Urine cell-free DNA multi-omics to detect MRD and predict survival in bladder cancer patients

Cell-Free DNA: Features and Attributes Shaping the Next Frontier in Liquid Biopsy

Cell-free DNA (cfDNA) is changing the face of liquid biopsy as a minimally invasive tool for disease detection and monitoring, with its main applications in oncology and prenatal testing, and rising roles in transplant patient monitoring. However, the processes of cfDNA biogenesis, fragmentation, and clearance are complex and require further investigation. Evidence suggests that cfDNA production relates to mechanisms of cell death and DNA repair, both of which further influence fragment size and its applicability as a biomarker. An emerging domain, cfDNA fragmentomics is being explored for advancing the field of diagnostics using non-mutational signatures such as fragment size ratios and methylation patterns. Thus, this review examines structural diversity in cfDNA with various fragment sizes. In examining these cfDNA subsets, we discuss their distinct biological origins and potential clinical utility. Development of sequencing methodologies has broadened the application of cfDNA in diagnosing cancers and organ-specific pathologies, as well as directing personalized therapies. This has been achieved by identifying and uncovering different subsets of cfDNA in biofluids using different methodologies and biofluids. Different cfDNA subsets provide important insights regarding genomic and epigenetic features, enhancing the understanding of gene regulation, tissue-specific functions, and disease progression. Advancement of these key areas further asserts increasing clinical relevance for the use of cfDNA as a biomarker. Continued exploration of cfDNA subsets is expected to drive further innovation in liquid biopsy and its integration into routine clinical practice.

Novel Urinary Biomarkers for the Detection of Bladder Cancer

Bladder cancer (BCa) is a highly recurrent malignancy that requires sensitive and noninvasive diagnostic and predictive markers. Conventional diagnostic tools, such as cystoscopy and urine cytology, are far from ideal in terms of sensitivity, specificity, and patient compliance. In this narrative review, the development of novel urinary markers for the diagnosis of BCa is highlighted, with a focus on their application in the clinical arena, detection accuracy, and future potential. An extensive analysis of new urinary biomarkers, including proteinuria-based tests, DNA methylation biomarkers, and RNA-based molecular panels, has been conducted. Various molecular tests, such as Cxbladder®, Bladder EpiCheck®, and UroSEEK, are highly sensitive and clinically valid. Urinary biomarkers provide a promising noninvasive alternative for traditional BCa diagnostics with enhanced specificity and the possibility of early diagnosis. Future research should focus on large-scale clinical validation and standardization of biomarkers to facilitate their use in routine clinical practice.

Chromatin accessibility states affect transrenal clearance of plasma DNA: Implications for urine-based diagnostics

BACKGROUND

Urinary cell-free DNA (ucfDNA) is a valuable resource for truly non-invasive liquid biopsy. UcfDNA comprises transrenal ucfDNA passing from the bloodstream through the glomeruli and locally shed urinary-tract ucfDNA. Understanding their differences in characteristics may enable new diagnostic applications.

METHODS

We analyzed 136 ucfDNA samples from healthy controls, pregnant women, patients with chronic kidney diseases (CKDs), and bladder cancer using massively parallel sequencing. Fragmentomic characteristics including fragment sizes and 5' end motifs were deduced. The relationship between ucfDNA and chromatin accessibility was examined by overlapping ucfDNA with open chromatin regions (OCRs, lacking histones) and heterochromatin regions (HCRs, tightly packed with histones).

FINDINGS

Compared with urinary-tract ucfDNA, the transrenal ucfDNA was shorter and enriched for C-ends. The transrenal ucfDNA was over-represented in OCRs but depleted in HCRs, indicating an interplay between the glomerular filtration barrier and the effective cfDNA size. In patients with proteinuria (preeclampsia and CKDs), the amount of ucfDNA from HCRs increased, suggesting elevated glomerular permeability of histone-bound plasma DNA molecules. In oncology, the use of hypomethylation signals in HCRs enhanced bladder cancer detection, with an area under the receiver operating characteristic curve of 0.93.

CONCLUSIONS

Chromatin accessibility states impact the transrenal clearance of plasma DNA, likely through the size restriction of the glomerular barrier. This realization has enabled the rational development of novel approaches for detecting or monitoring renal dysfunction and urological cancers.

