Sensitive MRD Detection from Lymphatic Fluid after Surgery in HPV-Associated Oropharyngeal Cancer

PURPOSE

Our goal was to demonstrate that lymphatic drainage fluid (lymph) has improved sensitivity in quantifying postoperative minimal residual disease (MRD) in locally advanced human papillomavirus (HPV)-associated oropharyngeal squamous cell carcinoma (OPSCC) compared with plasma, and leverage this novel biofluid for patient risk stratification.

EXPERIMENTAL DESIGN

We prospectively collected lymph samples from neck drains of 106 patients with HPV (+) OPSCC, along with 67 matched plasma samples, 24 hours after surgery. PCR and next-generation sequencing were used to quantify cancer-associated cell-free HPV (cf-HPV) and tumor-informed variants in lymph and plasma. Next, lymph cf-HPV and variants were compared with TNM stage, extranodal extension (ENE), and composite definitions of high-risk pathology. We then created a machine learning model, informed by lymph MRD and clinicopathologic features, to compare with progression-free survival (PFS).

RESULTS

Postoperative lymph was enriched with cf-HPV compared with plasma (P < 0.0001) and correlated with pN2 stage (P = 0.003), ENE (P < 0.0001), and trial-defined pathologic risk criteria (mean AUC = 0.78). In addition, the lymph mutation number and variant allele frequency were higher in pN2 ENE (+) necks than in pN1 ENE (+) (P = 0.03, P = 0.02) or pN0-N1 ENE (-) (P = 0.04, P = 0.03, respectively). The lymph MRD-informed risk model demonstrated inferior PFS in high-risk patients (AUC = 0.96, P < 0.0001).

CONCLUSIONS

Variant and cf-HPV quantification, performed in 24-hour postoperative lymph samples, reflects single- and multifeature high-risk pathologic criteria. Incorporating lymphatic MRD and clinicopathologic feature analysis can stratify PFS early after surgery in patients with HPV (+) head and neck cancer. See related commentary by Shannon and Iyer, p. 1223.

Early detection of malignant and pre-malignant peripheral nerve tumors using cell-free DNA fragmentomics

Early detection of neurofibromatosis type 1 (NF1) associated peripheral nerve sheath tumors (PNST) informs clinical decision-making, potentially averting deadly outcomes. Here, we describe a cell-free DNA (cfDNA) fragmentomic approach which distinguishes non-malignant, pre-malignant and malignant forms of NF1 PNST. Using plasma samples from a novel cohort of 101 NF1 patients and 21 healthy controls, we validated that our previous cfDNA copy number alteration (CNA)-based approach identifies malignant peripheral nerve sheath tumor (MPNST) but cannot distinguish among benign and premalignant states. We therefore investigated the ability of fragment-based cfDNA features to differentiate NF1-associated tumors including binned genome-wide fragment length ratios, end motif analysis, and non-negative matrix factorization deconvolution of fragment lengths. Fragmentomic methods were able to differentiate pre-malignant states including atypical neurofibromas (AN). Fragmentomics also adjudicated AN cases suspicious for MPNST, correctly diagnosing samples noninvasively, which could have informed clinical management. Overall, this study pioneers the early detection of malignant and premalignant peripheral nerve sheath tumors in NF1 patients using plasma cfDNA fragmentomics. In addition to screening applications, this novel approach distinguishes atypical neurofibromas from benign plexiform neurofibromas and malignant peripheral nerve sheath tumors, enabling more precise clinical diagnosis and management.

GAiN: An integrative tool utilizing generative adversarial neural networks for augmented gene expression analysis

Big genomic data and artificial intelligence (AI) are ushering in an era of precision medicine, providing opportunities to study previously under-represented subtypes and rare diseases rather than categorize them as variances. However, clinical researchers face challenges in accessing such novel technologies as well as reliable methods to study small datasets or subcohorts with unique phenotypes. To address this need, we developed an integrative approach, GAiN, to capture patterns of gene expression from small datasets on the basis of an ensemble of generative adversarial networks (GANs) while leveraging big population data. Where conventional biostatistical methods fail, GAiN reliably discovers differentially expressed genes (DEGs) and enriched pathways between two cohorts with limited numbers of samples (n = 10) when benchmarked against a gold standard. GAiN is freely available at GitHub. Thus, GAiN may serve as a crucial tool for gene expression analysis in scenarios with limited samples, as in the context of rare diseases, under-represented populations, or limited investigator resources.

Genomic approaches to cancer and minimal residual disease detection using circulating tumor DNA

Liquid biopsies using cell-free circulating tumor DNA (ctDNA) are being used frequently in both research and clinical settings. ctDNA can be used to identify actionable mutations to personalize systemic therapy, detect post-treatment minimal residual disease (MRD), and predict responses to immunotherapy. ctDNA can also be isolated from a range of different biofluids, with the possibility of detecting locoregional MRD with increased sensitivity if sampling more proximally than blood plasma. However, ctDNA detection remains challenging in early-stage and post-treatment MRD settings where ctDNA levels are minuscule giving a high risk for false negative results, which is balanced with the risk of false positive results from clonal hematopoiesis. To address these challenges, researchers have developed ever-more elegant approaches to lower the limit of detection (LOD) of ctDNA assays toward the part-per-million range and boost assay sensitivity and specificity by reducing sources of low-level technical and biological noise, and by harnessing specific genomic and epigenomic features of ctDNA. In this review, we highlight a range of modern assays for ctDNA analysis, including advancements made to improve the signal-to-noise ratio. We further highlight the challenge of detecting ultra-rare tumor-associated variants, overcoming which will improve the sensitivity of post-treatment MRD detection and open a new frontier of personalized adjuvant treatment decision-making.

