Development of digital PCR probe assays targeting SNPs to monitor co-cultured cell lines

Cancer is driven by genetic alterations causing abnormal cell proliferation and invasion. Cancer heterogeneity refers to the diversity and variability observed within or between tumors, causing major issues in developing novel anti-cancer therapies targeting all cellular subtypes. To tackle this, more representative cancer models are developed to more accurately mimic the complex tumor environment and its diversity. This helps improve drug response studies and reveals important molecular mechanisms of cancer. However, downstream analytical methods for profiling the effects of these more complex models are costly and time-consuming and face practical challenges, limiting their feasibility in laboratory settings. This master’s thesis aimed to develop and evaluate a probe-based digital polymerase chain reaction (dPCR) setup with high sensitivity and specificity for monitoring various cell lines in a co-culture over time. The designed probes target cell line unique single nucleotide polymorphisms (SNPs) of each myxoid liposarcoma (MLS) and a fibrosarcoma human-derived cell line. In his thesis, a method was developed for monitoring co-cultures with up to four different cell lines with reliable quantification using dPCR analysis, proving to be both sensitive and efficient enough for our application. While this thesis project focused on MLS and fibrosarcoma cell lines, the workflow can be applied to other cell types, including immune cells or various cancer cell lines, as long as unique SNPs are identified. The method and workflow provide profiling of complex cell cultures and could be utilized for a deeper understanding of therapeutic responses across various culture model systems.

Department dc:contributor.department

Chalmers tekniska högskola / Institutionen för life sciences

Year dc:date.issued

2024

Author dc:creator

• Frisk, Emma

Advisor dc:contributor.supervisor

• Ståhlberg, Anders

• Heterogeneity
• Digital PCR
• Co-culture
• Myxoid liposarcoma
• Monitor
• Probe
• SNP

Language dc:language.iso

eng

Handle dc:identifier.uri

https://hdl.handle.net/20.500.12380/307906

OAI record oai:identifier

https://odr.chalmers.se/oai/request?verb=GetRecord&metadataPrefix=dim&identifier=oai%3Aodr.chalmers.se%3A20.500.12380%2F307906