Experimental study on differences in clivus chordoma bone invasion: an iTRAQ-based quantitative proteomic analysis

Pilot Study of High-Dose Pemetrexed in Patients with Progressive Chordoma

PURPOSE

Chordomas are ultrarare tumors of the axial spine and skull-base without approved systemic therapy. Most chordomas have negative expression of thymidylate synthase (TS), suggesting a potential for responding to the antifolate agent pemetrexed, which inhibits TS and other enzymes involved in nucleotide biosynthesis. We evaluated the therapeutic activity and safety of high-dose pemetrexed in progressive chordoma.

PATIENTS AND METHODS

Adult patients with previously treated, progressive chordoma participated in an open-label, single-institution, single-arm, pilot clinical trial of intravenous pemetrexed 900 mg/m2 every 3 weeks and supportive medications of folic acid, vitamin B12, and dexamethasone. The primary endpoint was objective response rate according to RECIST v1.1. Secondary endpoints included adverse events, progression-free survival (PFS), tumor molecular profiles, and alterations in tissue and blood-based biomarkers.

RESULTS

Fifteen patients were enrolled and the median number of doses administered was 15 (range, 4-31). One patient discontinued treatment due to psychosocial issues after four cycles and one contracted COVID-19 after 13 cycles. Of the 14 response-evaluable patients, 2 (14%) achieved a partial response and 10 (71%) demonstrated stable disease. Median PFS was 10.5 months (95% confidence interval: 9 months-undetermined) and 6-month PFS was 67%. Adverse events were expected and relatively mild, with one grade 3 creatinine increased, and one each of grade 3 and 4 lymphopenia. No grade 5 adverse events, unexpected toxicities, or dose-limiting toxicities were observed. Several patients reported clinical improvement in disease-related symptoms.

CONCLUSIONS

High-dose pemetrexed appears tolerable and shows objective antitumor activity in patients with chordoma. Phase II studies of high-dose pemetrexed are warranted.

Methylation-based reclassification and risk stratification of skull-base chordomas

BACKGROUND

Skull-base chordomas are rare malignant bone cancers originating from the remnant of the notochord. Survival is variable, and clinical or molecular factors cannot reliably predict their outcomes. This study therefore identified epigenetic subtypes that defined new chordoma epigenetic profiles and their corresponding characteristics.

METHODS

Methylation profiles of 46 chordoma-resected neoplasms between 2008 and 2014, along with clinical information, were collected. K-means consensus clustering and principal component analysis were used to identify and validate the clusters. Single-sample gene set enrichment analysis, methylCIBERSORT algorithm, and copy number analysis were used to identify the characteristics of the clusters.

RESULTS

Unsupervised clustering analysis confirmed two clusters with a progression-free survival difference. Gene set enrichment analysis indicated that the early and late estrogen response pathways and the hypoxia pathway were activated whereas the inflammatory and interferon gamma responses were suppressed. Forty-six potential therapeutic targets corresponding to differentially methylated sites were identified from chordoma patients. Subgroups with a worse outcome were characterized by low immune cell infiltration, higher tumor purity, and higher stemness indices. Moreover, copy number amplifications mostly occurred in cluster 1 tumors and the high-risk group. Additionally, the presence of a CCNE1 deletion was exclusively found in the group of chordoma patients with better outcome, whereas RB1 and CDKN2A/2B deletions were mainly found in the group of chordoma patients with worse outcome.

CONCLUSIONS

Chordoma prognostic epigenetic subtypes were identified, and their corresponding characteristics were found to be variable.

Proteomics and phosphoproteomics of chordoma biopsies reveal alterations in multiple pathways and aberrant kinases activities

Background

Chordoma is a slow-growing but malignant subtype of bone sarcoma with relatively high recurrence rates and high resistance to chemotherapy. It is urgent to understand the underlying regulatory networks to determine more effective potential targets. Phosphorylative regulation is currently regarded as playing a significant role in tumorigenesis, and the use of tyrosine kinase inhibitors in clinical practice has yielded new promise for the treatment of a variety of sarcoma types.

Materials and methods

We performed comprehensive proteomic and phosphoproteomic analyses of chordoma using four-dimensional label-free liquid chromatography–tandem mass spectrometry (LC-MS/MS) and bioinformatics analysis. The potential aberrantly expressed kinases and their functions were validated using western blotting and CCK-8 assays.

