Loss of mice before the end of the experiment and reason of sacrification. CRS: CIC-rearranged sarcoma; DDLPS: dedifferentiated liposarcoma; LMS: leiomyosarcoma; SynSa: synovial sarcoma.

Gastrointestinal stromal tumors (GIST) are the most common mesenchymal tumors of the gastrointestinal tract. While imatinib and other tyrosine kinase inhibitors have improved the survival of patients with advanced GIST, these treatments are not curative. Additionally, drug resistance eventually develops in most cases. Therefore, there is an unmet need to develop new therapeutic strategies for advanced GIST. This study is the first to comprehensively analyze the molecular epidemiology of urokinase plasminogen activator receptor-associated protein (uPARAP/Endo180/CD280) expression in GIST, highlighting its potential as an attractive target for targeted therapy. We analyzed uPARAP expression in GIST samples using tissue microarrays (TMAs) constructed from clinically annotated patient samples and GIST xenograft specimens. Our results demonstrated that all clinical GIST samples were positive for uPARAP expression, with high expression found in 79% (52/66) of samples. There was no statistically significant correlation between uPARAP expression and relevant clinical parameters, including gender, sample status (primary tumor or metastatic lesion), clinical outcome, mutation status, primary tumor location, and risk class, indicating that uPARAP has no prognostic role in this setting. In xenograft GIST samples, high uPARAP expression was found in 53% (8/15) of models, with a homogeneous distribution of expression in the majority of the samples. This study emphasizes the potential of uPARAP as a druggable target and paves the way for further (pre)clinical evaluation of anti-uPARAP therapy in advanced GIST.

Average number of apoptotic cells evaluated on (A) H&E and (B) cPARP IHC staining. C, Double-strand break formation shown by γH2AX IHC staining. The results show the mean ± standard deviation. Statistical significance was calculated using the Mann–Whitney U test, *P < 0.05. ns, not significant.

Supplemental Figure 5: Overview of representative tumor sections of STS336SynSa on day 16, treated with A) vehicle, B) doxorubicin, C) trabectedin, D) lurbinectedin, E) ecubectedin, and F) PM54. Tumors treated with ecubectedin and PM54 showed alteration in the myxoid stroma after treatment, potentially explaining the absence of tumor volume shrinkage despite the increase in mitosis and decrease in apoptosis. SynSa: synovial sarcoma.

List of treatment groups, models, number of tumors included at the start of the experiment and the number of tumors included in the analysis. Tumors from mice that were sacrificed prior to the end of the experiment (e.g., due to unethical tumor volume >2000mm 3 or body weight loss), were not included in the analysis. Tumors excluded from analysis of phase 2 of the STS336SynSa experiment concerns tumors from mice designated to the group intended for follow-up at any point in the experiment (i.e., any moment between days 0 and 41). CRS: CIC-rearranged sarcoma; DDLPS: dedifferentiated liposarcoma; LMS: leiomyosarcoma; SynSa: synovial sarcoma

Abstract Trabectedin, prototype of the ecteinascidin class of drugs, is a known second- or later-line therapeutic option for advanced soft tissue sarcoma (STS). We evaluated the antitumor activity of two novel synthetic trabectedin derivatives, ecubectedin and PM54, in selected patient-derived xenograft (PDX) STS models. In total, 364 Naval Medical Research Institutenu/nu mice were transplanted bilaterally with two leiomyosarcoma (LMS), two dedifferentiated liposarcoma (DDLPS), one synovial sarcoma (SynSa), and one CIC-rearranged sarcoma (CRS) PDX models. Mice were randomized to six groups and treated via tail vein injection with (i) vehicle, (ii) doxorubicin, (iii) trabectedin, (iv) lurbinectedin, (v) ecubectedin, or (vi) PM54. Treatment was given on days 1, 8, and 15, and mice were sacrificed on day 16. The SynSa experiment included extra mice to investigate posttreatment xenograft evolution. Antitumor activity was assessed by tumor volume measurement, histopathologic, and immunohistochemical analyses. In all LMS and DDLPS models, ecubectedin and PM54 led to tumor growth delay compared with trabectedin. Histopathologic evaluation of treated tumors showed moderately increased antitumor activity of novel ecteinascidins compared with trabectedin. The CRS model showed tumor shrinkage in response to ecubectedin (63% regression from baseline) and PM54 (24% regression from baseline), while the SynSa model showed tumor volume stabilization. Both translocation-related models showed significant antitumor effect on histopathologic evaluation in response to the novel drugs compared with trabectedin. Ecubectedin and PM54 have modest antitumor activity in STS PDX models, with the strongest effects seen in the translocation-related sarcoma models, showing the potential of this class of drugs in the treatment of STS. Significance: Advanced STS remains without truly effective therapeutic options. Translocation-related sarcomas demonstrate higher vulnerability to next-generation ecteinascidin treatment compared with more complex sarcoma subtypes. This vulnerability builds upon known literature and could be exploited in future clinical trials using the next-generation ecteinascidins.

