Liquid biopsy in non‐Hodgkin's lymphoma

The implication of next-generation sequencing in the diagnosis and clinical management of non-Hodgkin lymphomas

Next generation sequencing (NGS) is a technology that broadens the horizon of knowledge of several somatic pathologies, especially in oncological and oncohematological pathology. In the case of NHL, the understanding of the mechanisms of tumorigenesis, tumor proliferation and the identification of genetic markers specific to different lymphoma subtypes led to more accurate classification and diagnosis. Similarly, the data obtained through NGS allowed the identification of recurrent somatic mutations that can serve as therapeutic targets that can be inhibited and thus reducing the rate of resistant cases. The article's purpose is to offer a comprehensive overview of the best ways of integrating of next-generation sequencing technologies for diagnosis, prognosis, classification, and selection of optimal therapy from the perspective of tailor-made medicine.

Significance of multiple tumor markers measurements in conversion surgery for unresectable locally advanced pancreatic cancer

BACKGROUND

This study aimed to evaluate the significance of multiple tumor markers (TMs) measurements in determining the indications for conversion surgery (CS) in the management of unresectable locally advanced pancreatic cancer (UR-LAPC).

METHODS

A total of 103 patients with UR-LAPC, treated between 2008 and June 2021, were enrolled in this study. Three TMs, including carbohydrate antigen 19-9 (CA19-9), carcinoembryonic antigen (CEA), and Duke pancreatic monoclonal antigen type 2 (DUPAN-2), were measured.

RESULTS

Twenty-five patients (24%) underwent CS. The median preoperative treatment period was 9.5 months. The median survival time (MST) from the initial treatment for patients with CS was significantly longer than that for patients without surgery (34.6 vs. 18.9 months, P < 0.001). The number of elevated TMs before CS was one in five patients and two in five patients, while 15 patients had normal levels of all three TMs. Notably, the MST from the initial treatment for patients with all three preoperative normal TMs levels was favorable for 70.5 months. In contrast, patients with one or two preoperatively elevated TMs levels had a significantly worse prognosis (25.4 and 21.0 months, respectively, P < 0.001). Furthermore, the relapse-free survival of patients with three preoperative normal TMs levels was significantly longer than those with one or two elevated TMs levels (21.9 vs. 11.3 or 3.0 months, respectively, P < 0.001). Non-normal values of all TMs before CS were identified as independent poor prognostic factors.

CONCLUSIONS

Simultaneous measurement and assessment of the three TMs levels may help determine the surgical indications for UR-LAPC after systemic anticancer treatment.

Circulating tumor DNA in B-cell lymphoma: technical advances, clinical applications, and perspectives for translational research

Noninvasive disease monitoring and risk stratification by circulating tumor DNA (ctDNA) profiling has become a potential novel strategy for patient management in B-cell lymphoma. Emerging innovative therapeutic options and an unprecedented growth in our understanding of biological and molecular factors underlying lymphoma heterogeneity have fundamentally increased the need for precision-based tools facilitating personalized and accurate disease profiling and quantification. By capturing the entire mutational landscape of tumors, ctDNA assessment has some decisive advantages over conventional tissue biopsies, which usually target only one single tumor site. Due to its non- or minimal-invasive nature, serial and repeated ctDNA profiling provides a real-time picture of the genetic composition and facilitates quantification of tumor burden any time during the course of the disease. In this review, we present a comprehensive overview of technologies used for ctDNA detection and genotyping in B-cell lymphoma, focusing on pre-analytical and technical requirements, the advantages and limitations of various approaches, and highlight recent advances around improving sensitivity and suppressing technical errors. We broadly review potential applications of ctDNA in clinical practice and for translational research by describing how ctDNA might enhance lymphoma subtype classification, treatment response assessment, outcome prediction, and monitoring of measurable residual disease. We finally discuss how ctDNA could be implemented in prospective clinical trials as a novel surrogate endpoint and be utilized as a decision-making tool to guide lymphoma treatment in the future.

Management of relapsed or refractory large B-cell lymphoma in patients ineligible for CAR-T cell therapy

INTRODUCTION

Chimeric antigen receptor T (CAR-T) therapy has revolutionized the treatment of relapsed/refractory large B-cell lymphoma (LBCL). However, patients who are excluded or have no access to CAR-T represent a challenge for clinicians and have generally a dismal outcome. The landscape for this category of patients is constantly evolving: new agents have been approved in the last 2-3 years, alone or in combination, and novel treatment modalities are under investigations.