Abstract 3359: Sensitive detection of locoregional MRD after head and neck cancer surgery

Background: Plasma cell-free DNA (cfDNA) has low sensitivity to detect locoregional molecular residual disease (MRD) immediately after surgery for limited-stage head and neck cancer. To enhance locoregional MRD sensitivity, we utilize a novel biofluid proximal to the primary tumor: the serosanguinous fluid collected by surgical drains inserted into the wound bed following regional lymph node dissection. We demonstrate that cancer-associated cfDNA in the surgical drain fluid (SDF) is a sensitive biomarker of locoregional MRD detection, risk stratification, and prognostication.

Methods: We extracted DNA from 168 SDFs, 48 paired plasmas, and 44 tumor specimens collected 24 hours after surgery from 90 patients: 74 HPV (+) oropharyngeal cancers (OPC), 8 HPV (-) oral cancers, 2 thyroid cancers, and 6 benign neck pathologies. SDFs were also collected at 0, 6, 12, and 24 hours after surgery from 11 HPV (+) patients. We applied TaqMan qPCR to our specimens to quantify cell-free HPV (cf-HPV), a proxy for cancer-associated cfDNA in HPV (+) malignancies. We then measured the association between cf-HPV and extranodal extension (ENE), AJCC 8 staging, and established clinical and pathological risk criteria from 4 HPV (+) OPC clinical trials. We validated our findings using HPV next-generation sequencing. We also compared the predictive value of high-risk pathology with cf-HPV MRD for HPV (+) OPC recurrences. Lastly, we developed a second assay for cell-free BRAF V600E (cf-V600E) in thyroid cancer SDF.

Results: Serially collected SDF revealed cf-HPV decreased continuously from 0 to 24 hours postoperative, and that the 24-hour timepoint stratified detectable versus undetectable persistent residual disease. At 24 hours, SDF was significantly more enriched with cf-HPV compared to plasma (P &lt; 0.0001). In a subset of 9 patients, HPV genotype and detection in SDF were 100% concordant between NGS and PCR. Strikingly, SDF cf-HPV was 11-fold higher in pN2 patients versus pN1/N0 (P = 0.02) and 15-fold higher in cases with ENE (P = 0.003), suggesting SDF reflects aggressive nodal pathology and captures locoregional MRD. When we classified our patients according to established clinical and pathological risk criteria, we found significantly higher SDF cf-HPV among high-risk patients (AUC = 0.77). Crucially, in HPV (+) patients treated with surgery alone, SDF MRD detected 100% of locoregional recurrences, while plasma MRD and high-risk pathology detected 0%. Lastly, as proof of concept, we demonstrated SDF cf-V600E detection in the context of high-risk thyroid cancer.

Conclusions: Surgical drain fluid cancer-associated cfDNA is a novel minimally invasive biomarker. Our SDF assay was strongly associated with high-risk criteria and detected locoregional relapse with 100% sensitivity compared to 0% in plasma. Our data suggest that SDF liquid biopsy is ultra-sensitive and has the potential to inform postoperative molecular-based risk stratification.

Citation Format: Noah Earland, Ricardo J. Ramirez, Sophie P. Gerndt, Peter K. Harris, Andrew I. Hearn, Matthew Inkman, Jeffrey J. Szymanski, Nick Semenkovich, Benjamin M. Wahle, Zhongping Xu, Kevin Chen, Jin Zhang, Jose P. Zevallos, Aadel A. Chaudhuri. Sensitive detection of locoregional MRD after head and neck cancer surgery [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3359.

Abstract 997: Cell-free DNA fragmentomics distinguish between benign, pre-malignant and malignant peripheral nerve sheath tumors in neurofibromatosis type 1

Background: Malignant peripheral nerve sheath tumors (MPNST) are aggressive soft tissue sarcomas that, in the setting of neurofibromatosis type 1 (NF1), arise within pre-malignant atypical neurofibroma (AN) and benign plexiform neurofibroma (PN). Early surgical resection improves prognosis, however, early detection by imaging and tissue biopsies is challenging due to tissue heterogeneity. In this multi-institutional study we analyze fragmentomic profiles of plasma cell free DNA (cfDNA) to non-invasively distinguish between NF1 associated PN, AN and MPNST. Accurate classification would inform clinical care: standards of care for PN is observation, AN is narrow-margin resection, and MPNST is wide-margin resection.

Methods: We performed whole genome sequencing of plasma cfDNA samples from healthy controls (n = 21), patients with PN (n = 113), AN (n = 39) and MPNST (n = 71). cfDNA fragment profiles were analyzed using two complementary approaches. First, we used unsupervised non-negative matrix factorization (NMF) to obtain global fragment length signatures to infer tumor fragment length distributions. The optimal cutpoint was determined after receiver operating characteristic analysis by Youden’s index in one-versus-one (OVO) disease state comparisons. Additionally, we implemented a bin-wise fragmentomic analysis based on DELFI, training a classifier on the ratios of short (100-150bp) and long (151-220bp) fragments in 5 megabase regions across the genome and arm-level features.

Results: NMF accurately distinguished disease states on OVO comparisons: MPNST v AN (acc 0.71), MPNST v PN (acc 0.75), MPNST v healthy (acc 0.84), AN v PN (acc 0.70), AN v healthy (acc 0.80) and PN v healthy (acc 0.87). Accuracies were moderately improved in nearly all conditions with bin-wise fragmentomics: MPNST v AN (acc 0.62), MPNST v PN (acc 0.83), MPNST vs healthy (acc 0.86), AN v PN (acc 0.87), AN vs healthy (acc 0.72) and PN vs healthy (acc 0.88). Strikingly, the two AN with the DELFI scores most closely resembling MPNST were separately identified by independent clinical care teams to have very high-risk features and recent history warranting short-interval follow up.

