Clinical sequencing of soft tissue and bone sarcomas delineates diverse genomic landscapes and potential therapeutic targets

Rapid Malignant Transformation of a Biopsy Proven Sporadic Soft Tissue Schwannoma to Spindle Cell MPNST With TP53 Mutation as an Early Event

Malignant peripheral nerve sheath tumors (MPNSTs) primarily originate from the neurofibromatosis 1 (NF1)- associated and/or sporadic neurofibromas. Reports of malignant transformation from a sporadic soft tissue schwannoma are rare. In most tumors documented in this context so far, the malignant component is an epithelioid MPNST with a strong and diffuse S100 positivity. We present a patient diagnosed with a sporadic soft tissue schwannoma on core biopsy, which underwent rapid malignant transformation to a spindle cell type MPNST. Somatic tumor profiling of the excision specimen revealed NF2 loss, TP53, NRAS, and subclonal RICTOR gene mutations. A retrospective immunohistochemical stain for p53 on the core biopsy demonstrated an aberrant staining pattern, indicating an early effect of TP53 in the process of malignant transformation.

Leiomyosarcoma Therapeutic Approaches and Future Directions

Leiomyosarcomas (LMS) are mesenchymal malignancies with smooth muscle differentiation that most commonly arise in the uterus, retroperitoneum, and extremity. Clinical course is variable, and management differs by site of origin. Recently completed and ongoing clinical trials are optimizing LMS management, and multidisciplinary care by an expert team is essential to navigate the nuances and provide optimal care. Advances in molecular characterization have improved diagnosis and identification of novel prognostic factors and systemic therapies. This article provides an overview of LMS presentation, diagnosis, molecular features, and clinical management, and highlights advancements in LMS biology and treatment.

Genomic, transcriptomic, and immunogenomic landscape of over 1300 sarcomas of diverse histology subtypes

Given their rarity and diversity, a fundamental understanding of the genomic underpinnings for many sarcoma subtypes is still lacking. To better define the molecular landscape of this group of diseases, we perform matched whole exome sequencing and RNA sequencing on a cohort of 1340 sarcoma tumor specimens. We identify recurrent somatic mutations and observe an increased mutational burden in metastatic vs. primary samples (p < 0.001). We observe frequent copy number alterations including whole genome doubling, with this feature being more common in metastatic tumors (p = 0.026). Estimation of immune cell abundances followed by hierarchical clustering identifies five immune subtypes ranging from low to high and we observe inferior overall survival in immune deplete clusters compared to immune enriched (p < 0.01). Interestingly, GIST predominantly form a distinct "immune intermediate" cluster that is marked by a specific enrichment for NK cells (FDR < 0.01).

Insights into the role of histone lysine demethylases in bone homeostasis and skeletal diseases: A review

Histone lysine demethylases (KDMs), as important epigenetic regulators, are involved in various biological processes such as energy metabolism, apoptosis, and autophagy. Recent research shows that KDMs activate or silence downstream target genes by removing lysine residues from histone tails, and participate in the regulation of bone marrow mesenchymal stem cells (BM-MSCs), osteoblasts (OB), osteoclasts (OC), chondrocytes and other skeletal cell development, differentiation and formation. Moreover, several members of the KDM family affect the occurrence and development of bone diseases such as osteoporosis (OP), osteoarthritis (OA), osteosarcoma (OS), by regulating target genes. Specific regulation mechanisms of KDMs suggest new strategies for bone disease treatment and prevention. Despite the unique function and importance of KDMs in the skeletal system, previous studies have never systematically summarized their specific role, molecular mechanism, and clinical treatment in bone physiology and pathology. Therefore, this review summarises the expression pattern, intracellular signal transduction, and mechanism of action of the KDM family in several bone physiological and pathological conditions, aiming to highlight the important role of KDMs in bone diseases and provide a reference for the future treatment of bone diseases.

Advancements in bone malignancy research through next-generation sequencing focussed on osteosarcoma, chondrosarcoma, and Ewing sarcoma

Next-generation sequencing (NGS) technologies have revolutionized bone cancer research, enabling detailed insights into the genetic, transcriptional, and epigenetic layers of these malignancies. This overview discusses the pivotal role of NGS in enhancing the diagnosis, prognosis, and treatment of primary bone cancers such as osteosarcoma, chondrosarcoma, and Ewing sarcoma. By facilitating the identification of novel genetic mutations, gene fusions, and epigenetic alterations, NGS supports the development of personalized medicine approaches and targeted therapies, significantly impacting clinical outcomes. The utilization of various NGS platforms, including Illumina, SOLiD, and Ion Torrent, has provided comprehensive genomic profiles that inform targeted treatment strategies and enable early detection through liquid biopsies and circulating tumor DNA (ctDNA) analysis. Despite the profound clinical benefits, the integration of NGS into routine practice faces challenges such as technical limitations, complex data interpretation, and substantial infrastructure requirements. Future directions involve technological improvements, combinatorial omics approaches, and extensive validation through clinical trials to confirm the efficacy of NGS-guided interventions. These advancements promise to further enhance the precision and effectiveness of bone cancer management, offering hope for more tailored and effective therapeutic outcomes.

Botensilimab (Fc-enhanced anti-cytotoxic lymphocyte-association protein-4 antibody) Plus Balstilimab (anti-PD-1 antibody) in Patients With Relapsed/Refractory Metastatic Sarcomas

PURPOSE

Outcomes for patients with advanced sarcomas are poor and there is a high unmet need to develop novel therapies. The purpose of this phase I study was to define the safety and efficacy of botensilimab (BOT), an Fc-enhanced anti-cytotoxic lymphocyte-association protein-4 antibody, plus balstilimab (BAL), an anti-PD-1 antibody, in advanced sarcomas.

METHODS

BOT was administered intravenously (IV) at 1 mg/kg or 2 mg/kg once every 6 weeks in combination with BAL IV at 3 mg/kg once every 2 weeks for up to 2 years. The primary end point was to determine dose-limiting toxicities during the dose-escalation period. Secondary end points include objective response rate (ORR), duration of response (DOR), disease control rate, and progression-free survival (PFS) by RECIST 1.1. Exploratory end points include assessing patient biomarkers including tumor mutational burden, cytokines, and PD-L1 expression.

RESULTS

Overall, 64 patients with sarcoma were treated; all were evaluable for safety and 52 for efficacy. The most common treatment-related adverse event (TRAE) was diarrhea/colitis occurring in 35.9% of patients, with grade 3 in 6.3% of patients. No grade 4 or 5 TRAEs were reported. For all evaluable patients, ORR was 19.2% (95% CI, 9.6 to 32.5), and 27.8% (95% CI, 9.7 to 53.5) for evaluable patients with angiosarcoma (n = 18); 33.3% in visceral and 22.2% in cutaneous subtypes. Median PFS for evaluable patients was 4.4 months (95% CI, 2.8 to 6.1), with a 6-month PFS rate of 36% (95% CI, 22 to 50) and a median DOR of 21.7 months (95% CI, 1.9 to not reached).

CONCLUSION

The combination of BOT/BAL demonstrated promising efficacy and safety in a large cohort of heavily pretreated sarcoma patients. This encouraging activity warrants further investigation (ClinicalTrials.gov identifier: NCT03860272).

Case Report: Lasting complete response to pembrolizumab in mismatch repair-deficient cardiac sarcoma: a genomic characterization

Sarcomas are traditionally considered "cold" tumors with poor response to immunotherapy. However, evidence accumulating over the last years shows that immune checkpoint inhibitors (ICIs) may have a role in selected sarcoma patients according to predictive markers. Here, we report the case of a woman diagnosed with a primary cardiac undifferentiated sarcoma. Following failure of standard first line chemotherapy, high-throughput sequencing (HTS) revealed a high tumor mutational burden (TMB), pathogenic mutations in FAT1 and NOTCH2 and a microsatellite instability (MSI)-associated signature. Immunohistochemistry confirmed mismatch repair-deficiency (MMRd) and abundant CD8+ tumor-infiltrating lymphocytes (TILs), in the absence of tertiary lymphoid structures. The patient was, therefore, treated with the ICI pembrolizumab, reaching a complete response that continues to persist at last follow-up, more than seven years from initial diagnosis and nearly six years from initiation of ICI treatment. This case illustrates the importance of performing HTS in rare sarcomas given the availability of efficient therapies, such as those for tumors displaying high TMB or MMRd/MSI. In agreement with other reports, it supports the contention that MMRd/MSI status and high numbers of TILs are valuable predictive markers of response to immunotherapy in sarcomas.

The genomic landscape of distant metastatic endometrial cancer

OBJECTIVE

The molecular underpinnings of primary treatment-naïve endometrial carcinoma (EC) are well described. Here we sought to characterize the genomic landscape of distant metastatic EC.

METHODS

Distant metastatic ECs from a total of 1888 cases subjected to a clinical panel sequencing between 4/2015 and 6/2020 were identified, and their genomic profiles, affected pathways and actionable alterations were compared to those of 711 primary ECs. Wilcoxon and Fisher's exact tests were used for continuous and categorical variables, respectively, and p-values adjusted for multiple hypothesis-testing.

