ATP1B1::PRKACA fusion-defined intraductal oncocytic papillary neoplasm of the pancreas: a case report

Introduction

Background

Cystic and intraductal neoplasms of the pancreas constitute less than 5% of all pancreatic tumors (1). Intraductal oncocytic papillary neoplasm (IOPN) of the pancreas is a rare intraductal cystic neoplasm, and although large-scale incidence data are limited, a 2016 imaging series reported that IOPN constituted 4.5% of intraductal neoplasms (2). IOPN was first described by Adsay et al. in 1996 as a distinct intraductal neoplasm defined by complex arborizing papillary structures with delicate fibrovascular cores lined by stratified oncocytic cells in a myxoid background (3). The 2010 World Health Organization (WHO) classification subsequently grouped IOPN under intraductal papillary mucinous neoplasm (IPMN) as the oncocytic subtype (4). Molecular profiling later showed that IOPNs lack the KRAS, GNAS, and RNF43 alterations characteristic of IPMN and instead harbor recurrent ATP1B1::PRKACB, DNAJB1::PRKACA, and ATP1B1::PRKACA fusions, supporting their recognition as a distinct entity in the 2019 WHO classification (5-11). These fusions result in constitutive protein kinase A activation and are thought to drive mitochondrial accumulation and the characteristic oncocytic phenotype (10). Clinically, IOPNs often present as large cystic-solid masses, typically approximately 4.5 to 6 cm, and may mimic pancreatic ductal adenocarcinoma or other intraductal neoplasms on imaging (2,4,12). Reported adverse features include large size, main pancreatic duct involvement, and associated invasive carcinoma, although non-invasive IOPNs generally have favorable outcomes after complete resection (12).

Rationale and knowledge gap

The IOPN literature has grown steadily since the molecular characterization of the entity, with multiple case reports and small series describing the morphologic, molecular, and clinical spectrum of the disease (13-18). ATP1B1::PRKACA fusion-defined IOPN and mixed IOPN/pancreaticobiliary-type morphology have each been described, and we therefore consider these features of the present case confirmatory of established literature rather than novel (8-10,18). The principal gap addressed here concerns preoperative diagnosis: current commercial pancreatic cyst fluid molecular panels target KRAS, GNAS, and loss of heterozygosity (LOH) but do not include RNA-based detection of the PRKACA/PRKACB fusions that define IOPN, and can therefore misclassify an IOPN as low-risk on cyst fluid testing alone. A secondary, less well-characterized observation is the co-occurrence of a likely pathogenic SMAD4 variant in a non-invasive PRKACA fusion-defined IOPN, an alteration nearly absent in published IOPN cohorts (6,7). No biological or clinical implications can be drawn from a single case.

Objective

We report an ATP1B1::PRKACA fusion-defined IOPN with morphologically heterogeneous (oncocytic and pancreaticobiliary-type) features and a coexisting likely pathogenic SMAD4 variant, in a high-risk surgical patient in whom the standard KRAS/GNAS/LOH cyst fluid panel was negative. We frame this report along four tiers: (I) confirmatory features that align with the established IOPN literature (PRKACA fusion and mixed morphology); (II) the primary teaching point, namely the limitation of a standard KRAS/GNAS/LOH cyst fluid panel that does not include PRKACA/PRKACB fusion detection; (III) a secondary observation of a coexisting SMAD4 variant in a non-invasive IOPN; and (IV) a hypothesis-generating implication: prospective evaluation of fusion-inclusive cyst fluid testing in selected cases. We present this article in accordance with the CARE reporting checklist (available at https://apc.amegroups.com/article/view/10.21037/apc-26-0021/rc).

Case presentation

Clinical history and decision-making timeline

A 70-year-old woman with autoimmune cholangitis, compensated cirrhosis, cardiac sarcoidosis, and systolic heart failure (ejection fraction of 40–45%) was referred for management of a pancreatic cystic lesion. Initially diagnosed as a pseudocyst in 2014, the lesion had been under surveillance at our center since 2017 with serial imaging. Her cardiac history was notable for surgical repair of a left ventricular (LV) apical aneurysm in 2019 with implantable cardioverter-defibrillator placement. She required long-term anticoagulation for an LV apical thrombus identified in 2020.