Supplemental Figure 2: Evolution of absolute tumor volume of individual tumors from day 1 to day 16 (A-F) or from day 1 to day 17 and to day 41 (G). Statistical significance indicate either tumor growth or shrinkage, whereas non-significance indicates tumor volume stabilization. * p<0.05, CRS: CIC-rearranged sarcoma; DDLPS: dedifferentiated liposarcoma; LMS: leiomyosarcoma; STS: soft tissue sarcoma; TV: tumor volume; ns: not significant; SynSa: synovial sarcoma.

Tumor volume assessment in STS models after treatment.

Evaluation of mitotic and apoptotic activity Arrows indicate whether mitotic or apoptotic activity was significantly higher (↑), lower (↓) or not statistically different (=) compared to trabectedin. Statistically significant changes were calculated using the Mann-Whitney U test, compared to trabectedin. CRS: CIC-rearranged sarcoma; DDLPS: dedifferentiated liposarcoma; H&E: hematoxylin and eosin; LMS; leiomyosarcoma; SynSa; synovial sarcoma

Supplemental Figure 3: Relative change of individual tumor volumes from baseline (here indicated as 0), on day 16 (A-F) or day 41 (G), sorted per treatment for each experiment.

Average number of mitotic cells evaluated on (A) H&E and (B) mitotic activity shown by pHH3 IHC staining. C, Percentage of Ki-67–positive cells. The results show the mean ± standard deviation. Statistical significance was calculated using the Mann–Whitney U test, *P < 0.05. ns, not significant.

Background Malakoplakia is a rare, chronic granulomatous inflammatory condition that primarily affects the genitourinary tract, albeit rarely renal allografts. This article highlights the clinical presentation and radiological features of renal allograft malakoplakia and aims to identify knowledge gaps by a pooled analysis of case reports.Methods This study contains a detailed case report focusing on the presentation and radiological evolution of renal allograft malakoplakia, followed by a pooled analysis of 38 histologically confirmed cases, extracted from 34 publications. Descriptive statistics were applied.Results Malakoplakia of the renal allograft generally affects female (79%), middle-aged (mean 48 years) kidney transplant recipients in the first 2 years after transplantation (68.4%, mean 19 months), with a history of recurrent E. coli UTIs (87%) and considered at high immunological risk (70%). Acute kidney injury (AKI) was the most common presentation of allograft malakoplakia (84% of cases). Three main patterns can be differentiated on imaging: parenchymal lesions (40%), abscess-like formations (34%), and pseudotumoral masses (26%). Ultrasound, CT, MRI, and FDG-PET-CT can result in initial detection, assess disease extent, and treatment response. However, these imaging modalities cannot reliably differentiate malakoplakia from malignant or other infectious processes, making histopathological confirmation essential for definitive diagnosis. There are no standardized treatment protocols, nor guidelines concerning antibiotic duration, reduction of immunosuppression, and definition of remission. Despite treatment, one-fifth of cases result in graft failure and one-fifth in death.Conclusions Renal allograft malakoplakia is a rare but serious condition that in worst cases leads to graft loss and death. Prospective studies are needed to establish standardized diagnostic and therapeutic approaches, including the potential role of FDG-PET-CT in monitoring treatment response.

Supplemental Figure 4: Evolution of body weight during treatment, presented as relative body weight (% change from normalized baseline) ± standard deviation. Figure 2F depicts the first phase of the experiment of STS336SynSa, while Figure 2G depicts the complete experiment. Mice sacrificed prior to end of experiment are removed from data after date of scarification. 3x/4x: 3 or 4 mice of the same group were sacrificed on the same day; * p<0.05; CRS: CIC-rearranged sarcoma; DDLPS: dedifferentiated liposarcoma; LMS: leiomyosarcoma; ns: not significant; STS: soft tissue sarcoma; TV: tumor volume; SynSa: synovial sarcoma.

A–G, Evolution of tumor volume during treatment, presented as relative tumor volume (% change from normalized baseline) ± standard deviation. F, The first 16 days of the STS336SynSa experiment. G, The complete experiment, including the follow-up period after the first 16 days. Tumors from mice sacrificed prior to the end of the experiments were not included in statistical evaluation. Statistical significance is indicated for ecubectedin or PM54 compared with trabectedin at the end of the experiment (day 16 or 41). *, P < 0.05. 3×/4×: 3 or 4 mice of the same group were sacrificed on the same day. TV, tumor volume.

Supplementary Table S1 from Efficacy of the Kinase Inhibitor SU11248 against Gastrointestinal Stromal Tumor Mutants Refractory to Imatinib Mesylate

Supplemental Figure 1:Patient-derived xenograft model characterization: alpha-SMA: alpha smooth muscle actin; CD99: cluster of differentiation 99; CRS: CIC-rearranged sarcoma; DDLPS: dedifferentiated liposarcoma; EMA: epithelial membrane antigen; FISH: fluorescent in situ hybridization; HLA-A: human leukocyte antigen-A; H&E hematoxylin & eosin; LMS: leiomyosarcoma; MDM2: mouse double minute homolog 2; SynSa: synovial sarcoma; TLE-1: transducing-like enhancer of split 1; UZLX: University Hospitals Leuven xenograft.

