst its applicability in carcinomas is well established, the low incidence and heterogeneity of bone and soft tissue sarcomas explains the less well-established knowledge considering liquid biopsy in these highly malignant mesenchymal neoplasms.

MATERIALS AND METHODS

A systematic literature review adhering to the PRISMA guidelines initially identified 920 studies, of whom 68 original articles could be finally included, all dealing with clinical applicability of liquid biopsy in sarcoma. Studies were discussed within two main chapters, i.e. translocation-associated and complex-karyotype sarcomas.

RESULTS

Overall, data on clinical applicability of liquid biopsy in 2636 patients with > 10 different entities of bone and soft tissue sarcomas could be summarised. The five most frequent tumour entities included osteosarcoma (n = 602), Ewing sarcoma (n = 384), gastrointestinal stromal tumour (GIST; n = 203), rhabdomyosarcoma (n = 193), and leiomyosarcoma (n = 145). Of 11 liquid biopsy analytes, largest evidence was present for ctDNA and cfDNA, investigated in 26 and 18 studies, respectively.

CONCLUSIONS

This systematic literature review provides an extensive up-to-date overview about the current and potential future uses of different liquid biopsy modalities as diagnostic, prognostic, and disease monitoring markers in sarcoma.

New Insights from Long-Term Clinical Use of Circulating Tumor DNA-Based Minimal Residual Disease Monitoring in Translocation-Associated Sarcomas

INTRODUCTION

Assessment of circulating tumor DNA (ctDNA) as a means to monitor disease activity in translocation-associated tumors has become very popular in clinical practice. However, there are still few studies on its clinical application to date. Our study evaluates the clinical applicability of ctDNA as a biomarker for monitoring minimal residual disease (MRD) in patients with translocation-associated sarcomas.

METHODS

In this retrospective study, we correlated 285 ctDNA samples from 34 patients diagnosed with translocation-associated sarcoma with the clinical course and images. Blood samples were collected at multiple time points during follow-up (median: 97 weeks, range: 7-398).

RESULTS

We discovered a significant association between ctDNA levels and the clinical course of the disease, particularly noting differences between patients in remission or with progressive disease (p = 0.001). Furthermore, although we noted that ctDNA levels remained undetectable in a few cases of unilocular recurrence (n = 3), they were consistently higher in patients with multilocular recurrence (n = 14; p = 0.008).

CONCLUSION

Monitoring ctDNA levels provides highly specific, additional information enabling early recurrence detection in patients with translocation-associated sarcomas during the follow-up and can be integrated into clinical practice. However, MRD monitoring by ctDNA quantification alone does not allow the reliable detection of 100% of unilocular recurrences and should be complemented by the use of conventional imaging techniques.

INTRODUCTION

Assessment of circulating tumor DNA (ctDNA) as a means to monitor disease activity in translocation-associated tumors has become very popular in clinical practice. However, there are still few studies on its clinical application to date. Our study evaluates the clinical applicability of ctDNA as a biomarker for monitoring minimal residual disease (MRD) in patients with translocation-associated sarcomas.

METHODS

In this retrospective study, we correlated 285 ctDNA samples from 34 patients diagnosed with translocation-associated sarcoma with the clinical course and images. Blood samples were collected at multiple time points during follow-up (median: 97 weeks, range: 7-398).

RESULTS

We discovered a significant association between ctDNA levels and the clinical course of the disease, particularly noting differences between patients in remission or with progressive disease (p = 0.001). Furthermore, although we noted that ctDNA levels remained undetectable in a few cases of unilocular recurrence (n = 3), they were consistently higher in patients with multilocular recurrence (n = 14; p = 0.008).

CONCLUSION

Monitoring ctDNA levels provides highly specific, additional information enabling early recurrence detection in patients with translocation-associated sarcomas during the follow-up and can be integrated into clinical practice. However, MRD monitoring by ctDNA quantification alone does not allow the reliable detection of 100% of unilocular recurrences and should be complemented by the use of conventional imaging techniques.

Clinically relevant fusion oncogenes: detection and practical implications

Mechanistically, chimeric genes result from DNA rearrangements and include parts of preexisting normal genes combined at the genomic junction site. Some rearranged genes encode pathological proteins with altered molecular functions. Those which can aberrantly promote carcinogenesis are called fusion oncogenes. Their formation is not a rare event in human cancers, and many of them were documented in numerous study reports and in specific databases. They may have various molecular peculiarities like increased stability of an oncogenic part, self-activation of tyrosine kinase receptor moiety, and altered transcriptional regulation activities. Currently, tens of low molecular mass inhibitors are approved in cancers as the drugs targeting receptor tyrosine kinase (RTK) oncogenic fusion proteins, that is, including ALK, ABL, EGFR, FGFR1-3, NTRK1-3, MET, RET, ROS1 moieties. Therein, the presence of the respective RTK fusion in the cancer genome is the diagnostic biomarker for drug prescription. However, identification of such fusion oncogenes is challenging as the breakpoint may arise in multiple sites within the gene, and the exact fusion partner is generally unknown. There is no gold standard method for RTK fusion detection, and many alternative experimental techniques are employed nowadays to solve this issue. Among them, RNA-seq-based methods offer an advantage of unbiased high-throughput analysis of only transcribed RTK fusion genes, and of simultaneous finding both fusion partners in a single RNA-seq read. Here we focus on current knowledge of biology and clinical aspects of RTK fusion genes, related databases, and laboratory detection methods.

Experimentally Deduced Criteria for Detection of Clinically Relevant Fusion 3′ Oncogenes from FFPE Bulk RNA Sequencing Data

Drugs targeting receptor tyrosine kinase (RTK) oncogenic fusion proteins demonstrate impressive anti-cancer activities. The fusion presence in the cancer is the respective drug prescription biomarker, but their identification is challenging as both the breakpoint and the exact fusion partners are unknown. RNAseq offers the advantage of finding both fusion parts by screening sequencing reads. Paraffin (FFPE) tissue blocks are the most common way of storing cancer biomaterials in biobanks. However, finding RTK fusions in FFPE samples is challenging as RNA fragments are short and their artifact ligation may appear in sequencing libraries. Here, we annotated RNAseq reads of 764 experimental FFPE solid cancer samples, 96 leukemia samples, and 2 cell lines, and identified 36 putative clinically relevant RTK fusions with junctions corresponding to exon borders of the fusion partners. Where possible, putative fusions were validated by RT-PCR (confirmed for 10/25 fusions tested). For the confirmed 3′RTK fusions, we observed the following distinguishing features. Both moieties were in-frame, and the tyrosine kinase domain was preserved. RTK exon coverage by RNAseq reads upstream of the junction site were lower than downstream. Finally, most of the true fusions were present by more than one RNAseq read. This provides the basis for automatic annotation of 3′RTK fusions using FFPE RNAseq profiles.