FUNDING

The Innovation and Technology Commission of the Hong Kong SAR Government (InnoHK initiative) and the Li Ka Shing Foundation supported this study.

Circulating tumor DNA: a revolutionary approach for early detection and personalized treatment of bladder cancer

Bladder cancer is a malignant tumor with a high global incidence and recurrence rate. Traditional diagnostic methods, such as cystoscopy and urine cytology, have limitations in sensitivity and specificity, particularly in detecting low-grade bladder cancer. Circulating tumor DNA (ctDNA) offers a non-invasive alternative, reflecting tumor genetic characteristics through blood samples. It demonstrates high sensitivity and repeatability, making it a promising tool for early detection, recurrence monitoring, and treatment evaluation. Clinical studies have shown that ctDNA not only detects tumor burden but also captures dynamic tumor mutations, aiding in personalized treatment strategies. Despite its potential, clinical implementation of ctDNA faces challenges, including optimization of detection techniques, standardization, and the cost of testing. This paper explores the role of ctDNA in advancing bladder cancer diagnosis and treatment, with a focus on refining its clinical application and guiding future research toward improved patient outcomes.

Phase II Trial of Risk-Enabled Therapy After Neoadjuvant Chemotherapy for Muscle-Invasive Bladder Cancer (RETAIN 1)

PURPOSE

Cisplatin-based neoadjuvant chemotherapy (NAC) followed by cystectomy is the standard of care for patients with muscle-invasive bladder cancer (MIBC). Mutations in DNA damage repair genes are associated with pathologic downstaging after NAC. We hypothesized that a combination of biomarker selection and clinical staging would identify patients for cystectomy-sparing active surveillance (AS).

PATIENTS AND METHODS

We conducted a single-arm, phase II, noninferiority trial to evaluate a risk-adapted approach for MIBC. Patients with cT2-T3N0M0 MIBC underwent NAC with accelerated methotrexate, vinblastine, doxorubicin, and cisplatin (AMVAC). Pre-NAC transurethral bladder tumor specimens were sequenced for mutations in ATM, ERCC2, FANCC, and RB1. Patients with ≥1 mutation and cT0 post-NAC began AS. The primary end point was metastasis-free survival (MFS) at 2 years for the entire cohort with the null hypothesis rejected if the lower bound exact one-sided 95% CI exceeds 64%.

RESULTS

Seventy patients were enrolled, 33 (47%) had a mutation, and 25 (36%) began per-protocol AS. With a median follow-up of 40 months, the 2-year MFS for all patients was 72.9% (lower bound exact one-sided 95% CI, 62.8). The 2-year MFS was 76.0% in the AS group (95% CI, 54.2 to 88.4) and 71.1% (95% CI, 55.5 to 82.1) in the remaining patients. In the AS group, 17 patients (68%) had some recurrence and 12 (48%) were metastasis-free with an intact bladder. The 2-year overall survival (OS) was 84.3% (95% CI, 73.4 to 91.0); OS was 88.0% (95% CI, 67.3 to 96.0) and 82.2% (95% CI, 67.6 to 90.7) in the AS and not-AS groups, respectively.

CONCLUSION

Patients with MIBC treated with AMVAC followed by a risk-adapted approach to local consolidation achieved a 2-year MFS rate of 73%. The primary end point was not met, but 17% of all enrolled patients and 48% of the AS group avoided cystectomy without metastatic disease.

Development of a Technique for Diagnosis and Screening of Superficial Bladder Cancer by Cell-Pellet DNA From Urine Sample

Bladder cancer (BCa) is the most common malignancy of the urinary system with high incidence and recurrence rates. There are several ways to detect BCa. However, different approaches have different accuracy, which essentially depends on the sensitivity and specificity of the technique. Alternative noninvasive diagnostic tools for BCa are needed. We isolated and compared urinary cell-pellet DNA (cpDNA), cell-free DNA, and exosomal DNA from patients with localized BCa. Consequently, we analyzed 12 tissues and cpDNA samples by next-generation sequencing and then used bioinformatic tools to analyze genomic and transcriptomic alterations in coding and noncoding sequences. Then, cpDNA and tissue DNA from 12 patients were analyzed using next-generation sequencing to verify that the genomic characteristics of cpDNA are concordant with those of tissue. We also detected somatic mutation patterns between tissues and their corresponding cpDNA samples. An overlapping variant analysis was performed based on somatic mutation data and a high similarity was observed. Moreover, we identified frequently mutated signaling pathways. In these results, several point mutations were analyzed in FGFR3, TTN, and LEPROTL1 from the cpDNA of patients with BCa. Tumor mutational burden analysis showed that cpDNA had no significant difference in tumor mutational burden compared with tumor tissue. These results provide that cpDNA is a potential diagnostic source for detecting and managing BCa using alternative noninvasive methods from patient urine. Our findings may serve as a clinical tool for early detection or recurrence screening of nonmuscle invasive BCa using urinary cpDNA.

