Monitoring and adapting cancer treatment using circulating tumor DNA kinetics: Current research, opportunities, and challenges

Circulating tumor DNA (ctDNA) has emerged as a biomarker with wide-ranging applications in cancer management. While its role in guiding precision medicine in certain tumors via noninvasive detection of susceptibility and resistance alterations is now well established, recent evidence has pointed to more generalizable use in treatment monitoring. Quantitative changes in ctDNA levels over time (i.e., ctDNA kinetics) have shown potential as an early indicator of therapeutic efficacy and could enable treatment adaptation. However, ctDNA kinetics are complex and heterogeneous, affected by tumor biology, host physiology, and treatment factors. This review outlines the current preclinical and clinical knowledge of ctDNA kinetics in cancer and how early on-treatment changes in ctDNA levels could be applied in clinical research to collect evidence to support implementation in daily practice.

Association between Genetic Variants and Cisplatin-Induced Nephrotoxicity: A Genome-Wide Approach and Validation Study

This study aims to evaluate genetic risk factors for cisplatin-induced nephrotoxicity by investigating not previously studied genetic risk variants and further examining previously reported genetic associations. A genome-wide study (GWAS) was conducted in genetically estimated Europeans in a discovery cohort of cisplatin-treated adults from Toronto, Canada, followed by a candidate gene approach in a validation cohort from the Netherlands. In addition, previously reported genetic associations were further examined in both the discovery and validation cohorts. The outcome, nephrotoxicity, was assessed in two ways: (i) decreased estimated glomerular filtration rate (eGFR), calculated using the Chronic Kidney Disease Epidemiology Collaboration formula (CKD-EPI) and (ii) increased serum creatinine according to the Common Terminology Criteria for Adverse Events v4.03 for acute kidney injury (AKI-CTCAE). Four different Illumina arrays were used for genotyping. Standard quality control was applied for pre- and post-genotype imputation data. In the discovery cohort (n = 608), five single-nucleotide polymorphisms (SNPs) reached genome-wide significance. The A allele in rs4388268 (minor allele frequency = 0.23), an intronic variant of the BACH2 gene, was consistently associated with increased risk of cisplatin-induced nephrotoxicity in both definitions, meeting genome-wide significance (β = −8.4, 95% CI −11.4–−5.4, p = 3.9 × 10⁻⁸) for decreased eGFR and reaching suggestive association (OR = 3.9, 95% CI 2.3–6.7, p = 7.4 × 10⁻⁷) by AKI-CTCAE. In the validation cohort of 149 patients, this variant was identified with the same direction of effect (eGFR: β = −1.5, 95% CI −5.3–2.4, AKI-CTCAE: OR = 1.7, 95% CI 0.8–3.5). Findings of our previously published candidate gene study could not be confirmed after correction for multiple testing. Genetic predisposition of BACH2 (rs4388268) might be important in the development of cisplatin-induced nephrotoxicity, indicating opportunities for mechanistic understanding, tailored therapy and preventive strategies.

Treatment outcomes and survival following definitive (chemo)radiotherapy in HPV-positive oropharynx cancer: Large-scale comparison of DAHANCA vs PMH cohorts

We compare outcomes in two large-scale contemporaneously treated HPV-positive (HPV+) oropharynx cancer (OPC) cohorts treated with definitive radiotherapy/chemoradiotherapy (RT/CRT). p16-confirmed HPV+ OPC treated between 2007 and 2015 at PMH and DAHANCA were identified. Locoregional failure (LRF), distant metastasis (DM), and overall survival (OS) were compared. Multivariable analysis (MVA) calculated adjusted-hazard-ratio (aHR) with 95% confidence interval (95% CI), adjusting for cohort, age, gender, performance status, smoking pack-years, T-category and N-category and chemotherapy. Compared to PMH (n = 701), DAHANCA (n = 1174) contained lower TNM-8T-categories (T1-T2: 77% vs 56%), N-categories (N0-N1: 77% vs 67%) and stages (stage I: 63% vs 44% (all P < .001). PMH used standard-fractionation CRT in 69% (481) while 31% (220) received hypofractionated or moderately accelerated RT-alone. All DAHANCA patients were treated with moderately accelerated RT; 96% (1129) received nimorazole (NIM) and 73% (856) concurrent weekly cisplatin. DAHANCA had shorter overall-treatment-time (P < .001), lower gross tumor (66-68 vs 70 Gy) and elective neck (50 vs 56 Gy) doses. Median follow-up was 4.8 years. DAHANCA had higher 5-year LRF (13% vs 7%, aHR = 0.47 [0.34-0.67]), comparable DM (7% vs 12%, aHR = 1.32 [0.95-1.82]), but better OS (85% vs 80%, aHR = 1.30 [1.01-1.68]). CRT patients had a lower risk of LRF (aHR 0.56 [0.39-0.82]), DM (aHR 0.70 [0.50-1.00]) and death (aHR 0.39 [0.29-0.52]) vs RT-alone. We observed exemplary outcomes for two large-scale trans-Atlantic HPV+ OPC cohorts treated in a similar manner. Concurrent chemotherapy was a strong, independent prognostic factor for all endpoints. Our findings underscore the need for a very careful approach to de-intensification of treatment for this disease.