Malignant triton tumor (MTT) is a rare subset (5%) of malignant peripheral nerve sheath tumors (MPNSTs), classified as soft-tissue sarcomas. MTT is an orphan disease characterized by rhabdomyoblastic differentiation, therapeutic resistance, and a sinister prognosis. The neoplasms classically arise at the trunk, head and neck region, and extremities. In 50% of the cases, MTT is associated with neurofibromatosis type 1 (NF1), a relatively common autosomal dominant cancer-prone disorder of the central nervous system. Few cases of MTT in the gastrointestinal tract have been published, including esophagus, duodenum, and rectum. In this article, we present what we believe to be the first report of MTT in the common bile duct. A multidisciplinary approach was the key in establishing this particular diagnosis, and workup included endoscopic ultrasound, endoscopic retrograde cholangiopancreatography, pathological staining, and genetic testing. Literature focusing on MTT remains scarce, and patients with MTT are often included with other subtypes in broader studies of MPNST. Therefore, our literature review covers MPNST and focusses on MTT where appropriate. It provides the current understanding of tumor epidemiology, genetics, and diagnostic workup, and discusses therapeutic challenges and future perspectives. Our case report underlines the value of cholangioscopy-guided biopsies, and honoring patient's autonomy in end-of-life setting.

Supplementary Fig. 6. One histologically representative picture of cPARP staining in control group versus IDRX-42_25 treatment group in the experiment with UZLX-GIST9KIT11+17.

CONTEXT:Nodular fasciitis (NF), myositis ossificans/fibro-osseous pseudotumor of the digits (MO/FP) and aneurysmal bone cyst (ABC) are grouped under the category of 'USP6-associated neoplasms' (UANs) due to their shared characteristic of an underlying USP6 rearrangement. OBJECTIVE:Our aim in this study is to investigate the diversity of USP6 rearrangements in UANs. DESIGN:We performed a clinicopathological and molecular investigation using targeted RNA sequencing on 124 cases of NF, 19 cases of MO/PF and 32 cases of ABC. Additionally, NF cases were scored for the presence of typical morphological features to assess their correlation with the detected USP6 fusion partner. RESULTS:In 85.4% of NF cases (88/103), we identified a USP6 rearrangement, with 46.6% exhibiting the classic MYH9::USP6 fusion and 53.4% displaying non-MYH9::USP6 fusions. Notably, classic histological features of NF strongly correlated with the presence of the MYH9::USP6 fusion, while specific NF locations (e.g. intramuscular, intra-articular and intradermal) were significantly associated with non-MYH9 fusions. This study identified 22 novel USP6 fusion partners, demonstrating the fusion diversity within UANs. Additionally, there was minimal overlap in USP6 fusion partners between different UAN types. CONCLUSIONS:A significant entity- and location-specific USP6 fusion partner diversity was revealed among the UAN members. This supports the hypothesis that this diversity may be linked to the cell of origin. Additionally, molecular analysis can be valuable in diagnosing non-classical NF.

INTRODUCTION:Dedifferentiated liposarcoma (DDLPS) is a fairly common subtype of soft tissue sarcoma, but relatively little is known about the clinical course and prognostic factors of this mesenchymal malignancy. METHODS:We performed a retrospective analysis of patients diagnosed with DDLPS at the University Hospital Leuven, Belgium between 1991 and 2022 based on an established clinical database and patient records. RESULTS:We identified 259 patients with DDLPS, with the retroperitoneum as most common location of the primary tumor (47.5%). 204/259 patients (78.8%) patients had primary surgery. Radiotherapy was administered in the pre- (46/259, 17.8%) or postoperative setting (51/259, 19.7%). At diagnosis 28/259 (10.8%) patients presented with locally inoperable disease and 26/259 (10.0%) with synchronous metastasis. In patients who had primary surgery, local relapses were seen in 114/259 (44.0%) patients and 80/259 (30.9%) patients developed metachronous metastasis. A total of 48/259 (18.5%) patients developed both local relapse and metastasis. Patients with inoperable or metastatic disease were often treated with systemic therapy. The most common first-line systemic therapies were doxorubicin (51/98, 52.0%), doxorubicin combined with ifosfamide (12/98, 12.2%) and different types of experimental treatments (18/98, 18.4%). The median overall survival from first diagnosis of DDLPS to death of all causes was 70.5 months (95% confidence interval [CI] 56.6-98.6) for all patients, 10.9 months (95% CI 3.6-29.2) in patients with inoperable disease, 28.4 months (95% CI 1.3-199.3) for patients with local relapse and only 9.4 months (95% CI 1.2-25.9) for patients with metastatic disease. We identified lower age, primary surgery, absence of synchronous metastasis, absence of local relapse and treatment with experimental therapy as statistically significant favorable prognostic factors. CONCLUSIONS:DDLPS is a subtype of soft tissue sarcoma with an aggressive clinical course and very poor prognosis, especially in patients with inoperable or metastatic disease. The results with classic chemotherapy are poor, and experimental treatments may be a preferred choice for individual patients. Data from this retrospective series can inform the design of future prospective and ongoing trials in this setting.