Tracking Neoantigens by Personalized Circulating Tumor DNA Sequencing during Checkpoint Blockade Immunotherapy in Non-Small Cell Lung Cancer

The evolutionary dynamics of tumor-associated neoantigens carry information about drug sensitivity and resistance to the immune checkpoint blockade (ICB). However, the spectrum of somatic mutations is highly heterogeneous among patients, making it difficult to track neoantigens by circulating tumor DNA (ctDNA) sequencing using "one size fits all" commercial gene panels. Thus, individually customized panels (ICPs) are needed to track neoantigen evolution comprehensively during ICB treatment. Dominant neoantigens are predicted from whole exome sequencing data for treatment-naïve tumor tissues. Panels targeting predicted neoantigens are used for personalized ctDNA sequencing. Analyzing ten patients with non-small cell lung cancer, ICPs are effective for tracking most predicted dominant neoantigens (80-100%) in serial peripheral blood samples, and to detect substantially more genes (18-30) than the capacity of current commercial gene panels. A more than 50% decrease in ctDNA concentration after eight weeks of ICB administration is associated with favorable progression-free survival. Furthermore, at the individual level, the magnitude of the early ctDNA response is correlated with the subsequent change in tumor burden. The application of ICP-based ctDNA sequencing is expected to improve the understanding of ICB-driven tumor evolution and to provide personalized management strategies that optimize the clinical benefits of immunotherapies.

Titin mutation in circulatory tumor DNA is associated with efficacy to immune checkpoint blockade in advanced non-small cell lung cancer

Background

Only a fraction of patients with advanced non-small cell lung cancer (NSCLC) respond well to immune checkpoint blockade (ICB) therapy. Here, we investigated whether Titin (TTN) mutation, which has been demonstrated to be a predictive biomarker in tissue-based analysis, can identify patients with a greater likelihood in response to ICB based on circulatory tumor DNA (ctDNA) sequencing.

Methods

In this retrospective analysis, 92 patients with advanced NSCLC from two independent cohorts who received ICB treatment were included. A probe panel covering all exons of TTN was developed and validated to detect TTN mutation in ctDNA. Baseline plasma samples were collected and subjected to ctDNA sequencing with the TTN probe panel.

Results

Of the 92 patients, 28.3% harbored TTN mutation in their baseline ctDNA. Progression-free survival was significantly improved in patients with the mutated TTN (212 days and 334.5 days for cohort 1 and 2) compared to those without the mutation (113 days and 147 days for cohort 1 and 2). Objective response to ICB treatment (40% for TTN^mut and 15.8% for TTN^wt in cohort 1; 50% for TTN^mut and 23.4% for TTN^wt in cohort 2) was common in patients with mutated TTN. Stratified analysis showed a generally predictive potential of TTN mutation in patients with advanced NSCLC.

Conclusions

The presence of mutated TTN in pre-treatment peripheral blood was associated with favorable objective response and survival with ICB administration. Therefore, circulatory TTN mutation may be applicable for guiding ICB immunotherapy in patients with NSCLC.

Genomic landscapes by multiregion sequencing combined with circulation tumor DNA detection contribute to molecular diagnosis in glioblastomas

Glioblastoma is a highly aggressive brain malignancy with a poor prognosis. Its high intratumor heterogeneity contributes to therapeutic resistance, tumor progression and recurrence. We sequenced 31 loci in 11 patients with glioblastoma (including one patient with samples available from the primary and recurrent tumors) to determine the genetic basis and intratumor heterogeneity of glioblastoma. By analyzing the somatic mutations, known driver genes were identified, including EGFR, PTEN and TP53, and the MUC16 gene exhibited the highest mutation rate in the samples examined. Through an evolutionary analysis of the sequencing results, the EGFR p.L861Q mutation was determined to play a role in the progression from the primary tumor to a relapsing tumor in one patient. We analyzed 1403 genes in blood-derived ctDNA that were previously revealed to play a role in tumorigenesis and the progression of cancer. Somatic mutations identified through ctDNA sequencing that match the results of multipoint exon sequencing in tumor tissues were detected, such as EGFR p.L861Q. These findings provide new insights into the intratumor heterogeneity and evolution of glioblastoma. In addition, ctDNA detection in blood samples represents a convenient method to dynamically identify the genetic changes and new therapeutic targets during the treatment of glioblastoma.