RESULTS

Distant EC metastases (n = 137) of the lung (n = 66, 48 %), liver (n = 21, 15 %), soft tissue (n = 15, 11 %), distant lymph nodes (n = 15, 11 %), gastrointestinal tract (n = 10, 7 %), central nervous system (n = 5, 4 %), bone (n = 4, 3 %), and renal system (n = 1, 1 %) were included. Distant EC metastases were most commonly of copy number (CN)-high/TP53 abnormal (42 %) or CN-low/no specific molecular profile (NSMP) (39 %) molecular subtype; 18 % were microsatellite instability (MSI)-high/mismatch repair (MMR)-deficient and 1 % were of POLE molecular subtype. Distant EC metastases were significantly more chromosomally unstable compared to primary ECs across molecular subtypes (p < 0.0001). CTNNB1 mutations were more prevalent in distant CN-low/NSMP and MSI-high/MMR-deficient metastases compared to primary ECs (q < 0.1). Clinically actionable alterations were significantly less common in metastatic ECs (27 % vs 37 % primary; p = 0.025). PI3K, p53 and epigenetic pathways were the most altered pathways among all anatomic sites.

CONCLUSIONS

Distant metastatic ECs are more frequently chromosomally unstable but less commonly exhibit hypermutator phenotypes. Exploitation of genetic differences of metastatic EC is warranted for targeted treatment strategy development.

Myxofibrosarcoma with epithelioid morphology: A clinicopathological study of 44 cases with emphasis on differential diagnosis

AIMS

Epithelioid myxofibrosarcoma (eMFS) is an aggressive morphological variant associated with high rates of local recurrence and metastatic disease. The clinicopathological understanding of this disease is currently limited to a few small case-series.

METHODS AND RESULTS

We reviewed 44 cases of eMFS and classified them based on the presence of focal (< 50%) or diffuse (> 50%) epithelioid morphology and Fédération Nationale des Centres de Lutte Contre le Cancer (FNCLCC) grade. The patients (28 males; 16 females) had a median age of 71 years (range = 14-90 years). The proximal extremity was the most common site (n = 21), followed by the trunk (n = 11), distal extremity (n = nine) and head/neck (n = two). Of cases with known depth of involvement (n = 41), 39 involved the subcutis, one was limited to the dermis and one limited to the skeletal muscle. Most cases (n = 34, 77%) demonstrated diffuse (> 50%) epithelioid morphology and were FNCLCC grade 3 (n = 29, 66%). Follow-up data were available for 22 patients. Two developed local recurrence and 10 developed metastases, frequently to regional lymph nodes. All metastatic tumours had a primary lesion with diffuse epithelioid morphology (P = 0.09). There was no association between grade and recurrent or metastatic disease (P = 0.67 and 0.90, respectively). Three cases initially diagnosed as eMFS, one in the neck and two in the axilla, were found to have NRAS Q61R mutations and a high tumour mutation burden and/or ultraviolet (UV)-light DNA mutational signature.

CONCLUSIONS

These findings suggest that UV-driven malignancies (including melanoma or sarcomatoid squamous cell carcinoma) may histologically mimic eMFS and should be considered in cases of eMFS presenting at atypical anatomical sites.

Subtype-Specific Patterns of Tumor Purity and Mutation Load Suggest Treatment Implications: A Cross-Sectional Analysis of 7494 Soft Tissue and Bone Sarcomas (MSK Cohort)

OBJECTIVES

Sarcomas are complex mesenchymal malignancies whose molecular characteristics can significantly influence treatment strategies. This study aimed to investigate the relationship between tumor purity, mutation load, and clinical characteristics across sarcoma subtypes, focusing on potential implications for therapeutic stratification.

METHODS

This study analyzed the molecular characteristics of 7494 sarcoma cases from the Soft Tissue and Bone Sarcoma (MSK, Nat Commun 2022) data set using available case analysis. Correlations between tumor purity, mutation load, age, and sex were analyzed using nonparametric methods, with subtype-specific analyses conducted using Kruskal-Wallis tests and Bonferroni-corrected post hoc comparisons. A comprehensive analysis of mutation patterns was performed using microsatellite instability (MSI) status.

RESULTS

Significant correlations between mutation load and tumor purity (ρ=0.320, P <0.001) were identified, with marked heterogeneity across subtypes. Tumor purity ranged from 20.0% in brain sarcomas to 78.5% in dermatofibrosarcoma protuberans. Age-related molecular changes were observed in brain (ρ=0.711, P =0.006) and skin sarcomas (ρ=0.450, P =0.006), suggesting distinct evolutionary patterns. A subset of hypermutated, microsatellite stable cases (0.15%) with mutation loads exceeding 100 mutations/mb were identified, suggesting alternative mechanisms of genomic instability. MSI-high status was rare (0.24%) but associated with higher mutation loads (median: 25.84 vs. 2.42, P <0.001), particularly in uterine sarcomas (0.7% prevalence).

CONCLUSIONS

The identification of distinct molecular patterns across sarcoma subtypes challenge existing morphology-based classification systems and may hold implications for therapeutic stratification. These findings may help inform future immunotherapeutic and molecular-guided approaches to treatment in sarcoma patients, particularly for elderly patients with brain sarcomas or females with uterine sarcomas.

Functional combinatorial precision medicine for predicting and optimizing soft tissue sarcoma treatments

Soft tissue sarcomas (STS) are rare, heterogeneous tumors with poor survival outcomes, primarily due to reliance on cytotoxic chemotherapy and lack of targeted therapies. Given the uniquely individualized nature of STS, we hypothesized that the ex vivo drug sensitivity platform, quadratic phenotypic optimization platform (QPOP), can predict treatment response and enhance combination therapy design for STS. Using QPOP, we screened 45 primary STS patient samples, and showed improved or concordant patient outcomes that are attributable to QPOP predictions. From a panel of approved and investigational agents, QPOP identified AZD5153 (BET inhibitor) and pazopanib (multi-kinase blocker) as the most effective combination with superior efficacy compared to standard regimens. Validation in a panel of established patient lines and in vivo models supported its synergistic interaction, accompanied by repressed oncogenic MYC and related pathways. These findings provide preliminary clinical evidence for QPOP to predict STS treatment outcomes and guide the development of novel therapeutic strategies for STS patients.

Self-assembled patient-derived tumor-like cell clusters for personalized drug testing in diverse sarcomas

Several patient-derived tumor models have emerged recently. However, soft tissue sarcomas (STSs) present a challenge in developing preclinical drug-testing models due to their non-epithelial and complex nature. Here, we report a model termed patient-derived tumor-like cell clusters (PTCs) derived from STS patients. PTCs result from the self-assembly and proliferation of mesenchymal stem cells (MSCs), epithelial cells, and immune cells, faithfully recapitulating the morphology and function of the original tumors. Through standardized culture and drug-response assessment protocols, PTCs facilitate personalized drug testing, evaluating hundreds of therapies within two weeks. Notably, PTCs exhibit 100% accuracy in distinguishing between complete or partial response and disease progression. We demonstrate the utility of PTCs in guiding chemotherapy selection for a patient with relapse and metastases following conventional therapy, who exhibited a positive response after non-conventional therapy identified through PTC. These findings underscore the potential of PTCs for prospective use in clinical decision-making regarding therapy selection.

Monocyte-lineage tumor infiltration predicts immunoradiotherapy response in advanced pretreated soft-tissue sarcoma: phase 2 trial results

Immunoradiotherapy holds promise for improving outcomes in patients with advanced solid tumors, including in soft-tissue sarcoma (STS). However, the ideal combination of treatment modalities remains to be determined, and reliable biomarkers to predict which patients will benefit are lacking. Here, we report the results of the STS cohort of the SABR-PDL1 phase II trial that evaluated the anti-PDL1 atezolizumab combined with stereotactic body radiation therapy (SBRT) delivered concurrently with the 2nd cycle to at least one tumor site. Eligible patients received atezolizumab until progression or unmanageable toxicity, with SBRT at 45 Gy in 3 fractions). The primary endpoint was one-year progression-free survival (PFS) rate with success defined as 13 patients achieving 1-year PFS. Sixty-one heavily pretreated patients with STS (median 5 prior lines; 52% men; median age 54 years; 28% leiomyosarcoma) were enrolled across two centers (France, Spain). SBRT was delivered to 55 patients (90%), with the lung being the most commonly irradiated site (50%). After a median follow-up of 45 months, the one-year PFS rate was 8.3% [95% CI: 3.6-18.1]. Median PFS and overall survival were 2.5 and 8.6 months, respectively. Best responses included partial responses (5%) and stable disease (60%). Immune profiling revealed increased immunosuppressive tumor-associated macrophages (e.g., IL4I1, HES1) and monocyte-recruiting chemokines in non-responders. Higher monocyte/lymphocyte ratios (MonoLR) in tumor and blood correlated with progression. PD-L1 status, lymphoid infiltration, and tertiary-lymphoid structures were not predictive. Although the primary endpoint was not met, this study highlights MonoLR imbalance as a potential biomarker to identify STS patients likely to benefit from immunoradiotherapy. EudraCT No. 2015-005464-42; Clinicaltrial.gov number: NCT02992912.

Genomic Profiling of Cardiac Angiosarcoma Reveals Novel Targetable KDR Variants, Recurrent MED12 Mutations, and a High Burden of Germline POT1 Alterations

PURPOSE

Cardiac angiosarcoma is a rare, aggressive malignancy with limited treatment options. Both sporadic and familial cases occur, with recent links to germline POT1 mutations. The genomic landscape of this disease is poorly understood.

