Conventional Skull Base Chordoma in a Ugandan Adult Male, Presenting with Prolonged Headache: A Case Report

Abstract

Background

Chordomas are uncommon malignant neoplasms arising from notochordal remnants, most commonly affecting the axial skeleton, mainly the skull base and sacrococcygeal region. Skull base chordoma may be asymptomatic or cause progressive headache before focal symptoms prompt imaging. In resource-limited settings, diagnostic work-up is often prolonged as the patient is managed with analgesics without prompt and satisfactory investigation. We report a case of conventional Chordoma arising at the skull base, in a patient with long standing headache.

Case Presentation

A 49-year-old man presenting with a more than one-year history of intermittent and progressive worsening headache. After he reported an episode of facial numbness, examination documented preserved facial sensation. There was no other focal neurological clinical abnormality. Head CT imaging revealed an expansile, destructive midline skull base mass (bone erosion) occupying the region of the skull base, sphenoid paranasal sinus extending into the ethmoid. An invasive biopsy through the sphenoid sinuses was obtained for histopathologic evaluation, which showed morphology consistent with chordoma, supported by IHC showing positivity for EMA, pan-cytokeratin, and S100, with negative CK7, CK20, and CD34. The Ki-67 proliferation index was less than 5%. The integrated findings strongly supported conventional chordoma. Brachyury was unavailable. At last documented review, the patient was clinically stable and surgical management was planned; however the patient was lost to follow-up on subsequent attempts.

Conclusion

Progressive headache with a newly reported focal neurological symptom warrants appropriate imaging and specialist assessment. In a destructive midline skull base mass, the combined morphology and immunophenotype strongly support chordoma, while the absence of brachyury confirmation remains a limitation.

Introduction

Chordomas are uncommon malignant neoplasms derived from embryonic notochordal remnants, accounting for approximately 1–4% of primary bone tumours.^1,2 They most frequently involve the clivus (base of skull) and sacrococcygeal region.³ Despite their slow growth, chordomas are locally aggressive with a high recurrence rate.⁴ Diagnosis relies on a combination of anatomic location, histologic features and immunohistochemistry.² Conventional chordoma typically contains physaliphorous cells (mildly atypical epithelioid cells with bubbly/mucoid filled cytoplasm) in a myxoid matrix and commonly expresses cytokeratins, EMA, and S100; nuclear brachyury is particularly useful in distinguishing it from mimics.¹ Chondrosarcoma and epithelial malignancies can mimic chordoma, as such the anatomic site, morphology, and immunophenotype must be interpreted together; nuclear brachyury provides more specific support for notochordal differentiation when available.⁵ We report a Ugandan patient who presented with history of prolonged headache was treated as presumed migraine before an episode of sensory symptom prompted head and Neck CT scan, and biopsy. The case illustrates the value of radiological, and morphological correlation with the available immunohistochemical panel when brachyury cannot be performed.

Case Presentation

A 49-year-old man presented with a persistent, intermittently worsening dull headache for more than one year. Before the lesion was identified, headache had been managed symptomatically and as presumed migraine with intermittent paracetamol 1g three time daily. Sometimes he took over the counter Ibuprofen capsule 400mg thrice daily during severe pain. The clinical basis and date of the earlier migraine diagnosis, treatment durations, and individual drug responses were not documented, as the patient had been seeking care from another peripheral facility. His headaches persisted despite treatment; in October 2025 he reported an episode of facial numbness that resolved spontaneously. He denied visual disturbance, facial asymmetry, nasal discharge, and other focal symptoms.

At the documented assessment, blood pressure was 118/75 mm Hg, pulse 76/min, axillary temperature 36.6 °C, Glasgow Coma Scale score 15/15, and gait was normal. No objective focal deficit was documented, including no demonstrable facial sensory deficit at examination. The history of facial numbness without an objective examination finding, therefore refer patient’s subjective observations, without proof of a persistent sensory loss.

Full blood count showed a red cell count of 5.89 × 10⁶/µL (local reference interval 4.35–5.65 × 10⁶/µL) and haemoglobin 15.9 g/dL; white cell and platelet counts were normal. Renal and liver function tests were reported as unremarkable; a blood smear showed no hemoparasites. These findings did not establish the diagnosis.

Contrast-enhanced head CT showed an expansile, destructive midline skull base mass centered at the clival region, with bone erosion and extension into the sphenoid and ethmoid sinuses (Figure 1). Tumor dimensions and detailed relationships to the cavernous sinuses, carotid arteries, dura, and optic structures were not documented in the material available for this report. No MRI or systemic staging study was documented at the time of this report. Endoscopic assessment identified a protruding sphenoid sinus mass, from which fragmented biopsy tissue was obtained. ENT consultation and endoscopic examination of the sphenoid sinuses revealed a large protruding mass, of which fragmented tissues were biopsied and submitted for histopathological analysis as shown in Figure 1 below.