Unleashing the power of urine‑based biomarkers in diagnosis, prognosis and monitoring of bladder cancer (Review)

Bladder cancer (BCa) is a prevalent malignant neoplasm of the urinary tract with high incidence rate, frequent recurrence and rapid disease progression. Conventional approaches for diagnosing, prognosticating and monitoring BCa often rely on invasive procedures such as cystoscopy and tissue biopsy, which are associated with high costs and low patient compliance for follow‑up. Liquid biopsies have advantages, such as being non‑invasive, real‑time, and reproducible, in obtaining diverse biomarkers derived from cellular, molecular, proteomic and genetic signatures in urine or plasma samples. Although plasma‑based biomarkers have been clinically validated, urine provides greater specificity for directly assessing biological materials from urological sources. The present review summarizes advancements and current limitations in urinary protein, genetic and epigenetic biomarkers for disease progression and treatment response of BC, compares performance and application scenarios of urine and blood biomarkers and explores how urinary biomarkers may serve as an alternative or complementary tool to traditional diagnostic methods. The integration of urine‑based or plasma‑based biomarkers into existing diagnostic workflows offers promising avenues for improving accuracy and efficiency of diagnosis in the management of BCa. Notably, the emergence of synthetic biomarkers and urine metabolites, combined with artificial intelligence or bioinformatic technologies, has promise in the screening of potential targets. Continued research and validation efforts are needed to translate these findings into routine clinical practice, ultimately improving patient outcomes and decreasing the burden of BCa.

Pilot study: Urine cell-free DNA with low-pass whole genome sequencing can detect and molecularly type upper tract urothelial carcinomas

OBJECTIVES

Upper tract urothelial carcinoma (UTUC) is an aggressive disease that is challenging to biopsy and diagnose, frequently yielding nondiagnostic cytology and tissue specimens. Therefore, UTUC is often late stage when diagnosed, with poor outcomes. Cell-free tumor DNA (cfDNA) may improve UTUC early diagnosis and assessments of heterogeneity, treatment response, and recurrence but has not been studied in the urine from patients with UTUC. This study aimed to detect recurrent, diagnostic UTUC cytogenetic abnormalities by low-pass whole genome sequencing (LPWGS) and to compare urine-derived and plasma cfDNA against abnormalities identified in patient tumor tissue.

METHODS

Cell-free tumor DNA extracted from voided urine and plasma before nephroureterectomy in 4 patients with UTUC was compared with genomic DNA from formalin-fixed, paraffin-embedded tumor tissue after LPWGS.

RESULTS

Abnormal autosomal genomic regions were highest in tissue (n = 11,843), intermediate in urine (n = 5,072) and lowest in plasma (n = 763), with a high concordance of flagged regions identified in tissue and urine (r = 0.88). Pairwise analysis of whole chromosome gains/losses and subchromosomal alterations between tissue and urine showed nearly identical patterns in all 4 patients (r = 0.88-0.99) in contrast to plasma (r < 0.25). Abnormal genomic regions identified by LPWGS showed a high degree of overlap (100% for tumor tissue, 94% for urine cfDNA) with cBioPortal UTUC-associated genes.

CONCLUSIONS

We demonstrated the superiority of urine vs plasma cfDNA when LPWGS was used to identify UTUC-associated gene abnormalities. Voided urine cfDNA molecular signatures are highly concordant with matched tumor tissue on chromosomal and subchromosomal levels, emphasizing its feasibility as a noninvasive biomarker for UTUC detection and surveillance.