HPV Sequencing Facilitates Ultrasensitive Detection of HPV Circulating Tumor DNA

PURPOSE

Human papillomavirus (HPV) DNA offers a convenient circulating tumor DNA (ctDNA) marker for HPV-associated malignancies, but current methods, such as digital PCR (dPCR), provide insufficient accuracy for clinical applications in patients with low disease burden. We asked whether a next-generation sequencing approach, HPV sequencing (HPV-seq), could provide quantitative and qualitative assessment of HPV ctDNA in low disease burden settings.

EXPERIMENTAL DESIGN

We conducted preclinical technical validation studies on HPV-seq and applied it retrospectively to a prospective multicenter cohort of patients with locally advanced cervix cancer (NCT02388698) and a cohort of patients with oropharynx cancer. HPV-seq results were compared with dPCR. The primary outcome was progression-free survival (PFS) according to end-of-treatment HPV ctDNA detectability.

RESULTS

HPV-seq achieved reproducible detection of HPV DNA at levels less than 0.6 copies in cell line data. HPV-seq and dPCR results for patients were highly correlated (R ² = 0.95, P = 1.9 × 10^-29) with HPV-seq detecting ctDNA at levels down to 0.03 copies/mL plasma in dPCR-negative posttreatment samples. Detectable HPV ctDNA at end-of-treatment was associated with inferior PFS with 100% sensitivity and 67% specificity for recurrence. Accurate HPV genotyping was successful from 100% of pretreatment samples. HPV ctDNA fragment sizes were consistently shorter than non-cancer-derived cell-free DNA (cfDNA) fragments, and stereotyped cfDNA fragmentomic patterns were observed across HPV genomes.

CONCLUSIONS

HPV-seq is a quantitative method for ctDNA detection that outperforms dPCR and reveals qualitative information about ctDNA. Our findings in this proof-of-principle study could have implications for treatment monitoring of disease burden in HPV-related cancers. Future prospective studies are needed to confirm that patients with undetectable HPV ctDNA following chemoradiotherapy have exceptionally high cure rates.

Antitumor immune effects of preoperative sitravatinib and nivolumab in oral cavity cancer: SNOW window-of-opportunity study

BACKGROUND

Sitravatinib, a tyrosine kinase inhibitor that targets TYRO3, AXL, MERTK and the VEGF receptor family, is predicted to increase the M1 to M2-polarized tumor-associated macrophages ratio in the tumor microenvironment and have synergistic antitumor activity in combination with anti-programmed death-1/ligand-1 agents. SNOW is a window-of-opportunity study designed to evaluate the immune and molecular effects of preoperative sitravatinib and nivolumab in patients with oral cavity squamous cell carcinoma.

METHODS

Patients with newly-diagnosed untreated T2-4a, N0-2 or T1 >1 cm-N2 oral cavity carcinomas were eligible. All patients received sitravatinib 120 mg daily from day 1 up to 48 hours pre-surgery and one dose of nivolumab 240 mg on day 15. Surgery was planned between day 23 and 30. Standard of care adjuvant radiotherapy was given based on clinical stage. Tumor photographs, fresh tumor biopsies and blood samples were collected at baseline, at day 15 after sitravatinib alone, and at surgery after sitravatinib-nivolumab combination. Tumor flow cytometry, multiplex immunofluorescence staining and single-cell RNA sequencing (scRNAseq) were performed on tumor biopsies to study changes in immune-cell populations. Tumor whole-exome sequencing and circulating tumor DNA and cell-free DNA were evaluated at each time point.

RESULTS

Ten patients were included. Grade 3 toxicity occurred in one patient (hypertension); one patient required sitravatinib dose reduction, and one patient required discontinuation and surgery delay due to G2 thrombocytopenia. Nine patients had clinical-to-pathological downstaging, with one complete response. Independent pathological treatment response (PTR) assessment confirmed a complete PTR and two major PTRs. With a median follow-up of 21 months, all patients are alive with no recurrence. Circulating tumor DNA and cell-free DNA dynamics correlated with clinical and pathological response and distinguished two patient groups with different tumor biological behavior after sitravatinib alone (1A) versus sitravatinib-nivolumab (1B). Tumor immunophenotyping and scRNAseq analyses revealed differential changes in the expression of immune cell populations and sitravatinib-targeted and hypoxia-related genes in group 1A vs 1B patients.

CONCLUSIONS

The SNOW study shows sitravatinib plus nivolumab is safe and leads to deep clinical and pathological responses in oral cavity carcinomas. Multi-omic biomarker analyses dissect the differential molecular effects of sitravatinib versus the sitravatinib-nivolumab and revealed patients with distinct tumor biology behavior.

TRIAL REGISTRATION NUMBER

NCT03575598.

Cell-free DNA and circulating tumor cell kinetics in a pre-clinical head and neck Cancer model undergoing radiation therapy

BACKGROUND

Monitoring circulating tumor DNA (ctDNA) and circulating tumor cells (CTCs), known as liquid biopsies, continue to be developed as diagnostic and prognostic markers for a wide variety of cancer indications, mainly due to their minimally invasive nature and ability to offer a wide range of phenotypic and genetic information. While liquid biopsies maintain significant promising benefits, there is still limited information regarding the kinetics of ctDNA and CTCs following radiation therapy which remains a vital treatment modality in head and neck cancers. This study aims to describe the kinetics of ctDNA and CTCs following radiation exposure in a preclinical rabbit model with VX2 induced buccal carcinoma.