Figure 1.

Contrast-enhanced head ct in axial (A), coronal (B), and sagittal (C) planes, showing an expansile destructive midline skull base mass centered at the clivus, with extension into the sphenoid and ethmoid sinuses and associated bone erosion.

Histopathology Findings

Hematoxylin and eosin sections showed lobulated architecture separated by fibrous septa, with cords and nests of mild atypical epithelioid tumor cells in abundant myxoid matrix. Many cells had vacuolated, physaliphorous cytoplasm and low mitotic activity (Figure 2). Tumor cells stained positively for pan-cytokeratin, EMA, and S100 and negatively for CK7, CK20, and CD34 (Figures 3 and 4). The higher power magnification for the positive S100, panCK and EMA have been provided as a separate supplementary file. Ki-67 labelling was less than 5%. Brachyury immunostaining was unavailable. The radiologic and pathologic findings were interpreted as conventional skull base chordoma. The clinical timeline is summarized in Table 1.

Figure 2.

H&E sections at lower (A) and higher (B) magnification. Lobules and cords of epithelioid tumor cells lie in myxoid stroma; the higher magnification shows vacuolated physaliphorous cells. Scale bars are shown in the artwork.

Figure 3.

IHC: CK20 (A), CK7 (B), and CD34 (C) show no tumor-cell staining; EMA (D) shows tumor-cell positivity. Scale bars are shown in the artwork.

Figure 4.

Immunohistochemistry: S100 (A) and pan-cytokeratin (B) show tumor-cell positivity; Ki-67 (C) labels fewer than 5% of tumor nuclei in the sampled area. Scale bars are shown in the artwork.

Table 1.

Timeline

Period	Event
1 year before diagnosis	Intermittent, worsening headaches treated with paracetamol, intermittently sumatriptan, and ibuprofen during severe episodes; exact dates unavailable.
October 2025	Patients reported facial numbness; examination did not demonstrate a persistent objective sensory deficit.
21st November 2025	CT demonstrated destructive clival mass.
27th November 2025	Endoscopic sinus biopsy of skull base lesion.
4th December 2025	Histological diagnosis
April 2026	Clinically stable; Patient referred for surgical management. Subsequent imaging, treatment, and outcome have not been confirmed.
30th August 2026	Lost to follow up, several attempts made.

Final Diagnosis

Conventional chordoma of the skull base.

Treatment and Outcome

The patient is lost to follow up.

Discussion

Chordoma is an uncommon malignant tumor that primarily occurs along the axial spine.⁶ Chordomas arise from primitive notochordal remnants along the axial skeleton.⁷ Although the tumor can appear at any age, the majority occur in patients between the ages of 40 and 60 years; they are uncommon before the age of 20.² Studies have shown that Chordomas are more male-predilected than female, with a male-to-female ratio of 3:2.⁷ The reported annual global incidence is 0.08 per 100,000 cases.⁸ There is limited information on the incidence of Chordoma in Sub-Saharan Africa, with no explicit studies carried out in Uganda to estimate the incidence.⁹ Clinical presentation of Chordomas depends on the site and size of the tumour.⁷ Chordomas are most commonly located at the cranial base, sacrum, and the spine at 38.7%, 34.3%, and 27.0%, respectively.¹⁰ Chordomas of the skull base present clinically with headache, cranial nerve deficits, or sinonasal symptoms, depending on the extent of invasion.³ Unfamiliar presentations such as nasal obstruction, nasal bleeding, and cerebrospinal fluid rhinorrhoea have been documented.¹¹ Chordomas clinically present as slow-growing tumours with locally invasive features and limited distant metastases, occurring only in advanced-stage disease.¹²

In this patient, the clinical presentation was relatively subtle despite significant anatomical involvement and a notably large tumor mass at a critical anatomic location. The prolonged headache and later subjective facial numbness illustrate a diagnostic challenge: a progressive skull base lesion can initially resemble a primary headache disorder. Available records do not establish why imaging was deferred, whether financial or referral barriers contributed, or whether migraine was formally diagnosed. Persistent headaches prompted physician review, during which organ function tests, full blood count, and a contrasted head CT scan were done. The CBC, RFT and LFT were all unremarkable. These tests are non-specific and are not used to diagnose chordoma, but rather to rule out possible systemic inflammatory disorders and tropical haemoparasite diseases.¹³

The contrasted head CT scan showed a destructive bone lesion of the skull base extending to involve the sphenoid and ethmoid paranasal sinuses measuring 33mm in the widest diameter. This is consistent with most skull base chordomas,^2,3 which explains the patient’s protracted headaches and facial numbness.³

Histopathological analysis of the biopsy using H&E stain showed atypical large epithelioid cells with bubbly cytoplasm (physaliphorous cells) in abundant myxoid stroma, consistent with Chordoma.^2,7 The main differential diagnoses were chondrosarcoma, chordoid Meningioma, and metastatic carcinomas.⁶ Furthermore, IHCs were requested; panCK, EMA, CK7, CK20, S100, CD34 and Ki67.

