Impact of Biomarker-Matched Therapies on Outcomes in Patients with Sarcoma Enrolled in Early-Phase Clinical Trials (SAMBA 101)

Designing Clinical Trials for Patients With Rare Cancers: Connecting the Zebras

The field of rare cancer research is rapidly transforming, marked by significant progress in clinical trials and treatment strategies. Rare cancers, as defined by the National Cancer Institute, occur in fewer than 150 cases per million people each year, yet they collectively represent a significant portion of all cancer diagnoses. Because of their infrequency, these cancers pose distinct challenges for clinical trials, including limited patient populations, geographical dispersion, and a general lack of awareness of treatment options. Economic limitations further complicate drug development, making initiatives such as the Orphan Drug Act essential for incentivizing research. The advent of next-generation sequencing (NGS) and precision medicine has been instrumental in identifying actionable genetic alterations in parallel with an explosion in the development of genomically targeted therapies, immunotherapies, and antibody drug conjugates. Advances in clinical NGS, precision medicine, and tumor-agnostic therapies have become central to the progress in rare cancer research. The development and approval of tumor-agnostic drugs, such as BRAF, NTRK, and RET inhibitors, and immunotherapy for mismatch repair deficient/microsatellite instability-high status cancers highlight the potential of personalized treatments across diverse cancer types and across the age spectrum. Collaborative trials from cooperative groups including SWOG DART, ASCO TAPUR, NCI-MATCH, pediatric COG-match, DRUP, IMPRESS, and innovative registrational basket and platform trials (eg, VE-Basket, ROAR, LIBRETTO-001, ARROW), along with patient advocacy group-run trials like TRACK, are enhancing access to clinical trials. In addition, artificial intelligence has the potential to improve the trial matching process. An integrated approach, combining these innovations in collaboration with multiple stakeholders, is crucial for advancing rare cancer research, offering hope for better patient outcomes and quality of life.

Next‑generation sequencing failure rates in rare tumors: A real‑world single‑institution analysis

Reported next-generation sequencing (NGS) failure rates vary widely and are primarily based on studies of common tumor types. The present study aimed to estimate NGS failure rates in rare tumors and their association with preanalytical variables and sequencing methods in a single institution. Patients with sarcomas, rare carcinomas, and rare melanomas who underwent NGS between January 2022 and October 2023 were eligible for participation in the present study. NGS was performed as whole exome/transcriptome sequencing (WETS) based on hybrid capture or multigene commercial targeted panel. Clinicopathological and NGS-related data were extracted from clinical charts. Univariable logistic regression models were constructed with the outcome variable NGS failure and the following explanatory variables: Assay, sampling method, tissue type, and storage time. A total of 102 NGS reports from 86 patients with sarcomas (73.3%), rare carcinomas (16.3%), and melanomas (10.5%) were included. The median age of the patients was 40 years [interquartile range (IQR), 23-61 years]. Samples were obtained by biopsy (51%) and surgery (48%) and were collected from soft tissue (92.1%) or bone (7.9%) lesions. The median storage time was 2.5 months (IQR, 1.3-4.6 months). Targeted panel and WETS were used in 39.2 and 60.8% of reports, respectively. NGS failure due to insufficient material quantity or quality was observed in 14.7% of tests, corresponding to 4.7% of patients. Repeated testing was successful in 7 out of 8 patients. WETS was significantly associated with a higher probability of NGS failure due to the insufficient quantity or quality of material compared to targeted panel (odds ratio, 11.4; 95% confidence interval, 1.4-90.4; P=0.022). In summary, our findings suggest that the NGS failure rates in rare tumors are comparable to the rates reported in prevalent neoplasms. WETS can be associated with more frequent NGS failure than targeted panel. Retesting can often overcome the initial NGS testing failure.

