The genomics of undifferentiated sarcoma of soft tissue: Progress, challenges and opportunities

Deciphering the role of liquid-liquid phase separation in sarcoma: Implications for pathogenesis and treatment

Liquid-liquid phase separation (LLPS) is a significant reversible and dynamic process in organisms. Cells form droplets that are distinct from membrane-bound cell organelles by phase separation to keep biochemical processes in order. Nevertheless, the pathological state of LLPS contributes to the progression of a variety of tumor-related pathogenic issues. Sarcoma is one kind of highly malignant tumor characterized by aggressive metastatic potential and resistance to conventional therapeutic agents. Despite the significant clinical relevance, research on phase separation in sarcomas currently faces several major challenges. These include the limited availability of sarcoma samples, insufficient attention from the research community, and the complex genetic heterogeneity of sarcomas. Recently, emerging evidence have elaborated the specific effects and pathways of phase separation on different sarcoma subtypes, including the effect of sarcoma fusion proteins and other physicochemical factors on phase separation. This review aims to summarize the multiple roles of phase separation in sarcoma and novel molecular inhibitors that target phase separation. These insights will broaden the understanding of the mechanisms concerning sarcoma and offer new perspectives for future therapeutic strategies.

Soft tissue sarcomas at the single-cell and spatial resolution: new markers and targets

Soft tissue sarcomas (STS) are heterogeneous and aggressive tumors, originating in connective tissues embryologically derived from the mesenchyme. Due to their rarity, crucial information about their biology is still lacking. In recent years, single-cell and spatial analyses have opened up new horizons in oncology, leading to the possibility of characterizing the internal architecture of the tumor at the single-cell and spatial levels. This review summarizes the first results acquired through these revolutionary methods for different types of STS. We discuss tumor cell populations and their evolution, interactions between tumor cells and the microenvironment, new prognostic markers, and clinically important targets. Finally, we examine the challenges presented by the single-cell and spatial omics of STS and the future perspectives in this field.

Local relapse patterns after preoperative radiotherapy of limb and trunk wall soft tissue sarcomas: Prognostic role of imaging and pathologic response factors

Purpose

To retrospectively identify clinical, pathologic, or imaging factors predictive of local relapse (LR) after preoperative radiotherapy (RT) for soft tissue sarcomas (STS).

Methods and Materials

This is a retrospective multicenter study of patients who underwent preoperative RT and surgery for limb or trunk wall STS between 2007 and 2018 in French Sarcoma Group centers and were enrolled in the "Conticabase". Patterns of LR were investigated taking into account the multimodal response after preoperative RT. Diagnostic and surgical samples were compared after systematic review by expert pathologists and patients were stratified by tumor grade. Log-rank tests and Cox models were used to identify prognostic factors for radiation response and LR.

Results

257 patients were included; 17 % had low-grade (LG), 72.5 % had high-grade (HG) sarcomas. In HG group, tumors were larger, mostly undifferentiated, and displayed more necrosis and perilesional edema after RT. Median follow-up was 32 months. Five-year cumulative incidence of LR was 20.3 % in the HG group versus 9.7 % in the LG group (p = 0.026). In multivariate analysis, trunk wall location (HR 6.79, p = 0.012) and proportion of viable tumor cellularity ≥ 20 % (HR 3.15, p = 0.018) were associated with LR. After adjusting for tumor location, combination of histotype and cellularity rate significantly correlated with LR. We described three prognostic subgroups for HG sarcomas, listed from the highest to lowest risk: undifferentiated sarcoma (US) with cellularity rates ≥ 20 %; non-US (NUS) with cellularity rates ≥ 20 % or US with cellularity rates < 20 %; and NUS with cellularity rates < 20 %, which shared similar prognostic risks with LG sarcomas.

Conclusions

HG and LG tumors have different morphological and biological behaviors in response to RT. Combination of cellularity rate with histotype could be a major prognostic for LR. Patients with undifferentiated HG sarcomas with cellularity rates ≥ 20 % after preoperative RT had the highest risk of LR and disease-specific death.

