Sacral Chordoma: Symptoms, Diagnosis, and Treatment

Sacral chordoma is a rare, slow-growing bone cancer that arises in the sacrum, the triangular bone at the base of the spine, from leftover cells of the notochord, the embryonic structure that forms before the backbone develops. Its hallmark symptom is persistent lower back pain that does not respond well to standard painkillers, and because that symptom mimics so many common conditions, diagnosis is frequently delayed by two years or more. Treatment centers on aggressive surgical removal, often supplemented with radiation, though the tumor’s location deep in the pelvis makes clean margins difficult and raises real concerns about nerve damage affecting bladder, bowel, and leg function.

Where Sacral Chordoma Comes From

During early development, the notochord acts as the scaffold around which the spine eventually forms. In most people, notochord remnants are quietly reabsorbed or persist as the jelly-like center of spinal discs. In chordoma, those remnants undergo malignant transformation. The tumor cells share both the microscopic appearance and the gene expression of notochord cells, particularly the transcription factor known as Brachyury (encoded by the gene TBXT).¹ Brachyury is not just a marker; it appears to be a driver. Research has found that extra copies of the Brachyury gene are present in a substantial share of chordoma tumors, and higher copy numbers correlate with higher expression of the protein, which in turn fuels tumor growth.² More recent work has shown that the gene can be amplified through unusual circular DNA structures outside normal chromosomes, which may explain both the tumor’s persistence and its tendency toward genetic instability.³

Who Gets It

Chordoma overall is rare, with an incidence under one per million people per year. A population-based analysis of over 6,000 U.S. cases found that the sacrum accounts for roughly a third of all chordomas, making it the second most common site after the skull base.⁴ Sacral chordoma skews older and more male than its cranial counterpart: about half of sacral cases occur in people 65 or older, and roughly 60% are in men. White patients are also disproportionately represented. These demographic patterns do not mean the disease cannot appear in younger adults or women; it can, and younger patients may actually face a higher risk of eventual metastasis.

Symptoms and the Problem of Late Diagnosis

The most common early complaint is low back pain, usually worse when sitting. Up to a third of patients also report urinary tract infections, constipation, or symptoms that mimic disc herniation.⁵ Because these symptoms overlap with everyday musculoskeletal problems, it is easy to see why sacral chordoma gets missed. A study of diagnostic delays found that the average time from first symptoms to diagnosis was about 2.3 years, with some patients waiting as long as eight years.⁶ A key clinical clue is that the pain responds poorly to non-steroidal anti-inflammatory drugs like ibuprofen or naproxen. Persistent, NSAID-resistant low back pain in someone over 40, especially if accompanied by bowel or bladder changes, should prompt imaging of the sacrum rather than another round of conservative back treatment.

On physical examination, a rectal exam sometimes reveals a palpable presacral mass, though this is not always present, particularly in earlier-stage disease. By the time symptoms are severe enough to trigger advanced imaging, the tumor has often grown quite large, which complicates both surgery and prognosis.

How Sacral Chordoma Is Diagnosed

Cross-sectional imaging is the starting point once suspicion arises. On CT, sacral chordoma typically appears as a large destructive lesion eating into the bone, often with characteristic chunky calcifications inside the tumor and a bulky soft-tissue component extending forward into the pelvis. MRI adds crucial detail: the mass usually shows mixed signals on different sequences, lights up brightly on fluid-sensitive sequences, restricts diffusion, and enhances unevenly with contrast, often with non-enhancing areas in the center suggesting necrosis or mucin pools.⁷

PET/CT with a standard glucose tracer can help distinguish chordoma from other sacral cancers, because chordomas tend to have relatively low metabolic activity compared to more aggressive sacral tumors. A study comparing chordomas to other sacral malignancies found that a low tumor-to-liver uptake ratio was the most useful differentiating feature, with the ratio being significantly lower in chordomas.⁸

Imaging alone cannot confirm the diagnosis. Biopsy is essential, and it reveals the hallmark features: large cells with enormous, bubble-filled cytoplasm (called physaliferous cells) sitting in a mucus-rich background.⁹ Immunostaining for Brachyury protein is the confirmatory test. In one analysis of biopsy specimens, Brachyury was expressed in 96% of cases tested, making it an extremely reliable marker.¹⁰ The biopsy tract itself matters: it must be placed so that the surgeon can remove it along with the tumor during the definitive operation, since seeding the biopsy tract with tumor cells is a real risk.