Given her extensive comorbidities, the multidisciplinary tumor board in September 2024 recommended continued close surveillance of the pancreatic lesion. However, repeat endoscopic ultrasound-guided fine-needle aspiration (EUSFNA) on January 22, 2025, was complicated by poor oral intake and abdominal cramping, requiring emergency department evaluation.

Endoscopic drainage was not pursued because drainage of pancreatic fluid collections is appropriate only after sufficient exclusion of alternative diagnoses such as cystic neoplasms. In this case, chronicity since 2014, symptomatic presentation, rapid interval growth, large pancreatic-head location, solid/nodular components, and atypical cytology raised concern for neoplasia and made pseudocyst-directed drainage inappropriate.

Subsequent imaging with computed tomography (CT) of the abdomen and pelvis on February 11, 2025, revealed that the pancreatic head mass had increased in size to 11 cm × 7.7 cm from 8.4 cm × 6.1 cm on a CT from 2 weeks prior (Figure 1). Considering this progression, her case was reviewed again at the multidisciplinary Pancreas tumor board on February 20, 2025, and the decision was made to proceed with surgical resection despite her comorbidities (Table 1).

Figure 1 Clinical timeline. Chronologic summary of the case from initial cyst identification [2014] through surveillance, rapid interval growth in early 2025, multidisciplinary review, pancreaticoduodenectomy with portal vein resection (April 2025), discharge home (April 30, 2025), and most recent follow-up (May 1, 2026; disease-free at approximately 12 months postoperatively). Embedded preoperative CT panels demonstrate the cyst at 8.4 cm × 6.1 cm on January 31, 2025 and at 11 cm × 7.7 cm on February 11, 2025, illustrating the rapid two-week interval growth that prompted surgical resection. CT, computed tomography; EUS-FNA, endoscopic ultrasound-guided fine-needle aspiration.

Imaging and early investigations

Preoperative laboratory studies were largely unremarkable with mild leukocytosis (11.3 ×10³/µL; reference 4.0–11.0 × 10³/µL) and anemia (hemoglobin 10.8 g/dL; reference 12.0–16.0 g/dL), while the comprehensive metabolic panel was within normal limits. The contrast-enhanced CT revealed a complex 11.0 cm × 7.7 cm multiloculated cystic mass in the pancreatic head with enhancing nodular components. The mass extended inferiorly with additional cystic components in the right retroperitoneum and pelvis, measuring up to 7 cm, resulting in right hydronephrosis likely due to mass effect on the ureter.

EUS-FNA confirmed a large heterogeneous cystic lesion with fluid cytology revealing mostly degenerative debris with only rare, atypical epithelial cells showing nuclear enlargement and prominent nucleoli. Cyst fluid analysis showed no high-risk features: carcinoembryonic antigen (CEA) was 53 ng/mL, amylase 28,924 U/L, and glucose <4.3 mg/dL. DNA was present in moderate quantity but of poor quality. Standard molecular panel of GNAS, KRAS, and LOH was negative, with the cyst molecular profile interpreted as benign in risk stratification. Despite these reassuring findings, the rapid growth and imaging characteristics warranted surgical exploration.

Perioperative course

The patient was admitted on the day of surgery for a planned pancreaticoduodenectomy. Intraoperatively, dense adhesions around the pancreas and duodenum were lysed to achieve adequate mobilization. A replaced right hepatic artery was identified and preserved. The tumor was found to be adherent to the portal vein, necessitating a partial portal vein resection with primary repair. Standard pancreaticoduodenectomy was performed with negative frozen section margins for all resection margins. The reconstruction included pancreaticojejunostomy, hepaticojejunostomy, and gastrojejunostomy. Two Jackson-Pratt drains were placed for postoperative drainage.

Intraoperative hemodynamics were notable for vasoplegia requiring multiple vasopressors for support. The patient received infusions of epinephrine (up to 8 µg/min) and norepinephrine (8 µg/min) in the context of her baseline cardiomyopathy. Estimated blood loss was approximately 500 mL, and one unit of packed red blood cells was transfused. She was successfully extubated at the end of the case and transferred to the surgical intensive care unit. Postoperative recovery was uneventful. Vasopressors were weaned by postoperative day 2, and the patient was discharged home on April 30, 2025. At most recent chart review on May 1, 2026 (approximately 12 months postoperatively), the patient remained disease-free with no clinical evidence of recurrence.