AREAS COVERED

Thereafter, we reviewed the currently available therapeutic strategies: conventional chemotherapy, Antibody-drug conjugate ADC (mainly polatuzumab and loncastuxumab), bispecific antibodies (CD19/CD3 and focus on novel CD20/CD3 Abs), immunomodulatory drugs (covering tafasitamab and lenalidomide, checkpoint inhibitors mainly in PMBL), small molecules (selinexor, BTK and PI3K inhibitors), and the role of radiotherapy.

EXPERT OPINION

Navigating this scenario, will uncover new challenges, including identifying an ideal sequence for these therapies, the most effective combinations, and search for consistent predictive factors to help selecting the appropriate population of LBCL patients. At present, supporting clinical research for CAR-T ineligible patients, a new and challenging group, must remain a major focus that is complementary to advances in CAR T-cell therapy.

Incorporation of next-generation sequencing in clinical practice using solid and liquid biopsy for patients with non-Hodgkin's lymphoma

Although next-generation sequencing (NGS) data on lymphomas require further validation before being implemented in daily practice, the clinical application of NGS can be considered right around the corner. The aim of our study was to validate an NGS lymphoid panel for tissue and liquid biopsy with the most common types of non-Hodgkin’s lymphoma [follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBCL)]. In this series, 372 somatic alterations were detected in 93.6% (44/47) of the patients through tissue biopsy. In FL, we identified 93 somatic alterations, with a median of 7.4 mutations per sample. In DLBCL, we detected 279 somatic variants with a median of 8.6 mutations (range 0–35). In 92% (24/26) of the cases, we were able to detect some variant in the circulating tumor DNA. We detected a total of 386 variants; 63.7% were detected in both types of samples, 13.2% were detected only in the circulating tumor DNA, and 23% were detected only in the tissue biopsy. We found a correlation between the number of circulating tumor DNA mutations, advanced stage, and bulky disease. The genetic alterations detected in this panel were consistent with those previously described at diagnosis. The liquid biopsy sample is therefore a complementary tool that can provide new genetic information, even in cases where a solid biopsy cannot be performed or an insufficient sample was obtained. In summary, we describe and analyze in this study the findings and difficulties encountered when incorporating liquid biopsy into clinical practice in non-Hodgkin’s lymphoma at diagnosis.

Advances in Lymphoma Molecular Diagnostics

Lymphomas encompass a diverse group of malignant lymphoid neoplasms. Over recent years much scientific effort has been undertaken to identify and understand molecular changes in lymphomas, resulting in a wide range of genetic alterations that have been reported across all types of lymphomas. As many of these changes are now incorporated into the World Health Organization’s defined criteria for the diagnostic evaluation of patients with lymphoid neoplasms, their accurate identification is crucial. Even if many alterations are not routinely evaluated in daily clinical practice, they may still have implications in risk stratification, treatment, prognosis or disease monitoring. Moreover, some alterations can be used for targeted treatment. Therefore, these advances in lymphoma molecular diagnostics in some cases have led to changes in treatment algorithms. Here, we give an overview of and discuss advances in molecular techniques in current clinical practice, as well as highlight some of them in a clinical context.

Extracellular genetic materials and their application in clinical practice

This study reviews the possible origins, functional roles, and diagnostic applications of 'extracellular genetic material' (EGM), a novel term introduced to cover DNA, RNA, and DNA/RNA-related molecules released from all types of cells into the extracellular region. The literature on EGMs shows them to play a dual role in diverse, fine-tuning mechanisms involved in both homeostasis and pathological events, including cancerogenesis and genometastasis. Recent developments in the next-generation technology have provided successful applications of low quantities of genomic materials into the diagnostic field, yielding high sensitivity and specificity in test results. Also, the successful application of EGMs into diagnostics has afforded promising outcomes for researchers and clinicians. This study of EGM provides a deeper understanding of the subject as an area of interest, especially cell-free DNA, aiming toward the eventual development of new therapeutic applications and diagnostic strategies.

Liquid biopsy in lymphoma: Molecular methods and clinical applications

In this article, we broadly review the application of cfDNA analysis to the diagnosis and management of lymphoma. We introduce the advantages of cfDNA measurement over conventional tissue biopsy and describe how cfDNA may be utilized for both genotyping and detection of minimal residual disease. First, we discuss genotyping, beginning with differences in identifying mutations from the blood plasma vs. from circulating cells. We review the technical distinctions between PCR- and NGS-based assays and describe two important applications of NGS-based cfDNA tests, namely the identification of resistance mutations and classification of disease subtype. We discuss difficulties in genotyping diseases with low burden of tumor cells and the application of cfDNA assays in these contexts. Second, we describe the utility of ctDNA measurement in assessing MRD. We cover recent advances in the assessment of pre-treatment disease burden as a prognostic biomarker, detection of molecular response to therapy, and early detection of relapsing disease. Third, we explore select emerging areas of research in ctDNA technologies that show promise in boosting the performance of existing ctDNA-based assays. These include cell-free DNA fragment structure analysis or 'fragmentomics', epigenetic modifications, and novel circulating analytes such as tumor-educated platelets and extracellular vesicular DNA. We also discuss alternative analytes to blood plasma for tumor detection, such as urine, saliva, and stool. Finally, we present a case that highlights potential applications of ctDNA approaches to the management of patients with lymphoma, while also defining important prerequisite advances before this can be fully realized. We close with a look to the future of cfDNA applications, outlining one potential timeline and path forward towards routine clinical application.

