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YUe Pu



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    P1.03 - Biology (ID 161)

    • Event: WCLC 2019
    • Type: Poster Viewing in the Exhibit Hall
    • Track: Biology
    • Presentations: 1
    • Moderators:
    • Coordinates: 9/08/2019, 09:45 - 18:00, Exhibit Hall
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      P1.03-22 - A Novel Method for Detecting Low Abundant Mutants in Three Types of Liquid Biopsies by Capturing Mutant-Alleles (ID 1332)

      09:45 - 18:00  |  Author(s): YUe Pu

      • Abstract
      • Slides

      Background

      Liquid biopsy can facilitate early detection of cancers, treatment selection, and disease monitoring. Improved methods to detect low abundant circulating tumor DNA (ctDNA) are needed for clinical samples including plasma, pleural effusion, and cerebrospinal fluid that carry a large amount of wild-type DNA.

      Method

      We have developed a novel method, namely PEAC, with an ultra-high sensitivity to detect low abundant mutants from ctDNA through mutant capturing followed by Sanger sequencing or next-generation sequencing (NGS). This novel approach combines the high discrimination power of locked–nucleic acid (LNA) modified nucleotide sequence and short probes as bait to capture mutant fragment under an optimized temperature. Mutant fragments bound by biotin-labelled, LNA-modified probes are enriched by streptavidin beads and amplified by PCR, and then sequenced for detection.

      Result

      Using circulating cell-free DNA (cfDNA) reference standards, we demonstrated that PEAC technology can enrich mutants up to 5000-fold (panel B of the figure below) and empower to detect clinically relevant EGFR mutants such as L858R, 19Del, and T790M mutant at the abundance as low as 0.01-0.1% by Sanger sequencing or NGS analysis. The clinical implications of PEAC technology were further validated using ctDNA from liquid biopsy specimens of non-small cell lung cancer (NSCLC) patients. EGFR L858R, 19DEL or T790M mutants were detected at the abundance >50% after PEAC enrichment from plasma samples of NSCLC patients, whereas the corresponding ctDNA samples without PEAC enrichment were undetectable by Sanger sequencing and hardly detected by NGS analysis. One cerebrospinal fluid and two pleural effusion samples had dominated 19DEL, L858R and T790M peaks after PEAC enrichment, respectively, but exhibited almost the background signal levels prior to PEAC.

      peac fig.png

      Conclusion

      PEAC technology can enrich ctDNA from body fluids of cancer patients to detect ultra-low abundant clinically relevant mutants. Combined with other methods including NGS, the technology may serve as an attractive detection method in clinical practice.

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    P2.03 - Biology (ID 162)

    • Event: WCLC 2019
    • Type: Poster Viewing in the Exhibit Hall
    • Track: Biology
    • Presentations: 1
    • Moderators:
    • Coordinates: 9/09/2019, 10:15 - 18:15, Exhibit Hall
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      P2.03-27 - Discovery of WNK1-ROS1 Fusion in a Lung Adenocarcinoma Patient and the Precise Guidance for Targeted Therapies (ID 2122)

      10:15 - 18:15  |  Author(s): YUe Pu

      • Abstract
      • Slides

      Background

      Lung cancer can be driven by activation of tyrosine kinases including EGFR mutations, ALK, ROS1, RET, or NTRK fusions. New partners of gene fusions remain to be identified and their response to targeted therapy need be carefully evaluated in the clinical practice.

      Method

      A targeted next-generation sequencing (NGS) panel was used to analyze DNA extracted from tumor tissue and plasma samples from a lung adenocarcinoma patient. The fusion detected by NGS panel was confirmed by Sanger sequencing.

      Result

      Using a targeted NGS lung cancer panel, we identified a novel ROS1 fusion from a 39-year old Chinese female with lung adenocarcinoma. No EGFR, MET, KRAS, ALK, ROS1 or other driver mutations of lung cancer were detected in the patient. Intron 25 of WNK1 was translocated to intron 33 of ROS1 (Figure blow), which resulted in an in-frame fusion transcript of WNK1-ROS1 at the breakpoints of exon 25 and exon 34, respectively. Sanger sequencing confirmed the fusion and the breakpoints. This novel WNK1-ROS1 fusion encoded a chimera protein of which the transmembrane and kinase domains of ROS1 remained intact. The patient received treatment with crizotinib targeting to ROS1, and partial response was achieved 3 months later. Resistance to crizotinib occurred at 5 months after the treatment. Analysis of the ctDNA from the patient’s plasma sample identified ROS1 G2032R mutation, a well-known mechanism of ROS1 resistance to crizotinib. The patient was subsequently treated with TPX-0005, which is effective to ROS1 G2032R mutant. Decreased CEA level was observed 2 months after TPX-0005 treatment, suggesting the patient was responsive to the targeted therapy.

      wnk1-ros1 fusion.png

      Conclusion

      We identified a lung adenocarcinoma patient with a novel WNK1-ROS1 fusion who was sensitive to crizotinib and developed crizotinib resistant ROS1 G2032R mutation at progression but appeared to be responsive to the new generation of TPX-0005 therapy. These results suggest that WNK1-ROS1 fusion is a new molecular mechanism leading to lung adenocarcinoma and targetable to ROS1 tyrosine kinase inhibitors.

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