Gross pathology

Gross examination of the Whipple specimen (head of pancreas, duodenum, and bile duct) revealed a 10.8 cm multiloculated cystic mass in the posterior pancreas with intervening septa and papillary projections involving the main pancreatic duct. The ampulla, duodenum, and bile duct appeared grossly uninvolved. Histologically, approximately half of the lesion showed classic IOPN morphology, with complex papillary and cribriform architecture composed of high-grade oncocytic cells with abundant eosinophilic granular cytoplasm, prominent nucleoli, interspersed goblet cells, and surrounding myxoid stroma (Figure 2). The remaining approximately half showed flatter, less arborizing pancreaticobiliary-type architecture with cuboidal-to-columnar epithelium, high-grade nuclear atypia, intraepithelial neutrophils, and scattered cells with eosinophilic oncocytic cytoplasm. These areas resembled pancreaticobiliary-type IPMN morphologically, but in the setting of a fusion-defined IOPN are best interpreted as “IPMN-like” or “pancreaticobiliary-type” morphologic heterogeneity within the IOPN rather than definitive evidence of a separate collision neoplasm (Figure 3). Immunohistochemical stains showed CD117 positivity in the classic oncocytic foci and absent staining in the pancreaticobiliary-like foci; hepatocyte paraffin-1 (HepPar1) was positive in both components. EMA, CDX-2, and CK7 supported epithelial differentiation, and chromogranin and synaptophysin were negative, ruling out a neuroendocrine neoplasm (Figure 4). Next-generation sequencing was performed on these different foci after appropriate patient consent was obtained. No invasive carcinoma was present in the entirely submitted 10.8 cm cystic mass. All 23 lymph nodes retrieved were negative for metastatic disease, and all surgical resection margins were negative for dysplasia and carcinoma.

Figure 2 IOPN, H&E stain at progressive magnifications [4× (A), 10× (B), 20× (C), 40× (D)]. Complex arborizing papillary architecture lined by multilayered oncocytic epithelium (A,B). Higher magnifications demonstrate characteristic oncocytic cells with abundant eosinophilic granular cytoplasm, uniform round to oval nuclei, and prominent nucleoli (C,D). H&E, hematoxylin and eosin; IOPN, intraductal oncocytic papillary neoplasm.

Figure 3 H &E-stained area within IOPN showing histologic features resembling pancreatobiliary-type IPMN. At 20x (A, left), complex papillary proliferation with abundant stromal inflammation. At 40x (B, right), papillae are lined by cuboidal to columnar epithelium with less prominent oncocytic features, nuclear stratification, and associated inflammatory infiltrate in the stroma. IOPN, intraductal oncocytic papillary neoplasm; IPMN, intraductal papillary mucinous neoplasm.

Figure 4 Immunohistochemical findings supporting IOPN. CD117 immunohistochemistry demonstrates diffuse cytoplasmic positivity in oncocytic epithelium at 10x (A, left). HepPar1 immunohistochemistry highlights the neoplastic oncocytic cells at 20x (B, right). These findings support the diagnosis of IOPN. IOPN, intraductal oncocytic papillary neoplasm.

Molecular profiling

Molecular analysis revealed an ATP1B1::PRKACA fusion characteristic of IOPN. Importantly, no KRAS or GNAS mutations were detected, supporting distinction from conventional IPMN. A SMAD4 variant was also detected: an in-frame deletion in exon 9 (p.C363_L367del), classified as likely pathogenic by tumor DNA sequencing, identified in the foci with pancreaticobiliary-like morphology. The clinical and biological significance of this SMAD4 finding in a PRKACA fusion-driven, non-invasive IOPN is unknown and discussed below.

All procedures performed in this study were in accordance with the ethical standards of the institutional and/or national research committee(s) and with the Declaration of Helsinki and its subsequent amendments. Written informed consent was obtained from the patient for the publication of this case report and accompanying images. A copy of the written consent is available for review by the editorial office of this journal.

Discussion

Key findings

IOPN is a WHO-recognized distinct intraductal cystic neoplasm of the pancreas characterized by recurrent PRKACA/PRKACB fusions and generally favorable disease-specific survival after complete resection (11,12). Reported tumors characteristically involve the main pancreatic duct and have an average size of approximately 6 cm (4). Our patient presented with a 10.8 cm mass with fibroinflammatory response within the pancreas and dense adhesions to the portal vein, requiring portal vein resection at the time of surgery.