Minimal residual disease as a target for liquid biopsy in patients with solid tumours

Metastasis is the leading cause of cancer-related death in patients with solid tumours. Current imaging technologies are not sufficiently sensitive to detect minimal residual disease (MRD; also known as measurable or molecular residual disease) after initial surgery or chemotherapy, pointing to the need for more sensitive tests to detect remaining traces of cancer in the body. Liquid biopsy, or the analysis of tumour-derived or tumour-induced cells or cellular products in the blood or other body fluids, has opened a new diagnostic avenue to detect and monitor MRD. Liquid biopsy is already used in clinical decision making for patients with haematological malignancies. Here, we review current knowledge on the use of circulating tumour DNA (ctDNA) to detect and monitor MRD in patients with solid tumours. We also discuss how ctDNA-guided MRD detection and characterization could herald a new era of novel 'post-adjuvant therapies' with the potential to eliminate MRD and cure patients before terminal metastatic disease is evident on imaging.

Current and Future Role of Circulating DNA in the Diagnosis and Management of Urothelial Carcinoma

The growing sophistication of tumor molecular profiling has helped to slowly transition oncologic care toward a more personalized approach in different tumor types, including in bladder cancer. The National Comprehensive Cancer Network recommends that all patients with stage IVA and stage IVB urothelial carcinoma have molecular analysis that integrates at least FGFR3 testing to help facilitate the selection of future therapeutic options. Sequencing of tumor-derived tissue is the mainstay to obtain this genomic testing, but as in other cancers, there has been extensive research into the integration of liquid biopsies in longitudinal management. Liquid biopsies broadly refer to the isolation of both cellular and noncellular tumor components including proteins and nucleic acids such as mRNA and circulating free DNA within a liquid sample. Although protein-based testing and testing of circulating tumor cells are options, the bulk of promising research in bladder cancer is investigating the role of plasma-based circulating tumor DNA (ctDNA). Currently, a universal consensus on optimal preanalytic and analytic approaches has not been fully defined, and the exact role that liquid biopsies should have in screening, diagnosis, prognostication, treatment selection, and monitoring is not yet known. Still, it can be expected that ctDNA testing will be a part of appropriate management of muscle-invasive bladder cancer and metastatic bladder cancer in the near future. In this review, the goal is to provide a practical overview of the current and future role of ctDNA in bladder cancer including ongoing trials.

Liquid biopsy through non-blood fluids: The show must go on

Image 1.

5-Hydroxymethylcytosine Profiles of cfDNA in Urine as Diagnostic, Differential Diagnosis and Prognostic Markers for Multiple Myeloma

BACKGROUND

An effective urine-based method for the diagnosis, differential diagnosis and prognosis of multiple myeloma (MM) has not yet been developed. Urine cell-free DNA (cfDNA) carrying cancer-specific genetic and epigenetic aberrations may enable a noninvasive "liquid biopsy" for diagnosis and monitoring of cancer.

METHODS

We first identified MM-specific hydroxymethylcytosine signatures by comparing 64 MM patients, 23 amyloidosis (AM) patients and 59 healthy cohort. Then, we applied a machine learning algorithm to develop diagnostic and differential diagnosis model. Finally, the prognosis of MM patients was predicted based on their survival time at the last follow-up.

RESULTS

We identified 11 5hmC markers using logistic regression algorithm could effectively diagnosis MM (AUC = 0.902), and achieved 85.00% specificity and 85.71% sensitivity. These 11 markers could also effectively differential diagnosis MM (AUC = 0.805) with 88.89% specificity and 73.08% sensitivity. In addition, the prognostic prediction model also effectively predicted the prognosis of patients with MM (p < 0.01), of which 4 differential markers (RAPGEF2, BRD1, TET2, TRAF3IP2) could independently predict the prognosis of MM.

CONCLUSIONS

Together, our findings showed the value of urine cfDNA hydroxymethylcytosine markers in the diagnosis, differential diagnosis and prognosis of MM. Meantime, our study provides a promising and completely non-invasive method for the diagnosis, differential diagnosis and prognosis prediction of MM.

