Genome wide CRISPR/Cas9 screen identifies the coagulation factor IX (F9) as a regulator of senescence

Abstract

During this last decade, the development of prosenescence therapies has become an attractive strategy as cellular senescence acts as a barrier against tumour progression. In this context, CDK4/6 inhibitors induce senescence and reduce tumour growth in breast cancer patients. However, even though cancer cells are arrested after CDK4/6 inhibitor treatment, genes regulating senescence in this context are still unknown limiting their antitumour activity. Here, using a functional genome-wide CRISPR/Cas9 genetic screen we found several genes that participate in the proliferation arrest induced by CDK4/6 inhibitors. We find that downregulation of the coagulation factor IX (F9) using sgRNA and shRNA prevents the cell cycle arrest and senescent-like phenotype induced in MCF7 breast tumour cells upon Palbociclib treatment. These results were confirmed using another breast cancer cell line, T47D, and with an alternative CDK4/6 inhibitor, Abemaciclib, and further tested in a panel of 22 cancer cells. While F9 knockout prevents the induction of senescence, treatment with a recombinant F9 protein was sufficient to induce a cell cycle arrest and senescence-like state in MCF7 tumour cells. Besides, endogenous F9 is upregulated in different human primary cells cultures undergoing senescence. Importantly, bioinformatics analysis of cancer datasets suggest a role for F9 in human tumours. Altogether, these data collectively propose key genes involved in CDK4/6 inhibitor response that will be useful to design new therapeutic strategies in personalised medicine in order to increase their efficiency, stratify patients and avoid drug resistance.

Identification of oncogenes and tumor-suppressor genes with hepatocellular carcinoma: A comprehensive analysis based on TCGA and GEO datasets

“…F9 has been widely studied as a hemophilia defect factor ( Lu et al, 2019 ; Shapiro et al, 2021 ). Recent research has suggested that F9 may play a role in CD4 + T cell induction ( Cooper et al, 2009 ) and predict CDK4/6 inhibitor response in breast cancer ( Carpintero-Fernández et al, 2022 ). However, the role of F9 in the immunotherapy of HCC has not been reported.…”

Cellular senescence: a key therapeutic target in aging and diseases

“…Complementary to the phenotypic cell-based screening of chemicals, genetic screening of vulnerabilities of SnCs can provide new senescence targets for drug discovery. For example, genome-wide CRISPR/Cas9-based screening has been applied to identify genes that potentially regulate cellular senescence, such as SMARCB1, coagulation factor IX (F9), and KAT7 (132)(133)(134). With a deeper understanding of senescence biology and the discovery of more senescence targets, structure-based virtual screening should be feasible using certain key proteins and pathways regulating senescence.…”

Cellular Senescence and Ageing: Mechanisms and Interventions

“…Molecular changes at CDKs level have been reported in various cancer types making them an attractive potential target for new treatments. CDK inhibitors, in particular CDK4/6 inhibitors (Abemaciclib, Palbociclib and Ribociclib), induce cell-cycle arrest and subsequent senescence in several cancer cell lines and mouse models ( Asghar et al, 2015 ; Alvarez-Fernandez and Malumbres, 2020 ; Carpintero-Fernandez et al, 2022 ). Palbociclib is a drug for oestrogen-receptor-positive breast cancer (ER + ).…”

“…Additionally, evidence is building up that senescence is a stable, but not irreversible, cellular state. In fact, this novel characteristic of senescent cells has been attributed to the plasticity of their SASP in different contexts such as cancer, reprogramming and rejuvenation ( Mosteiro et al, 2016 ; Ocampo et al, 2016 ; Ritschka et al, 2017 ; Rhinn et al, 2019 ; Fafian-Labora et al, 2020 ; Carpintero-Fernandez et al 2022 ). Importantly, recent evidences show that the SASP is not unique and static as initially thought but that it is dynamic, changing with time depending on trigger, context and cellular type ( Hoare et al, 2016 ; Lee and Schmitt, 2019 ).…”