Surgery Is the Primary Treatment

Wide surgical removal, aiming to take out the entire tumor surrounded by a cuff of healthy tissue (called en bloc resection with negative margins), is the backbone of treatment. Getting clean margins has been shown to be a strong predictor of long-term disease control.¹¹ In one series of 29 patients who had combined anterior and posterior surgery, about 62% achieved wide margins, and the overall survival rate was roughly 84% at both five and ten years.¹² A multicenter study found that patients who underwent radical surgery had a three-year overall survival rate of 96%, compared to about 89% for those treated with radiation alone, a statistically significant difference.¹³

The anatomy of recurrence is worth understanding because it guides surgical planning. Recurrences tend to appear at the lateral edges of the remaining sacrum and sometimes in the cut ends of nearby muscles like the gluteus maximus or piriformis.¹⁴ One analysis of 18 patients found that recurrences showed up along the posterolateral margins despite what appeared to be wide resections, whereas ventral and proximal margins with narrower clearance did not recur as frequently.¹⁵ This asymmetry suggests that surgeons need to be especially aggressive along the sides and back of the sacrum, even if that means sacrificing more muscle tissue.

The Nerve Trade-Off

The sacrum houses nerve roots that control bladder, bowel, sexual function, and leg movement. Removing a tumor embedded in or pressing on these roots forces a difficult trade-off between oncologic completeness and quality of life. The specific nerves sacrificed matter enormously.

A systematic review of outcomes after sacrectomy found that preserving both S3 nerve roots kept normal bladder function intact in about 83% of patients and bowel function in 94%.¹⁶ But if both S2 roots were cut, no patients maintained normal bladder or bowel function. Walking ability also depended heavily on the S1 root: when both S2 roots were spared, normal ambulation was preserved in about 56% of patients, and when both S3 roots were spared, that rose to 94%. In a separate landmark study, researchers confirmed that saving at least one S3 root on either side was the critical threshold for retaining bladder and bowel control in most patients.¹⁷ In that data, when both S3 through S5 roots were sacrificed on both sides, all patients had abnormal function; when the sacrifice was limited to S4 and S5 with bilateral S3 preservation, bowel function was retained in all and bladder function in about 69%.

The good news, such as it is, comes from long-term follow-up. A study tracking bladder, bowel, and walking function over five years found that the decline from pre-operative function to one year after surgery did not continue to worsen afterward. Function at one year was essentially stable at five years, meaning that patients can expect whatever recovery they achieve in the first year to hold.¹⁸ Patients who had low sacrectomies (removing only the lower sacral segments) did significantly better at five years than those with mid or high sacrectomies.

Wound Complications After Sacral Surgery

Sacral tumor surgery carries a notably high rate of wound problems because of the anatomical location, long operating times, large dead spaces, and proximity to the rectum. A study of 387 sacral tumor operations found that roughly 29% of wounds broke down from infection or dehiscence. Surgical site infections occurred in about 13%, and wound dehiscence in about 16%.¹⁹ The infections were overwhelmingly caused by gut bacteria, with E. coli appearing in the majority of positive cultures, reflecting contamination from the nearby rectum. Previous radiation therapy, accidental rectal tears during surgery, longer operative times, and cerebrospinal fluid leaks all raised the infection risk.

A separate series focused on en bloc sacrectomies found an even higher infection rate of 57%, almost all of them polymicrobial.²⁰ These numbers underscore why meticulous wound planning, including soft-tissue reconstruction, is considered part of the operation rather than an afterthought.

Closing the Wound and Rebuilding the Pelvic Floor

After removing a large chunk of the sacrum, surgeons face a gaping defect that needs to be filled and covered. The specific reconstruction depends on how much bone was removed and whether the patient has had prior radiation. For partial sacrectomy patients with intact blood supply to the buttocks and no prior radiation, bilateral gluteal advancement flaps are typically the first choice.²¹ These use the patient’s own gluteal muscle and skin, rotated inward to fill the defect. For near-total sacrectomies or patients whose tissue has been damaged by radiation, more complex options come into play, including flaps based on the rectus abdominis muscle from the abdomen or even free tissue transfer from distant body sites.

Rebuilding the pelvic floor is just as important as covering the skin wound. Without a structural barrier, abdominal organs can herniate backward into the surgical defect. Some surgeons use synthetic mesh or acellular dermal matrices combined with muscle flaps from the inner thigh to create a new pelvic floor.²² These reconstructive details are not cosmetic concerns; they directly affect complication rates, recovery time, and whether the patient can sit and move comfortably afterward.

The Role of Radiation

Chordoma has historically been considered relatively resistant to conventional photon radiation, but higher-dose techniques, and especially proton beam therapy, have changed the picture. A study comparing outcomes in sacral chordoma patients who received post-operative radiation to those who did not found a dramatically lower local recurrence rate in the radiation group: 18% versus 57%. Among patients who received proton-beam radiation specifically, no local recurrences were observed.²³ The advantage of protons lies in their ability to deliver a high dose to the tumor bed while depositing less energy in the surrounding bowel, bladder, and other pelvic structures. Access remains a barrier, though, because proton therapy facilities are expensive and not available everywhere.