Advancing rare cancer research by MALDI mass spectrometry imaging: Applications, challenges, and future perspectives in sarcoma

MALDI mass spectrometry imaging (MALDI imaging) uniquely advances cancer research, by measuring spatial distribution of endogenous and exogenous molecules directly from tissue sections. These molecular maps provide valuable insights into basic and translational cancer research, including tumor biology, tumor microenvironment, biomarker identification, drug treatment, and patient stratification. Despite its advantages, MALDI imaging is underutilized in studying rare cancers. Sarcomas, a group of malignant mesenchymal tumors, pose unique challenges in medical research due to their complex heterogeneity and low incidence, resulting in understudied subtypes with suboptimal management and outcomes. In this review, we explore the applicability of MALDI imaging in sarcoma research, showcasing its value in understanding this highly heterogeneous and challenging rare cancer. We summarize all MALDI imaging studies in sarcoma to date, highlight their impact on key research fields, including molecular signatures, cancer heterogeneity, and drug studies. We address specific challenges encountered when employing MALDI imaging for sarcomas, and propose solutions, such as using formalin-fixed paraffin-embedded tissues, and multiplexed experiments, and considerations for multi-site studies and digital data sharing practices. Through this review, we aim to spark collaboration between MALDI imaging researchers and clinical colleagues, to deploy the unique capabilities of MALDI imaging in the context of sarcoma.

Low NT5DC2 expression predicts favorable prognosis and suppresses soft tissue sarcoma progression via ECM-receptor interaction pathway

BACKGROUND

Soft tissue sarcoma, a malignant tumor arising from mesenchymal tissues with poor prognosis. 5'-Nucleotidase Domain Containing 2 (NT5DC2) is a novel oncogene, and the precise involvement of NT5DC2 in soft tissue sarcoma were still undefined. Hence, our study aims to investigate NT5DC2 functions in soft tissue sarcoma progression.

METHODS

The tumor immune single-cell hub 2 (TISCH2) website, The Cancer Genome Atlas (TCGA) pan-cancer or sarcoma and Gene Expression Omnibus (GEO, GSE21122) databases were applied to visualize the NT5DC2 status in the sarcoma databases. The NT5DC2 protein expression in sarcoma tissues in our hospital was detected by using immunohistochemistry (IHC) and analyzed the associations between NT5DC2 expression and clinicopathological parameters. Real-time quantitative polymerase chain reaction (RT-qPCR), colony formation, 5-ethynyl-2'-deoxyuridine (EdU) assay, wound healing, transwell, flow cytometry and xenograft model were used to elucidate the effects of NT5DC2 downregulated by lentivirus in sarcoma cell.

RESULTS

The TISCH2 website detection found that NT5DC2 expression is enriched in malignant cells in sarcoma single-cell database. Furthermore, the TCGA-sarcoma database indicated that NT5DC2 expression correlates with metastasis, positive margin status, prognosis, and diagnostic value. Additionally, IHC staining showed that 40 % of soft tissue sarcoma patients present high expression of NT5DC2, and NT5DC2 upregulation is closely associated with poor prognosis. Functional verification analysis further revealed that downregulating NT5DC2 expression can suppress sarcoma progression through the ECM-receptor interaction pathway.

CONCLUSION

Low expression of NT5DC2 predicts a favorable prognosis in soft tissue sarcoma, and downregulated NT5DC2 expression can suppress sarcoma cell progression through the ECM-receptor interaction pathway.

A Modification of the American Joint Committee on Cancer Nomogram for Undifferentiated Sarcoma With External Validation and Risk Stratification

BACKGROUND

The aim of this study is to establish a model to predict the overall survival (OS) and stratify the risk of postoperative patients with undifferentiated sarcoma.

METHODS

A total of 452 postoperative patients with undifferentiated sarcoma in the trunk and extremity from the Surveillance, Epidemiology, and End Results database were enrolled as the training cohort. We collected a group of 163 undifferentiated sarcoma patients from our center as the external validation cohort. Cox proportional hazards regression model was used to screen survival-associated factors for the construction of the nomogram. Concordance-indexes (C-indexes), calibration curves, and receiver operating characteristics (ROCs) curves were applied for the discrimination and calibration of the nomogram. The cutoff value of nomogram-based total points was applied to stratify the risk of patients.