EXPERIMENTAL DESIGN

We conducted comprehensive genomic profiling of cardiac angiosarcoma to assess the burden of germline predisposition and identify other recurrent genomic alterations of clinical significance.

RESULTS

Six patients were female, and four were male. The median age at presentation was 40 years (range, 21-69 years). All cases with available follow-up exhibited an aggressive clinical course (6/8 patients died of disease). KDR alterations, including novel structural variants, were found in 9/11 cases at a rate significantly higher than that in noncardiac angiosarcomas. POT1 mutations were present in 45.5% of cardiac angiosarcoma cases. In three of five POT1-mutant cases, the germline status was confirmed through testing of normal tissue, and in one additional case, the germline status was inferred with high probability through allele frequency analysis. Additionally, we identified novel recurrent MED12 exon 2 mutations in POT1 wild-type cardiac angiosarcoma, suggesting an alternative path to cardiac angiosarcoma oncogenesis.

CONCLUSIONS

Cardiac angiosarcoma demonstrates a unique genetic profile, distinct from noncardiac angiosarcoma. This study highlights the role of germline POT1 burden on cardiac angiosarcoma development and demonstrates recurrent MED12 alterations for the first time. The reported KDR variants provide a potential avenue for the treatment of this aggressive disease. Given the prevalence of germline POT1 mutations reported in this study, germline genetic testing should be considered in patients diagnosed with cardiac angiosarcoma.

Insights into targeting LKB1 in tumorigenesis

Genetic alterations to serine-threonine kinase 11 (STK11) have been implicated in Peutz-Jeghers syndrome and tumorigenesis. Further exploration of the context-specific roles of liver kinase B1 (LKB1; encoded by STK11) observed that it regulates AMP-activated protein kinase (AMPK) and AMPK-related kinases. Given that both migration and proliferation are enhanced with the loss of LKB1 activity combined with the prevalence of STK11 genetic alterations in cancer biopsies, LKB1 was marked as a tumor suppressor. However, the role of LKB1 in tumorigenesis is paradoxical as LKB1 activates autophagy and reactive oxygen species scavenging while dampening anoikis, which contribute to cancer cell survival. Due to the pro-tumorigenic properties of LKB1, targeting LKB1 pathways is now relevant for cancer treatment. With the recent successes of targeting LKB1 signaling in research and clinical settings, and enhanced cytotoxicity of chemical compounds in LKB1-deficient tumors, there is now a need for LKB1 inhibitors. However, validating LKB1 inhibitors is challenging as LKB1 adaptor proteins, nucleocytoplasmic shuttling, and splice variants all manipulate LKB1 activity. Furthermore, STE-20-related kinase adaptor protein (STRAD) and mouse protein 25 dictate LKB1 cellular localization and kinase activity. For these reasons, prior to assessing the efficacy and potency of pharmacological candidates, the functional status of LKB1 needs to be defined. Therefore, to improve the understanding of LKB1 in physiology and oncology, this review highlights the role of LKB1 in tumorigenesis and addresses the therapeutic relevancy of LKB1 inhibitors.

Immune Biomarkers on Tissue Microarray Cores Support the Presence of Adjacent Tertiary Lymphoid Structures in Soft Tissue Sarcoma

Immunotherapy has emerged as a new treatment modality in some soft tissue sarcomas, particularly for tumors associated with tertiary lymphoid structures (TLSs). These structures are functional lymphoid aggregates, and their presence is indicative of an active anticancer immune response in the tumor microenvironment. The assessment of TLS as a predictive biomarker at scale on patient specimens remains challenging. Although tissue microarrays (TMAs) could facilitate this assessment, it is unclear whether small microarray cores can represent and identify associated TLS responses. We sought to use multiplex immunohistochemistry to identify key components of TLS: T cells, B cells, and dendritic cells. The multiplex panels (CD3, CD20, CD208, and PNAd) were applied to 80 cases both on TMAs and on their cognate available full-faced sections from epithelioid sarcoma and dedifferentiated/well-differentiated liposarcoma case series. TMAs were digitally scored for the number of immune cells using the HALO image analysis platform, and cognate full-faced sections were visually evaluated for the presence of TLS. An independent validation set of soft tissue sarcomas (N = 49) was stained with the CD3, CD20, and CD208, and scored by QuPath. A combined immune marker (defined as the presence of more than 24% CD3+ T cells, or 0.51% CD20+ B cells, or >0.14% CD208+ mature dendritic cells on tissue microarray cores) is highly specific (100%) and moderately sensitive (61%) to predict the existence of TLS on full-faced sections. The combined immune marker showed a sensitivity of 25% and specificity of 91% on the validation set. The combined immune marker assessed on tissue microarrays is highly specific in inferring the presence of TLS on cognate full-faced sections. Therefore, despite the small area sampled, tissue microarrays may be utilized to assess the clinical value of TLS on data sets where specificity is critical and large sample size can mitigate low-to-moderate sensitivity.

Histologic and Immunologic Factors Associated with Response to Immune Checkpoint Inhibitors in Advanced Sarcoma

PURPOSE

To characterize factors associated with response to immune checkpoint inhibitors (ICI) in advanced sarcoma.

EXPERIMENTAL DESIGN

This is a retrospective study with a cohort of 216 patients with advanced sarcoma treated with ICI between 2016 and 2023 at Stanford Health Care. Overall survival, progression-free survival (PFS), objective response rates (ORR) per RECIST criteria, and reason for ICI discontinuation were analyzed across histologic subtypes, ICI regimens, tumor mutational burden, and PD-L1 expression.

RESULTS

The overall ORR in the cohort was 16.7%. The histologic subtypes with the highest ORR were Kaposi sarcoma (KS, 66.7%), alveolar soft part sarcoma (ASPS, 50%), angiosarcoma (33.3%), myxofibrosarcoma (MFS, 28.6%), and undifferentiated pleomorphic sarcoma (UPS, 27.8%). The subtypes with the lowest ORR were osteosarcoma (0%), synovial sarcoma (0%), and liposarcoma (3.7%). The subtypes with the highest median PFS were KS (median not reached), ASPS (median not reached), MFS (27.4 months), and UPS (11.3 months). The ORR for sarcomas with PD-L1 ≥ 1% was 27.8% (P = 0.02), whereas the ORR for sarcomas with tumor mutational burden ≥10 mutations per megabase of DNA was 28.6% (P = 0.20).

CONCLUSIONS

ORR and PFS were highly variable across sarcoma histologic subtypes. In this large analysis, KS, ASPS, angiosarcoma, MFS, and UPS demonstrated the highest ORR and longest PFS while osteosarcoma, synovial sarcoma, and liposarcoma had the lowest ORR and shortest PFS. PD-L1 expression was also associated with increased ORR. Our findings provide further insight into understanding the sarcoma histologic and immunologic factors that correspond with response to ICI.

Age-related genomic alterations and chemotherapy sensitivity in osteosarcoma: insights from cancer genome profiling analyses

BACKGROUND

Osteosarcoma, the most common primary bone malignancy, has a complex genetic basis and two incidence peaks. In younger patients, the standard treatment involves wide surgical resection combined with adjuvant chemotherapy; however, the role of chemotherapy in elderly patients remains controversial. The aims of this study were to investigate genetic differences between younger and elderly patients with osteosarcoma and to identify genetic signatures associated with chemotherapy response.

METHODS

Genetic alterations were analyzed using cancer genome profiling data for 204 patients with osteosarcoma obtained from the Center for Cancer Genomics and Advanced Therapeutics.

RESULTS

The mutation spectrum was consistent with previous results for osteosarcoma. CCNE1, MCL1, MYC, and RB1 alterations were significantly associated with a younger age, while CDK4, CDKN2A, CDKN2B, H3F3A, KMT2D, MDM2, RAC1, and SETD2 alterations were significantly associated with an older age. Age, unsupervised clustering of gene alterations, and MYC amplifications were significantly associated with the response to ifosfamide. Notably, both clustered mutation signatures and MYC amplification were correlated with age.

CONCLUSIONS

These findings suggest that distinct oncogenic mechanisms contribute to differential sensitivity to chemotherapy in younger and elderly patients. Cancer genome profiling may aid in chemotherapy selection, and its early implementation is recommended to optimize treatment strategies.

Comprehensive mutational profiling identifies new driver events in cutaneous leiomyosarcoma

BACKGROUND

Cutaneous leiomyosarcoma (cLMS) is a rare soft-tissue neoplasm, showing smooth muscle differentiation, that arises from the mesenchymal cells of the dermis. To date, genetic investigation of these tumours has involved studies with small sample sizes and limited analyses that identified recurrent somatic mutations in RB1 and TP53, copy number gain of MYOCD and IGF1R, and copy number loss of PTEN.

OBJECTIVES

To better understand the molecular pathogenesis of cLMS, we comprehensively explored the mutational landscape of these rare tumours to identify candidate driver events.

METHODS

In this retrospective, multi-institutional study, we performed whole-exome sequencing and RNA sequencing in 38 cases of cLMS.

