CRISPR/Cas9 system as a genetic screen for identifying biomarkers in cancer immunotherapy

The advancement in high throughput genetic sequencing and our understanding of immune system functioning has brought about a paradigm shift in therapeutic strategies. The capacity to probe into molecular and genetic pathways associated with a particular disease offers the capacity to develop precision medicine tailored to suit the needs of an individual patient. This is in stark contrast to traditional disease-specific or targeted therapeutic strategies. Immunotherapy is one such example that holds unlimited hope to offer a personalised therapeutic product for a disease that is genetically unique to an individual.

Immunotherapies have achieved significant clinical efficacy that is noteworthy in diseases such as cancer and autoimmunity. The capacity to intervene in the cancer-related molecular pathways through the blocking of immune checkpoint receptors shows the translation of concepts of immunology to therapy.

However, to develop immunotherapies, biomarkers are key prerequisites. These biomarkers offer insight into the correlation of disease onset and progression with the genetic build, mutation, and interactions with the immune system of the host. This information can be vital in assessing the therapeutic strategy that would best suit a patient’s needs. Thus there is a need for the genetic screen to identify biomarkers, the scope of which until recent times remained limited. However, the discovery of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR Associated Nuclease 9 (Cas9) system and its potential applications have helped to overcome the existing challenges in biomarker identification.

CRISPR/Cas9 is a simple and precise technique that enables genetic manipulation of a part or of the entire genome of an organism by introducing specific changes to the DNA sequence through addition, deletion, or substitution of base pairs. This creates unlimited scope for CRISPR in functional genomics, and the CRISPR screen is one such example. The CRISPR screen brings together the programmable RNAi and the versatile genome and epigenome editing tool onto the same platform. This platform in combination with CRISPR/Cas9 and its variants can produce different types of screens such as knockdown, loss of function and gain of function screens, analysed through the arrayed screen or pooled screen techniques. Through these genetic screens, transient expressions of PD-L1 biomarkers on the cell surface of immune cells within tumour microenvironment have been studied. Similarly, the CRISPR screen has identified TNC, an extracellular matrix, and FOXC, a transcription factor as prognostic biomarkers in lung and breast cancer respectively.

Additionally, CRISPR/Cas9 genetic screens also help in identifying resistance mechanisms in tumours. For example, the genes related to SWI/SNF chromatin remodelling complex and PBRM1 genes have been found to be responsible for developing resistance in tumours against immunotherapies. Consequently, their knock-out increases the sensitivity of the tumour to the immunotherapies, thus giving us an insight into the molecular pathway involved. ‘The versatility, reliability and specificity of CRISPR screen render it a promising player in medical genetic researches.’ (Xue et al, 2016, p.96). With the rapid advancements in genome editing technologies, CRISPR/Cas9 screens hold the promise to identify stronger biomarkers for diagnosis and therapeutic intervention.


Xue H, Ji L, Gao A, GaoA et al. (2016). ‘CRISPR-Cas9 for medical genetic screens: applications and future perspectives’, Journal of Medical Genetics,53, p.91-97.

Mukherjee S. (2019). ‘Genomics-Guided Immunotherapy for Precision Medicine in Cancer’, Cancer biotherapy & radiopharmaceuticals, 34(8), p.487–497. DOI: 10.1089/cbr.2018.2758

Ajina, R., Zamalin, D., and Weiner, L. M. (2019). ‘Functional genomics: paving the way for more successful cancer immunotherapy’, Briefings in functional genomics, 18(2), p.86–98. DOI: 10.1093/bfgp/ely017

Wolf, Y. and Samuels Y. (2018). ‘Cancer research in the era of immunogenomics’, ESMO Open, 3(e000475). DOI: 10.1136/esmoopen-2018-000475

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