RESULTS

A nomogram was developed incorporating four independent factors: age, tumor site, eighth AJCC stage, and radiotherapy. The nomogram showed good prognostic accuracy and excellent agreement in the training and validation cohort, with C-indexes of .701 (95% confidence interval [CI]: .683-.719) and .700 (95% CI: 0.659-.741), respectively. Furthermore, we identified the best cutoff value of nomogram total points (103.2) as the predicted risk and divided the patients into a high-risk group and a low-risk group. Significant differences in OS between the two groups were indicated in the training cohort and external validation cohort, showing the appreciable clinical validity and clinical utility of the nomogram (P < .001).

CONCLUSION

This nomogram provides an insightful and applicable tool for individual evaluations and the distinguishment of risk for patients with undifferentiated sarcoma.

Sarcoma care in the era of precision medicine

Sarcoma subtype classification is currently mainly based upon histopathological morphology. Molecular analyses have emerged as an efficient addition to the diagnostic workup and sarcoma care. Knowledge about the sarcoma genome increases, and genetic events that can either support a histopathological diagnosis or suggest a differential diagnosis are identified, as well as novel therapeutic targets. In this review, we present diagnostic, therapeutic, and prognostic molecular markers that are, or might soon be, used clinically. For sarcoma diagnostics, there are specific fusions highly supportive or pathognomonic for a diagnostic entity-for instance, SYT::SSX in synovial sarcoma. Complex karyotypes also give diagnostic information-for example, supporting dedifferentiation rather than low-grade central osteosarcoma or well-differentiated liposarcoma when detected in combination with MDM2/CDK4 amplification. Molecular treatment predictive sarcoma markers are available for gastrointestinal stromal tumor (GIST) and locally aggressive benign mesenchymal tumors. The molecular prognostic markers for sarcomas in clinical practice are few. For solitary fibrous tumor, the type of NAB2::STAT6 fusion is associated with the outcome, and the KIT/PDGFRA pathogenic variant in GISTs can give prognostic information. With the exploding availability of sequencing technologies, it becomes increasingly important to understand the strengths and limitations of those methods and their context in sarcoma diagnostics. It is reasonable to believe that most sarcoma treatment centers will increase the use of massive-parallel sequencing soon. We conclude that the context in which the genetic findings are interpreted is of importance, and the interpretation of genomic findings requires considering tumor histomorphology.

New established cell lines from undifferentiated pleomorphic sarcoma for in vivo study

As a high-grade soft-tissue sarcoma (STS), undifferentiated pleomorphic sarcoma (UPS) is highly recurrent and malignant. UPS is categorized as a tumor of uncertain differentiation and has few options for treatment due to its lack of targetable genetic alterations. There are also few cell lines that provide a representative model for UPS, leading to a dearth of experimental research. Here, we established and characterized new cell lines derived from two recurrent UPS tissues. Cells were obtained from UPS tissues by mincing, followed by extraction or dissociation using enzymes and culture in a standard culture environment. Cells were maintained for several months without artificial treatment, and some cell clones were found to be tumorigenic in an immunodeficient mouse model. Interestingly, some cells formed tumors in vivo when injected after aggregation in a non-adherent culture system for 24 h. The tissues from in vivo study and tissues from patients shared common histological characteristics. Pathways related to the cell cycle, such as DNA replication, were enriched in both cell clones. Pathways related to cell-cell adhesion and cell-cell signaling were also enriched, suggesting a role of the mesenchymal-to-epithelial transition for tumorigenicity in vivo. These new UPS cell lines may facilitate research to identify therapeutic strategies for UPS. [BMB Reports 2023; 56(4): 258-264].

Efficacy and safety of fruquintinib as third- or further-line therapy for patients with advanced bone and soft tissue sarcoma: a multicenter retrospective study

PURPOSE

Fruquintinib is an oral small-molecule angiogenesis inhibitor, markedly specifically inhibited vascular endothelial growth factor 2 (VEGFR2). This retrospective study aimed to evaluate the safety and efficacy of fruquintinib, or in combination with immunotherapy or chemotherapy in patients with bone and soft tissue sarcoma (STS), who have failed at least secondary-line treatment.