TP53INP2 promotes mitophagic degradation of YAP to impede dedifferentiated liposarcoma development

Dedifferentiated liposarcoma (DDLPS) accounts for 15-20% of liposarcoma (LPS) and has high rates of local recurrence and distant metastasis. Hyperactivation of yes-associated protein (YAP) has been implicated in DDLPS development. However, the mechanisms that drive aberrant YAP signaling remain largely unknown. Here, we show that tumor protein p53 inducible nuclear protein 2 (TP53INP2) is a potential negative modulator of the malignant progression of DDLPS. The TP53INP2 protein expression level in tumor tissues from 79 patients with DDLPS decreased progressively. Compared with primary tumors, recurrent tumors also exhibited reduced TP53INP2 expression. More importantly, low TP53INP2 expression is correlated with poor prognosis. TP53INP2 gain- or loss-of-function experiments in DDLPS cell lines showed profound inhibitory effects on processes and properties linked with cancer malignancy, such as proliferation, migration, stemness and dedifferentiation. Mechanistically, TP53INP2 is located mainly in mitochondria and promotes mitophagic degradation of YAP in a VDAC1-dependent manner. The WW domain in YAP and the PPTY motif in VDAC1 are required for their interaction. Taken together, these data demonstrate that TP53INP2 represses the malignant progression of DDLPS by inactivating YAP via a mitophagy-dependent mechanism and that TP53INP2 may constitute a novel prognostic biomarker for advanced DDLPS.

Safety and Efficacy of Percutaneous Cryoablation for Recurrent or Metastatic Soft-Tissue Sarcoma in Adult Patients

BACKGROUND. Treatment options are limited in patients with recurrent or metastatic disease after initial treatment of soft-tissue sarcoma (STS) by surgical resection, radiation, or systemic therapy. Percutaneous cryoablation may provide a complementary minimally invasive option in this setting. OBJECTIVE. The purpose of this article was to assess the safety and efficacy of percutaneous cryoablation performed for local control of treatment-refractory recurrent or metastatic STS. METHODS. This single-institution retrospective study included adult patients who underwent percutaneous cryoablation from January 2016 to April 2023 to achieve local control of recurrent or metastatic STS after earlier treatment (surgery, radiation, or chemotherapy). For each treated lesion, a single interventional radiologist rereviewed intraprocedural images to assess for adequate coverage by the ice ball of the entire lesion and a 5-mm or greater margin in all dimensions. Complications and outcomes were extracted from medical records. The primary end point for procedure efficacy was 1-year local progression-free survival. RESULTS. The study included 141 patients (median age, 66 years; 90 women, 51 men) who underwent 217 cryoablation procedures to treat 250 recurrent or metastatic STS lesions. The most common STS histologic types were leiomyosarcoma (56/141) and liposarcoma (39/141). Lesions had a mean long-axis diameter of 2.0 cm (range, 0.4-11.0 cm). Adequate ice-ball coverage was achieved for 82% (204/250) of lesions. The complication rate was 2% (4/217), including three major complications and one minor complication. Patients' median postablation follow-up was 25 months (range, 3-80 months). Local progression-free survival rate was 86% at 1 year and 80% at 2 years. The chemotherapy-free survival rate was 45% at 1 year and 31% at 2 years. The overall survival (OS) rate was 89% at 1 year and 80% at 2 years. In Kaplan-Meier analysis, leiomyosarcoma, in comparison with liposarcoma, had significantly higher local progression-free survival but no significant difference in OS. In multivariable analysis, factors independently associated with an increased risk for local progression included inadequate ice-ball coverage (HR = 7.34) and a lesion location of peritoneum (HR = 3.63) or retroperitoneum (HR = 3.71) relative to lung. CONCLUSION. Percutaneous cryoablation has a favorable safety and efficacy profile in patients with recurrent or metastatic STS after earlier treatments. CLINICAL IMPACT. Percutaneous cryoablation should be considered for local control of treatment-refractory STS.

Establishing biomarkers for soft tissue sarcomas

INTRODUCTION

Soft tissue sarcomas (STS) are a rare and diverse group of tumors. Curative options are limited to localized disease, with surgery being the mainstay. Advanced stages are associated with a poor prognosis. Currently, the prognosis of the patient is based on histological classification and clinical characteristics, with only a few biomarkers having entered clinical practice.

AREAS COVERED

This article covers extensive recent research that has established novel potential biomarkers based on genomics, proteomics, and clinical characteristics. Validating and incorporating these biomarkers into clinical practice can improve prognosis, prediction of recurrence, and treatment response. Relevant literature was collected from PubMed, Scopus, and clinicaltrials.gov databases (November 2023).

EXPERT OPINION

Currently, defining prognostic markers in soft tissue sarcomas remains challenging. More studies are required, especially to personalize treatment through advanced genetic profiling and analysis using individual tumor and patient characteristics.