IOPN remains rare, but a growing case-report and case-series literature has accumulated since its molecular characterization (13-17). Recent molecular-pathologic studies have expanded the recognized morphologic spectrum of IOPN. Tanaka et al. analyzed 22 pancreatobiliary IOPNs, including cases with atypical or IPMN-like morphology, and found PRKACA/PRKACB fusions across this expanded spectrum (18). More directly relevant to the present case, Vyas et al. described 6 pancreaticobiliary neoplasms with PRKACA fusions, three of which were diagnosed as “IPMN with mixed oncocytic and pancreaticobiliary or gastric features”, supporting that mixed “IPMN-PB”-like morphology is a recognized pattern in fusion-positive oncocytic neoplasms (9). These data support interpreting “IPMN-like” areas in a fusion-defined IOPN as part of the morphologic spectrum of IOPN, while recognizing that morphology alone cannot always distinguish true mixed/collision neoplasms from morphologic heterogeneity within one neoplasm. IOPN also remains diagnostically challenging because it overlaps radiologically and morphologically with IPMN of pancreaticobiliary type, intraductal tubulopapillary neoplasm, neuroendocrine neoplasm, and intraductal acinar cell carcinoma (2,12,19,20). The differential diagnosis relies on combined morphology, immunohistochemistry, and molecular testing. IOPNs harbor PRKACA/PRKACB fusions and typically lack the KRAS/GNAS mutations characteristic of IPMN, as seen in Table 2 (7,8).

SMAD4/DPC4 expression is typically preserved in intraductal components of IOPN (6,7). Genetically, IOPN is distinct from IPMN and often lacks KRAS/GNAS mutations, with recurrent PRKACA/PRKACB fusions (6-8). In our case, a likely pathogenic SMAD4 variant was detected in the area with pancreaticobiliary-like morphology. We do not interpret this finding as evidence of high-grade dysplasia transformation, because IOPNs are high-grade dysplastic lesions by definition and the conventional SMAD4 progression model was established primarily in KRAS-driven pancreatic neoplasia.

No biological or clinical implications can be drawn from the likely pathogenic SMAD4 finding in this single case. Additional cases with paired regional sequencing, SMAD4 immunohistochemistry, and longer follow-up will be needed to determine whether SMAD4 alterations occur reproducibly in IOPN and whether they have any prognostic significance.

Strengths and limitations

This case highlights the importance of molecular analysis for accurate characterization of intraductal pancreatic neoplasms with overlapping morphologic features. It also illustrates an important limitation of standard pancreatic cyst fluid molecular testing: a panel focused on KRAS, GNAS, and LOH will not detect the PRKACA/PRKACB fusions that define IOPN. However, the ATP1B1::PRKACA fusion in this patient was identified on the resection specimen, not prospectively on cyst fluid. This single case therefore does not establish the analytical sensitivity, specificity, cost-effectiveness, or clinical utility of universal cyst-fluid fusion testing. Additional limitations include the degraded quality of cyst-fluid DNA, possible sampling bias from cystic rather than mural components, and a follow-up duration of approximately 12 months, which remains short relative to the natural history of IOPN, in which recurrences have been reported up to 10 years postoperatively (12).

Comparison with similar research

The morphology matches previous IOPN descriptions while the ATP1B1::PRKACA fusion aligns with the molecular profile established (3,4,11,12). Mixed IOPN and IPMN histology has been reported rarely (9,18).

Like most reported cases, our patient presented with a large cystic-solid mass mimicking malignancy (12). Non-invasive IOPNs show excellent outcomes supporting aggressive resection when feasible (12).

Explanations of findings

ATP1B1::PRKACA represents one of three recurrent IOPN fusions, though ATP1B1::PRKACB predominates (8). CD117 immunohistochemical staining showed strong positivity in areas with classic oncocytic features and negative staining in pancreaticobiliary-type morphology. CD117 demonstrates remarkable specificity for IOPNs among the pancreatic intraductal neoplasms with 94.1% of IOPNs showing positive staining compared to minimal expression in IPMNs (21) (Figure 4).

