Applications of spatially resolved omics in the field of endocrine tumors

Abstract

Endocrine tumors derive from endocrine cells with high heterogeneity in function, structure and embryology, and are characteristic of a marked diversity and tissue heterogeneity. There are still challenges in analyzing the molecular alternations within the heterogeneous microenvironment for endocrine tumors. Recently, several proteomic, lipidomic and metabolomic platforms have been applied to the analysis of endocrine tumors to explore the cellular and molecular mechanisms of tumor genesis, progression and metastasis. In this review, we provide a comprehensive overview of spatially resolved proteomics, lipidomics and metabolomics guided by mass spectrometry imaging and spatially resolved microproteomics directed by microextraction and tandem mass spectrometry. In this regard, we will discuss different mass spectrometry imaging techniques, including secondary ion mass spectrometry, matrix-assisted laser desorption/ionization and desorption electrospray ionization. Additionally, we will highlight microextraction approaches such as laser capture microdissection and liquid microjunction extraction. With these methods, proteins can be extracted precisely from specific regions of the endocrine tumor. Finally, we compare applications of proteomic, lipidomic and metabolomic platforms in the field of endocrine tumors and outline their potentials in elucidating cellular and molecular processes involved in endocrine tumors.

Keywords: endocrine tumors; liquid chromatography-mass spectrometry; mass spectrometry imaging; microextraction; multi-omics; spatially resolved microproteomics.

Figure 1

The ionization principles for SIMS-MSI, MALDI-MSI and DESI-MSI. A mass spectrometer is at least composed of ion source, mass analyzer and detector. Different ion sources determine different ionization process. (A) Ionization process of SIMS-MSI. A primary ion beam possessing energy strikes the sample surface, causing the interaction between the ions and the surface. The interaction processes bring about the emission of atoms and molecules from the sample surface. (B) Ionization process of MALDI-MSI. Before the analysis, the matrix is applied to the sample surface. The matrix forms co-crystals with the analytes. The co-crystals can absorb the laser’s energy upon laser irradiation. The energy uptake then causes evaporation and desorption/ionization of the analytes. (C) Ionization process of DESI-MSI. It is carried out by applying pneumatically-assisted electrospray, which produces charged solvent droplets directly at the sample surface. The charged droplets impact the surface and produce gaseous ions.

Figure 2

Schemes of sample preparation for MSI and microproteomics. (A) Preparation protocols of fresh frozen tissues and FFPE tissue blocks for MSI and LMD or LMJ guided microproteomics. The fresh frozen tissue is sliced into sections by cryo-microtome and the tissue sections are placed on ITO slides or non-conductive slides. Then the tissue sections can be processed with MSI (For MALDI-MSI, matrix applying before data acquisition is necessary). The tissue section can also be processed with LMD or LMJ. For LMD, the region of interest within the tissue section is cut off and extracted, followed by LC-MS. For LMJ, the extracts obtained from the target region within the tissue surface can be directly analyzed by LC-MS. After data acquisition, data analysis is performed. For the FFPE tissue block, it is sliced into tissue sections by microtome. These FFPE tissue sections can be analyzed by MSI or LC-MS until they are treated with deparaffinization, rehydration and antigen retrieval. (B) Preparation protocols of cytologic samples for MSI. The cytologic samples are collected by FNA. The cytologic samples are smeared onto the ITO slides or non-conductive slides for the analysis of MSI.

Figure 3

(A) Principle of the Arcturus laser capture microdissection. A thermolabile membrane on bottom face of the cap is placed on the tissue section. The infrared (IR) laser activates the membrane which extends to the tissue. The adhesion force of the tissue to the activated membrane exceeds that to the glass slide. The selected area is removed from the tissue. (B) Principle of the Zeiss’s PALM microdissection. The tissue section is mounted on a polyethylene napthalate (PEN) membrane coated glass slide. After selecting the region of interest, ultraviolet (UV) laser ablates the surrounding cells and cuts away the selected area, which is then transported into a collection tube by a defined laser pulse against gravity. (C) Principle of the Leica LMD microdissection. The tissue section is mounted on the PEN membrane glass slide and placed upside down on the stage. The target tissue is dissected by the laser and directly falls into a collection tube underneath the tissue section. (D) Principle of liquid microjunction extraction. The probe aspirates the extraction solvent and dispenses a portion onto the tissue surface to create a liquid microjunction between the probe and the tissue surface. After a predefined extraction time, analytes that are soluble in the solvent are extracted into the liquid microjunction. The extracted solution can be analyzed by LC-MS directly.