The panCK and EMA expressions showed diffuse positive cytoplasmic and membranous stain, respectively, confirming epithelial differentiation characteristic of chordomas.⁵ IHC S100 showed diffuse nuclear and cytoplasmic positivity, of which interpretation in the context of positive EMA and panCK, taking into consideration the H&E stain morphology, and radiological presentation are suggestive of Chordoma.^2,5 The IHC stains CK7, CK20, and CD34 were all negative, arguing against metastatic mucinous carcinomas and vascular tumours. CK7, CK20, and CD34 negativity are ancillary; negative CK7/CK20 results do not exclude every metastatic carcinoma.² The Ki-67 was less than 5%, consistent with a low proliferation rate. Ki-67 alone is not diagnostic of Chordomas, however chordomas are known to have low proliferation indices as seen in this case.¹⁴ S100 expression, together with pan-cytokeratin and EMA positivity, the characteristic morphology, and the midline clival location, strongly supported chordoma; none of these stains alone excluded every relevant mimic.² Chondrosarcoma can be myxoid and S100 positive, but usually lacks the epithelial marker expression seen here, where as Chordoid Meningioma are negative for S100 and panCK.⁵ The most specific IHC stain for Chordoma is brachyury, which stains positively only in cells with notochordal origin.⁵ In our setting, we did not have access to brachyury.

Despite the low Ki-67, Chordomas remain clinically aggressive due to local invasiveness, difficulty in achieving complete resection, and management implications with a high rate of recurrences.⁷ Treatment of localized skull base chordoma requires specialist multidisciplinary planning. Current multidisciplinary management generally considers maximal safe surgical resection followed by high-dose, conformal radiotherapy; proton therapy is an option in centres with access and suitable anatomy.^6,7

Limitations

The IHC Brachyury testing for confirmation of Chordoma was unavailable for this case. The earlier headache assessment and treatment response were incompletely documented. Detailed CT anatomic relationships, MRI and staging information were unavailable in the supplied records, and the patient could not be followed up after referral, surgery and further outcome management cannot be reported. As a single case, we can not use these observations to establish a general frequency of diagnostic delay or a causal explanation for it to financial, referral, or access factors. Despite several attempts, the patient was lost to follow-up, and this is a significant limitation for the long term documentation of the earlier planned surgical intervention.

Conclusion

Progressive headache accompanied by a newly reported focal neurological symptom warrants appropriate neuroimaging and specialist review. In this patient, a destructive midline skull base mass with characteristic mildly atypical physaliphorous cellular morphology, with positive pan-cytokeratin, EMA, and S100 expression strongly supported conventional chordoma. The lack of brachyury testing and follow-up remain limitations in the current case. Multidisciplinary treatment planning and long-term surveillance are important for this locally aggressive tumor.

Funding Statement

There is no funding to report.

Abbreviations

CD, Cluster of differentiation; CK, Cytokeratin; CT, Computer tomography; EMA, Epithelial membrane antigen; ENT, Ear, nose, and throat; FBC, Full blood count; H&E, Hematoxylin and Eosin; IHC, Immunohistochemistry; IHK, International Hospital Kampala; LFT, Liver function test; OD, Once daily; panCK, Pan cytokeratin; RBC, Red blood cell; RFT, Renal function test.

Data Sharing Statement

De-identified case materials are available from the corresponding author, Okello Malcom Mark, upon reasonable request, subject to patient confidentiality and institutional policy.

Ethics Approval and Consent to Participate

Ethics statement is not applicable.

Consent for Publication

Written informed consent was obtained from the patient for publication of this case report and accompanying images.

Author Contributions

All authors made a significant contribution to the work reported, whether that is in the conception, study design, execution, acquisition of data, analysis and interpretation, or in all these areas; took part in drafting, revising or critically reviewing the article; gave final approval of the version to be published; have agreed on the journal to which the article has been submitted; and agree to be accountable for all aspects of the work.

Disclosure

The authors declare no competing interests.