METHODS

Seven rabbits were inoculated with VX2 cells in the buccal mucosa and subjected to radiation. At selected time points, blood sampling was performed to monitor differing levels of ctDNA and CTC. Plasma ctDNA was measured with quantitative PCR for papillomavirus E6 while CTCs were quantified using an immunomagnetic nanoparticles within a microfluidic device. Comparisons of CTC detection with EpCAM compared to multiple surface markers (EGFR, HER2 and PSMA) was evaluated and correlated with the tumor size.

RESULTS

Plasma ctDNA reflects the overall tumor burden within the animal model. Analysis of correlations between ctDNA with tumor and lymph node volumes showed a positive correlation (R = 0.452 and R = 0.433 [p < 0.05]), respectively. Over the course of treatment, ctDNA levels declined and quickly becomes undetectable following tumor eradication. While during the course of treatment, ctDNA levels were noted to rise particularly upon initiation of radiation following scheduled treatment breaks. Levels of CTCs were observed to increase 1 week following inoculation of tumor to the primary site. For CTC detection, the use of multiple surface markers showed a greater sensitivity when compared to detection using only EpCAM. Plasma CTC levels remained elevated following radiation therapy which may account for an increased shedding of CTCs following radiation.

CONCLUSION

This study demonstrates the utility of ctDNA and CTCs detection in response to radiation treatment in a preclinical head and neck model, allowing for better understanding of liquid biopsy applications in both clinical practice and research development.

Longitudinal health utility and symptom-toxicity trajectories in patients with head and neck cancers

BACKGROUND

This study examined long-term health utility and symptom-toxicity trajectories among patients with head and neck cancer (HNC).

METHODS

For patients diagnosed with HNC (2014-2019), Health Utility Index 3 (HUI-3), Edmonton Symptom Assessment Scale (ESAS), and MD Anderson Symptom Inventory (MDASI) surveys (including both the core and head and neck cancer modules) were prospectively collected at multiple time points (at the baseline, after surgery, during radiotherapy, and 3, 6, 12, and 24 months after treatment). Locally estimated scatterplot smoothing plots were generated to describe HUI-3, ESAS, and MDASI trajectories over time by clinicodemographic factors, treatment modality, and tumor subsite. Contributions of clinical factors were assessed with univariable and multivariable analyses.

RESULTS

In 800 patients, the treatment modality and the tumor subsite produced unique HUI-3, ESAS, and MDASI trajectories. Patients treated with surgery alone experienced rapid improvements in HUI-3, ESAS, and MDASI scores postoperatively. Among patients treated with chemoradiotherapy, patients with nasopharyngeal carcinoma had greater declines in HUI-3 during treatment in comparison with patients with oropharyngeal carcinoma, but they had similar ESAS/MDASI scores. Among patients treated with radiotherapy, patients with laryngeal carcinoma had better HUI-3/ESAS/MDASI scores than those with oropharyngeal carcinoma during treatment, but they slowly converged after treatment. Female sex, an age > 75 years, a household income < $40,000, a Charlson comorbidity score > 1, an Eastern Cooperative Oncology Group performance status > 0 (at the baseline), and current smoking were independently associated with worse HUI-3 trajectories. HUI-3 had mild to moderate correlations (ρ = 0.2-0.5) with individual symptom-toxicity trajectories.

CONCLUSIONS

Long-term HUI-3 trajectories are associated with tumor subsite, clinicodemographic, and treatment factors, and this may be partly explained by relationships with symptoms/toxicities. Separate evaluations by subsite and treatment should occur in health utility and symptom-toxicity studies of HNC.

LAY SUMMARY

This study indicates that the long-term health utility and symptoms/toxicities of patients with the most common head and neck cancers (ie, squamous cell carcinomas and nasopharyngeal carcinomas) differ over time with a variety of factors, including the tumor anatomic site, treatment volume, clinicodemographic characteristics (eg, age, human papillomavirus status, tumor stage, gender, smoking status, alcohol status, education, and comorbidities), and treatment modalities. Generalizations across all head and neck cancers should be strongly discouraged. Future studies should evaluate health utility, symptoms and toxicities, and patient need assessments separately for each anatomic site and treatment modality.

Pan-cancer analysis of longitudinal metastatic tumors reveals genomic alterations and immune landscape dynamics associated with pembrolizumab sensitivity

Serial circulating tumor DNA (ctDNA) monitoring is emerging as a non-invasive strategy to predict and monitor immune checkpoint blockade (ICB) therapeutic efficacy across cancer types. Yet, limited data exist to show the relationship between ctDNA dynamics and tumor genome and immune microenvironment in patients receiving ICB. Here, we present an in-depth analysis of clinical, whole-exome, transcriptome, and ctDNA profiles of 73 patients with advanced solid tumors, across 30 cancer types, from a phase II basket clinical trial of pembrolizumab (NCT02644369) and report changes in genomic and immune landscapes (primary outcomes). Patients stratified by ctDNA and tumor burden dynamics correspond with survival and clinical benefit. High mutation burden, high expression of immune signatures, and mutations in BRCA2 are associated with pembrolizumab molecular sensitivity, while abundant copy-number alterations and B2M loss-of-heterozygosity corresponded with resistance. Upon treatment, induction of genes expressed by T cell, B cell, and myeloid cell populations are consistent with sensitivity and resistance. We identified the upregulated expression of PLA2G2D, an immune-regulating phospholipase, as a potential biomarker of adaptive resistance to ICB. Together, these findings provide insights into the diversity of immunogenomic mechanisms that underpin pembrolizumab outcomes.

