Liquid biopsies: the newest tool for diagnosing and treating tumors

Two recent PLOS Medicine studies indicate that innovations in liquid biopsy could become the new, fast, and less invasive method for detecting and tracking tumors.

One of the studies examined the efficacy of liquid biopsy in treating muscle-invasive bladder cancer (MIBC)¹ and the other investigated liquid biopsy as a biomarker for peripheral nerve tumors, which in rare cases can occur in the prostate.² Both papers were led by Aadel A. Chaudhuri, MD, PhD, and conducted at Washington University School of Medicine, St. Louis, Missouri.

Liquid biopsy and bladder cancer

This study implemented a next-generation sequencing approach called urine Cancer Personalized Profile by Deep Sequencing (uCAPP-Seq) to detect urine tumor DNA (utDNA) in patients with localized bladder cancer.

Aadel A. Chaudhuri, MD, PhD

“For bladder cancer, if a urine biopsy can detect whether the early chemotherapy totally eradicated the tumor, it could help some patients avoid major surgery to remove the bladder,” explained Chaudhuri in a news release.³

Chaudhuri et al also found that the approach can be used “to noninvasively infer tumor mutational burden (TMB)” to identify patients who are candidates for early immune checkpoint blockade.

Between April 2019 and November 2020, Chaudhuri et al collected paired blood and urine samples from 42 patients on the day of curative-intent radical cystectomy. A similar sample was taken from 15 healthy patients to later compare the pathologic complete response (pCR) and survival outcomes between the groups.

Of the enrolled patients, 76% (32/42) were men, 64% (27/42) were smokers, and the average age was 69 (50-86) years. Seventy-six percent (32/42) had confirmed diagnosis of MIBC, and among them, 59% (19/32) received neoadjuvant chemotherapy.

In comparing the samples, results found that the median utDNA level was 0% in healthy patients versus 2.4% in patients with bladder cancer (P = .006). When comparing the samples of those who had minimal residual disease (MRD; n = 16) versus those who achieved a pCR (n = 26), median utDNA levels were 4.3% and 0%, respectively (P = .002).

Additionally, positive utDNA MRD detection was significantly correlated with the absence of pCR (P <.001; sensitivity, 81%; specificity, 81%) and utDNA MRD-positive patients had worse progression-free survival (HR, 7.4; 95% CI, 1.4-38.9; P = .02) than utDNA MRD-negative patients.

TMB findings, determined by the number of non-silent mutations detected in urine cell-free DNA (cfDNA), suggested that 58% of patients may have been candidates for treatment with early immune checkpoint blockade.

From these findings, the authors of this study concluded, “Our approach has the potential to facilitate more personalized treatment interventions for MIBC in the future, such as curative-intent bladder-sparing approaches, adjuvant treatment with immune checkpoint blockade, and targeted systemic therapy administration.”

Liquid biopsy and peripheral nerve tumors

In this multi-institutional study, investigators used fragment size analysis and ultra-low-pass whole genome sequencing (ULP-WGS) of plasma cfDNA to distinguish malignant peripheral nerve sheath tumors (MPNSTs) from plexiform neurofibroma (PN) in patients with neurofibromatosis type 1 (NF1).

In describing the background for this study, Chaudhuri said, “For NF1, if we can distinguish between tumors that are cancerous versus precancerous, we open the door to early cancer detection in hereditary conditions that predispose people to developing cancer.”³

Also of note for urologists, recent research includes prostate cancer as one of the cancers associated with NF1.⁴

Blood and plasma samples were collected from 53 patients with NF1 who had MPNST and PN tumors. 23 participants had PN (23 plasma samples), 14 participants had MPNST (46 plasma samples), and there were 16 healthy participants (16 plasma samples).

During this study, Silico enrichment was performed for short cfDNA fragments, copy number analysis was performed to evaluate tumor fraction, and ULP-WGS was performed to differentiate MPNST from PN. This noninvasive classifier had an 86% pretreatment accuracy (91% specificity, 75% sensitivity) and 89% accuracy on serial analysis (91% specificity, 83% sensitivity).

Results showed that patients with MPNST had plasma cfDNA with a shorter fragmentation profile versus patients with PN or healthy patients. Plasma cfDNA in patients with MPNST or PN also had focal copy number loss that was not seen in healthy patients and MPNST patient cfDNA had significantly greater tumor genomic instability versus PN patient cfDNA.

In addition, tumor fraction of MPNST plasma had a significant correlation with tumor size (P = .024) and serial cfDNA analysis demonstrated a relationship between tumor fraction levels and treatment response to therapy and MRD detection prior to relapse.

These findings suggest that cfDNA fragment analysis paired with ULP-WGS could be a new biomarker for treatment response as well as a screening assay for early detection of MPNST in patients. The outcomes of this study also represent the first evidence of distinguishing between benign and malignant tumors using liquid biopsy in patients with a heritable cancer predisposition syndrome.

Regarding the promising nature of both studies, Chaudhuri said, “Our studies demonstrate ways that cancer management could improve with liquid biopsies that accurately diagnose and monitor tumors at various stages of the disease.”³

References

1. Chauhan PS, Chen K, Babbra RK, et al. Urine tumor DNA detection of minimal residual disease in muscle-invasive bladder cancer treated with curative-intent radical cystectomy: a cohort study. Published online August 31, 2021. PLOS Med. doi:10.1371/journal.pmed.1003732

2. Syzmanski JJ, Sundby RT, Jones PA, et al. Cell-free SNA ultra-low-pass whole genome sequencing to distinguish malignant peripheral nerve sheath tumor (MPNST) from its benign precursor lesion: a cross-sectional study. Published online August 31, 2021. PLOS Med. doi:10.1371/journal.pmed.1003734

3. Liquid biopsies may aid diagnosis, treatment of bladder, nerve tumors. Newswise. September 1, 2021. Accessed August September 30, 2021. https://www.newswise.com/articles/liquid-biopsies-may-aid-diagnosis-treatment-of-bladder-nerve-tumors?sc=sphr&xy=10016681

4. Landry JP, Schertz KL, Chiang YJ, et al. Comparison of Cancer Prevalence in Patients With Neurofibromatosis Type 1 at an Academic Cancer Center vs in the General Population From 1985 to 2020. JAMA Netw Open. 2021;4(3):e210945. doi: 10.1001/jamanetworkopen.2021.0945