Conclusions: This study demonstrates that the spectrum of benign, pre-malignant and malignant peripheral nerve sheath tumors have distinct, disease state specific fragmentomic signatures. Fragmentomics alone outperformed our previously published copy number based cfDNA classifier in all conditions, most notably in low mutational burden healthy, PN and AN states. Finally, preliminary clinical vignettes suggest that this approach may be able to inform surveillance intervals by identifying higher risk premalignant lesions. Together, this work has the potential to enable earlier detection of clinically actionable AN and early-stage MPNST, thereby improving survival outcomes.

Citation Format: Alex C. Pan, Russell Taylor Sundby, Jeffrey J. Szymanski, Paul A. Jones, Peter K. Harris, Aadel A. Chaudhuri, Angela C. Hirbe, Jack F. Shern. Cell-free DNA fragmentomics distinguish between benign, pre-malignant and malignant peripheral nerve sheath tumors in neurofibromatosis type 1 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 997.

Genomic Patterns of Malignant Peripheral Nerve Sheath Tumor (MPNST) Evolution Correlate with Clinical Outcome and Are Detectable in Cell-Free DNA

Malignant peripheral nerve sheath tumor (MPNST), an aggressive soft-tissue sarcoma, occurs in people with neurofibromatosis type 1 (NF1) and sporadically. Whole-genome and multiregional exome sequencing, transcriptomic, and methylation profiling of 95 tumor samples revealed the order of genomic events in tumor evolution. Following biallelic inactivation of NF1, loss of CDKN2A or TP53 with or without inactivation of polycomb repressive complex 2 (PRC2) leads to extensive somatic copy-number aberrations (SCNA). Distinct pathways of tumor evolution are associated with inactivation of PRC2 genes and H3K27 trimethylation (H3K27me3) status. Tumors with H3K27me3 loss evolve through extensive chromosomal losses followed by whole-genome doubling and chromosome 8 amplification, and show lower levels of immune cell infiltration. Retention of H3K27me3 leads to extensive genomic instability, but an immune cell-rich phenotype. Specific SCNAs detected in both tumor samples and cell-free DNA (cfDNA) act as a surrogate for H3K27me3 loss and immune infiltration, and predict prognosis.

SIGNIFICANCE

MPNST is the most common cause of death and morbidity for individuals with NF1, a relatively common tumor predisposition syndrome. Our results suggest that somatic copy-number and methylation profiling of tumor or cfDNA could serve as a biomarker for early diagnosis and to stratify patients into prognostic and treatment-related subgroups. This article is highlighted in the In This Issue feature, p. 517.

Abstract B006: Development of a NF1-MPNST-PDX liquid biopsy model using whole-genome sequencing and quantitative PCR of mouse-derived cell-free DNA

Background: Malignant Peripheral Nerve Sheath Tumors (MPNST) are aggressive, NF1-associated soft tissue sarcomas with a dismal 40% 5-year survival rate, high rates of disease relapse and metastasis, and limited treatment options. Our lab has generated a collection of patient-derived xenograft (PDX) models, which recapitulate the variety of genetic changes that occur in human NF1-MPNST. Longitudinal analysis of PDX tumor burden in preclinical studies is currently limited to imprecise tumor measurement or expensive and time-consuming imaging modalities such as MRI. These methods of analysis fail to allow for the early detection of tumor formation, the assessment of treatment-response dynamics, the formation of resistant subclones, or the detection of molecular residual disease. Liquid biopsies using plasma-derived cell-free DNA (cfDNA) have been successful in addressing these challenges in the context of multiple solid tumor types including MPNST by our group previously (Szymanski et al. 2021). However, liquid biopsy of cfDNA in the context murine model systems is quite limited, primarily due the challenge of collecting sufficient plasma for analysis. We hypothesize that we can detect and longitudinally track tumor burden in response to treatment using human-tumor-specific quantitative PCR (qPCR) and whole-genome sequencing of sequentially collected PDX-bearing murine plasma to develop a NF1-MPNST-PDX liquid biopsy model. Methods: To address this challenge, we sequentially collected ≈50 µL of murine plasma weekly from two independent groups of NF1-MPNST-PDX-bearing mice and corresponding PDX-free controls for up to six weeks. The first group consisted of six PDX-bearing mice who underwent whole-genome sequence of murine-derived plasma cfDNA and paired PDX tissue. The second group consisted of fifteen NF1-MPNST-PDX-bearing mice and five PDX-free controls; plasma cfDNA samples collected from this group underwent human-specific LINE-1 qPCR, which should only detect human DNA derived from implanted PDX and allow for longitudinal tracking of tumor burden. Results: We serially collected ≈50 µL of plasma weekly from NF1-MPNST-PDX mice with no obvious impact on mouse survival or weight. Mean total cfDNA yield from the terminally collected samples was 1.12 ± 1.02 ng per uL plasma (n=21) for PDX-bearing animals with cfDNA fragments canonically appearing between 70 and 450 bps as determined by electropherogram. Whole-genome sequencing of murine plasma cfDNA revealed broad genomic aneuploidy detectable in NF1-MPNST-PDX plasma which corresponded to alterations present in PDX tissue, including MPNST-specific chromosome 8q gain, corresponding with our earlier findings (Dehner et al. 2021). Human-specific LINE-1 qPCR showed specific enrichment of tumor-derived LINE-1 in NF1-MPNST-PDX-bearing mice compared to PDX-free mice which showed no human LINE-1 enrichment. Conclusion: Our data suggest that PDX plasma cfDNA may be an informative biomarker that can be non-invasively collected and used to track tumor burden in NF1-MPNST-PDX models.