High sensitivity ctDNA assays in genitourinary malignancies: current evidence and future directions

In the recent decade, analysis of circulating tumor DNA (ctDNA) has improved cancer care by allowing for rapid detection of actionable molecular targets. A new generation of circulating DNA tests is now becoming available commercially. These tests are characterized by a superior limit of detection of 0.01% vaF or better, allowing for the detection of radiologically occult molecular residual disease (MRD). MRD tests have the potential to revolutionize neoadjuvant and adjuvant treatment. In addition, these tests can be used as tumor markers to assess disease response. We reviewed the current evidence for the use of high-sensitivity MRD assays with particular focus on the genitourinary tumors. Multiple studies have now been reported in urothelial, renal, and recently testicular carcinoma. We find that the sensitivity varies across tumor types in the adjuvant setting and may reach a high of 100% in urothelial cancer. Specificity in tumor-informed MRD appears to be preserved across tumor types (98%-100%). Several trials are now prospectively validating MRD testing in biomarker integral studies, mainly in urothelial carcinoma.

Liquid Biopsies Based on Cell-Free DNA Integrity as a Biomarker for Cancer Diagnosis: A Meta-Analysis

Liquid biopsies have been identified as a viable source of cancer biomarkers. We aim to evaluate the diagnostic accuracy of cell-free DNA integrity (cfDI) in liquid biopsies for cancer. A comprehensive literature search was conducted through PubMed, Embase, Web of Science, and Cochrane Library up to June 2024. Seventy-two study units from forty-six studies, comprising 4286 cancer patients, were identified and evaluated. The Quality Assessment for Studies of Diagnostic Accuracy-2 (QUADAS-2) was used to assess study quality. Meta-regression analysis was employed to investigate the underlying factors contributing to heterogeneity, alongside an evaluation of publication bias. The bivariate random-effect model was utilized to compute the primary diagnostic outcomes and their corresponding 95% confidence intervals (CIs). The pooled sensitivity, specificity, and positive and negative likelihood ratios of cfDI in cancer diagnosis were 0.70 and 0.77, 3.26 and 0.34, respectively. The overall area under the curve was 0.84, with a diagnostic odds ratio of 10.63. This meta-analysis suggested that the cfDI index has a promising potential as a non-invasive and accurate diagnostic tool for cancer. Study registration: The study was registered at PROSPERO (reference No. CRD42021276290).

Survival prediction landscape: an in-depth systematic literature review on activities, methods, tools, diseases, and databases

Survival prediction integrates patient-specific molecular information and clinical signatures to forecast the anticipated time of an event, such as recurrence, death, or disease progression. Survival prediction proves valuable in guiding treatment decisions, optimizing resource allocation, and interventions of precision medicine. The wide range of diseases, the existence of various variants within the same disease, and the reliance on available data necessitate disease-specific computational survival predictors. The widespread adoption of artificial intelligence (AI) methods in crafting survival predictors has undoubtedly revolutionized this field. However, the ever-increasing demand for more sophisticated and effective prediction models necessitates the continued creation of innovative advancements. To catalyze these advancements, it is crucial to bring existing survival predictors knowledge and insights into a centralized platform. The paper in hand thoroughly examines 23 existing review studies and provides a concise overview of their scope and limitations. Focusing on a comprehensive set of 90 most recent survival predictors across 44 diverse diseases, it delves into insights of diverse types of methods that are used in the development of disease-specific predictors. This exhaustive analysis encompasses the utilized data modalities along with a detailed analysis of subsets of clinical features, feature engineering methods, and the specific statistical, machine or deep learning approaches that have been employed. It also provides insights about survival prediction data sources, open-source predictors, and survival prediction frameworks.

Advances in Liquid Biopsy for Diagnosis of Bladder Cancer

Bladder cancer (BCa) is the most common malignancy of the urinary system. It has a high recurrence rate and requires longterm follow-up. Significant advances in BCa research have been made in recent years; however, the initial diagnosis and follow-up of BCa relies on cystoscopy, which is an invasive and expensive procedure. Over the past decade, liquid biopsies (e.g., blood and urine) have proven to be highly efficient methods for the discovery of BCa biomarkers. This noninvasive sampling method is used to analyze unique tumor components released into body fluids and enables serial sampling and longitudinal monitoring of tumor progression. Several liquid biopsy biomarkers have been studied extensively and have shown promising results in the clinical applications of BCa, including early detection, microscopic residual disease detection, recurrence prediction, and treatment response. Therefore, this review aims to provide an update on various new liquid biopsy markers and the advantages and current limitations of liquid biopsy in the diagnosis of BCa.