PATIENTS AND METHODS

We performed a retrospective analysis of advanced bone and STS patients who received fruquintinib containing third- or further-line therapy in Shanghai Jiao Tong University Affiliated Sixth People's and the Affiliated Hospital of Jiangxi University of Traditional Chiese Medicine from September 2019 to February 2022. All of them had accepted at least anthracyclines-based chemotherapy. For the experimental group, 25 cases, the patients took a basic dose of fruquintinib 3-5 mg once a day for 21 days per 4 weeks as a cycle until the disease progression or intolerable toxicity. The other 20 patients in the control group received the best supportive care. The patients were evaluated by computed tomography (CT) or MRI once 2 months or symptoms worse. The DCR, progression-free survival (PFS), and adverse reactions of the drug were recorded and reviewed.

RESULTS

The DCR in patients receiving fruquintinib therapy was 80.0%. The median PFS (mPFS) in the fruquintinib-containing therapy group was significantly longer than that in the control group (4.8 vs. 1.4 months; P  < 0.001). The mPFS in the fruquintinib group, the fruquintinib-OI group and the fruquintinib-chemotherapy group were 3.2 months [95% confidence interval (CI), 2.0-7.9], 4.9 months (95% CI, 3.0-9.9) and 4.2 months (95% CI, 2.6-6.6) respectively, all of them were longer than the mPFS of 1.4 months (95% CI, 0.3-2.5) in the control group ( P  < 0.001).

CONCLUSION

Fruquintinib was reported for the first time to have favorable efficacy and safety as an optional treatment for patients with advanced bone and STS who failed in multi-line therapies.

The impact of additional pathology analysis on the diagnosis and management of soft tissue tumours: a 10-year,retrospective study

In order to characterise soft tissue tumours, pathologists often utilise specialised additional tests, or may seek opinions from subspecialist pathologists due to rarity or complex morphology. Additionally, further review may be sought by subspecialist sarcoma pathologists, such as those at our tertiary referral centre in Sydney, Australia. The aim of this study was to examine the impact on diagnosis and management of this external review, following diagnosis at a specialised sarcoma unit. We collated the results of all additional external ancillary tests and specialist reviews over a 10-year period and characterised the impact on the preliminary diagnosis as 'confirmed', 'new' or 'no clear diagnosis'. We subsequently noted whether the additional findings resulted in a clinically significant change in management. Of the 136 cases sent away, 103 patients had their initial diagnosis confirmed, 29 patients received a new diagnosis and, for four patients, the diagnosis remained uncertain. Nine of the 29 patients receiving a new diagnosis had their management altered. This study demonstrated that within our specialised sarcoma unit, the majority of diagnoses provided by our specialist pathologists are confirmed on additional external testing and review, but external review does provide additional assurance and benefit to the patient.

Undifferentiated sarcoma of bladder with sarcomatoid carcinoma: A case report

Compared with bladder urothelial cell carcinoma, the incidence of bladder undifferentiated sarcoma and bladder sarcomatoid carcinoma is low, and the number of cases is rare. The lack of studies with larger samples has led to insufficient understanding of these diseases. It is even rarer to report that these two types of diseases occur simultaneously in the bladder of a patient. Radical cystectomy does not seem to delay the recurrence and metastasis of the tumor. Whether adjuvant chemoradiotherapy is needed in a timely manner and the timing of the corresponding treatment need to be further studied.

Large mirror brain metastases from primary undifferentiated sarcoma of the breast: case report and review of the literature

Primary breast sarcomas are rare high-grade tumors with a reported incidence of <1% of breast malignancies. Its dissemination to the CNS is exceptional and only one is found in the literature. The authors described the case of a 22-year-old female with history of a breast undifferentiated sarcoma that present with two large bilateral retrolenticular brain metastases. Both lesions were excised in the same procedure and she underwent adjuvant therapy. She died 24 months after surgery. Despite being aggressive lesions, aggressive treatment of primary breast sarcomas including brain metastases excision, should be considered in order to improve overall survival.