Citation Format: Paul A. Jones, Wenjia Feng, Xiaochun Zhang, Peter K. Harris, Taylor Sundby, Jeffrey J. Szymanski, Divya Srihari, Faridi Qaium, Jack F. Shern, Aadel A. Chaudhuri, Angela C. Hirbe. Development of a NF1-MPNST-PDX liquid biopsy model using whole-genome sequencing and quantitative PCR of mouse-derived cell-free DNA [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr B006.

Integrative analysis of urine cell-free DNA for the detection of residual disease in localized bladder cancer patients

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Background: We previously developed a liquid biopsy assay to measure urine tumor DNA (utDNA) levels based on detection of single nucleotide variants (SNVs) in urine cell-free DNA (cfDNA). Nonsilent SNV detection in urine from muscle-invasive bladder cancer (MIBC) patients prior to radical cystectomy (RC) was associated with pathologic residual disease and worse progression-free survival (Chauhan et al., PLOS Medicine, 2021). Given the multiple types of genomic alterations present in bladder cancer (BC), here we developed a multi-omics approach for estimating utDNA levels without restricting our approach to SNVs. We performed ultra-low pass whole genome sequencing (ULP-WGS) based copy number analysis and urine Cancer Personalized Profiling by deep Sequencing (uCAPP-Seq) of urine cell-free DNA to predict pathologic complete response (pCR) in localized BC patients. Methods: We acquired urine preoperatively from 65 BC patients (69% muscle-invasive) on the day of standard-of-care RC, and after neoadjuvant chemotherapy in 48% of patients. We performed ULP-WGS of urine cfDNA from all 65 BC patients and 11 healthy adults. utDNA levels based on genome-wide copy number alterations (CNAs) in urine cfDNA was estimated using ichorCNA. In order to derive a SNV-based utDNA level as well, uCAPP-Seq was applied to urine cfDNA samples derived from 42 patients using a 145 kb panel of 49 consensus driver genes commonly mutated in MIBC. Results: In our cohort of 65 BC patients, 55% of patients achieved pCR ( n = 36) while 45% had residual disease detected in their surgical sample (no pCR; n = 29). Comparing ULP-WGS-derived utDNA levels between the groups, patients with no pCR had significantly higher CNA-derived tumor fractions in urine compared to patients with pCR (median 8.9% vs 1.8%, p = 0.01) and healthy adults ( n = 11) (median 8.9% vs 0%, p = 0.006). Further analysis with uCAPP-Seq in 42 patients revealed that nonsilent SNV-based utDNA detection correlated significantly with the absence of pCR ( p < 0.001) with a sensitivity of 81% and specificity of 81%. Moreover, utDNA-positive patients exhibited significantly worse progression-free survival compared to utDNA-negative patients (HR = 7.4; 95% CI: 1.4–38.9; p = 0.02). Conclusions: Bladder cancer patients who did not attain a pCR at the time of RC had greater genome-wide copy number alterations and nonsilent single nucleotide variants in their urine cfDNA compared to patients with pCR. These results suggest that integrative multi-omics of urine derived from MIBC patients has potential real-world clinical impact for bladder-sparing approaches in select patients.

Correction: Urine tumor DNA detection of minimal residual disease in muscle-invasive bladder cancer treated with curative-intent radical cystectomy: A cohort study

[This corrects the article DOI: 10.1371/journal.pmed.1003732.].

Urine tumor DNA detection of minimal residual disease in muscle-invasive bladder cancer treated with curative-intent radical cystectomy: A cohort study

BACKGROUND

The standard of care treatment for muscle-invasive bladder cancer (MIBC) is radical cystectomy, which is typically preceded by neoadjuvant chemotherapy. However, the inability to assess minimal residual disease (MRD) noninvasively limits our ability to offer bladder-sparing treatment. Here, we sought to develop a liquid biopsy solution via urine tumor DNA (utDNA) analysis.

METHODS AND FINDINGS

We applied urine Cancer Personalized Profiling by Deep Sequencing (uCAPP-Seq), a targeted next-generation sequencing (NGS) method for detecting utDNA, to urine cell-free DNA (cfDNA) samples acquired between April 2019 and November 2020 on the day of curative-intent radical cystectomy from 42 patients with localized bladder cancer. The average age of patients was 69 years (range: 50 to 86), of whom 76% (32/42) were male, 64% (27/42) were smokers, and 76% (32/42) had a confirmed diagnosis of MIBC. Among MIBC patients, 59% (19/32) received neoadjuvant chemotherapy. utDNA variant calling was performed noninvasively without prior sequencing of tumor tissue. The overall utDNA level for each patient was represented by the non-silent mutation with the highest variant allele fraction after removing germline variants. Urine was similarly analyzed from 15 healthy adults. utDNA analysis revealed a median utDNA level of 0% in healthy adults and 2.4% in bladder cancer patients. When patients were classified as those who had residual disease detected in their surgical sample (n = 16) compared to those who achieved a pathologic complete response (pCR; n = 26), median utDNA levels were 4.3% vs. 0%, respectively (p = 0.002). Using an optimal utDNA threshold to define MRD detection, positive utDNA MRD detection was highly correlated with the absence of pCR (p < 0.001) with a sensitivity of 81% and specificity of 81%. Leave-one-out cross-validation applied to the prediction of pathologic response based on utDNA MRD detection in our cohort yielded a highly significant accuracy of 81% (p = 0.007). Moreover, utDNA MRD-positive patients exhibited significantly worse progression-free survival (PFS; HR = 7.4; 95% CI: 1.4-38.9; p = 0.02) compared to utDNA MRD-negative patients. Concordance between urine- and tumor-derived mutations, determined in 5 MIBC patients, was 85%. Tumor mutational burden (TMB) in utDNA MRD-positive patients was inferred from the number of non-silent mutations detected in urine cfDNA by applying a linear relationship derived from The Cancer Genome Atlas (TCGA) whole exome sequencing of 409 MIBC tumors. We suggest that about 58% of these patients with high inferred TMB might have been candidates for treatment with early immune checkpoint blockade. Study limitations included an analysis restricted only to single-nucleotide variants (SNVs), survival differences diminished by surgery, and a low number of DNA damage response (DRR) mutations detected after neoadjuvant chemotherapy at the MRD time point.