Results

Compared with paired normal muscle tissues, 1,139 differentially expressed proteins (DEPs) and 776 differentially phosphorylated proteins (DPPs) were identified in chordoma tumor tissues. The developmentally significant Wnt-signaling pathway and oxidative phosphorylation were aberrant in chordoma. Moreover, we predicted three kinases (AURA, CDK9, and MOK) with elevated activity by kinase-pathway network analysis (KiPNA) and verified their increased expression levels. The knockdown of these kinases markedly suppressed chordoma cell growth, and this was also the case for cells treated with the CDK9 inhibitor AZD4573. We additionally examined 208 proteins whose expression and phosphorylation levels were synergetically altered.

Conclusions

We herein depicted the collective protein profiles of chordomas, providing insight into chordomagenesis and the potential development of new therapeutic targets.

PTEN is recognized as a prognostic-related biomarker and inhibits proliferation and invasiveness of skull base chordoma cells

Objective

This work aimed to examine the function of phosphatase and tensin homologue deleted on chromosome 10 (PTEN) in skull base chordoma (SBC) at the clinical and cellular levels.

Methods

Totally 65 paraffin-embedded and 86 frozen specimens from 96 patients administered surgery were analyzed. Immunohistochemical staining and quantitative real-time polymerase chain reaction were performed, and the associations of PTEN expression with clinical features were assessed. At the cellular level, PTEN was knocked down by the siRNA approach in the UCH-1 cell line, and cell proliferation and invasion were detected by the CCK-8 and migration assays, respectively.

Results

At the protein level, PTEN expression was increased in non-bone-invasive tumor samples in comparison with bone-invasive specimens (p = 0.025), and elevated in soft SBCs in comparison with hard tumors (p = 0.017). Increased PTEN protein expression was associated with decreased risk of tumor progression (p = 0.002; hazard ratio = 0.981, 95% confidence interval: 0.969–0.993). At the gene expression level, the cut-off value was set at 10.5 after ROC curve analysis, and SBC specimens were divided into two groups: PTEN high group, ΔCt value below 10.5; PTEN low group, ΔCt value above 10.5. In multivariate regression analysis of PFS, the risk of tumor progression was increased in PTEN low group tumors in comparison with PTEN high group SBCs (p = 0.006). In the CCK-8 assay, in comparison with control cells, PTEN knockdown cells had increased absorbance, suggesting elevated cell proliferation rate. In the invasion assay, the number of tumor cells penetrating into the lower chamber was significantly increased in the PTEN knockdown group compared with control cells.

Conclusions

Decreased PTEN expression in SBC, at the protein and gene levels, is associated with reduced PFS. PTEN knockdown in chordoma cells led to enhanced proliferation and invasiveness.

A Cystic Clival Chordoma with CT and MRI Unconventional Appearances

We present the first case of clival cystic chordoma with extradural location, transdural transgression, and moderate bone involvement in a 10-year-old girl. Chordoma showed unconventional appearances on computed tomography (CT) and magnetic resonance imaging (MRI), due to cystic components, extradural space location with extensive intradural extension, moderate superficial bone involvement. Surgery confirmed the extradural location and histopathological examination revealed cystic chordoma. MRI and CT findings were not characteristic for a single lesion; differential diagnoses included cystic lesions such as epidermoid and dermoid cyst, ecchordosis physaliphora, and benign notochordal cell tumors.

Clivus chordomas: Heterogeneous tumor extension requires adapted surgical approaches

OBJECTIVE

Clivus chordomas are semi-malignant, but infiltratively growing tumors. Currently, a widely-accepted treatment concept encompasses maximal, but safe, surgical resection and radiotherapy. Caused by the size and the tumor extension, different surgical approaches, especially in recurrent cases, might be necessary.

METHODS

Retrospective review of 50 patients on whom 70 surgeries were performed: 29 in primary and 41 in recurrent cases. Based on MRI images, all cases were asserted according to the size and the extension of the tumor. Used surgical approaches were evaluated. Postoperative complications, neurological function prior to and after the surgery, the extent of tumor resection on postoperative MR images were assessed and progression-free survival was calculated.