Development of a Novel Immune Infiltration-Related ceRNA Network and Prognostic Model for Sarcoma

Due to the rarity and heterogeneity, it is challenging to explore and develop new therapeutic targets for patients with sarcoma. Recently, immune cell infiltration in the tumor microenvironment (TME) was widely studied, which provided a novel potential approach for cancer treatment. The competing endogenous RNA (ceRNA) regulatory network has been reported as a critical molecular mechanism of tumor development. However, the role of the ceRNA regulatory network in the TME of sarcoma remains unclear. In this study, gene expression data and clinical information were obtained from The Cancer Genome Atlas (TCGA) sarcoma datasets, and an immune infiltration-related ceRNA network was constructed, which comprised 14 lncRNAs, 13 miRNAs, and 23 mRNAs. Afterward, we constructed an immune infiltration-related risk score model based on the expression of IRF1, MFNG, hsa-miR-940, and hsa-miR-378a-5p, presenting a promising performance in predicting the prognosis of patients with sarcoma.

Identification of Subtype-Specific Metastasis-Related Genetic Signatures in Sarcoma

Background: Sarcomas are heterogeneous rare malignancies constituting approximately 1% of all solid cancers in adults and including more than 70 histological and molecular subtypes with different pathological and clinical development characteristics.

Method: We identified prognostic biomarkers of sarcomas by integrating clinical information and RNA-seq data from TCGA and GEO databases. In addition, results obtained from cell cycle, cell migration, and invasion assays were used to assess the capacity for Tanespimycin to inhibit the proliferation and metastasis of sarcoma.

Results: Sarcoma samples (N = 536) were divided into four pathological subtypes including DL (dedifferentiated liposarcoma), LMS (leiomyosarcoma), UPS (undifferentiated pleomorphic sarcomas), and MFS (myxofibrosarcoma). RNA-seq expression profile data from the TCGA dataset were used to analyze differentially expressed genes (DEGs) within metastatic and non-metastatic samples of these four sarcoma pathological subtypes with DEGs defined as metastatic-related signatures (MRS). Prognostic analysis of MRS identified a group of genes significantly associated with prognosis in three pathological subtypes: DL, LMS, and UPS. ISG15, NUP50, PTTG1, SERPINE1, and TSR1 were found to be more likely associated with adverse prognosis. We also identified Tanespimycin as a drug exerting inhibitory effects on metastatic LMS subtype and therefore can serve a potential treatment for this type of sarcoma.

Conclusions: These results provide new insights into the pathogenesis, diagnosis, treatment, and prognosis of sarcomas and provide new directions for further study of sarcoma.

The Study of Sarcoma Microenvironment Heterogeneity Associated With Prognosis Based on an Immunogenomic Landscape Analysis

Microenvironment-driven tumor heterogeneity causes the limitation of immunotherapy of sarcomas. Nonetheless, systematical studies of various molecular levels can enhance the understanding of tumor microenvironment (TME) related to prognosis and provide novel insights of precision immunotherapy. Three prognostic-related TME phenotypes were identified by consensus clustering of the relative infiltration of 22 immune cells from 869 samples of sarcomas. Additionally, integrative immunogenomic analysis is applied to explore the characteristics of different TME groups. The results revealed that most of the immune cell infiltration is higher in the better prognostic group, which are more affected by lower DNA methylation levels and fewer copy number variations in the worse prognostic group. The signaling pathway crosstalk analysis suggested that the changes in the TME will cause considerable variation in the flow of information between pathways, especially when the degree of relative infiltration of immune cells is low, patient's endocrine system may also be significantly affected. Also, the endogenous competitive network analysis indicated that several differentially expressed long non-coding RNAs (lncRNAs) associated with the prognosis or tumor recurrence of sarcoma patients affected the regulatory relationship between miRNAs and different genes when the sarcoma microenvironment changes. In summary, the significant relationship between genetic alterations and prognostic-related TME characteristics in sarcomas were determined in this study. These findings may provide new clues for the treatment of sarcomas.