RESULTS

TP53 and RB1 were identified as significantly mutated and thus represent validated driver genes of cLMS. COSMIC mutational signatures SBS7a/b and DBS1 were recurrent; thus, ultraviolet light exposure may be an aetiological factor driving cLMS. Analysis of significantly recurrent somatic copy number alterations, which represent candidate driver events, found focal (< 10 Mb) deletions encompassing TP53 and KDM6B, and amplifications encompassing ZMYM2, MYOCD, MAP2K4 and NCOR1. A larger (24 Mb) recurrent deletion encompassing CYLD was also identified as significant. Significantly recurrent broad copy number alterations, involving at least half of a chromosome arm, included deletions of 6p/q, 10p/q, 11q, 12q, 13q and 16p/q, and amplification of 15q. Notably PTEN is located on 10q, RB1 on 13q and IGFR1 on 15q. Fusion gene analysis identified recurrent CRTC1/CRTC3::MAML2 fusions, as well as many novel fusions in individual samples.

CONCLUSIONS

Our analysis of the largest number of cases of cLMS to date highlights the importance of large cohort sizes and exploration beyond small targeted gene panels when performing molecular analyses, as it allowed a comprehensive exploration of the mutational landscape of these tumours and identification of novel candidate driver events. It also uniquely afforded the opportunity to compare the molecular phenotype of cLMS with LMS of other tissue types, such as uterine and soft-tissue LMS. Given that molecular profiling has resulted in the development of novel targeted treatment approaches for uterine and soft-tissue LMS, our study now allows the same opportunities to become available for patients with cLMS.

NTRK amplification occurs frequently in pan-TRK immunopositive dedifferentiated liposarcomas

The neurotrophic tyrosine kinase receptor (NTRK) gene family is of rising importance as their fusions are oncogenic, and specific target drugs are available to inhibit the chimera proteins. Pan-TRK antibody, which shows the overexpression of the NTRK1-2-3 genes, is a useful tool to detect tumors with or without NTRK gene alterations, due to high negative predictive value. Though it is well known that pan-TRK immunopositivity is usually not connected to NTRK fusion, the role of other possible genetic alterations is under-researched. In our previous work, we found 3 NTRK1 amplified cases out of 6 cases with recurrent NTRK1 tyrosine kinase domain mutation pair, so we extended our investigation to a larger series to estimate amplification frequency. Pan-TRK immunopositivity was seen in 76 of the 132 dedifferentiated liposarcomas cases, followed by NTRK1-2-3 break-apart FISH tests in 76 pan-TRK positive cases to detect oncogenic fusions or other copy number alterations of these genes. None of the pan-TRK immunopositive dedifferentiated liposarcomas showed absolutely certain sign of fusion, however, 18 (28%) cases showed amplification of one of the genes, 13 had polysomy, 34 were normal, 11 were not evaluable. The extent of pan-TRK immunoreaction showed a positive correlation (p = 0.002) with the NTRK status found by FISH. Analyzing publicly available data from large series of 265 liposarcoma samples consisting of both well-differentiated and dedifferentiated liposarcoma case, 23 (8.6%) cases showed a mutual exclusive amplification of the NTRK genomic loci in a non-preselected, independent patient population indicating that our findings are presented in other cohorts. Our results underline the so far not revealed frequent occurrence of NTRK amplifications which might be important in the TRK inhibition therapy.

Genomic profiling of intimal sarcoma reveals molecular subtypes with distinct tumor microenvironments and therapeutic implications

BACKGROUND

Intimal sarcoma is a rare and aggressive soft-tissue sarcoma with limited treatment options. We explored genomic profiles of intimal sarcoma to uncover therapeutic implications.

MATERIALS AND METHODS

We analyzed tumor tissues from patients with intimal sarcoma who visited the Seoul National University Hospital (SNUH) using whole-exome, whole-transcriptome, and clinical next-generation sequencing (NGS), integrated with intimal sarcoma NGS data from two public cohorts. We examined expression characteristics and tumor-infiltrating lymphocytes (TILs) according to molecular subtypes.

RESULTS

Our study included 42 samples in total. Thirty-three patients showing copy number variation (CNV) enrichment with frequent CDK4/MDM2 amplifications were classified as the CNV-high (CNV-H) subtype. Five patients showing predominant MLH1 mutations or homozygous deletions were classified as the microsatellite instability-high-like (MSI-H-like) subtype. Hallmark pathways up-regulated in the CNV-H subtype included Wnt β-catenin and Hedgehog signaling. In the MSI-H-like subtype, interferon-γ response, tumor necrosis factor-α signaling via nuclear factor-κB, interferon-α response, inflammatory response, and interleukin-6-Jak-Stat3 signaling were up-regulated. CNV-H subtype samples predominantly showed an immune-desert phenotype, whereas MSI-H-like subtype samples predominantly showed an immune-inflamed phenotype. Two MSI-H-like subtype patients received pembrolizumab and experienced tumor shrinkage.

CONCLUSIONS

We identified two intimal sarcoma molecular subtypes. Compared with CNV-H, MSI-H-like is enriched in pathways associated with tumor immune responses and TILs. Further efforts and clinical trials to better define these molecular subtypes are warranted to open new avenues for personalized treatment approaches and improve patient outcomes.

Treatment of Retroperitoneal Well-Differentiated Liposarcoma with Combination of Penpulimab and Anlotinib: A Case Report and Literature Review

To observe the efficacy of combination therapy with Penpulimab and Anlotinib in the treatment of retroperitoneal well-differentiated liposarcoma. Retrospective analysis of clinical data of a patient with retroperitoneal well-differentiated soft tissue sarcoma admitted to Shaoxing People's Hospital, and review of relevant literature. The patient is a young male who experienced recurrence of retroperitoneal well-differentiated liposarcoma after two surgeries. After first-line treatment with Anlotinib combined with Penpulimab, the patient achieved almost complete remission with a progression free survival period of about 16 months. The first-line treatment of retroperitoneal well-differentiated soft tissue sarcoma using Anlotinib combined with Penpulimab resulted in a good prognosis.

Nivolumab and sunitinib in patients with advanced bone sarcomas: A multicenter, single-arm, phase 2 trial

BACKGROUND

Herein, we present the results of the phase 2 IMMUNOSARC study (NCT03277924), investigating sunitinib and nivolumab in adult patients with advanced bone sarcomas (BS).

METHODS

Progressing patients with a diagnosis of BS were eligible. Treatment was comprised of sunitinib (37.5 mg/day on days 1-14, 25 mg/day afterword) plus nivolumab (3 mg/kg every 2 weeks). Primary end point was progression-free survival rate (PFSR) at 6 months based on central radiology review. Secondary end points were overall survival (OS), overall response rate (ORR) by Response Evaluation Criteria in Solid Tumors (RECIST) v1.1, and safety.

RESULTS

A total of 46 patients were screened, 40 patients entered the study, and 38 underwent central radiological review and were evaluable for primary end point. Median age was 47 years (range, 21-74). Histologies include 17 (43%) osteosarcoma, 14 chondrosarcoma (35%, 10 conventional, four dedifferentiated [DDCS]), eight (20%) Ewing sarcoma, and one (2%) undifferentiated pleomorphic sarcoma. The PFSR at 6 months was 42% (95% confidence interval [CI], 27-58). With a median follow-up of 39.8 months (95% CI, 37.9-41.7), the median PFS and OS were 3.8 months (95% CI, 2.7-4.8) and 11.9 months (95% CI, 5.6-18.2). ORR by RECIST was 5%, with two of 38 partial responses (one of four DDCS and one of 17 osteosarcoma), 19 of 38 (50%) stable disease, and 17 of 38 (45%) progressions. Grade ≥3 adverse events were neutropenia (six of 40, 15%), anemia (5/40, hypertension (6/40, 15%), 12.5%), ALT/AST elevation (5/40, 12.5%), and pneumonitis (1/40, 2.5%). Seventeen percent of patients discontinued treatment due to toxicity, including a treatment-related grade 5 pneumonitis CONCLUSION: The trial met its primary end point in the BS cohort with >15% of patients progression-free at 6 months. However, the toxicity profile of this regimen was relevant.

Biomimetic Targeted Co-Delivery System Engineered from Genomic Insights for Precision Treatment of Osteosarcoma

The high heterogeneity and severe side effects of chemotherapy are major factors contributing to the failure of osteosarcoma treatment. Herein, a comprehensive genomic analysis is conducted, and identified two prominent characteristics of osteosarcoma: significant cyclin-dependent kinases 4 (CDK4) amplification and homologous recombination repair deficiency. Based on these findings, a co-delivery system loaded with CDK4/6 inhibitors and poly ADP-ribose polymerase (PARP) inhibitors is designed. By employing metal-organic frameworks (MOFs) as carriers, issue of drug insolubility is effectively addressed, while also enabling controlled release in response to the tumor microenvironment. To enhance targeting capability and biocompatibility, the MOFs are further coated with a bio-membrane targeting B7H3. This targeted biomimetic co-delivery system possesses several key features: 1) it can precisely target osteosarcoma with high B7H3 expression; 2) the combination of CDK4/6 inhibitors and PARP inhibitors exhibits synergistic effects, significantly impairing tumor's DNA repair capacity; and 3) the system has the potential for combination with photodynamic therapy, amplifying DNA repair defects to maximize tumor cell eradication. Furthermore, it is observed that this co-delivery system can activate immune microenvironment, increasing CD8+ T cell infiltration and converting osteosarcoma from an immune-cold to an immune-hot tumor. In summary, the co-delivery system is an effective therapeutic strategy and holds promise as a novel approach for osteosarcoma treatment.