CONCLUSIONS

utDNA MRD detection prior to curative-intent radical cystectomy for bladder cancer correlated significantly with pathologic response, which may help select patients for bladder-sparing treatment. utDNA MRD detection also correlated significantly with PFS. Furthermore, utDNA can be used to noninvasively infer TMB, which could facilitate personalized immunotherapy for bladder cancer in the future.

Cell-free DNA ultra-low-pass whole genome sequencing to distinguish malignant peripheral nerve sheath tumor (MPNST) from its benign precursor lesion: A cross-sectional study

BACKGROUND

The leading cause of mortality for patients with the neurofibromatosis type 1 (NF1) cancer predisposition syndrome is the development of malignant peripheral nerve sheath tumor (MPNST), an aggressive soft tissue sarcoma. In the setting of NF1, this cancer type frequently arises from within its common and benign precursor, plexiform neurofibroma (PN). Transformation from PN to MPNST is challenging to diagnose due to difficulties in distinguishing cross-sectional imaging results and intralesional heterogeneity resulting in biopsy sampling errors.

METHODS AND FINDINGS

This multi-institutional study from the National Cancer Institute and Washington University in St. Louis used fragment size analysis and ultra-low-pass whole genome sequencing (ULP-WGS) of plasma cell-free DNA (cfDNA) to distinguish between MPNST and PN in patients with NF1. Following in silico enrichment for short cfDNA fragments and copy number analysis to estimate the fraction of plasma cfDNA originating from tumor (tumor fraction), we developed a noninvasive classifier that differentiates MPNST from PN with 86% pretreatment accuracy (91% specificity, 75% sensitivity) and 89% accuracy on serial analysis (91% specificity, 83% sensitivity). Healthy controls without NF1 (participants = 16, plasma samples = 16), PN (participants = 23, plasma samples = 23), and MPNST (participants = 14, plasma samples = 46) cohorts showed significant differences in tumor fraction in plasma (P = 0.001) as well as cfDNA fragment length (P < 0.001) with MPNST samples harboring shorter fragments and being enriched for tumor-derived cfDNA relative to PN and healthy controls. No other covariates were significant on multivariate logistic regression. Mutational analysis demonstrated focal NF1 copy number loss in PN and MPNST patient plasma but not in healthy controls. Greater genomic instability including alterations associated with malignant transformation (focal copy number gains in chromosome arms 1q, 7p, 8q, 9q, and 17q; focal copy number losses in SUZ12, SMARCA2, CDKN2A/B, and chromosome arms 6p and 9p) was more prominently observed in MPNST plasma. Furthermore, the sum of longest tumor diameters (SLD) visualized by cross-sectional imaging correlated significantly with paired tumor fractions in plasma from MPNST patients (r = 0.39, P = 0.024). On serial analysis, tumor fraction levels in plasma dynamically correlated with treatment response to therapy and minimal residual disease (MRD) detection before relapse. Study limitations include a modest MPNST sample size despite accrual from 2 major referral centers for this rare malignancy, and lack of uniform treatment and imaging protocols representing a real-world cohort.

CONCLUSIONS

Tumor fraction levels derived from cfDNA fragment size and copy number alteration analysis of plasma cfDNA using ULP-WGS significantly correlated with MPNST tumor burden, accurately distinguished MPNST from its benign PN precursor, and dynamically correlated with treatment response. In the future, our findings could form the basis for improved early cancer detection and monitoring in high-risk cancer-predisposed populations.

Abstract 543: ctDNA MRD detection from plasma and urine and personalized oncogenomic analysis in oligometastatic colorectal cancer

BACKGROUND: Circulating tumor DNA (ctDNA) can detect molecular residual disease (MRD) in plasma after curative-intent treatment of non-metastatic solid tumor malignancy when prior mutational knowledge from either tumor or pre-treatment plasma is available. We hypothesized that ctDNA MRD analysis without prior mutational knowledge could be performed to assess oligometastatic colorectal cancer (CRC) treated with curative intent by applying an error-corrected ultra-deep targeted sequencing approach. We also investigated urine as an alternative analyte for ctDNA MRD detection in this non-genitourinary setting.

METHODS: We applied AVENIO, a ctDNA technology derived from CAncer Personalized Profiling by deep Sequencing (CAPP-Seq) with integrated digital error suppression (iDES), to plasma, tumor, and urine samples acquired on the day of surgery from 24 prospectively enrolled oligometastatic CRC patients. We sequenced patients' white blood cell DNA to remove age-related clonal hematopoiesis variants. Plasma and urine ctDNA MRD detection were then correlated with residual disease present in tumor tissue, and adjuvant treatment strategies were proposed based on plasma ctDNA-inferred tumor mutational burden and targetable genomic alterations.