TP53 mutations in circulating tumor DNA in advanced epidermal growth factor receptor-mutant lung adenocarcinoma patients treated with gefitinib

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We evaluated 180 patients' EGFR and TP53 co-mutation types, who received gefitinib targeted therapy, through sequencing their ctDNA in plasma.

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Patients with TP53 mutation is predictive of poor survival.

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Patients with EGFR exon 19 and TP53 co-mutations had better prognosis value than those with EGFR L585R and TP53 co-mutations.

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4.Patients with TP53 mutations, especially in exons 6 and 7, had a lower response rate and shorter PFS and OS when treated with gefitinib.

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TP53 exon 5 mutation divided TP53 mutations in disruptive and non-disruptive types.

Tumor protein p53 (TP53) is a tumor suppressor gene and TP53 mutations are associated with poor prognosis in non-small cell lung cancer. However, the in-depth classification of TP53 and its relationship with treatment response and prognosis in epidermal growth factor receptor (EGFR)-mutant tumors treated with EGFR tyrosine kinase inhibitors are unclear. Circulating tumor DNA was prospectively collected at baseline in advanced treatment-naïve EGFR-mutant lung adenocarcinoma patients treated with gefitinib in an open-label, single-arm, prospective, multicenter, phase 2 clinical trial (BENEFIT trial) and analyzed using next-generation sequencing. Survival was estimated using the Kaplan–Meier method. Of the 180 enrolled patients, 115 (63.9%) harbored TP53 mutations. The median progression-free survival (PFS) and overall survival (OS) of patients with TP53-wild type tumors were significantly longer than those of patients with TP53-mutant tumors. Mutations in exons 5–8 accounted for 80.9% of TP53 mutations. Mutations in TP53 exons 6 and 7 were significantly associated with inferior PFS and OS compared to wild-type TP53. TP53 mutation also influenced the prognosis of patients with different EGFR mutations. Patients with TP53 and EGFR exon 19 mutations had significantly longer PFS and OS than patients with TP53 and EGFR L858R mutations, and both groups had worse survival than patients with only EGFR mutations. Patients with TP53 mutations, especially in exons 6 and 7, had a lower response rate and shorter PFS and OS when treated with gefitinib. Moreover, TP53 exon 5 mutation divided TP53 mutations in disruptive and non-disruptive types.

Exceptional response to brigatinib following alectinib failure in a patient with ALK fusion-positive duodenal carcinoma

Patients with advanced duodenal carcinoma typically have a poor prognosis due to limited practical chemotherapy options. While studies on genotype-directed therapy in patients with duodenal carcinoma is progressing, clinical data assessing the efficacy of molecularly targeted therapy remains scarce. We report the case of a 65-year-old woman diagnosed with anaplastic lymphocyte kinase (ALK) fusion-positive advanced duodenal carcinoma. The patient had been treated with alectinib for approximately 2 years for ALK-positive duodenal carcinoma but developed progressive liver metastases, indicating alectinib failure. During the disease progression, circulating tumor DNA (ctDNA) sequencing revealed the emergence of ALK L1196M mutation, which demonstrated sensitivity to brigatinib. After switching to brigatinib, marked shrinkage of liver metastases was observed. The patient maintained brigatinib treatment for 7 months until tumor progression. This is the first report demonstrating the efficacy of brigatinib after alectinib failure in a patient with duodenal carcinoma harboring ALK fusion. Furthermore, this case suggests that ctDNA sequencing can detect specific acquired mutations and help expand optimal treatment options for patients.