Radiation before surgery (neoadjuvant radiation) is also used in some centers with the idea of shrinking the tumor or sterilizing its margins, but prior radiation increases the risk of wound complications, as discussed above. The decision about timing is individualized, weighing tumor size, proximity to critical nerves, and the surgical team’s approach.

Targeted Therapy and Immunotherapy

For patients whose tumors recur, metastasize, or cannot be fully resected, systemic therapy enters the conversation. Chordoma lacks the high mutation rates that make some cancers vulnerable to checkpoint immunotherapy, and traditional chemotherapy has little effect. Targeted drugs that block specific growth-signaling pathways have been the main area of exploration.

A review of published targeted therapy trials found that the most commonly used drugs targeted receptors in the PDGFR, VEGFR, and mTOR pathways. Progression-free survival ranged widely across studies, from a few months to several years, with the best results seen when targeted drugs were combined with radiation rather than used alone.²⁴ A meta-analysis of tyrosine kinase inhibitors (TKIs) in advanced or metastatic chordoma reported a median progression-free survival of about 8.4 months and a median overall survival of roughly 37 months. Imatinib, the best-studied agent, showed a somewhat longer median overall survival of about 39 months compared to 25 months for other TKIs, but toxicity was substantial: 95% of patients experienced side effects, and serious adverse events occurred in over half.²⁵ These are not cures. Objective tumor shrinkage by standard criteria is rare. The drugs mostly stabilize disease for a time.

Because Brachyury is so central to chordoma biology and is expressed in virtually no normal adult tissues, it has been an attractive target for vaccine-based immunotherapy. A phase 2 trial combined a Brachyury-targeting vaccine with radiation therapy. The trial did not meet its predefined response goal, though two partial responses were observed and the median progression-free survival exceeded two years for the full cohort.²⁶ The approach confirmed safety but fell short of efficacy. Research continues, including efforts to combine immune strategies with other modalities.

Recurrence and Metastasis Patterns

Even after seemingly complete resection, sacral chordoma comes back frequently. Local recurrence rates across large series generally range from about 20% to over 40%, depending on the margin status and follow-up length. Metastatic disease, once thought uncommon, is now recognized to occur in roughly 18% of patients, with the lung as the most frequent destination.²⁷ Patients who had already experienced a local recurrence were about 2.5 times more likely to develop metastases than those who had not.

A larger cohort study of 221 sacral chordoma cases put the lung metastasis rate at about 20% overall, but it was much higher in recurrent cases (about 33%) versus newly diagnosed ones (about 13%).²⁸ Patients who developed lung metastases had significantly shorter overall survival (a median of about 7.5 years versus 12 years for those without lung spread) and much shorter recurrence-free survival. Larger tumor size and prior recurrence were the strongest associated factors. These findings reinforce the importance of long-term surveillance with periodic chest imaging even years after the initial treatment.

Rehabilitation and Living After Sacrectomy

Recovery from sacral chordoma surgery is not simply about cancer control; it is about learning to live with a fundamentally altered pelvis. In a series of 50 consecutive patients followed long term, bowel and bladder dysfunction increased from 46% before surgery to 68% afterward, closely matching what would be predicted based on which nerve roots were sacrificed.²⁹ Motor deficits, however, were less common than expected. Although 16% of patients were predicted to have weakness based on S1 nerve root sacrifice, only 6% had persistent motor problems at last follow-up, thanks in part to intensive physical therapy.

Rehabilitation after sacrectomy is complex and individualized. A case report illustrating the typical needs of a post-sacrectomy patient described multimodal pain management including nerve-pain medications, neurogenic bladder management with intermittent catheterization, routine colostomy care for bowel management, and treatment of post-operative urinary tract infection. With consistent physical and occupational therapy, the patient was able to walk independently with a rolling walker and was discharged home.³⁰ Pelvic floor therapy has emerged as an important part of post-surgical care for patients dealing with the lower motor neuron symptoms of bladder retention and constipation that result from nerve root loss.³¹

The psychological burden deserves mention too. Many patients are relatively young or middle-aged adults who suddenly face incontinence, sexual dysfunction, chronic pain, and mobility limitations. Research on quality of life in chordoma survivors remains thin, but what exists suggests that identifying the specific level of neurological injury and matching it to the right supportive therapies, rather than offering generic advice, produces meaningfully better outcomes. Connecting patients to both a physiatrist (rehabilitation medicine specialist) and a pelvic floor therapist early in the recovery process is increasingly seen as standard of care rather than optional.