RESULTS: Tumor-naïve plasma ctDNA analysis detected MRD at a median level of 0.62% with 95% sensitivity and 100% specificity. Plasma ctDNA MRD levels correlated with tumor size at the time of surgery (ρ= 0.68, P = 0.0003) and were significantly lower in patients without evidence of disease in their surgical specimen compared to those with residual tumor cells (P = 0.02). In urine, ctDNA MRD detection specificity remained high at 100%, but sensitivity was lower at 64%, with median levels being 11-fold lower than in plasma (P &lt; 0.0001). Cell-free DNA fragments containing mutations were shorter in urine with an average size of 150.1 bp, compared to 180.2 bp in plasma (P &lt; 0.0001). Personalized ctDNA MRD oncogenomic analysis revealed that 81% of patients had a high inferred tumor mutational burden (&gt;10 mutations/megabase), and 10% also had a targetable PIK3CA mutation.

CONCLUSION: Tumor-naïve plasma ctDNA analysis can sensitively and specifically detect MRD in patients with oligometastatic CRC after neoadjuvant chemotherapy. Urine-based ctDNA MRD detection is also feasible in these patients; however, it is less sensitive than plasma. Analysis of oligometastatic CRC patients' ctDNA MRD also revealed potentially actionable results that might have implications for personalized adjuvant treatment regimens.

Citation Format: Bruna Pellini, Nadja Pejovic, Wenjia Feng, Noah Earland, Peter K. Harris, Abul Usmani, Jeffrey J. Szymanski, Farid Qaium, Jacqueline Mudd, Hyun Kim, Benjamin Tan, Ryan C. Fields, Aadel A. Chaudhuri. ctDNA MRD detection from plasma and urine and personalized oncogenomic analysis in oligometastatic colorectal cancer [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 543.

Tracking minimal residual disease with urine tumor DNA in muscle-invasive bladder cancer after neoadjuvant chemotherapy

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Background: Standard-of-care for muscle-invasive bladder cancer (MIBC) consists of neoadjuvant chemotherapy (NAC) followed by radical cystectomy. The inability to noninvasively assess minimal residual disease (MRD) after NAC limits our ability to offer bladder-sparing treatment. We perform urine tumor DNA (utDNA) analysis to identify pathologic complete response (pCR) at the time of cystectomy in patients receiving NAC. Methods: We applied CAPP-Seq to urine cell-free DNA samples acquired on the day of radical cystectomy from 19 MIBC patients treated with NAC. utDNA variant-calling was performed without prior tumor mutational knowledge using a panel of 49 consensus driver genes mutated in MIBC. The utDNA level for each patient was represented by the duplex-supported non-silent driver mutation with the highest variant allele fraction (vAF) after removing germline variants. We also serially tracked utDNA variants in two patients before, during, and after NAC. Results: Comparing patients with residual disease detected in their cystectomy specimen ( n = 10) to those who achieved a pCR ( n = 9), median utDNA levels were 2.4% vs. 0%, respectively ( P = 0.006). Using an optimal utDNA threshold to define MRD detection, positive utDNA MRD was highly correlated with the absence of pCR ( P = 0.003). Analysis of two patients’ serial urine samples revealed utDNA dynamics that were consistent with treatment responses in real-time. In one patient who ultimately achieved a pCR, four non-silent driver mutations were detectable pre-NAC, including ERCC2 N238S (7.8% vAF) associated with increased chemosensitivity. One week after starting NAC, ERCC2 N238S increased by 1.6-fold in urine, as did PIK3CA E726K which increased by 8.4-fold. Four weeks post-NAC, however, all mutations previously detected in this patient’s urine became undetectable, consistent with the patient’s pCR and long-term disease-free survival. Conversely, another patient harbored two non-silent driver mutations in PLEKHS1 (1.9% vAF) and KMT2D (4.9% vAF) pre-NAC. One week after starting NAC, both mutations decreased dramatically by 8.0- and 4.3-fold, respectively. By three weeks post-NAC, however, these mutations progressively increased by 5.2-fold on average, which correlated with a lack of pCR as well as post-treatment disease progression. Two newly detected non-silent driver mutations in ARID1A and ERBB2 also emerged on NAC and persisted following completion of chemotherapy , likely reflecting the development of treatment resistance. Conclusions: utDNA MRD after NAC but before radical cystectomy for MIBC correlated significantly with pathologic response, which could help personalize patient selection for bladder-sparing treatments in the future. Serial monitoring of utDNA variants during NAC can reveal dynamic mutational changes that reflect real-time treatment responses as well as ultimate disease-free survival.

ctDNA MRD Detection and Personalized Oncogenomic Analysis in Oligometastatic Colorectal Cancer From Plasma and Urine

We hypothesized that circulating tumor DNA (ctDNA) molecular residual disease (MRD) analysis without prior mutational knowledge could be performed after neoadjuvant chemotherapy to assess oligometastatic colorectal cancer (CRC) treated surgically with curative intent. We also investigated urine as an alternative analyte for ctDNA MRD detection in this nongenitourinary setting.

PATIENTS AND METHODS

We applied AVENIO targeted next-generation sequencing to plasma, tumor, and urine samples acquired on the day of curative-intent surgery from 24 prospectively enrolled patients with oligometastatic CRC. Age-related clonal hematopoiesis was accounted for by removing variants also present in white blood cells. Plasma and urine ctDNA MRD were correlated with tumor cells detected in the surgical specimen, and adjuvant treatment strategies were proposed based on ctDNA-inferred tumor mutational burden (iTMB) and targetable alterations.

RESULTS

Seventy-one percent of patients were treated with neoadjuvant chemotherapy. Tumor-naive plasma ctDNA analysis detected MRD at a median level of 0.62% with 95% sensitivity and 100% specificity, and 94% and 77% sensitivity when only considering patients treated with neoadjuvant chemotherapy and putative driver mutations, respectively. In urine, ctDNA MRD detection specificity remained high at 100%, but sensitivity decreased to 64% with median levels being 11-fold lower than in plasma (P < .0001). Personalized ctDNA MRD oncogenomic analysis revealed 81% of patients might have been candidates for adjuvant immunotherapy based on high iTMB or targeted therapy based on actionable PIK3CA mutations.