Genetic, Epigenetic and Transcriptome Alterations in Liposarcoma for Target Therapy Selection

Liposarcoma (LPS) is one of the most common adult soft-tissue sarcomas (STS), characterized by a high diversity of histopathological features as well as to a lesser extent by a spectrum of molecular abnormalities. Current targeted therapies for STS do not include a wide range of drugs and surgical resection is the mainstay of treatment for localized disease in all subtypes, while many LPS patients initially present with or ultimately progress to advanced disease that is either unresectable, metastatic or both. The understanding of the molecular characteristics of liposarcoma subtypes is becoming an important option for the detection of new potential targets and development novel, biology-driven therapies for this disease. Innovative therapies have been introduced and they are currently part of preclinical and clinical studies. In this review, we provide an analysis of the molecular genetics of liposarcoma followed by a discussion of the specific epigenetic changes in these malignancies. Then, we summarize the peculiarities of the key signaling cascades involved in the pathogenesis of the disease and possible novel therapeutic approaches based on a better understanding of subtype-specific disease biology. Although heterogeneity in liposarcoma genetics and phenotype as well as the associated development of resistance to therapy make difficult the introduction of novel therapeutic targets into the clinic, recently a number of targeted therapy drugs were proposed for LPS treatment. The most promising results were shown for CDK4/6 and MDM2 inhibitors as well as for the multi-kinase inhibitors anlotinib and sunitinib.

Clinico-Genomic Profiling of Conventional and Dedifferentiated Chondrosarcomas Reveals TP53 Mutation to Be Associated with Worse Outcomes

PURPOSE

Chondrosarcomas are the most common primary bone tumor in adults. Isocitrate dehydrogenase 1 (IDH1) and IDH2 mutations are prevalent. We aimed to assess the clinico-genomic properties of IDH mutant versus IDH wild-type (WT) chondrosarcomas as well as alterations in other genes.

EXPERIMENTAL DESIGN

We included 93 patients with conventional and dedifferentiated chondrosarcoma for which there were available clinical next-generation sequencing data. Clinical and genomic data were extracted and compared between IDH mutant and IDH WT chondrosarcomas and between TP53 mutant and TP53 WT chondrosarcomas.

RESULTS

IDH1 and IDH2 mutations are prevalent in chondrosarcoma (50.5%), more common in chondrosarcomas arising in the extremities, associated with higher age at diagnosis, and more common in dedifferentiated chondrosarcomas compared with grades 1-3 conventional chondrosarcoma. There was no difference in survival based on IDH mutation in univariate and multivariate analyses. TP53 mutation was the next most prevalent (41.9%) and is associated with worse overall survival and metastasis-free survival in both univariate and multivariate analyses. TP53 mutation was also associated with higher risk of recurrence following curative-intent surgery and worse survival among patients that presented with de novo metastatic disease.

CONCLUSIONS

IDH mutations are prevalent in chondrosarcoma though were not associated with survival outcomes in this cohort. TP53 mutations were the next most common alteration and were associated with worse outcomes.

Circulating tumor DNA in clinical trials for solid tumors: Challenges and current applications

Tumor derived biomarkers including circulating tumor DNA (ctDNA) and/or circulating tumors cells (CTCs) may be detected and quantified through liquid biopsy (LB). ctDNA analysis through LB is a validated tool for monitoring response to systemic treatment and detecting molecular mechanisms of resistance at the time of progression of advanced stage malignancies. Several applications of ctDNA have been investigated in the diagnostic phase of cancer or in the post-curative treatment surveillance phase (e.g., minimal residual disease assessment after neoadjuvant or adjuvant therapy). Recently, the improvement of ctDNA technology and its implementation have affected early phase trials design, with significant changes in the inclusion and randomization phases. Implementation of LB has resulted in large-scale development of academic programs aimed at exploiting all the potential applications of ctDNA, such as patients extended molecular screening, molecular oriented treatment decision making, monitoring of anti-cancer treatments response. In this rapid evolving field, the challenge is no longer the technique, but the evaluation of the results and the interpretation of their impact on diagnosis, prognosis, or therapeutic decision. Leading research cancer centers may favor education for scientific community, by capturing data on this evolving technology and sharing knowledge. In this review we summarize the main applications and challenges of ctDNA genotyping in clinical trials, with special focus on ongoing studies. We finally describe the most important next generation academic and industry-sponsored programs addressing early cancer detection and prevention in high-risk populations through ctDNA genotyping.