Systematic review of staging bone marrow involvement in B cell lymphoma by flow cytometry

The clinical relevance of flow cytometry (FC)-based bone marrow involvement (BMI) in B cell non-Hodgkin lymphoma (B-NHL) is not well established. We conducted a systematic review of MEDLINE regarding the use of FC to establish BMI in B-NHL to determine the prevalence of BMI by FC, to understand the interrelation between FC and bone marrow biopsy (BMB), and to explore the prognostic impact of BMI by FC. Relevant exclusion criteria included publication before 2010. Eleven publications (of 18 screened) were included, with 2803 patients involved. Relevant methodological details were often unreported. The prevalence of BMI by FC varied based on histological subtypes included. The median kappa agreement between BMB and FC was 0.68 and the type of discordance (FC+/BMB- vs. FC-/BMB+) was highly variable across studies. Only 4 studies (all in diffuse large B cell lymphoma) assessed the prognostic impact of BMI by FC. Two found a worse prognosis for patients with FC+/BMB- than those without BMI. To conclude, studies assessing BMI by FC are retrospective, of low methodological quality and with heterogeneous findings.

Genetic mutations and features of mantle cell lymphoma: a systematic review and meta-analysis

Mantle cell lymphoma (MCL) is an incurable rare subtype of non-Hodgkin lymphoma and is subject to relapse and therapeutic resistance. Molecular aberrations in MCL affect pathogenesis, prognosis, and therapeutic response. In this systematic review, we searched 3 databases and selected 32 articles that described mutations in MCL patients. We then conducted a meta-analysis using a Bayesian multiregression model to analyze patient-level data in 2127 MCL patients, including prevalence of mutations. In tumor or bone marrow samples taken at diagnosis or baseline, ATM was the most frequently mutated gene (43.5%) followed by TP53 (26.8%), CDKN2A (23.9%), and CCND1 (20.2%). Aberrations were also detected in IGH (38.4%) and MYC (20.8%), primarily through cytogenetic methods. Other common baseline mutations were NSD2 (15.0%), KMT2A (8.9%), S1PR1 (8.6%), and CARD11 (8.5%). Our data also show a change in mutational status from baseline samples to samples at disease progression and present mutations of interest in MCL that should be considered for future analysis. The genes with the highest mutational frequency difference (>5%) are TP53, ATM, KMT2A, MAP3K14, BTK, TRAF2, CHD2, TLR2, ARID2, RIMS2, NOTCH2, TET2, SPEN, NSD2, CARD11, CCND1, SP140, CDKN2A, and S1PR1. These findings provide a summary of the mutational landscape of MCL. The genes with the highest change in mutation frequency should be included in targeted next-generation sequencing panels for future studies. These findings also highlight the need for analysis of serial samples in MCL. Patient-level data of prevalent mutations in MCL provide additional evidence emphasizing molecular variability in advancing precision medicine initiatives in MCL.

Application of liquid biopsy for surgical management of pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest forms of cancer. Although drug development over the past decade has gradually improved the prognosis of PDAC, the prognosis remains extremely poor. The predominant determinant of a poor prognosis is that patients are already at the advanced stage when they are diagnosed. Therefore, it is essential to detect early-stage PDAC to ensure a good prognosis. However, in general, being asymptomatic at the early stage makes the detection of early-stage PDAC very difficult. Recently, much attention has been focused on the utility of a liquid biopsy as a biomarker. Theoretically, early-stage tumors can be detected even under asymptomatic conditions. A number of studies on liquid biopsies have been reported so far. Several biomarkers, including circulating tumor DNA (ctDNA), circulating tumor cells (CTCS), and exosomes, are used in liquid biopsies, with the potential to be applied to the clinical setting. Each biomarker is reported to have different utilities, such as the detection of early-stage disease, the differential diagnosis of PDAC from other types of pancreatic tumors, the prediction of the prognosis or risk of recurrence, and monitoring the treatment response. In this review, we focus on ctDNA, CTCS, and exosomes as representative liquid biopsy biomarkers and describe the specific functions of each biomarker in the treatment of PDAC. Furthermore, we discuss the application of liquid biopsies, especially for the surgical management of PDAC.