RESULTS

Tumor size was estimated as small (< 5 cm³) in 8, as medium (5-20 cm³) in 21, as large (20-100 cm³) in 17, and as giant (> 100 cm³) in 4 patients. Most frequently used surgical approaches in primary cases were the transsphenoidal one and midfacial degloving (51.7 % and 17.2 %, respectively). In recurrent cases, dependent on the tumor extension, transsphenoidal (21.9 %), retrosigmoidal (29.3 %), and pterional (19.5 %) approaches, as well as midfacial degloving (17.1 %) were used. Due to the vast tumor extension and infiltration, gross total or near total resection could be achieved in 12 patients (24 %), only. There was no mortality and no major complications in primary cases. In recurrences, however, postoperative hemorrhages and strokes emerged in 4.9 % and 7.1 %. Minor complications occurred in 17.1 % and were dominated by CSF leaks (12.2 %), both in primary in recurrent cases. While most cranial nerve impairments were caused by tumor infiltration of the cavernous sinus, and hence have not improved by treatment, the sixth nerve palsy as a consequence of tumor mass compression, could significantly be improved by surgery. Following surgery, patients were subjected to radiotherapy (68.9 % for primary cases, and 36.6 % for recurrences) mainly with carbon ions. Overall, 5-year progression-free survival was 44.7 %.

CONCLUSION

Caused by the heterogenous pattern of growth of clivus chordomas, surgical approaches should be chosen individually. Vast and infiltrative tumor extension constitute major limitations of surgical resection, and hence result in poor progression-frees survival.

Clinicopathological and Prognostic Characteristics in Extra-Axial Chordomas: An Integrative Analysis of 86 Cases and Comparison With Axial Chordomas

BACKGROUND

Currently, clinical characteristics and prognostic factors of extra-axial chordoma (EAC) remain poorly understood.

OBJECTIVE

To characterize clinicopathological characteristics in a large EAC cohort and investigate their correlation with survival. We also attempted to compare these outcomes with axial chordoma (AC).

METHODS

Medline and Embase searches (from inception to February 28, 2018) were conducted to identify eligible studies as per predefined criteria. The local database at our center was also retrospectively reviewed to include additional patients.

RESULTS

Forty-three studies from the literature and 86 patients from our local institute were identified, resulting in a total of 86 EAC patients and 75 AC patients for analysis. Overall, EAC had similar characteristics to AC, except for having higher CAM5.2 expression, common lobular growth pattern, and better prognosis. Whereas wide surgical resection was consistently associated with favorable survival in both EAC and AC cohorts on univariate analyses, most parameters showed differential prognostic implications between the 2 groups. Significant prognostic factors for local recurrence-free survival on multivariate analysis included type of surgery in both cohorts and tumor Brachyury expression and adjuvant radiotherapy in AC cohort. Multivariate analysis of overall survival demonstrated that type of surgery, tumor Brachyury expression, and duration of symptoms were significant predictors in the AC cohort, whereas none of the analyzed parameters were predictive of overall survival for the EAC group.

CONCLUSION

These data suggest potentially distinct biological behaviors between EAC and AC and may provide useful information to better understand the prognostic characteristics and improve the outcome prediction of EAC patients.

Natural Growth Dynamics of Untreated Skull Base Chordomas In Vivo

OBJECTIVE

To study the natural growth dynamics of skull base chordomas.

METHODS

A retrospective study of skull base chordomas was performed. Patients with ≥2 preoperative magnetic resonance (MR) images and with pathologically confirmed chordomas were enrolled. All clinical data and MR images were studied.

RESULTS

Twenty-one patients with pathologically confirmed skull base chordomas were enrolled. The mean volume of the tumors at diagnosis was 19.9 ± 17.0 cm³, with a mean interval examination period of 22.4 ± 26.1 (range, 3-113) months. The mean tumor volume change was approximately 15.4 ± 16.3 cm³. The mean specific growth rate was 8% ± 9% per month, and the mean specific growth volume was 0.8 ± 0.7 cm³ per month. The tumor MR signal index grade, female gender, no dura mater breakthrough, endophytic type, small tumors, and soft tumor texture were related to a higher tumor growth rate (P < 0.05), and small tumors showed the greatest growth rate compared with the middle-sized and large tumors. Curve estimation was performed using a power function (R² = 0.545).