Multiomics analysis of homologous recombination deficiency across cancer types

There remains ongoing debate regarding the association of homologous recombination deficiency (HRD) with patient survival across various malignancies, highlighting the need for a comprehensive understanding of HRD's role in different cancer types. Based on data from databases, we conducted a multivariable omics analysis on HRD in 33 cancer types, focusing mainly on 23 cancers in which HRD was significantly associated with patient overall survival (OS) rates. This analysis included the mechanisms related to patient prognosis, gene expression, gene mutation, and signaling pathways. In this study, HRD was found to be significantly associated with patient prognosis, but its impact varied among different cancers. HRD was linked to different outcomes for patients with distinct tumor subtypes and was correlated with clinical features such as clinical stage and tumor grade. Driver gene mutations, including TP53, MUC4, KRAS, HRAS, FLG, ANK3, BRCA2, ATRX, FGFR3, NFE2L2, MAP3K1, PIK3CA, CIC, FUBP1, ALB, CTNNB1, and MED12, were associated with HRD across specific cancer types. We also analyzed differentially expressed genes (DEGs) and differentially methylated regions (DMRs) in relation to HRD levels in these cancers. Furthermore, we explored the correlation between HRD and signaling pathways, as well as immune cell infiltration. Overall, our findings contribute to a comprehensive understanding of HRD's multifaceted role in cancer.

Targeting liposarcoma: unveiling molecular pathways and therapeutic opportunities

In recent years, an increasing number of studies have utilized molecular biology techniques to reveal important molecular heterogeneity among different subtypes of liposarcoma. Each subtype exhibits distinct genetic patterns and molecular pathways, which may serve as important targets for molecular therapy. In the present review, we focus on the molecular characteristics, molecular diagnostics, driver genes, and molecular mechanisms of liposarcoma. We also discuss the clinical research progress of related targeted therapies, with an aim to provide a reference and crucial insights for colleagues in the field.

Development and validation of a novel immune-related prognostic model and the potential metastatic mechanism in synovial sarcoma

Background

Several clinical trials have shown that immunotherapy plays a pivotal role in the treatment of patients with metastatic synovial sarcoma. Immune-related genes (IRGs) have been demonstrated to predict the immunotherapy response in certain malignant tumours. However, the clinical significance of IRGs in patients with synovial sarcoma (SS) is still unclear.

Methods

We first combined the immune-related ImmPort gene set to search for SS related to metastatic and differentially expressed immune-related genes (DEIRGs) in the GSE40021 dataset from the GEO database. The soft tissue sarcoma database in TCGA was used for univariate Cox regression analyses to identify DEIRGs that were related to overall survival and to build an immune-related prognostic assessment model.

Results

The study screened a total of six DEIRGs that were closely related to prognosis in metastatic SS. Further analysis showed that there was no significant difference in the expression of several immune checkpoints between the two groups in the GSE40021 data. Moreover, the GREM2 and CTSS genes were significantly expressed in metastatic patients. Further verification of clinical SS tissues from our centre by RT-qPCR analysis demonstrated reduced infiltration of activated NK cells and macrophages but increased M2-type macrophages in metastatic patients. Together, our study successfully constructed an immune-related prognostic assessment model and probably explains the poor efficacy of PD-1 inhibitors for SS patients.

Conclusion

The research deepens our understanding of the tumor immune microenvironment and proposes a new immune mechanism for metastatic SS. Early intervention and reversal of immunosuppressive microenvironmental changes are expected to delay metastasis and improve survival.

Classification of pediatric soft and bone sarcomas using DNA methylation-based profiling

Pediatric sarcomas present heterogeneous morphology, genetics and clinical behavior posing a challenge for an accurate diagnosis. DNA methylation is an epigenetic modification that coordinates chromatin structure and regulates gene expression, determining cell type and function. DNA methylation-based tumor profiling classifier for sarcomas (known as sarcoma classifier) from the German Cancer Research Center (Deutsches Krebsforschungszentrum) was applied to 122 pediatric sarcomas referred to a reference pediatric oncology hospital. The classifiers reported 88.5% of agreement between histopathological and molecular classification confirming the initial diagnosis of all osteosarcomas and Ewing sarcomas. The Ewing-like sarcomas were reclassified into sarcomas with BCOR or CIC alterations, later confirmed by orthogonal diagnostic techniques. Regarding the CNAs profile, osteosarcomas had several chromosomal gains and losses as well as chromothripsis, whereas Ewing sarcomas had few large events, such as amplifications of chromosomes 8 and 12. The molecular classification together with clinical and histopathological assessment could improve the diagnosis of pediatric sarcomas although there are limitations to deal with more rare classes. This study provides an increase in the number of sarcomas evaluated for DNA methylation profiling in the pediatric population.

Analysis of cancer multigene panel testing for osteosarcoma in pediatric and adults using the center for cancer genomics and advanced therapeutics database in Japan

BACKGROUND

Osteosarcoma (OS) is the most common primary malignant bone tumor. Despite advances in multimodal chemotherapy, prognosis for metastatic or recurrent OS remains poor. Next-generation sequencing (NGS) can uncover new therapeutic options by identifying potentially targetable alterations. This study analyzed NGS data from the Center for Cancer Genomics and Advanced Therapeutics (C-CAT) database in Japan, comparing findings with the Memorial Sloan-Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) data from the United States.

METHODS

We sequenced tumor and/or germline DNA from 223 high-grade OS samples using the FoundationOne® CDx or OncoGuideTM NCC Oncopanel System, and the FoundationOne® Liquid CDx for multigene panel testing (2019-2023). Genomic alterations were interpreted using the Cancer Knowledge Database (CKDB), with potentially actionable genetic events categorized into A-F levels.

RESULTS

Analysis of 223 high-grade OS samples revealed 1684 somatic mutations in 167 genes and 1114 copy number alterations in 89 genes. Potentially actionable alterations were identified in 94 patients (42.2 %) at CKDB Levels A-C. These included 2 cases with NTRK fusions (0.9 %; Level A), one case with TMB-high (0.4 %; Level A), 3 with ERBB amplifications (1.3 %; Level B), and 88 cases (39.5 %) with alterations such as CDK4 amplification, PTEN deletion/mutation, and others (Level C). Co-occurring amplifications of KIT, KDR, and PDGFRA at the 4q12 locus were found in 8 cases (3.6 %), while VEGFA and CCND3 co-amplifications at the 6p12-21 locus were seen in 33 cases (14.8 %). These gene amplifications, also reported in US studies, are targetable by multi-kinase inhibitors, although the C-CAT cohort's profiles differed from US cohorts like MSK-IMPACT.

CONCLUSIONS

Precision medicine for rare tumors still poses challenges. In this Japanese cohort, 42.2 % of high-grade OSs had potentially actionable alterations per CKDB. Concurrent gene amplifications of KIT, KDR, and PDGFRA at 4q12, and VEGFA and CCND3 at 6p12-21, might offer promising therapeutic options for patients with recurrent/metastatic OS resistant to conventional chemotherapy.

Molecular Profiling Defines Three Subtypes of Synovial Sarcoma

Synovial Sarcomas (SS) are characterized by the presence of the SS18::SSX fusion gene, which protein product induce chromatin changes through remodeling of the BAF complex. To elucidate the genomic events that drive phenotypic diversity in SS, we performed RNA and targeted DNA sequencing on 91 tumors from 55 patients. Our results were verified by proteomic analysis, public gene expression cohorts and single-cell RNA sequencing. Transcriptome profiling identified three distinct SS subtypes resembling the known histological subtypes: SS subtype I and was characterized by hyperproliferation, evasion of immune detection and a poor prognosis. SS subtype II and was dominated by a vascular-stromal component and had a significantly better outcome. SS Subtype III was characterized by biphasic differentiation, increased genomic complexity and immune suppression mediated by checkpoint inhibition, and poor prognosis despite good responses to neoadjuvant therapy. Chromosomal abnormalities were an independent significant risk factor for metastasis. KRT8 was identified as a key component for epithelial differentiation in biphasic tumors, potentially controlled by OVOL1 regulation. Our findings explain the histological grounds for SS classification and indicate that a significantly larger proportion of patients have high risk tumors (corresponding to SS subtype I) than previously believed.

The Impact of Li-Fraumeni and Germline Retinoblastoma Mutations on Leiomyosarcoma Initiation, Outcomes, and Genetic Testing Recommendations

PURPOSE

Leiomyosarcomas (LMS) are clinically and molecularly heterogeneous, occurring mostly in sporadic but also syndromic settings. The role of pathogenic germline variants (PGV) as LMS drivers and their impact on outcomes remains uncertain.

EXPERIMENTAL DESIGN

We performed a comprehensive clinicopathologic and molecular analysis using a tumor-normal DNA next-generation sequencing assay (Memorial Sloan Kettering-Integrated Mutational Profiling of Actionable Cancer Targets) of germline-associated LMS compared with sporadic LMS.

