Rare coexistence of three novel CDCA7-ALK, FSIP2-ALK, ALK-ERLEC1 fusions in a lung adenocarcinoma patient who responded to Crizotinib

Zhao, Guojiang; Chen, Lin; Xiao, Mingzhe; Yang, Sheng

doi:10.1016/j.lungcan.2020.12.013

Cited by 3 publications

(4 citation statements)

References 6 publications

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“…[10][11][12] The emergence of NGS technology and modern computational tools allows the identification of multiple fused genes in parallel. 13 Many large DNA-based NGS (DNA-NGS) panels have been developed to detect SNVs, insertions/deletions, and fused genes. 14 However, breakpoints are unpredictable, and any fusion detection requires a great many probes to cover a large range of genomes.…”

Section: Introductionmentioning

confidence: 99%

“…However, these technologies have a common limitation in identifying multiple fused genes simultaneously 10‐12 . The emergence of NGS technology and modern computational tools allows the identification of multiple fused genes in parallel 13 . Many large DNA‐based NGS (DNA‐NGS) panels have been developed to detect SNVs, insertions/deletions, and fused genes 14 .…”

Section: Introductionmentioning

confidence: 99%

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Development and validation of an RNA sequencing panel for gene fusions in soft tissue sarcoma

Zhang

et al. 2022

Cancer Science

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Gene fusions are one of the most common genomic alterations in soft tissue sarcomas (STS), which contain more than 70 subtypes. In this study, a custom‐designed RNA sequencing panel including 67 genes was developed and validated to identify gene fusions in STS. In total, 92 STS samples were analyzed using the RNA panel and 95.7% (88/92) successfully passed all the quality control parameters. Fusion transcripts were detected in 60.2% (53/88) of samples, including three novel fusions (MEG3–PLAG1, SH3BP1–NTRK1, and RPSAP52–HMGA2). The panel demonstrated excellent analytic accuracy, with 93.9% sensitivity and 100% specificity. The intra‐assay, inter‐assay, and personnel consistencies were all 100.0% in four samples and three replicates. In addition, different variants of ESWR1–FLI, COL1A1–PDGFB, NAB2–STAT6, and SS18–SSX were also identified in the corresponding subtypes of STS. In combination with histological and molecular diagnosis, 14.8% (13/88) patients finally changed preliminary histology‐based classification. Collectively, this RNA panel developed in our study shows excellent performance on RNA from formalin‐fixed, paraffin‐embedded samples and can complement DNA‐based assay, thereby facilitating precise diagnosis and novel fusion detection.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Development and validation of an RNA sequencing panel for gene fusions in soft tissue sarcoma

Zhang

et al. 2022

Cancer Science

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“…To comprehensively study the discovery of IGR events in lung cancer, we searched PubMed publications and conference abstracts for reports of intergenic fusion cases. By June 2021, a total of 74 IGR cases were identified by DNA-based NGS in 19 single-case reports or cohort studies 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 ( Supplementary Table S3 , available at https://doi.org/10.1016/j.esmoop.2022.100405 ). Fifty-three of those cases were ALK fusions.…”

Section: Discussionmentioning

confidence: 99%

Characterizing kinase intergenic-breakpoint rearrangements in a large-scale lung cancer population and real-world clinical outcomes

Yao

Ma³

et al. 2022

ESMO Open

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“…Comparing the commonly altered genes between PR and RR, we found that FSIP2 was mutated more frequently after relapse; however, the result was not significant (Figure 4B). Several studies demonstrated that FSIP2 was associated with metastasis and drug response in breast cancers [34,35]; therefore, we suspected that FSIP2 mutation might contribute to the survival advantage of disseminated lesions. We next compared the TMB and TNB between paired PR and RR but found no obvious difference (Figure 4C).…”

Section: Genetic and Transcriptional Distinction Between Pr And Rrmentioning

confidence: 94%

Dysregulated Immune and Metabolic Microenvironment Is Associated with the Post-Operative Relapse in Stage I Non-Small Cell Lung Cancer

Zhang

Xiao²,

Zhu³

et al. 2022

Cancers

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The underlying mechanism of post-operative relapse of non-small cell lung cancer (NSCLC) remains poorly understood. We enrolled 57 stage I NSCLC patients with or without relapse and performed whole-exome sequencing (WES) and RNA sequencing (RNA-seq) on available primary and recurrent tumors, as well as on matched tumor-adjacent tissues (TATs). The WES analysis revealed that primary tumors from patients with relapse were enriched with USH2A mutation and 2q31.1 amplification. RNA-seq data showed that the relapse risk was associated with aberrant immune response and metabolism in the microenvironment of primary lesions. TATs from the patients with relapse showed an immunosuppression state. Moreover, recurrent lesions exhibited downregulated immune response compared with their paired primary tumors. Genomic and transcriptomic features were further subjected to build a prediction model classifying patients into groups with different relapse risks. We show that the recurrence risk of stage I NSCLC could be ascribed to the altered immune and metabolic microenvironment. TATs might be affected by cancer cells and facilitate the invasion of tumors. The immune microenvironment in the recurrent lesions is suppressed. Patients with a high risk of relapse need active post-operative intervention.

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Rare coexistence of three novel CDCA7-ALK, FSIP2-ALK, ALK-ERLEC1 fusions in a lung adenocarcinoma patient who responded to Crizotinib

Cited by 3 publications

References 6 publications

Development and validation of an RNA sequencing panel for gene fusions in soft tissue sarcoma

Development and validation of an RNA sequencing panel for gene fusions in soft tissue sarcoma

Characterizing kinase intergenic-breakpoint rearrangements in a large-scale lung cancer population and real-world clinical outcomes

Dysregulated Immune and Metabolic Microenvironment Is Associated with the Post-Operative Relapse in Stage I Non-Small Cell Lung Cancer

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