Postoperative tumor treatment strategies: From basic research to clinical therapy

Despite progression in advanced treatments for malignant tumors, surgery remains the primary treatment intervention, which removes a large portion of firm tumor tissues; however, the postoperative phase poses a possible risk for provincial tumor recurrence and metastasis. Consequently, the prevention of tumor recurrence and metastasis has attracted research attention. In this review, we summarized the postoperative treatment strategies for various tumors from both basic research and clinical perspectives. We delineated the underlying factors contributing to the recurrence of malignant tumors with a substantial prevalence rate, related molecular mechanisms of tumor recurrence post‐surgery, and related means of monitoring recurrence and metastasis after surgery. Furthermore, we described relevant therapeutic approaches for postoperative tumor recurrence, including chemotherapy, radiation therapy, immunotherapy, targeted therapy, and photodynamic therapy. This review focused on the emerging technologies used for postoperative tumor treatment in recent years in terms of functional classification, including the prevention of postoperative tumor recurrence, functional reconstruction, and monitoring of recurrence. Finally, we discussed the future development and deficiencies of postoperative tumor therapy. To understand postoperative treatment strategies for tumors from clinical treatment and basic research and further guide the research directions for postoperative tumors.

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.

Recommendations for the collection and annotation of biosamples for analysis of biomarkers in neurofibromatosis and schwannomatosis clinical trials

INTRODUCTION

Neurofibromatosis 1 and schwannomatosis are characterized by potential lifelong morbidity and life-threatening complications. To date, however, diagnostic and predictive biomarkers are an unmet need in this patient population. The inclusion of biomarker discovery correlatives in neurofibromatosis 1/schwannomatosis clinical trials enables study of low-incidence disease. The implementation of a common data model would further enhance biomarker discovery by enabling effective concatenation of data from multiple studies.

METHODS

The Response Evaluation in Neurofibromatosis and Schwannomatosis biomarker working group reviewed published data on emerging trends in neurofibromatosis 1 and schwannomatosis biomarker research and developed recommendations in a series of consensus meetings.

RESULTS

Liquid biopsy has emerged as a promising assay for neurofibromatosis 1/schwannomatosis biomarker discovery and validation. In addition, we review recommendations for a range of biomarkers in clinical trials, neurofibromatosis 1/schwannomatosis-specific data annotations, and common data models for data integration.

CONCLUSION

These Response Evaluation in Neurofibromatosis and Schwannomatosis consensus guidelines are intended to provide best practices for the inclusion of biomarker studies in neurofibromatosis 1/schwannomatosis clinical trials, data, and sample annotation and to lay a framework for data harmonization and concatenation between trials.

Surpassing sensitivity limits in liquid biopsy

Attenuation of cell-free DNA clearance in vivo is an alternative strategy to maximize recovery.

Phase I trial of Ganitumab plus Dasatinib to Cotarget the Insulin-Like Growth Factor 1 Receptor and Src Family Kinase YES in Rhabdomyosarcoma

PURPOSE

Antibodies against insulin-like growth factor (IGF) type 1 receptor have shown meaningful but transient tumor responses in patients with rhabdomyosarcoma (RMS). The SRC family member YES has been shown to mediate IGF type 1 receptor (IGF-1R) antibody acquired resistance, and cotargeting IGF-1R and YES resulted in sustained responses in murine RMS models. We conducted a phase I trial of the anti-IGF-1R antibody ganitumab combined with dasatinib, a multi-kinase inhibitor targeting YES, in patients with RMS (NCT03041701).

PATIENTS AND METHODS

Patients with relapsed/refractory alveolar or embryonal RMS and measurable disease were eligible. All patients received ganitumab 18 mg/kg intravenously every 2 weeks. Dasatinib dose was 60 mg/m2/dose (max 100 mg) oral once daily [dose level (DL)1] or 60 mg/m2/dose (max 70 mg) twice daily (DL2). A 3+3 dose escalation design was used, and maximum tolerated dose (MTD) was determined on the basis of cycle 1 dose-limiting toxicities (DLT).