Tumor-Naïve Multimodal Profiling of Circulating Tumor DNA in Head and Neck Squamous Cell Carcinoma

PURPOSE

Circulating tumor DNA (ctDNA) enables personalized treatment strategies in oncology by providing a noninvasive source of clinical biomarkers. In patients with low ctDNA abundance, tumor-naïve methods are needed to facilitate clinical implementation. Here, using locoregionally confined head and neck squamous cell carcinoma (HNSCC) as an example, we demonstrate tumor-naïve detection of ctDNA by simultaneous profiling of mutations and methylation.

EXPERIMENTAL DESIGN

We conducted CAncer Personalized Profiling by deep Sequencing (CAPP-seq) and cell-free Methylated DNA ImmunoPrecipitation and high-throughput sequencing (cfMeDIP-seq) for detection of ctDNA-derived somatic mutations and aberrant methylation, respectively. We analyzed 77 plasma samples from 30 patients with stage I-IVA human papillomavirus-negative HNSCC as well as plasma samples from 20 risk-matched healthy controls. In addition, we analyzed leukocytes from patients and controls.

RESULTS

CAPP-seq identified mutations in 20 of 30 patients at frequencies similar to that of The Tumor Genome Atlas (TCGA). Differential methylation analysis of cfMeDIP-seq profiles identified 941 ctDNA-derived hypermethylated regions enriched for CpG islands and HNSCC-specific methylation patterns. Both methods demonstrated an association between ctDNA abundance and shorter fragment lengths. In addition, mutation- and methylation-based ctDNA abundance was highly correlated (r > 0.85). Patients with detectable pretreatment ctDNA by both methods demonstrated significantly worse overall survival (HR = 7.5; P = 0.025) independent of clinical stage, with lack of ctDNA clearance post-treatment strongly correlating with recurrence. We further leveraged cfMeDIP-seq profiles to validate a prognostic signature identified from TCGA samples.

CONCLUSIONS

Tumor-naïve detection of ctDNA by multimodal profiling may facilitate biomarker discovery and clinical use in low ctDNA abundance applications.

Liquid Biopsy Goes Viral: Next-Generation Sequencing to Enhance HPV Detection

Liquid biopsy approaches for the detection of viral DNA can provide important information for the diagnosis and identification of virally-associated cancers. Here we discuss the next-generation sequencing (NGS)-based CaptHPV method for the detection and characterization of plasma human papillomavirus (HPV) DNA in HPV-associated cancers and its potential clinical utility.

Abstract 563: cfDNA-based analysis of minimal residual disease and T-cell receptor clonality as predictors of relapse in stage 3 NSCLC treated with chemoradiotherapy and durvalumab

Introduction: Durvalumab immunotherapy has rapidly emerged as standard treatment for stage 3 NSCLC patients following definitive chemoradiotherapy (CRT). Multiple novel immunotherapeutic strategies are in development to enhance the chance of cure in this setting as well. There exists a critical need to identify blood-based biomarkers capable of predicting clinical benefit from adjuvant immunotherapy as well selecting patients at high-risk of relapse for further drug development. Cell-free DNA (cfDNA)-based analysis of both minimal residual disease (MRD) and T-cell receptor (TCR) clonality have immense potential to predict and monitor response to adjuvant immunotherapy. In this study, we have combined innovative cfDNA measures of MRD (CAPPseq), TCR clonality (CapTCR-seq) and methylation (cfMeDIPseq) as potential predictive biomarkers of disease progression in stage 3 NSCLC patients treated with CRT and durvalumab.

Methods: Stage 3 NSCLC patients undergoing CRT and durvalumab were recruited prospectively to undergo serial blood collections at baseline, pre- and post- durvalumab. CAPPseq and cfMeDIPseq were performed as measures of MRD. TCR repertoire analysis (CapTCR-seq) was performed on cfDNA using hybrid-capture TCR sequencing and TCR diversity/clonality was estimated using the Shannon's index. Correlations between MRD, TCR clonality, response and progression-free survival (PFS) were examined using logistic/cox regression.

Results: 79 stage 3 NSCLC patients have been prospectively recruited and undergone serial blood collection. CAPPseq, cfMeDIPseq and capTCR-seq have been completed in 22 patients (5 primary progression on CRT, 17 received durvalumab). Tumor cfDNA was detectable by CAPPseq at baseline in 14 patients. High correlation between tumor cfDNA detected by CAPPseq and cfMeDIPseq was found (R=0.68, p&lt;0.0001). Failure to clear MRD with CRT plus durvalumab was associated with significantly increased risk of recurrence with a median PFS of 5.0 vs 15.0 months (p&lt;0.0001). Lower TCR clonality measured pre-durvalumab trended with lower likelihood of response (OR 0.82, p=0.09) and worse PFS (HR 1.16 P=0.10). Importantly, a decrease in TCR clonality compared to baseline, signaling the lack of clonal expansion on treatment, was significantly associated with a worse PFS (p=0.05). A decrease in TCR clonality of 50% after CRT was associated with a worse PFS (HR 3.5, p=0.14). CAPPseq, cfMeDIPseq and capTCR-seq analyses are ongoing in the full cohort.

Conclusions: Failure to clear MRD and decreasing TCR clonality as assessed by cfDNA was highly correlated with increased risk of recurrence and reduced PFS with consolidation durvalumab. This innovative approach has significant potential to define a new biomarker for the use and development of adjuvant immunotherapy.

