Molecular Characterization and Clinical Outcomes of Pancreatic Neuroendocrine Neoplasms Harboring PAK4-NAMPT Alterations

Ibrahim Azar; Husain Yar Khan; Sahar F Bannoura; Nishant Gandhi; Md Hafiz Uddin; Misako Nagasaka; Jun Gong; Bassel Nazha; Khalil Choucair; Nikhil Vojjala; Moh'd M Khushman; Heloisa P Soares; Wafik S El-Deiry; Philip Agop Philip; Bassel El-Rayes; Herbert Chen; Emil Lou; Irfana Muqbil; Alex Patrick Farrell; Jeffrey Swensen; Matthew James Oberley; Chadi Nabhan; Sanjay Goel; Anthony F Shields; Ramzi M Mohammad; Boris C Pasche; Asfar S Azmi

doi:10.1200/OA-24-00032

Molecular Characterization and Clinical Outcomes of Pancreatic Neuroendocrine Neoplasms Harboring PAK4-NAMPT Alterations

JCO Oncol Adv. 2025 May 2;2(1):e2400032. doi: 10.1200/OA-24-00032. eCollection 2025.

Authors

Ibrahim Azar^{1

2}, Husain Yar Khan^{2

3}, Sahar F Bannoura³, Nishant Gandhi⁴, Md Hafiz Uddin³, Misako Nagasaka⁵, Jun Gong⁴, Bassel Nazha⁶, Khalil Choucair³, Nikhil Vojjala¹, Moh'd M Khushman⁷, Heloisa P Soares⁸, Wafik S El-Deiry⁹, Philip Agop Philip¹⁰, Bassel El-Rayes¹¹, Herbert Chen¹¹, Emil Lou¹², Irfana Muqbil¹³, Alex Patrick Farrell⁴, Jeffrey Swensen⁴, Matthew James Oberley⁴, Chadi Nabhan⁴, Sanjay Goel⁴, Anthony F Shields³, Ramzi M Mohammad³, Boris C Pasche³, Asfar S Azmi³

Affiliations

¹ IHA Hematology Oncology, Pontiac, MI.
² Wayne State University, Detroit, MI.
³ Barbara Ann Karmanos Cancer Institute, Detroit, MI.
⁴ Caris Life Sciences, Phoenix, AZ.
⁵ University of California Irvine, Orange, CA.
⁶ Winship Cancer Institute of Emory University, Atlanta, GA.
⁷ Washington University Medical Campus, Saint Louis, MO.
⁸ University of Utah, Salt Lake City, UT.
⁹ Brown University, Providence, RI.
¹⁰ Henry Ford Health, Detroit, MI.
¹¹ University of Alabama School of Medicine, Birmingham, AL.
¹² Masonic Cancer Center/University of Minnesota School of Medicine, Minneapolis, MN.
¹³ Lawrence Technological University, Southfield, MI.

Abstract

Purpose: The mammalian target of rapamycin (mTOR) inhibitor everolimus is US Food and Drug Administration-approved for advanced pancreatic neuroendocrine neoplasms (pNENs), yet resistance is common, necessitating the identification of resistance mechanisms for effective treatment strategies. Previous studies suggest that targeting the aberrant expression of mTOR regulators p21-activated kinase 4 (PAK4) and nicotinamide phosphoribosyl transferase (NAMPT) sensitizes pNENs to everolimus. In this study, we queried a large real-world data set of pNENs, characterizing the molecular and immune landscapes, as well as the clinical outcomes associated with aberrant PAK4 and NAMPT expression.

Methods: Two-hundred and ninety-four pNEN cases were analyzed using next-generation sequencing and whole-exome/whole-transcriptome sequencing. We stratified patients into clusters on the basis of median cutoff.

Results: High expression of genes activated in response to mTOR activation was found in NAMPT-high and PAK4-high groups. Enrichment of PI3K/AKT/mTOR and glycolysis pathways was observed in these tumors. Higher mutation rates in multiple endocrine neoplasia type 1, alpha thalassemia/mental retardation syndrome X-linked, TSC2, SETD2, and CCNE1 were observed in high NAMPT and PAK4 clusters. Immune analysis revealed enrichment in inflammatory response pathways, IL2/STAT5 signaling, and immune checkpoint genes. Increased neutrophils, natural killer cells, and macrophages were found in PAK4-high/NAMPT-high tumors. Analysis of real-world patient data revealed that high PAK4 (P = .0428) or NAMPT (P = .0002) expression individually correlated with lower overall survival in all neuroendocrine neoplasms (NEN) cohorts, while the combined high expression of both was associated with the worst outcomes (P = .0002). Similar trends were observed in pancreatic NEN cohorts.

Conclusion: Our study demonstrates that PAK4-high/NAMPT-high pNENs are associated with distinct molecular and immune profiles. Further investigation is warranted to determine if dual PAK4 and NAMPT blockade enhances the efficacy of immunotherapeutics.