RESULTS

Thirteen eligible patients, median age 18 years (range 8-29) enrolled. Median number of prior systemic therapies was 3; all had received prior radiation. Of 11 toxicity-evaluable patients, 1/6 had a DLT at DL1 (diarrhea) and 2/5 had a DLT at DL2 (pneumonitis, hematuria) confirming DL1 as MTD. Of nine response-evaluable patients, one had a confirmed partial response for four cycles, and one had stable disease for six cycles. Genomic studies from cell-free DNA correlated with disease response.

CONCLUSIONS

The combination of dasatinib 60 mg/m2/dose daily and ganitumab 18 mg/kg every 2 weeks was safe and tolerable. This combination had a disease control rate of 22% at 5 months.

Minimal residual disease in solid tumors: an overview

Minimal residual disease (MRD) is termed as the small numbers of remnant tumor cells in a subset of patients with tumors. Liquid biopsy is increasingly used for the detection of MRD, illustrating the potential of MRD detection to provide more accurate management for cancer patients. As new techniques and algorithms have enhanced the performance of MRD detection, the approach is becoming more widely and routinely used to predict the prognosis and monitor the relapse of cancer patients. In fact, MRD detection has been shown to achieve better performance than imaging methods. On this basis, rigorous investigation of MRD detection as an integral method for guiding clinical treatment has made important advances. This review summarizes the development of MRD biomarkers, techniques, and strategies for the detection of cancer, and emphasizes the application of MRD detection in solid tumors, particularly for the guidance of clinical treatment.

Muscle invasive bladder cancer: where is the field headed?

INTRODUCTION

The standard treatment for muscle-invasive bladder cancer (MIBC) is cisplatin-based neoadjuvant chemotherapy (NAC) followed by radical cystectomy or upfront radical cystectomy for cisplatin-ineligible patients. In those who are ineligible for or refuse radical cystectomy, trimodal therapy with chemoradiation is offered. However, with the success of immune checkpoint inhibitors (ICI) and antibody-drug conjugates such as enfortumab vedotin in the metastatic setting, several trials are implementing these drugs in the neoadjuvant setting for cisplatin ineligible patients. Indeed, nivolumab is approved as adjuvant therapy for high-risk muscle-invasive urothelial carcinoma.

AREAS COVERED

Clinical trials using ICI, ICI/ICI, and ICI/chemotherapy combination therapies in the perioperative setting have been completed. These clinical trials have demonstrated that neoadjuvant ICI are safe and have encouraging pCR, making them promising treatment options. Neoadjuvant enfortumab vedotin alone and in combination with pembrolizumab is also being studied, and preliminarily to have promising activity. ICI is also being combined with radiation therapy (RT) and early data indicate that ICI combined with RT or chemo-RT may be safe with promising activity.

EXPERT OPINION

Biomarkers are urgently needed to identify appropriate treatment options for individual patients. The use of novel treatment approaches and biomarkers will help shape the future of precision therapy for MIBC and enable bladder preservation.

Emerging Roles of Circulating Tumor DNA for Increased Precision and Personalization in Radiation Oncology

Recent breakthroughs in circulating tumor DNA (ctDNA) technologies present a compelling opportunity to combine this emerging liquid biopsy approach with the field of radiogenomics, the study of how tumor genomics correlate with radiotherapy response and radiotoxicity. Canonically, ctDNA levels reflect metastatic tumor burden, although newer ultrasensitive technologies can be used after curative-intent radiotherapy of localized disease to assess ctDNA for minimal residual disease (MRD) detection or for post-treatment surveillance. Furthermore, several studies have demonstrated the potential utility of ctDNA analysis across various cancer types managed with radiotherapy or chemoradiotherapy, including sarcoma and cancers of the head and neck, lung, colon, rectum, bladder, and prostate . Additionally, because peripheral blood mononuclear cells are routinely collected alongside ctDNA to filter out mutations associated with clonal hematopoiesis, these cells are also available for single nucleotide polymorphism analysis and could potentially be used to detect patients at high risk for radiotoxicity. Lastly, future ctDNA assays will be utilized to better assess locoregional MRD in order to more precisely guide adjuvant radiotherapy after surgery in cases of localized disease, and guide ablative radiotherapy in cases of oligometastatic disease.