Citation Format: Sally CM Lau, Shirin Soleimani, Jinfeng Zou, Justin Burgener, Shelley Kuang, Stephanie WY Wong, Malcolm Ryan, Ben X. Wang, Stephanie Pedersen, Devalben Patel, Penelope A. Bradbury, Geoffrey Liu, Natasha Leighl, Ming S. Tsao, Pamela S. Ohashi, Scott V. Bratman, Trevor Pugh, Frances A. Shepherd, Adrian G. Sacher. cfDNA-based analysis of minimal residual disease and T-cell receptor clonality as predictors of relapse in stage 3 NSCLC treated with chemoradiotherapy and durvalumab [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 563.

Outcome and treatment toxicity in east-indian versus white-canadian patients with oral cavity cancer following postoperative (chemo-)radiotherapy delivered under similar multidisciplinary care: A propensity-matched cohort study

PURPOSE

We compare clinical behaviour of East-Indians and White-Canadians with oral cavity squamous cell carcinoma (OSCC) treated at a Western institution within a uniform health care system.

MATERIALS/METHODS

Newly diagnosed OSCC patients who underwent postoperative (chemo-)radiotherapy (PORT/POCRT) between 2005 and 2017 were included. Data on ethnicity and other variables were extracted from patient-questionnaires, a prospective database and supplemented by chart review. Baseline characteristics were compared between East-Indian versus White-Canadian groups. A propensity-matched (1:1 ratio) of East-Indian versus White-Canadian cohorts was generated to compare locoregional control (LRC), distant control (DC), overall survival (OS), and acute and late toxicities.

RESULTS

A total of 53 East-Indian and 467 White-Canadian OSCC patients were identified. Compared to White-Canadians, East-Indian patients were younger, had less exposure to smoking and alcohol (p < 0.001), but more chewed betel (areca) nut /tobacco (43% vs 0.2%, p < 0.001). Buccal/retromolar-trigone/lower gingiva primaries were more common in East-Indians (49% vs 25%, p < 0.001). Median follow-up was 5.0 years. Propensity-score paired analysis revealed inferior 3-year LRC (68% vs 81%, p = 0.030), non-significantly lower OS (61% vs 75%, p = 0.257), but similar DC (81% vs 87%, p = 0.428) in East-Indian versus White-Canadian patients. Actuarial rate of toxicities was higher in East-Indians vs White-Canadians: acute toxicity at 6 weeks: 47% vs 30%, p = 0.012; chronic trismus at 5-years: 16% vs 2%, p = 0.013.

CONCLUSION

East-Indian OSCC patients have a greater betel nut/ chewable tobacco exposure compared to White-Canadians and a different distribution of OSCC sites. Propensity-matched cohort analysis showed lower LRC and higher toxicities in East-Indian OSCC patients, suggesting a complicated interaction between genetic/biological and life-style factors.

Senescence, Necrosis, and Apoptosis Govern Circulating Cell-free DNA Release Kinetics

The kinetics of circulating cell-free DNA (cfDNA) release may provide a real-time assessment of induced cell death. However, there is a limited understanding of the underlying biological rationale for cfDNA release following distinct treatments and cell death mechanisms. Here, we uncover a complex interplay between apoptosis, necrosis, and senescence in determining cfDNA release kinetics. Utilizing multiple in vitro and in vivo preclinical models, we show how cfDNA release is modulated through a combination of apoptotic and senescent triggers and inhibitors. Interestingly, we identify treatment-induced senescence as a previously unrecognized determinant of cfDNA kinetics that can counteract its release. Necrosis is the predominant cell death mechanism that consistently contributes to cfDNA release in response to ionizing radiation, and, surprisingly, apoptosis plays a comparatively minor role in some tumors. Based on our results, we propose a model to explain cfDNA release from cells over time, with important implications for future studies.

The impact of the variation of imaging parameters on the robustness of Computed Tomography radiomic features: A review

The field of radiomics is at the forefront of personalized medicine. However, there is concern that high variation in imaging parameters will impact robustness of radiomic features and subsequently the performance of the predictive models built upon them. Therefore, our review aims to evaluate the impact of imaging parameters on the robustness of radiomic features. We also provide insights into the validity and discrepancy of different methodologies applied to investigate the robustness of radiomic features. We selected 47 papers based on our predefined inclusion criteria and grouped these papers by the imaging parameter under investigation: (i) scanner parameters, (ii) acquisition parameters and (iii) reconstruction parameters. Our review highlighted that most of the imaging parameters are disruptive parameters, and shape along with First order statistics were reported as the most robust radiomic features against variation in imaging parameters. This review identified inconsistencies related to the methodology of the reviewed studies such as the metrics used for robustness, the feature extraction techniques, the reporting style, and their outcome inclusion. We hope this review will aid the scientific community in conducting research in a way that is more reproducible and avoids the pitfalls of previous analyses.