HepPar1 expression is another helpful diagnostic marker for IOPNs, with granular cytoplasmic positivity in the oncocytic cells. The combination of CD117 and HepPar1 positivity in the setting of the characteristic oncocytic morphology and papillary architecture provides strong support for IOPN. The specificity of HepPar1 for IOPNs is limited because it is expressed in only 61% of cases; its utility lies in supporting the diagnosis within a comprehensive panel including molecular characterization (18). The explosive growth of 2.6 cm in 2 weeks deviates from typical IOPN behavior. Despite this aggressive presentation, the biology remained favorable with no invasion. The genetically distinct nature of IOPNs from IPMNs, with characteristic PRKACA/PRKACB fusions and typical absence of KRAS/GNAS mutations, helps distinguish these entities (7,8,10).

Implications and actions needed

Current KRAS/GNAS-based pancreatic cyst fluid molecular panels can miss IOPN when fusion testing is not included. Combined DNA/RNA-based platforms capable of detecting PRKACA/PRKACB fusions in cyst fluid have been developed and validated for selected pancreatic cyst classification (23,24). Rather than supporting routine universal fusion testing for all pancreatic cysts, this case supports awareness of this diagnostic gap and consideration of fusion-inclusive testing when standard molecular results are discordant with clinical, cytologic, or imaging features suspicious for an intraductal neoplasm. Given the rarity of IOPN, the cost-effectiveness and optimal clinical indications for RNA-based fusion testing require further study.

Complete resection remains the standard management for resectable IOPN when clinical and radiographic features support neoplasia, but treatment decisions should be individualized through multidisciplinary review and should account for operative risk, imaging features, cytology, molecular findings, and patient comorbidities. Excellent disease-specific survival has been reported, with one series showing no disease-specific deaths at median 7 years follow-up, though 46% experienced recurrence at 10 years (12). We do not draw therapeutic or prognostic conclusions from the SMAD4 finding in this single non-invasive case. Future therapeutic considerations may include molecular-targeted approaches exploiting PKA pathway dependencies identified through PRKACA/PRKACB fusion characterization, which may be relevant for rare unresectable cases or those with atypical molecular profiles (10). Pathologists should consider IOPN when encountering oncocytic intraductal lesions, particularly if KRAS/GNAS are wild type (7,8).

Conclusions

We describe successful management of a large, non-invasive IOPN of the pancreas that was initially interpreted clinically as a pancreatic pseudocyst in a high-risk patient. The ATP1B1::PRKACA fusion confirmed the diagnosis after resection. This case illustrates the diagnostic value of comprehensive tissue molecular profiling when morphology and standard cyst fluid testing are inconclusive.

IOPNs remain underrecognized as distinct intraductal neoplasms. Standard KRAS/GNAS-based cyst fluid panels may miss IOPN when PRKACA/PRKACB fusion testing is not included. This single case does not support universal fusion testing or resection regardless of comorbidity; rather, it supports multidisciplinary, case-specific evaluation and prospective study of fusion-inclusive cyst fluid testing in selected cysts with discordant clinical, imaging, cytologic, or molecular features.

Key questions remain: do different fusion partners affect prognosis? What drives the rare invasive cases? Can PKA-pathway-directed therapies treat unresectable disease? What is the significance of SMAD4 variants in fusion-defined IOPN?

Acknowledgments

None.

Footnote

Reporting Checklist: The authors have completed the CARE reporting checklist. Available at https://apc.amegroups.com/article/view/10.21037/apc-26-0021/rc

Peer Review File: Available at https://apc.amegroups.com/article/view/10.21037/apc-26-0021/prf

Funding: None.

Conflicts of Interest: All authors have completed the ICMJE uniform disclosure form (available at https://apc.amegroups.com/article/view/10.21037/apc-26-0021/coif). The authors have no conflicts of interest to declare.

Ethical Statement: The authors are accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved. All procedures performed in this study were in accordance with the ethical standards of the institutional and/or national research committee(s) and with the Declaration of Helsinki and its subsequent amendments. Written informed consent was obtained from the patient for the publication of this case report and accompanying images. A copy of the written consent is available for review by the editorial office of this journal.

Open Access Statement: This is an Open Access article distributed in accordance with the Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License (CC BY-NC-ND 4.0), which permits the non-commercial replication and distribution of the article with the strict proviso that no changes or edits are made and the original work is properly cited (including links to both the formal publication through the relevant DOI and the license). See: https://creativecommons.org/licenses/by-nc-nd/4.0/.

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