Immunotherapy in urothelial cancer: current status and future directions

INTRODUCTION

Since 2016, the progressive use of immune checkpoint inhibitors (ICIs) starting from second-line treatment has led to an improvement in overall survival in locally advanced and metastatic urothelial cancer (UC). Clinical trials are underway testing the role of ICIs since the first stages of the disease, alone or in combination with standard therapies.

AREAS COVERED

This review summarizes the current updated evidence regarding the role of ICIs in the different stages of UC, the ongoing clinical trials exploring the potential benefit of immunotherapy alone or in combination with standard-of-care therapies, as well as the promising association of ICIs with antibody-drug conjugates (ADCs).

EXPERT OPINION

In the first-line setting, ICIs alone in platinum-unfit patients have shown unconvincing results; the ongoing EV-302 trial will probably suggest enfortumab vedotin plus pembrolizumab as a new effective option. The optimal duration of maintenance immunotherapy is still to be determined, finding a balance with the risk-benefit profile. The clinical benefit of ICIs as second-line treatment is limited to a subset of patients that cannot be definitively established yet. In the next 5 years, a lot of new ADCs will likely emerge for the treatment of UC.

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.

Roles of non-coding RNAs in the metabolism and pathogenesis of bladder cancer

Bladder cancer (BC) is featured as the second most common malignancy of the urinary tract worldwide with few treatments leading to high incidence and mortality. It stayed a virtually intractable disease, and efforts to identify innovative and effective therapies are urgently needed. At present, more and more evidence shows the importance of non-coding RNA (ncRNA) for disease-related study, diagnosis, and treatment of diverse types of malignancies. Recent evidence suggests that dysregulated functions of ncRNAs are closely associated with the pathogenesis of numerous cancers including BC. The detailed mechanisms underlying the dysregulated role of ncRNAs in cancer progression are still not fully understood. This review mainly summarizes recent findings on regulatory mechanisms of the ncRNAs, long non-coding RNAs, microRNAs, and circular RNAs, in cancer progression or suppression and focuses on the predictive values of ncRNAs-related signatures in BC clinical outcomes. A deeper understanding of the ncRNA interactive network could be compelling framework for developing biomarker-guided clinical trials.

Measurable Residual Disease in Chronic Lymphocytic Leukemia: Current Understanding and Evolving Role in Clinical Practice

OPINION STATEMENT

Treatment of chronic lymphocytic leukemia (CLL) has evolved dramatically during the last decade, from chemoimmunotherapy (CIT)-based therapies to newer B-cell receptor (BCR) signaling targeting agents, which are sometimes given as continuous schemes. Response to treatment was traditionally defined according to clinical variables designed to assign a response category. Interest in assessing for deeper responses in CLL by the means of measurable residual disease (MRD) testing has been the subject of research during the last several years. Analyses and sub-analyses of clinical trials have shown that achieving undetectable MRD (uMRD) in CLL is an important prognostic factor. In this review, we summarize the available evidence about MRD in CLL, from the various assays available for measurement, the compartment to test, the impact of reaching uMRD according to the treatment regimen, and the results of fixed duration treatment guided by MRD trials. Finally, we summarize how MRD can be incorporated in clinical practice and how it may guide fixed duration treatment in the future should evidence continue to accumulate in that direction.

Approaches to Clinical Complete Response after Neoadjuvant Chemotherapy in Muscle-Invasive Bladder Cancer: Possibilities and Limitations

In the surgical oncology field, the change from a past radical surgery to an organ preserving surgery is a big trend. In muscle-invasive bladder cancer treatment, neoadjuvant chemotherapy (NAC) followed by radical cystectomy (RC) is the standard of care for muscle-invasive bladder cancer (MIBC) patients eligible for cisplatin. There is a growing interest in bladder preserving strategies after NAC because good oncologic outcome has been reported for pathologic complete response (pCR) patients after NAC, and many studies have continued to discuss whether bladder preservation treatment is possible for these patients. However, in actual clinical practice, decision-making should be determined according to clinical staging and there is a gap that cannot be ignored between clinical complete response (cCR) and pCR. Currently, there is a lack in a uniform approach to post-NAC restaging of MIBC and a standardized cCR definition. In this review, we clarify the gap between cCR and pCR at the current situation and focus on emerging strategies in bladder preservation in selected patients with MIBC who achieve cCR following NAC.