Abstract PO-086: Selective radiosensitization in preclinical models of HPV-negative squamous cell carcinoma

Background: Radiotherapy is a mainstay of curative treatment for squamous cell carcinomas (SCC) and is frequently combined with radiosensitizing drugs to improve efficacy. Outcomes for HPV-negative SCCs remain heterogeneous, in part due to variable resistance to ionizing radiation (IR) and modest benefit of existing radiosensitizing drugs. Hypothesis driven testing of novel radiosensitizing drugs has previously been limited due to a lack of robust, efficient, and reproducible methods to assess drug radiation combinations. Aims: To improve the throughput of preclinical studies on radiosensitizers, we have developed an in vitro system for assessing drug/radiation combinations, validated using the known radiosensitizing chemotherapeutic drug cisplatin. We extended the assay to assess the effect of ML-385, a NRF2 inhibitor that increases cellular reactive oxygen species (ROS), and abemaciclib and palbociclib, two CDK4/6 inhibitors predicted to radiosensitize cancer cells by inhibiting entry into more resistant phases of the cell cycle. Experimental Methods: We adapted the 9-day viability assay of Abazeed et al. (Cancer Res., 2013) to enable drug/radiation efficacy assessments. We first validated the assay’s ability to recapitulate clonogenic survival among 19 HPV-negative SCC cell lines. Drug/radiation experiments were performed in the 6 most radioresistant SCC cell lines. ROS levels after 4Gy IR was used to confirm NRF2 suppression. Flow cytometry was used to evaluate cell cycle phase. AKT inhibitor GSK690693 was used in combination with a NRF2 shRNA knockdown cell line to investigate the mechanism of sensitivity. Western blot was used to detect p16. Cellular response to multiple IR doses was summarized using an area-under-the-curve (AUC) metric. The delta AUC across drug doses was used to evaluate radiosensitization. Results: Among the 19 cell lines, AUCs with the clonogenic and 9-day viability assays were strongly correlated (Pearson r=0.74, p=3.00 × 10–4). Six (32%) of the cell lines were reproducibly radioresistant (AUC &gt;3.5) using both assays. All of these cell lines saw sensitization with cisplatin. None of these 6 cell lines harboured mutations in the canonical NRF2 pathway, whereas all 6 harboured either CCND1 amplification, CDKN2A mutation, or both. Only one cell line showed radiosensitization with the NRF2 inhibitor ML-385, an effect that was abrogated by PIK3CA or AKT pathway inhibition. In contrast, 5 of the 6 cell lines showed reproducible radiosensitization following CDK4/6 inhibition; with robust p16 expression detected in the lone unaffected cell line. Conclusion: The 9-day viability assay allows efficient evaluation of putative radiosensitizers. Our tests of putative radiosensitizing drugs in a cohort of radioresistant cell lines have identified CDK4/6 inhibitors to be of interest for further investigation in biomarker-selected populations.

Citation Format: Meghan Lambie, Rita Gill, Laurie Ailles, Scott V. Bratman. Selective radiosensitization in preclinical models of HPV-negative squamous cell carcinoma [abstract]. In: Proceedings of the AACR Virtual Special Conference on Radiation Science and Medicine; 2021 Mar 2-3. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(8_Suppl):Abstract nr PO-086.

Transitions in oral and gut microbiome of HPV+ oropharyngeal squamous cell carcinoma following definitive chemoradiotherapy (ROMA LA-OPSCC study)

Background

Oral and gut microbiomes have emerged as potential biomarkers in cancer. We characterised the oral and gut microbiomes in a prospective observational cohort of HPV+ oropharyngeal squamous cell carcinoma (OPSCC) patients and evaluated the impact of chemoradiotherapy (CRT).

Methods

Saliva, oropharyngeal swabs over the tumour site and stool were collected at baseline and post-CRT. 16S RNA and shotgun metagenomic sequencing were used to generate taxonomic profiles, including relative abundance (RA), bacterial density, α-diversity and β-diversity.

Results

A total of 132 samples from 22 patients were analysed. Baseline saliva and swabs had similar taxonomic composition (R² = 0.006; p = 0.827). Oropharyngeal swabs and stool taxonomic composition varied significantly by stage, with increased oral RA of Fusobacterium nucleatum observed in stage III disease (p < 0.05). CRT significantly reduced the species richness and increased the RA of gut-associated taxa in oropharyngeal swabs (p < 0.05), while it had no effect in stool samples. These findings remained significant when adjusted by stage, smoking status and antibiotic use.

Conclusions

Baseline oral and gut microbiomes differ by stage in this HPV+ cohort. CRT caused a shift towards a gut-like microbiome composition in oropharyngeal swabs. Stage-specific features and the transitions in oral microbiome might have prognostic and therapeutic implications.

Abstract PO-033: The impact of the variation of CT scanner on the prediction of HPV status in head & neck cancer patients

Radiomics involves the use of high-dimensional quantitative imaging features for predictive purposes. However, studies showed that these radiomic features are sensitive to the variability of imaging parameters (e.g., scanner model). One of the major challenges in radiomics lies in improving the robustness of quantitative features against the variation in the imaging dataset in multi-center studies. Here, we assess the impact of scanner choice on the computed tomography (CT)-derived radiomic features to predict association of oropharyngeal squamous cell carcinoma with human papillomavirus (HPV), which has a well-established impact on CT-derived radiomic features. This experiment was performed on CT image datasets acquired with two different scanner types. We demonstrate strong scanner dependency by developing a machine learning model to classify HPV status from radiological images. These experiments revealed the effect of scanner type on the robustness of the radiomic features, and the extent of this dependency is reflected on the performance of HPV prediction models. The result of this study highlighted the importance of implementing an appropriate approach to reduce the impact of the imaging domain radiomic features and consequently on the machine learning models.

Citation Format: Reza Reiazi, Collin Arrowsmith, Farnoosh Abbas-Aghababazadeh, Christopher Eles, Aria Rezaie, Scott V. Bratman, Andrew J. Hope, Benjamin Haibe-Kains. The impact of the variation of CT scanner on the prediction of HPV status in head & neck cancer patients [abstract]. In: Proceedings of the AACR Virtual Special Conference on Artificial Intelligence, Diagnosis, and Imaging; 2021 Jan 13-14. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(5_Suppl):Abstract nr PO-033.