CONCLUSION

Tumor-naive plasma ctDNA analysis can sensitively and specifically detect MRD in patients with oligometastatic CRC after neoadjuvant chemotherapy. Urine-based ctDNA MRD detection is also feasible; however, it is less sensitive than plasma because of significantly lower levels. Oligometastatic patients with detectable MRD may benefit from additional personalized treatment based on ctDNA-derived oncogenomic profiling.

Once-Per-Visit Alerts: A Means to Study Alert Compliance and Reduce Repeat Laboratory Testing

BACKGROUND

Clinical decision support alerts for laboratory testing have poor compliance. Once-per-visit alerts, triggered by reorder of a test within the same admission, are highly specific for unnecessary orders and provide a means to study alert compliance.

METHODS

Once-per-visit alerts for 18 laboratory orderables were analyzed over a 60-month period from September 2012 to October 2016 at a 1200-bed academic medical center. To determine correlates of alert compliance, we compared alerts by test and provider characteristics.

RESULTS

Overall alert compliance was 54.5%. In multivariate regression, compliance correlated with length of stay at time of alert, provider type, previous alerts in a patient visit, test ordered, total alerts experienced by ordering provider, and previous order status.

CONCLUSIONS

A diverse set of provider and test characteristics influences compliance with once-per-visit laboratory alerts. Future alerts should incorporate these characteristics into alert design to minimize alert overrides.

Short- and Long-term Biologic Variability of Galectin-3 and Other Cardiac Biomarkers in Patients with Stable Heart Failure and Healthy Adults

BACKGROUND

Galectin-3 (Gal-3) has been suggested as a prognostic biomarker in heart failure (HF) patients that may better reflect disease progression than traditional markers, including B-type natriuretic peptide (BNP) and cardiac troponins. To fully establish the utility of any biomarker in HF, its biologic variability must be characterized.

METHODS

To assess biologic variability, 59 patients were prospectively recruited, including 23 male and 16 female patients with stable HF and 10 male and 10 female healthy individuals. Gal-3, BNP, and high-sensitivity cardiac troponin I (hs-cTnI) were assayed at 5 time points within a 3-week period to assess short-term biologic variability. Long-term (3-month) biologic variability was assessed with samples collected at enrollment and after 4, 8, and 12 weeks.

RESULTS

Among healthy individuals, mean short-term biologic variability, expressed as intraindividual CV (CVI), was 4.5% for Gal-3, 29.0% for BNP, and 14.5% for hs-cTnI; long-term biologic variability was 5.5% for Gal-3, 34.7% for BNP, and 14.7% for hs-cTnI. In stable HF patients, mean short-term biologic variability was 7.1% for Gal-3, 22.5% for BNP, and 8.5% for hs-cTnI, and mean long-term biologic variability was 7.7% for Gal-3, 27.6% for BNP, and 9.6% for hs-cTnI.

CONCLUSIONS

The finding that Gal-3 has minimal intraindividual biological variability adds to its potential as a useful biomarker in HF patients.

Incidence of humoral hypercalcemia of malignancy among hypercalcemic patients with cancer

BACKGROUND

Malignancy-associated hypercalcemia (MAHC) is the most common cause of hypercalcemia among hospitalized patients. MAHC can result from the production of parathyroid hormone related peptide (PTHrP) which is known as humoral hypercalcemia of malignancy (HHM). HHM is commonly thought to account for approximately 80% of MAHC.

METHODS

We conducted a 12-year review of PTHrP testing at our institution to establish the prevalence of HHM among patients with MAHC.

RESULTS

A total of 524 PTHrP immunoassays were performed during the study period of which 470 tests qualified for inclusion in the analysis. Evidence of malignancy was found for 242 of 470 patients (51%). No etiology could be determined for 98 cases of MAHC (40%) and increased PTHrP contributed to 92 cases (38%) of MAHC. Age, race and gender were not associated with HHM. Increased PTHrP was observed at initial malignancy diagnosis in 20% of cases. PTHrP was never increased outside of the context of malignancy.

DISCUSSION

The prevalence of HHM among patients with MAHC is likely to be lower than previously described.

Impact on Patient Management and Outcome of Switching between 2 Contemporary Sensitive Cardiac Troponin Assays

BACKGROUND

Myocardial infarction is characterized by an increase of cardiac troponin I (cTnI) above the 99th percentile of a reference population. Our hospital switched from 1 contemporary cTnI assay to another and observed a doubling of cTnI results above the assays' respective 99th percentile cutoffs. We investigated the potential impact on inpatient management and outcomes.

METHODS

We performed a retrospective cohort study of 45 498 individuals with ≥1 cTnI result between January 2013 and June 2014. The Dimension cTnI assay was used in 2013; the Abbott Architect cTnI assay was used in 2014.

RESULTS

Before switching cTnI assays, 19.2% (4742/30 872) of patients had at least 1 of the first 3 cTnIs above the 99th percentile (0.07 μg/L). After switching to the Architect cTnI assay, 31.4% (4034/14 626) of patients had at least 1 cTnI above the 99th percentile (0.03 μg/L). This increase was due to the difference in the assays' 99th percentile cutoffs. Having an increased cTnI reported on the Architect assay that would not have been reported as such on the Dimension assay (0.03–0.06 μg/L) correlated with increased inpatient mortality, length of stay, non–ST elevation myocardial infarction diagnosis, therapeutic heparin use, and percutaneous coronary intervention, relative to individuals with cTnI &lt;0.03 μg/L.

CONCLUSIONS

The changes observed in patient outcomes and management were likely due to the increased sensitivity and lower 99th percentile cutoff of the Architect assay. It is important to recognize the potential impact that differences in sensitivity and assay configuration may have on patient management.