RESULTS

Among 285 LMS [120 soft-tissue LMS (STLMS) and 165 uterine LMS (ULMS)] with germline testing, 78 (27%, 43 STLMS and 35 ULMS) cases harbored PGV, with 35/78 (45%) of PGV carriers showing biallelic inactivation of the corresponding gene in the tumor (26 STLMS and nine ULMS). The most frequent germline predispositions were TP53 (Li-Fraumeni syndrome; 17 patients, 16 in STLMS) and RB1 (retinoblastoma; 13 patients, 11 in STLMS). Germline TP53 and somatic RB1 alterations often co-occurred in the tumor andvice versa. Other biallelically inactivated PGV were enriched in DNA damage repair-related genes: CHEK2, MSH2, MSH6, RAD51D, BRCA2, and FANCA. Monoallelic PGV were mostly in ULMS and associated with co-occurring TP53 and RB1 somatic alterations. Patients with STLMS with biallelic but not monoallelic PGV were significantly younger than patients with sporadic STLMS (median ages 38 vs. 52 vs. 58 years). No differences in disease-specific or progression-free survival were observed in germline-associated versus sporadic LMS regardless of biallelic status.

CONCLUSIONS

Although patients with ULMS had a relatively low proportion of PGV, a high percentage of patients with STLMS with PGV had tumor biallelic status, indicating that PGV drive tumorigenesis in these individuals. These findings have significant implications for genetic testing recommendations.

The landscape of drug sensitivity and resistance in sarcoma

Sarcomas are rare malignancies with over 100 distinct histological subtypes. Their rarity and heterogeneity pose significant challenges to identifying effective therapies, and approved regimens show varied responses. Novel, personalized approaches to therapy are needed to improve patient outcomes. Patient-derived tumor organoids (PDTOs) model tumor behavior across an array of malignancies. We leverage PDTOs to characterize the landscape of drug resistance and sensitivity in sarcoma, collecting 194 specimens from 126 patients spanning 24 distinct sarcoma subtypes. Our high-throughput organoid screening pipeline tested single agents and combinations, with results available within a week from surgery. Drug sensitivity correlated with clinical features such as tumor subtype, treatment history, and disease trajectory. PDTO screening can facilitate optimal drug selection and mirror patient outcomes in sarcoma. We could identify at least one FDA-approved or NCCN-recommended effective regimen for 59% of the specimens, demonstrating the potential of our pipeline to provide actionable treatment information.

Molecular markers of proliferation, DNA repair, and immune infiltration defines high-risk subset of resectable retroperitoneal sarcomas

INTRODUCTION

For retroperitoneal sarcomas (RPS), aggressive surgical resection offers the only chance for a cure; however, 5-year survival remains below 65%. Therefore, there is a critical need to identify drivers of poor clinical outcomes.

MATERIALS AND METHODS

To identify biomarkers of tumors likely to recur following curative intent resection, we performed genomic and transcriptomic sequencing for 47 and 34 patients, respectively, with non-metastatic RPS at a single, high-volume sarcoma center.

RESULTS

At the DNA level, alterations in TERT were associated with poor disease-free survival (DFS) and overall survival (OS). Increased RNA expression of gene sets related to growth signaling and DNA repair were associated with poor DFS and OS. Infiltration of CD8+ T-Cells and activated dendritic cells were associated with poor DFS and OS.

CONCLUSION

These findings may help to better identify and treat non-metastatic, high-risk RPS.

Translocation in bone and soft tissue sarcomas: a comprehensive epidemiological investigation

BACKGROUND

Limited epidemiological research has focused on translocations in soft tissue sarcomas, with no studies on bone sarcomas. This study aimed to clarify the epidemiology, prognosis, and genetic information of translocation-related sarcoma (TRS) and non-TRS patients.

MATERIALS AND METHODS

This retrospective cohort study used data from the Bone and Soft Tissue Tumor Registry in Japan (BSTTRJ) (2001-2019), the Kyushu University Hospital (KUH) repository (2001-2021), and a publicly available online dataset (MSK). The patients were categorized into TRS and non-TRS groups, and epidemiological, prognostic, and mutational diversity were compared.

RESULTS

This study included 25 383 participants, of whom 4864 (19.2%) were TRS and 20 519 (80.8%) were non-TRS patients. TRS patients had significantly younger onset ages (median: 43 years, interquartile range: 29-59 years) than non-TRS patients (median: 63 years, interquartile range: 46-73 years). In the MSK cohort, microsatellite instability and tumor mutation burden scores in non-TRS were higher than in TRS, although they were rather low compared with the pan-cancer analysis. In the BSTTRJ cohort, survival analyses with the propensity score matching revealed that patients with TRS had better overall [hazard ratio (HR): 0.71, 95% confidence interval (CI) 0.63-0.81], metastasis-free (HR: 0.75, 95% CI 0.67-0.84), and recurrence-free (HR: 0.47, 95% CI 0.39-0.57) survival.

CONCLUSIONS

This study highlights differences in the epidemiology and genetic rearrangements of sarcoma.

Comprehensive Genomic Assessment of Advanced-Stage GI Stromal Tumors Using the Japanese National Center for Cancer Genomics and Advanced Therapeutics Database

PURPOSE

Clinical utility of comprehensive genomic profiling (CGP) for precision medicine has become evident. Although there are several reports on the genomic landscape of GI stromal tumors (GISTs), large-scale data specific to GIST are limited, especially in Asia. Additionally, the applicability of molecular-targeted agents identified using CGP has not been extensively examined. We investigated the status of genomic alterations in Japanese patients with advanced GISTs using the National Center for Cancer Genomics and Advanced Therapeutics (C-CAT) database to identify novel treatment strategies and drug development.

MATERIALS AND METHODS

We retrospectively reviewed the clinical and CGP data of patients with advanced-stage GIST registered in the C-CAT database to assess the genomic landscape and potential actionable alterations.

RESULTS

Data from 144 patients were reviewed. Oncogenic alterations were detected frequently in KIT (78%), CDKN2A (37%), CDKN2B (29%), RB1 (11%), STK11 (10%), TP53 (9%), PDGFRA (6%), and SDHB (6%). Loss of CDKN2A/CDKN2B was only observed in KIT/PDGFRA-mutated GISTs, while alterations in SDHA/SDHB were only detected in KIT/PDGFRA wild-type GISTs. Among 119 KIT/PDGFRA-mutated GISTs, 95 (80%) had oncogenic genomic alterations and 29 (24%) had actionable alterations, excluding KIT and PDGFRA. However, among 25 KIT/PDGFRA wild-type GISTs, 22 (88%) had oncogenic alterations and 11 (44%) had actionable alterations. Representative candidate drugs for genome-matched therapies in KIT/PDGFRA-mutated and wild-type GISTs were as follows: pembrolizumab for tumor mutation burden-high in one and two patients, respectively; poly-adenosine diphosphate ribose polymerase inhibitors for alterations related to homologous recombination deficiency in 12 and one patient, respectively; NTRK inhibitor for ETV6-NTRK3 fusion in one with KIT/PDGFRA wild-type GIST; and human epidermal growth factor receptor 2-antibody-drug conjugate in one with KIT/PDGFRA-mutated GIST.

CONCLUSION

This study highlights the genomic landscape of advanced GISTs and the important role of CGP in identifying rational molecular-targeted therapeutic options.

Novel MEN1-associated retroperitoneal pleomorphic liposarcoma

Soft tissue sarcomas are rarely associated with mutations of the MEN1 gene. We report a patient with a large retroperitoneal pleomorphic liposarcoma harboring a rare mutation of the MEN1 gene not previously reported to be associated with soft tissue sarcomas. This report expands the known spectrum of MEN1-associated cancers.

Inhibition of Aberrantly Overexpressed Polo-like Kinase 4 Is a Potential Effective Treatment for DNA Damage Repair-Deficient Uterine Leiomyosarcoma

PURPOSE

Uterine leiomyosarcoma (LMS) is an aggressive sarcoma and a subset of which exhibits DNA repair defects. Polo-like kinase 4 (PLK4) precisely modulates mitosis, and its inhibition causes chromosome missegregation and increased DNA damage. We hypothesize that PLK4 inhibition is an effective LMS treatment.

EXPERIMENTAL DESIGN

Genomic profiling of clinical uterine LMS samples was performed, and homologous recombination (HR) deficiency scores were calculated. A PLK4 inhibitor (CFI-400945) with and without an ataxia telangiectasia mutated (ATM) inhibitor (AZD0156) was tested in vitro on gynecologic sarcoma cell lines SK-UT-1, SKN, and SK-LMS-1. Findings were validated in vivo using the SK-UT-1 xenograft model in the Balb/c nude mouse model. The effects of CFI-400945 were also evaluated in a BRCA2-knockout SK-UT-1 cell line. The mechanisms of DNA repair were analyzed using a DNA damage reporter assay.

RESULTS

Uterine LMS had a high HR deficiency score, overexpressed PLK4 mRNA, and displayed mutations in genes responsible for DNA repair. CFI-400945 demonstrated effective antitumor activity in vitro and in vivo. The addition of AZD0156 resulted in drug synergism, largely due to a preference for nonhomologous end-joining DNA repair. Compared with wild-type cells, BRCA2 knockouts were more sensitive to PLK4 inhibition when both HR and nonhomologous end-joining repairs were impaired.

CONCLUSIONS

Uterine LMS with DNA repair defects is sensitive to PLK4 inhibition because of the effects of chromosome missegregation and increased DNA damage. Loss-of-function BRCA2 alterations or pharmacologic inhibition of ATM enhanced the efficacy of the PLK4 inhibitor. Genomic profiling of an advanced-stage or recurrent uterine LMS may guide therapy.