Abstract PO-034: The prediction of mandibular osteoradionecrosis in head and neck cancer patients using CT-derived radiomics features

Osteoradionecrosis (ORN), or bone death, is a multifactorial late complication caused by radiotherapy (RT), that diminishes the bone’s ability to withstand trauma and avoid infection. In head and neck cancer (HNC), ORN most commonly manifests in the mandible. It is influenced by RT-induced factors and patient-related parameters. The most effective way to limit RT-induced ORN is to reduce mandibular volumes receiving high RT doses. However, this strategy may also result in a reduced dose to the tumor due to its proximity to the mandible, and therefore must be restricted to only the patients deemed most vulnerable to mandibular ORN. The objective of this study was to design a prognostic model based on RT-planning CT-derived radiomic features extracted from mandible contours along with the patient’s clinical features to predict the probability of mandibular ORN from the end of RT to the onset of ORN in HNC patients. We hypothesized that these features are related to mandibular ORN and that incorporating them into a prediction model will help to identify patients at risk of mandibular ORN after HNC RT. Patient data was retrospectively collected from the Princess Margaret Cancer Centre, University Health Network and based on the following inclusion criteria: patients had (1) had status regarding radiation-induced bone toxicity, (2) the time to the toxicity event was recorded, and (3) head RT-planning CT images in addition to mandible contours. Then, the patient’s history was reviewed by radiation oncologists to collect clinical features. Quantitative image features were then extracted from the segmented mandible for each patient. Finally, multivariable models, a binary classifier, and a regressor were independently trained on three sets of features (radiomic, demo-clinical, and both) to predict the patient’s risk of ORN and the time between the end of RT and the start of ORN respectively. In total, we analyzed CT images from 92 OPC patients with known ORN status (55 positive, 37 negative). We extracted a total of 1877 radiomic features from the manually-segmented Mandible from each patient. Initially, cases were labelled with their status regarding presence and time to radiation toxicity. Top 50, most relevant and least redundant, features were with mRMRe were used for both binary classification and regression models to predict time to the mandibular ORN. Model training upon radiomics and clinical features resulted in the higher accuracy value of 0.93 (AUCROC) compared to the only radiomics features (0.92) and clinical model (0.74). The distribution of AUC values was significantly wider in models trained on clinical features than radiomics or radiomics plus clinical features.

Citation Format: Reza Reiazi, Mattea Welch, Scott V. Bratman, Andrew J. Hope, Benjamin Haibe-Kains. The prediction of mandibular osteoradionecrosis in head and neck cancer patients using CT-derived radiomics features [abstract]. In: Proceedings of the AACR Virtual Special Conference on Artificial Intelligence, Diagnosis, and Imaging; 2021 Jan 13-14. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(5_Suppl):Abstract nr PO-034.

Comparing unilateral vs. bilateral neck management in lateralized oropharyngeal cancer between surgical and radiation oncologists: An international practice pattern survey

BACKGROUND

Management of the neck in oropharyngeal carcinoma varies due to a lack of clarity of patterns of lymphatic drainage and concern of failure in the contralateral neck. With recent advances in transoral surgical techniques, surgical management has become increasingly prevalent as the primary treatment modality. We compare international practice patterns between surgical and radiation oncologists.

METHODS

A survey of neck management practice patterns was developed and pilot tested by 6 experts. The survey comprised items eliciting the nature of clinical practice, as well as patterns of neck management depending on extent of nodal disease and location and extent of primary site disease. Proportions of surgical and radiation oncologists treating the neck bilaterally were compared using the chi-squared statistic.

RESULTS

Two-hundred and twenty-two responses were received from 172 surgical oncologists, 44 radiation oncologists, 3 medical oncologists, and 3 non-oncologists from 32 different countries. For tongue base cancers within 1 cm of midline (67% vs. 100%, p < 0.001), and for tonsil cancers with extension to the medial 1/3 of the soft palate (65% vs. 100%, p < 0.001) or tongue base (77% vs. 100%, p < 0.001), surgical oncologists were less likely to treat the neck bilaterally. For isolated tonsil fossa cancers with no nodal disease, both surgical and radiation oncologists were similarly likely to treat unilaterally (99% vs. 97%, p = NS). However, with increasing nodal burden, radiation oncologists were more likely to treat bilaterally for scenarios with a single node < 3 cm (15% vs. 2%, p < 0.001), a single node with extranodal extension (41% vs. 18%, p < 0.001), multiple positive nodes (55% vs. 23% p < 0.001), and node(s) > 6 cm (86% vs. 33%, p < 0.001). For tumors with midline extension, even with a negative PET in the contralateral neck, the majority of surgical and radiation oncologists would still treat the neck bilaterally (53% and 84% respectively).

CONCLUSIONS

The present study demonstrates significant practice pattern variability for management of the neck in patients with lateralized oropharyngeal carcinoma. Surgical oncologists are less likely to treat the neck bilaterally, regardless of tumor location or nodal burden. Even in the absence of disease in the contralateral neck on imaging, them majority of practitioners are likely to treat bilaterally when the disease approaches midline.

Prognostic value of clinical and radiologic extranodal extension and their role in the 8th edition TNM cN classification for HPV-negative oropharyngeal carcinoma

BACKGROUND/OBJECTIVES

We evaluate the performance between the TNM-8 versus TNM-7 cN-classification and explore the relative prognostic contribution of radiologic extranodal extension (rENE) for HPV-negative oropharyngeal cancer (HPV-OPC).

