Chapter 1 Abstract

Abstract Pituitary neuroendocrine tumors (PitNETs) are common intracranial neoplasms arising from anterior pituitary hormone-secreting cells, accounting for about 17% of brain tumors. Functional PitNETs cause systemic endocrine disorders through hormone hypersecretion, while non-functional types often remain silent until mass effects occur. Beyond endocrine dysregulation, PitNETs reshape their immune microenvironment and may influence systemic immunity through tumor-derived cytokines and hormones. Peripheral blood mononuclear cells (PBMCs), as mobile immune sentinels, offer a window into this tumor–host interaction, yet their role in PitNETs remains unclear. To address this, we combined bulk and single-cell RNA sequencing with immune profiling to map the systemic immune impact of PitNETs and identify PBMCs as dynamic biomarkers of disease progression and treatment response.

This tutorial provides a step-by-step guide to analyze multi-omics datasets and investigate the systemic immune effects of pituitary neuroendocrine tumors (PitNETs). We integrate bulk RNA-seq (883 tumors, 108 patient PBMCs, 175 healthy controls), single-cell RNA-seq (69 samples from tumors, normal pituitaries, and PBMCs), and clinical data to demonstrate key analysis strategies. This tutorial includes how to process data, characterize immune composition, and identify tumor-immune interactions.

Workflow highlights:

  • 1 Differential analysis of PBMCs from PitNET patients and healthy controls.

  • 2 Immune profiling of PitNET vs. normal PBMCs using scRNA-seq and bulk RNA-seq deconvolution.

  • 3 Postoperative monitoring of immune recovery in PitNET patients.

  • 4 Single-cell analysis of PitNET tissues, including cell type annotation and CNV assessment.

  • 5 Characterization of lineage-specific hormone and cytokine secretion profiles and tumor–blood ligand–receptor crosstalk.