Progress in histology specific treatments in soft tissue sarcoma

INTRODUCTION

Soft tissue sarcomas (STS) represent a heterogenous group of rare tumors, primarily treated with surgery. Preoperative radiotherapy is often recommended for extremity high-risk STS. Neoadjuvant chemotherapy, typically based on doxorubicin with ifosfamide, has shown efficacy in limbs and trunk wall STS. Second-line chemotherapy, commonly utilized in the metastatic setting, is mostly histology-driven. Molecular targeted agents are used across various histologies, and although the use of immunotherapy in STS is still in its early stages, there is increasing interest in exploring its potential.

AREAS COVERED

This article involved an extensive recent search on PubMed. It explored the current treatment landscape for localized and metastatic STS, focusing on the combined use of radiotherapy and chemotherapy for both extremity and retroperitoneal tumors, and with a particular emphasis on the most innovative histopathology driven therapeutic approaches. Additionally, ongoing clinical trials identified via clinicaltrials.gov are included.

EXPERT OPINION

Recently there have been advancements in the treatment of STS, largely driven by the outcomes of clinical trials. However further research is imperative to comprehend the effect of chemotherapy, targeted therapy and immunotherapy in various STS, as well as to identify biomarkers able to predict which patients are most likely to benefit from these treatments.

Genomic Landscape of Osteosarcoma of Bone in an Older-Aged Patient Population and Analysis of Possible Etiologies Based on Molecular Signature

Background: Osteosarcoma (OS), the most common primary malignant bone tumor, occurs mostly in the pediatric and adolescent (P/A) population where it has been subject to intense study whereas OS arising in the older-aged adult population has undergone less scrutiny. Materials and Methods: In this study, we assess the molecular aberrations detected in eight older adult patients (>59 years of age) with OS of bone by whole-exome sequencing (WES) on formalin-fixed, paraffin-embedded tissue and quantified the contributions of endogenous and exogenous mutational processes to tumor mutational burden and to tumorigenesis through computational analysis. Results: We identified 86 clinically significant somatic mutations. TP53 mutations occurred in OSs of three patients and one patient harbored a pathogenic germline mutation of TP53. Loss-of-heterozygosity of DNA-damage repair genes occurred in all six tumors evaluated. Computational analysis of single nucleotide variants within each tumor detected eight distinct mutagenic processes of which age-associated mutational processes, thiopurine chemotherapy, and defective homologous DNA recombination repair contributed the most to both tumor mutation burden and tumor pathogenesis. Conclusion: The genomic landscape of our older OS patients deciphered by WES is extremely diverse with only 15% of mutated somatic genes uncovered in our study previously described in P/A-enriched OS studies. Endogenous age-related mutagenic processes, defective DNA homologous recombination repair, and exogenous effects of chemotherapy are mainly responsible for pathogenic mutations in OS occurring in our cohort.

Multiregion exome sequencing indicates a monoclonal origin of esophageal spindle-cell squamous cell carcinoma

Esophageal spindle-cell squamous cell carcinoma (ESS) is a rare biphasic neoplasm composed of a carcinomatous component (CaC) and a sarcomatous component (SaC). However, the genomic origin and gene signature of ESS remain unclear. Using whole-exome sequencing of laser-capture microdissection (LCM) tumor samples, we determined that CaC and SaC showed high mutational commonality, with the same top high-frequency mutant genes, mutation signatures, and tumor mutation burden; paired samples shared a median of 25.5% mutation sites. Focal gains were found on chromosomes 3q29, 5p15.33, and 11q13.3. Altered genes were mainly enriched in the RTK-RAS signaling pathway. Phylogenetic trees showed a monoclonal origin of ESS. The most frequently mutated oncogene in the trunk was TP53, followed by NFE2L2, KMT2D, and MUC16. Prognostic associations were found for CDC27, LRP2, APC, and SNAPC4. Our data highlight the monoclonal origin of ESS with TP53 as a potent driver oncogene, suggesting new targeted therapies and immunotherapies as treatment options. © 2024 The Pathological Society of Great Britain and Ireland.

Advances in Soft Tissue and Bone Sarcoma

This Cancers Special Issue on bone and soft tissue sarcomas highlights the latest discoveries in soft tissue and bone cancers from the laboratory through to the clinics, from bench to bedside, and beyond [...].

A Review on Canine and Human Soft Tissue Sarcomas: New Insights on Prognosis Factors and Treatment Measures

Soft tissue sarcomas (STSs) represent a diverse group of tumors arising from mesenchymal cells, affecting both humans and animals, including dogs. Although STSs represent a class of rare tumors, especially in humans, they pose significant clinical challenges due to their potential for local recurrence and distant metastasis. Dogs, as a model for human STSs, offer several advantages, including exposure to similar environmental risk factors, genetic diversity among breeds, and the spontaneous development of tumors. Furthermore, canine tumors closely mimic the heterogeneity and complexity of human tumors, making them valuable for research into disease progression and treatment effectiveness. Current treatment approaches for STSs in both dogs and humans primarily involve surgery, radiation therapy, and chemotherapy, with treatment decisions based on tumor characteristics and patient factors. However, the development of novel therapeutic strategies is essential, given the high failure rate of new drugs in clinical trials. To better design new tailored treatments, comprehension of the tumor microenvironment (TME) is fundamental, since it plays a crucial role in STS initiation and progression by modulating tumor behavior, promoting angiogenesis, and suppressing immune responses. Notably, TME features include cancer-associated fibroblasts (CAFs), extracellular matrix (ECM) alterations, and tumor-associated macrophages (TAMs) that, depending on their polarization state, can affect immune responses and thus the patient's prognosis. In this review, new therapeutical approaches based on immunotherapy will be deeply explored as potential treatment options for both dogs and humans with STSs. In conclusion, this review provides an overview of the current understanding of STSs in dogs and humans, emphasizing the importance of the TME and potential treatment strategies.

p53 as a Potential Actionable Target in Myxofibrosarcoma: A Molecular and Pathologic Review of a Single-Institute Series

Myxofibrosarcoma (MFS) is a common adult soft tissue sarcoma characterized by high-local recurrence rate, poorly understood molecular pathogenesis, lack of specific prognostic markers, and effective targeted therapies. To gain further insights into the disease, we analyzed a well-defined group of 133 primary MFS cases. Immunohistochemical (IHC) staining for p53, MET, RET, and RB was performed. Twenty-five cases were analyzed by targeted resequencing of known cancer driver hotspot mutations, whereas 66 and 64 MFSs were examined for the presence of genetic variants in TP53 and MET gene, respectively. All clinical, histologic, immunostaining, and genetic variables were analyzed for their impact on 5-years overall survival (OS) and 5-years event-free survival (EFS). In our series, no grade I tumors relapsed and high grade are related to a positive MET immunostaining (P = .034). Both local recurrence (P = .038) and distal metastases (P = .016) correlated to the presence of "single nucleotide variant (SNV) plus copy number variation (CNV)" in TP53. Multivariate analysis revealed that age (>60 years), metastasis at presentation, and positive IHC-p53 signal are risk factors for a poor OS (P = .003, P = .000, and P = .002), whereas age (>60 years), synchronous metastasis, and tumor size (>10 cm) predict an unfavorable 5-years EFS (P = .011, P = .000, and P = .023). Considering the smaller series (n = 66) that underwent molecular screening, the presence of "SNV+CNV" in TP53 represents a risk factor for a worse 5-years EFS (hazard ratio, 2.5; P = .017). The present series confirms that TP53 is frequently altered in MFS (86.4% of cases), appearing to play an important role in MFS tumorigenesis and being a potentially drugable target. A positive p53 immunostainings is related to a poor diagnosis, and it is the presence of a single nucleotide genetic alterations in TP53 that is essential in conferring MFS an aggressive phenotype, thus supporting the use of molecular profiling in MFS to better define the role of p53 as a prognostic factor.

Spatial distribution of tumour immune infiltrate predicts outcomes of patients with high-risk soft tissue sarcomas after neoadjuvant chemotherapy

BACKGROUND

Anthracycline-based neoadjuvant chemotherapy (NAC) may modify tumour immune infiltrate. This study characterized immune infiltrate spatial distribution after NAC in primary high-risk soft tissue sarcomas (STS) and investigate association with prognosis.

METHODS

The ISG-STS 1001 trial randomized STS patients to anthracycline plus ifosfamide (AI) or a histology-tailored (HT) NAC. Four areas of tumour specimens were sampled: the area showing the highest lymphocyte infiltrate (HI) at H&E; the area with lack of post-treatment changes (highest grade, HG); the area with post-treatment changes (lowest grade, LG); and the tumour edge (TE). CD3, CD8, PD-1, CD20, FOXP3, and CD163 were analyzed at immunohistochemistry and digital pathology. A machine learning method was used to generate sarcoma immune index scores (SIS) that predict patient disease-free and overall survival (DFS and OS).

FINDINGS

Tumour infiltrating lymphocytes and PD-1+ cells together with CD163+ cells were more represented in STS histologies with complex compared to simple karyotype, while CD20+ B-cells were detected in both these histology groups. PD-1+ cells exerted a negative prognostic value irrespectively of their spatial distribution. Enrichment in CD20+ B-cells at HI and TE areas was associated with better patient outcomes. We generated a prognostic SIS for each tumour area, having the HI-SIS the best performance. Such prognostic value was driven by treatment with AI.

INTERPRETATION

The different spatial distribution of immune populations and their different association with prognosis support NAC as a modifier of tumour immune infiltrate in STS.