MATERIALS/METHODS

All HPV- OPC treated with IMRT between 2005 and 2016 were included. cENE was defined as unambiguous "fixation" of a neck mass or "skin involvement" on clinical examination. rENE was recorded by re-reviewing pre-treatment CT/MR. Disease-free survival (DFS) stratified by cENE or rENE were compared. Multivariable analyses (MVA) calculated the adjusted hazard ratio (aHR) for the separate cENE and rENE attributes and their combination. A refined cN-category incorporating both cENE and rENE parameters was proposed. The performance of the revision was compared to TNM-8 and TNM-7.

RESULTS

Of 361 HPV- OPC, 97 were cN0 and 264 were cN+ with 48 cENE+ and 72 rENE+ respectively. Median follow-up was 5.4 years. The 3-year DFS was lower in cENE+ vs cENE-negative (cENE-) (23% vs 45%; aHR = 1.68, p = 0.008) and rENE+ vs rENE-negative (rENE-) patients (29% vs 45%; aHR = 1.44, p = 0.037). The cENE+/rENE+ subset had the worse DFS vs cENE-/rENE+ or cENE-/rENE- (24%/37%/46%, p = 0.005). We propose a refined cN-category wherein any cENE-/rENE+ case is reclassified one N-stratum higher while any cENE+ case remains cN3b. The stage schema with the refined N-categorization outperformed TNM-8, and both outperformed TNM-7.

CONCLUSIONS

cENE and rENE are both prognostic but the cENE+/rENE+ subset has the worst outcome. The TNM-8 cN-categories improves outcome prediction compared to the TNM-7. Incorporation of rENE into TNM-8 cN-categories may further augment performance.

Serial Cell-free DNA Assessments in Preclinical Models

Studying circulating cell-free DNA (cfDNA) release within preclinical model systems provides opportunities to investigate the mechanisms and kinetics underlying this process under various conditions. We present a detailed protocol for longitudinal evaluation of cfDNA release through (1) seeding of cancer cell lines and establishment of xenograft tumors, (2) treatment of cancer cells and xenograft tumors, (3) serial collection of cell line media and xenograft blood, and (4) processing and isolation of cfDNA for (5) quantification of cfDNA by quantitative PCR.

For complete details on the use and execution of this protocol please refer to Rostami et al. (2020).

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Cell line media and xenograft blood can be serially collected after irradiation

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Small plasma volumes can be simultaneously purified for cell-free DNA (cfDNA)

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Cell line media can be diluted for quantification of cfDNA using quantitative PCR

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Human LINE-1 can be used for ultrasensitive detection of cfDNA

Healthcare resource utilization following unilateral versus bilateral radiation therapy for oropharyngeal carcinoma

PURPOSE

To describe differences in healthcare resource utilization between patients treated with bilateral vs. unilateral neck radiation therapy (RT) for lateralized oropharyngeal cancer.

METHODS

A propensity score matching strategy was used to identify two otherwise clinically similar cohorts of tonsillar cancer patients treated with either bilateral or unilateral neck RT. Cohorts were matched based on similar propensity scores for age, sex, ECOG performance status, pack-year smoking history, cT-category, cN-category, HPV-status, and use of concurrent chemotherapy. Short term (from start of RT to 3 months following end of RT) resource utilization included: 1) outpatient supportive care visits, 2) hospital admission, and 3) interventions (feeding tube insertion and outpatient intravenous hydration). Long-term resource utilization included feeding tube dependency at 1-year.

RESULTS

Among 559 patients with tonsillar cancer treated between 2004-2017, propensity score matching identified a unilateral neck RT cohort (n = 81) and bilateral neck RT cohort (n = 81) with similar clinical and treatment characteristics. Bilateral neck RT was associated with a higher likelihood of hospitalization (33% vs 12%, p < 0.01), outpatient IV hydration (33% vs 17%, p = 0.03), and feeding tube insertion (33% vs 10%, p < 0.001); a greater number of total days of hospitalization (110 vs 47 days, p < 0.01) and outpatient IV hydration (135 vs 72 days, p = 0.02); and higher total number of supportive clinic visits (1226 vs 1053 days, p = 0.04). In the long-term, bilateral RT was associated with higher rate of feeding tube dependency at 1-year (7% vs 0%, p < 0.001).

CONCLUSION

Bilateral RT for tonsillar cancer resulted in significant increase in health resource utilization.

Integration of intra-sample contextual error modeling for improved detection of somatic mutations from deep sequencing

Sensitive mutation detection by next-generation sequencing is critical for early cancer detection, monitoring minimal/measurable residual disease (MRD), and guiding precision oncology. Nevertheless, because of artifacts introduced during library preparation and sequencing, the detection of low-frequency variants at high specificity is problematic. Here, we present Espresso, an error suppression method that considers local sequence features to accurately detect single-nucleotide variants (SNVs). Compared to other advanced error suppression techniques, Espresso consistently demonstrated lower numbers of false-positive mutation calls and greater sensitivity. We demonstrated Espresso's superior performance in detecting MRD in the peripheral blood of patients with acute myeloid leukemia (AML) throughout their treatment course. Furthermore, we showed that accurate mutation calling in a small number of informative genomic loci might provide a cost-efficient strategy for pragmatic risk prediction of AML development in healthy individuals. More broadly, we aim for Espresso to aid with accurate mutation detection in many other research and clinical settings.