CONCLUSIONS

The skull base chordoma is a slow-growing tumor. The cases involving characteristics of female gender, endophytic type, small tumor size, and MR grade 3 showed a higher growth rate.

High Expression of TGF-β1 Predicting Tumor Progression in Skull Base Chordomas

OBJECTIVE

To investigate the expression characteristics and prognostic value of transforming growth factor β1 (TGF-β1) in primary skull base chordomas (SBCs).

METHODS

The mRNA expression levels of TGF-β1 were measured in 57 frozen samples from patients with primary SBCs. Clinical data collection, follow-up, correlations, and survival analyses were performed.

RESULTS

In the series of 57 patients (29 men and 28 women) with primary SBCs, the mean value of TGF-β1 mRNA was 1.713 with a median of 0.904. Twenty-four SBCs were soft type and 33 were hard type. The Mann-Whitney U test revealed that the expression level of TGF-β1 mRNA in hard type SBCs was significantly higher than the expression level found in the soft type (P = 0.03). The independent-samples median test suggested that the expression level of TGF-β1 mRNA in female patients' SBCs was significantly higher than that in male patients' SBCs (P = 0.01). Expression differences of TGF-β1 were not seen among different pathological subtypes, tumor blood supply, or degree of resection. The Spearman rank correlation coefficient clarified that TGF-β1 mRNA levels were not correlated with tumor diameter, preoperative Karnofsky Performance Status (KPS), postoperative KPS, follow-up KPS, age, or intraoperative blood loss. The multivariate Cox analysis revealed that pathological subtype (P = 0.008), expression level of TGF-β1 mRNA (P = 0.01), and tumor texture (P = 0.03) were all independent prognostic factors for tumor progression.

CONCLUSIONS

SBCs in female patients and SBCs with hard texture were prone to have high TGF-β1 mRNA expression. High expression of TGF-β1, hard tumor texture, and conventional subtype were all independent risk factors for tumor progression.

The Degree of Middle and Lower Clivus Invasion by Chordoma is Linked to Patient Prognosis Via Ki-67 Value

OBJECTIVE

The aim of this study was to discuss the relationship between Ki-67 values and the degree to which chordoma invade the clivus and to certify that the prognosis of chordoma is worse when it invades the middle and lower clivus than when it does not.

METHODS

We collected 56 cases of first-time chordoma illness in which patients received no treatment before surgery. Patients underwent craniocerebral magnetic resonance imaging and skull-base 3-dimensional computed tomography scans before the operation. We divided patients into 2 groups depending on the extent to which the middle and lower clivus were invaded. We classified patients with chordoma that did not significantly invade the middle and lower clivuses into a "noninvasive" group and the others into an "invasive" group. Ki-67 values were extracted from the pathological report after surgery. We use an independent χ² test to indicate that Ki-67 values for the invasive group were higher than those for the noninvasive group.

RESULTS

We grouped the data and did a statistical analysis. We found that the Ki-67 values are >5% for most patients in whom chordoma have eroded the middle-lower clivus, whereas it is ≤5% for patients in whom the middle-lower clivus region has not been invaded. Therefore, there is a correlation between Ki-67 value and the region of chordoma invading the clivus.

CONCLUSIONS

Statistical analysis revealed that Ki-67 values when the chordoma invaded the middle and lower clivus were significantly higher than when it did not. Thus, we can conclude that the prognosis is worse when chordoma invade the middle and lower clivus.

Immunophenotypic features of dedifferentiated skull base chordoma: An insight into the intratumoural heterogeneity

Chordomas are rare and low-grade malignant solid tumours, despite their histologically benign appearance, that arise in the bone from embryonic notochordal vestiges of the axial skeleton, a mesoderm-derived structure that is involved in the process of neurulation and embryonic development. Chordomas occurring in the skull base tend to arise in the basiocciput along the clivus. Three major morphological variants have been described (classical, chondroid, and atypical/dedifferentiated). The pathogenesis and molecular mechanisms involved in chordoma development remain uncertain. From a pathological standpoint, the microenvironment of a chordoma is heterogeneous, showing a dual epithelial-mesenchymal differentiation. These tumours are characterised by slow modality of biologic growth, local recurrence, low incidence of metastasis rates, and cancer stem cell (CSC) phenotype. The main molecular findings are connected with brachyury immunoexpression and activation of the downstream Akt and mTOR signalling pathways. The differentiation between typical and atypical chordomas is relevant because the tumoural microenvironment and prognosis are partially different. This review provides an insight into the recent and relevant concepts and histochemical markers expressed in chordomas, with special emphasis on dedifferentiated chordomas and their prognostic implications.

