Deep sequencing and automated histochemistry of human tissue slice cultures improve their usability as preclinical model for cancer research

Abstract

Cancer research requires models closely resembling the tumor in the patient. Human tissue cultures can overcome interspecies limitations of animal models or the loss of tissue architecture in in vitro models. However, analysis of tissue slices is often limited to histology. Here, we demonstrate that slices are also suitable for whole transcriptome sequencing and present a method for automated histochemistry of whole slices. Tumor and peritumoral tissue from a patient with glioblastoma was processed to slice cultures, which were treated with standard therapy including temozolomide and X-irradiation. Then, RNA sequencing and automated histochemistry were performed. RNA sequencing was successfully accomplished with a sequencing depth of 243 to 368 x 106 reads per sample. Comparing tumor and peritumoral tissue, we identified 1888 genes significantly downregulated and 2382 genes upregulated in tumor. Treatment significantly downregulated 2017 genes, whereas 1399 genes were upregulated. Pathway analysis revealed changes in the expression profile of treated glioblastoma tissue pointing towards downregulated proliferation. This was confirmed by automated analysis of whole tissue slices stained for Ki67. In conclusion, we demonstrate that RNA sequencing of tissue slices is possible and that histochemical analysis of whole tissue slices can be automated which increases the usability of this preclinical model.

Distinct Gene Expression Patterns of Ion Channels and Cytokines in Rat Primary Sensory Neurons During Development of Bone Cancer and Cancer Pain

“…However, it is also clear that with rat model alone cannot recapitulate all the features of bone cancer pain in humans, and the species differences in DEGs between rodents and humans is inevitable. As the development processes of primate nervous system are conserved across mammals ( Bakken et al, 2015 ), future studies better employ primate model or by using human tissue slice culture to improve the usability as preclinical model for bone cancer pain research ( Haehnel et al, 2019 ). In addition, studies have also reported the difference in pain mechanisms between males and females, thus, the findings in our current study in females need to be further investigated in males with other cancer cells probably unnecessary the female-specific breast cancer cells.…”

Peritumoral Microenvironment in High-Grade Gliomas: From FLAIRectomy to Microglia–Glioma Cross-Talk

“…Notwithstanding the extensive characterization of the transcriptome and proteome of the peritumoral area [ 61 , 62 , 63 , 64 , 65 , 66 ], little is known about the expression and involvement of miRNAs in this area and, more specifically, their role in the cross-talk between GBM and microglial cells. One of the first studies on the involvement of miRNAs in the pathogenesis of GBM was conducted by comparing their expression between the central tumor area, surgically and histopathologically recognized as frankly tumoral, and the peripheral glial area, without any evidence of tumor presence, by a surgeon’s macroscopical evaluation [ 39 ].…”

Glioblastoma Tissue Slice Tandem-Cultures for Quantitative Evaluation of Inhibitory Effects on Invasion and Growth

“…Also, artificial 2D or 3D matrices poorly mimic the in vivo situation, which consists, in addition to the ECM, of multiple cell types that are capable of influencing and interacting with tumor cells, and thus substantially affect their invasive potential [ 8 ]. Aiming at systems that provide an organotypic microenvironment with its required cellular complexity [ 9 , 10 ], more recent studies have developed tissue slice models in an air-liquid interface setting [ 11 , 12 , 13 , 14 ]. This also included tissue slice co-culture models.…”