FUNDING

Pharmamar; Italian Ministry of Health [RF-2019-12370923; GR-2016-02362609]; 5 × 1000 Funds-2016, Italian Ministry of Health; AIRC Grant [ID#28546].

Performance assessment of computational tools to detect microsatellite instability

Microsatellite instability (MSI) is a phenomenon seen in several cancer types, which can be used as a biomarker to help guide immune checkpoint inhibitor treatment. To facilitate this, researchers have developed computational tools to categorize samples as having high microsatellite instability, or as being microsatellite stable using next-generation sequencing data. Most of these tools were published with unclear scope and usage, and they have yet to be independently benchmarked. To address these issues, we assessed the performance of eight leading MSI tools across several unique datasets that encompass a wide variety of sequencing methods. While we were able to replicate the original findings of each tool on whole exome sequencing data, most tools had worse receiver operating characteristic and precision-recall area under the curve values on whole genome sequencing data. We also found that they lacked agreement with one another and with commercial MSI software on gene panel data, and that optimal threshold cut-offs vary by sequencing type. Lastly, we tested tools made specifically for RNA sequencing data and found they were outperformed by tools designed for use with DNA sequencing data. Out of all, two tools (MSIsensor2, MANTIS) performed well across nearly all datasets, but when all datasets were combined, their precision decreased. Our results caution that MSI tools can have much lower performance on datasets other than those on which they were originally evaluated, and in the case of RNA sequencing tools, can even perform poorly on the type of data for which they were created.

Clinical actionability of BRCA2 alterations in uterine leiomyosarcoma: a molecular tumor board case report and a cBioPortal comprehensive analysis

BACKGROUND

Uterine leiomyosarcoma (uLMS) represents one of the most common sarcoma histotypes, demonstrating an overall dismal prognosis. Previous studies reported uLMS to carry recurrent somatic BRCA2 homozygous deletions, related to significant clinical benefits from the use of PARP inhibitors.

METHODS

To investigate the prevalence in uLMS of genomic alterations (alt) in BRCA2 and other homologous recombination (HR) and DNA damage response (DDR) genes, cBioPortal was accessed and data were retrieved from studies including pan-sarcoma histologies. HR-/DDR-genes included BRCA1, BRCA2, ATM, BARD1, BRIP1, CHEK1, CHEK2, FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, FANCM, NBN, PALB2, RAD51C, RAD51D, RAD50, and ATR. Only oncogenic/likely oncogenic alterations were included according to OncoKB.

CLINICAL REPORT AND RESULTS

We reported a clinical case of a patient affected by a highly pretreated uLMS discussed at the European Institute of Oncology Molecular Tumor Board. A targeted next-generation sequencing panel demonstrated a somatic BRCA2 homozygous deletion (homDel). Upon access to Niraparib, a remarkable response of 15 months was observed before experiencing disease progression. In the genomic query, among 2393 cases, uLMS (n = 193) displayed 9 of all 31 BRCA2alt observed, representing the only sarcoma histotype showing an enrichment in BRCA2alt (4.66%; q < 0.001). All of 9 BRCA2alt were represented by homDel, which related to a high fraction of genome altered.

CONCLUSION

uLMS displays a significant frequency of somatic BRCA2alt homDel. Considering their dismal prognosis, further investigation is warranted to test the use of PARPi in uLMS, and particularly in the setting of BRCA1/2 alterations.

Loss of the DNA Repair Gene RNase H2 Identifies a Unique Subset of DDR-Deficient Leiomyosarcomas

Targeting the DNA damage response (DDR) pathway is an emerging therapeutic approach for leiomyosarcoma (LMS), and loss of RNase H2, a DDR pathway member, is a potentially actionable alteration for DDR-targeted treatments. Therefore, we designed a protein- and genomic-based RNase H2 screening assay to determine its prevalence and prognostic significance. Using a selective RNase H2 antibody on a pan-tumor microarray (TMA), RNase H2 loss was more common in LMS (11.5%, 9/78) than across all tumors (3.8%, 32/843). In a separate LMS cohort, RNase H2 deficiency was confirmed in uterine LMS (U-LMS, 21%, 23/108) and soft-tissue LMS (ST-LMS; 30%, 39/102). In the TCGA database, RNASEH2B homozygous deletions (HomDels) were found in 6% (5/80) of LMS cases, with a higher proportion in U-LMS (15%; 4/27) compared with ST-LMS (2%; 1/53). Using the SNiPDx targeted-NGS sequencing assay to detect biallelic loss of function in select DDR-related genes, we found RNASEH2B HomDels in 54% (19/35) of U-LMS cases with RNase H2 loss by IHC, and 7% (3/43) HomDels in RNase H2 intact cases. No RNASEH2B HomDels were detected in ST-LMS. In U-LMS patient cohort (n = 109), no significant overall survival difference was seen in patients with RNase H2 loss versus intact, or RNASEH2B HomDel (n = 12) versus Non-HomDel (n = 37). The overall diagnostic accuracy, sensitivity, and specificity of RNase H2 IHC for detecting RNA-SEH2B HomDels in U-LMS was 76%, 93%, and 71%, respectively, and it is being developed for future predictive biomarker driven clinical trials targeting DDR in U-LMS.

Palbociclib in Patients With Soft Tissue Sarcoma With CDK4 Amplifications: Results From the Targeted Agent and Profiling Utilization Registry Study

PURPOSE

Targeted Agent and Profiling Utilization Registry (TAPUR) is a phase II basket trial evaluating the antitumor activity of commercially available targeted agents in patients with advanced cancer and genomic alterations known to be drug targets. Results of a cohort of patients with soft tissue sarcoma with cyclin-dependent kinase 4 (CDK4) amplification treated with palbociclib are reported.

METHODS

Eligible patients had measurable disease, Eastern Cooperative Oncology Group performance status 0 to 2, adequate organ function, and no standard treatment options. The primary end point was disease control (DC), defined as objective response (OR) or stable disease (SD) of at least 16+ weeks duration (SD16+) according to RECIST v1.1. The DC rate was estimated with a 90% CI. Secondary end points included OR, progression-free survival (PFS), overall survival (OS), duration of response, duration of SD, and safety.

RESULTS

Forty-two patients with CDK4 amplification were enrolled. One patient was not evaluable for efficacy. One patient with partial response and 18 with SD16+ were observed for DC and OR rates of 46% (90% CI, 36 to 100) and 2% (95% CI, <1 to 13), respectively. Median PFS was 16 weeks (95% CI, 9 to 28) and median OS was 69 weeks (95% CI, 31 to 111) for evaluable patients. Twenty patients had at least one grade 3 to 4 adverse event (AE) at least possibly related to palbociclib, including alanine aminotransferase increase, anemia, fatigue, hypophosphatemia, leukopenia, neutropenia, and thrombocytopenia. No serious AEs were reported.

CONCLUSION

Palbociclib met prespecified criteria to declare a signal of antitumor activity in patients with sarcoma and CDK4 amplification.

Tumor-informed deep sequencing of ctDNA detects minimal residual disease and predicts relapse in osteosarcoma

Background

Current surveillance modalities of osteosarcoma relapse exhibit limited sensitivity and specificity. Although circulating tumor DNA (ctDNA) has been established as a biomarker of minimal residual disease (MRD) in many solid tumors, a sensitive ctDNA detection technique has not been thoroughly explored for longitudinal MRD detection in osteosarcoma.

Methods

From August 2019 to June 2023, 59 patients diagnosed with osteosarcoma at the First Affiliated Hospital of Sun Yat-sen University were evaluated in this study. Tumor-informed MRD panels were developed through whole exome sequencing (WES) of tumor tissues. Longitudinal blood samples were collected during treatment and subjected to multiplex PCR-based next-generation sequencing (NGS). Kaplan-Meier curves and Log-rank tests were used to compare outcomes, and Cox regression analysis was performed to identify prognostic factors.

Findings

WES analysis of 83 patients revealed substantial mutational heterogeneity, with non-recurrent mutated genes accounting for 58.1%. Tumor-informed MRD panels were successfully obtained for 85.5% of patients (71/83). Among 59 patients with successful MRD panel customization and available blood samples, 13 patients exhibited positive ctDNA detection after surgery. Patients with negative post-operative ctDNA had better event-free survival (EFS) compared to those with positive ctDNA, at 1-6 months after surgery, after adjuvant chemotherapy, and more than 6 months after surgery (p < 0.05). In both univariate and multivariate Cox regression analysis, ctDNA results emerged as a significant predictor of EFS (p < 0.05). ctDNA detection preceded positive imaging in 5 patients, with an average lead time of 92.6 days. Thirty-nine patients remained disease-free, with ctDNA results consistently negative or turning negative during follow-up.

Interpretation

Our study underscores the applicability of tumor-informed deep sequencing of ctDNA in osteosarcoma MRD surveillance and, to our knowledge, represents the largest cohort to date. ctDNA detection is a significant prognostic factor, enabling the early identification of tumor relapse and progression compared to standard imaging, thus offering valuable insights in guiding osteosarcoma patient management.

Funding

The Grants of National Natural Science Foundation of China (No. 82072964, 82072965, 82203798, 82203026), the Natural Science Foundation of Guangdong (No. 2023A1515012659, 2023A1515010302), and the Regional Combination Project of Basic and Applied Basic Research Foundation of Guangdong (No. 2020A1515110010).