HuR function and translational state analysis following global brain ischemia and reperfusion

Prolonged translation arrest in post-ischemic hippocampal CA1 pyramidal neurons precludes translation of induced stress genes and directly correlates with cell death. We evaluated the regulation of mRNAs containing adenine- and uridine-rich elements (ARE) by assessing HuR protein and hsp70 mRNA nuclear translocation, HuR polysome binding, and translation state analysis of CA1 and CA3 at 8 h of reperfusion after 10 min of global cerebral ischemia. There was no difference between CA1 and CA3 at 8 h of reperfusion in nuclear or cytoplasmic HuR protein or hsp70 mRNA, or HuR polysome association, suggesting that neither mechanism contributed to post-ischemic outcome. Translation state analysis revealed that 28 and 58 % of unique mRNAs significantly different between 8hR and NIC, in CA3 and CA1, respectively, were not polysome-bound. There was significantly greater diversity of polysome-bound mRNAs in reperfused CA3 compared to CA1, and in both regions, ARE-containing mRNAs accounted for 4-5 % of the total. These data indicate that posttranscriptional ARE-containing mRNA regulation occurs in reperfused neurons and contributes to post-ischemic outcome. Understanding the differential responses of vulnerable and resistant neurons to ischemia will contribute to the development of effective neuroprotective therapies.

Texture analysis of poly-adenylated mRNA staining following global brain ischemia and reperfusion

Texture analysis provides a means to quantify complex changes in microscope images. We previously showed that cytoplasmic poly-adenylated mRNAs form mRNA granules in post-ischemic neurons and that these granules correlated with protein synthesis inhibition and hence cell death. Here we utilized the texture analysis software MaZda to quantify mRNA granules in photomicrographs of the pyramidal cell layer of rat hippocampal region CA3 around 1h of reperfusion after 10min of normothermic global cerebral ischemia. At 1h reperfusion, we observed variations in the texture of mRNA granules amongst samples that were readily quantified by texture analysis. Individual sample variation was consistent with the interpretation that animal-to-animal variations in mRNA granules reflected the time-course of mRNA granule formation. We also used texture analysis to quantify the effect of cycloheximide, given either before or after brain ischemia, on mRNA granules. If administered before ischemia, cycloheximide inhibited mRNA granule formation, but if administered after ischemia did not prevent mRNA granulation, indicating mRNA granule formation is dependent on dissociation of polysomes. We conclude that texture analysis is an effective means for quantifying the complex morphological changes induced in neurons by brain ischemia and reperfusion.

Organelles do not colocalize with mRNA granules in post-ischemic neurons

Following global brain ischemia and reperfusion, it is well-established that neurons undergo a translation arrest that is reversible in surviving neurons, but irreversible in vulnerable neurons. We previously showed a correlation between translation arrest in reperfused neurons and the presence of granular mRNA-containing structures we termed "mRNA granules." Here we further characterized the mRNA granules in reperfused neurons by performing colocalization studies using fluorescent in situ hybridization for poly(A) mRNAs and immunofluorescence histochemistry for markers of organelles and mRNA-binding proteins. There was no colocalization between the mRNA granules and markers of endoplasmic reticulum, cis- or trans-Golgi apparatus, mitochondria, microtubules, intermediate filaments, 60S ribosomal subunits, or the HuR ligands APRIL and pp32. The mRNA granules colocalized with the neuronal marker NeuN regardless of the relative vulnerability of the neuron type. RNA immunoprecipitation of HuR from the cytoplasmic fraction of 8 h reperfused forebrains selectively isolated hsp70 mRNA suggesting the mRNA granules are soluble structures. Together, these results rule out several organelle systems and a known HuR pathway as being directly involved in mRNA granule function.

Translation arrest and ribonomics in post-ischemic brain: layers and layers of players

A persistent translation arrest (TA) correlates precisely with the selective vulnerability of post-ischemic neurons. Mechanisms of post-ischemic TA that have been assessed include ribosome biochemistry, the link between TA and stress responses, and the inactivation of translational components via sequestration in subcellular structures. Each of these approaches provides a perspective on post-ischemic TA. Here, we develop the notion that mRNA regulation via RNA-binding proteins, or ribonomics, also contributes to post-ischemic TA. We describe the ribonomic network, or structures involved in mRNA regulation, including nuclear foci, polysomes, stress granules, embryonic lethal abnormal vision/Hu granules, processing bodies, exosomes, and RNA granules. Transcriptional, ribonomic, and ribosomal regulation together provide multiple layers mediating cell reprogramming. Stress gene induction via the heat-shock response, immediate early genes, and endoplasmic reticulum stress represents significant reprogramming of post-ischemic neurons. We present a model of post-ischemic TA in ischemia-resistant neurons that incorporates ribonomic considerations. In this model, selective translation of stress-induced mRNAs contributes to translation recovery. This model provides a basis to study dysfunctional stress responses in vulnerable neurons, with a key focus on the inability of vulnerable neurons to selectively translate stress-induced mRNAs. We suggest a ribonomic approach will shed new light on the roles of mRNA regulation in persistent TA in vulnerable post-ischemic neurons.

Diverse clinical manifestations of pheochromocytomas

Many difficulties are encountered by clinicians in attempting to diagnose pheochromocytomas. We describe several patients with unusual clinical features. These include sudden death, cerebral hemorrhage, refractory congestive heart failure, acute abdominal pain, and hypercalcemia. In 2 patients, the rare association of this tumor and pregnancy was observed. Two subjects had sudden death, 1 during a pneumoencephalogram and another during an epidural block. The clinicians should be aware of these manifestations of pheochromocytomas.