Kinase Activity in Recurring Primary Skull Base Chordomas and Chondrosarcomas: Identification of Novel Pathways of Oncogenesis and Potential Drug Targets

BACKGROUND

Chordomas and chondrosarcomas can occur in the skull base. Currently, 45% of chordomas and 56% of chondrosarcomas recur within 5 years of surgery. The role of adjuvant therapy is highly debated. No pharmacotherapies have been approved by the U.S. Food and Drug Administration for chordomas or chondrosarcomas. High propensity for recurrence and lack of definitive adjuvant therapy necessitate additional basic science research to identify molecular anomalies associated with recurrent disease.

METHODS

We pooled tumor lysates from patients based on clinical criteria into 4 groups: primary chordomas, primary chordomas that recurred, primary chondrosarcomas, and primary chondrosarcomas that recurred. We used a peptide labeling method, isobaric tags for relative and absolute quantitation, to uniquely identify each tumor group. Phosphorylated peptides were identified and quantified via mass spectroscopy to determine and predict active kinases.

RESULTS

Six groups of phosphorylated peptides were associated with primary tumors that later recurred. Specific kinases associated with primary chordomas that recurred were FES and FER. Specific kinases associated with primary chondrosarcomas that recurred were FES, FER, SRC family kinases, PKC, ROCK, and mitogen-activated protein kinase signaling (JNK, ERK1, p38).

CONCLUSIONS

These data provide clinicians with a means to screen skull base chordomas and chondrosarcomas to help identify tumors with a propensity to recur. Many of these kinases can be efficaciously inhibited by Food and Drug Administration-approved drugs that have not yet been used in clinical trials for treatment of skull base chordomas or chondrosarcomas. Validation of kinases identified in this study may advance treatment options for patients with these tumors.

Clinical features and surgical outcomes of patients with skull base chordoma: a retrospective analysis of 238 patients

OBJECTIVE Skull base chordoma is relatively rare, and a limited number of reports have been published regarding its clinical features. Moreover, the factors associated with extent of resection, as well as the value of marginal resection for long-term survival, are still in question for this disease. The objective of this study was to investigate these factors by evaluating their clinical features and surgical outcomes. METHODS A retrospective analysis of 238 patients with skull base chordomas, who met the inclusion criteria, was performed. This study summarized the clinical features, selection of approaches, degree of resection, and postoperative complications by statistical description analyses; proposed modified classifications of tumor location and bone invasion; studied the contributions of the clinical and radiological factors to the extent of resection by Pearson χ², ANOVA, rank test, and binary logistic regression analysis; and estimated the differences in overall survival and progression-free survival rates with respect to therapeutic history, classification of tumor location, extent of bone invasion, and extent of tumor resection by the Kaplan-Meier method. A p value < 0.05 was considered statistically significant. RESULTS The study included 140 male and 98 female patients with a mean age of 38.1 years. Headache and neck pain (33.2%) and diplopia (29%) were the most common initial symptoms. Sphenoclival type accounted for the largest proportion of tumor location (59.2%); endophytic chordoma was the more common type of bone invasion (81.5%). Lateral open approaches were performed in two-thirds of the study population (78.6%). The rate of marginal resection was 66%, composed of gross-total resection (11.8%) and near-total resection (54.2%). Meningitis (8%) and CSF leakage (3.8%) were the most frequent complications. The mean follow-up period was 43.7 months. The overall survival and progression-free survival rates at 5 years were 76% and 45%, respectively. Recurrent tumor and larger tumor volume (≥ 40 cm³) were identified as risk factors of marginal resection. Patients who presented with recurrent tumor and underwent intralesional resection had a worse long-term outcome. CONCLUSIONS The classifications of both tumor location and bone invasion demonstrated clinical value. Marginal resection was more likely to be achieved for primary lesions with smaller volumes (< 40 cm³). The rate of CSF leakage declined due to improved dura mater repair with free fat grafts. Marginal resection, or gross-total resection when possible, should be performed in patients with primary chordomas to achieve better long-term survival.