A genome-wide CRISPR/Cas9-based functional screen uncovers the KLF4-Survivin/BIRC5 signaling pathway as a key regulator of cell fate following endoplasmic reticulum stress: Implications for tumor growth and therapeutic targeting

The growth and spread of tumors involve intricate interactions with the surrounding tissue microenvironment. As a tumor develops, it faces various stresses from its microenvironment, including hypoxia, nutrient deficiency, and acidosis. In response to these challenges, cancer cells can hijack existing cytoprotective mechanisms, such as the Unfolded Protein Response (UPR). The UPR activates signaling pathways at the translational and later transcriptional levels to alleviate cellular stress and prevent cell death. However, under unresolved or chronic endoplasmic reticulum (ER) stress, the UPR may paradoxically promote cell death. The precise mechanisms through which the UPR influences cellular fate during ER stress remain poorly understood. To address this knowledge gap, we employed a functional CRISPR-based genetic knockout screen to identify novel regulators of the UPR. Using a lentiviral genome-wide CRISPR-Cas9 knockout library, we identified over-represented sgRNAs (associated with pro-apoptotic genes) and underrepresented sgRNAs (associated with pro-survival genes) following ER stress induced by Thapsigargin and Tunicamycin. One of the top candidates identified was Survivin/BIRC5, a protein with anti-apoptotic and cell cycle regulatory activities and which is overexpressed in tumor cells compared to healthy tissues. Functional studies revealed that genetic or pharmacological inhibition of Survivin expression enhanced ER stress-induced apoptosis, but not apoptosis in response to other forms of stress. These findings were validated in multiple cancer cell lines, ruling out off-target effects. Mechanistically, ER stress led to PERK-dependent downregulation of Survivin, and overexpression of Survivin blocked Thapsigargin-induced apoptosis. In vivo xenograft models showed that combining Survivin ablation with PERK inhibition significantly delayed tumor growth and improved overall survival. Through a combination of bioinformatics analysis and loss-of-function studies, we identified the transcription factor KLF4 as a mediator of PERK-dependent effects on Survivin repression. Notably, CRISPR-mediated KLF4 knockout successfully rescued Survivin levels post-ER stress. Additionally, an analysis of TCGA data across various tumor types provided supporting evidence of a negative correlation between KLF4 and Survivin expression. In summary, this study unveils a novel regulatory axis, PERK-KLF4-Survivin, as a key determinant of cell fate in the cellular responses to ER stress. Targeting Survivin in conjunction with PERK inhibition showed promising antitumor effects in vivo. The growth and spread of tumors involve intricate interactions with the surrounding tissue microenvironment. As a tumor develops, it faces various stresses from its microenvironment, including hypoxia, nutrient deficiency, and acidosis. In response to these challenges, cancer cells can hijack existing cytoprotective mechanisms, such as the Unfolded Protein Response (UPR). The UPR activates signaling pathways at the translational and later transcriptional levels to alleviate cellular stress and prevent cell death. However, under unresolved or chronic endoplasmic reticulum (ER) stress, the UPR may paradoxically promote cell death. The precise mechanisms through which the UPR influences cellular fate during ER stress remain poorly understood. To address this knowledge gap, we employed a functional CRISPR-based genetic knockout screen to identify novel regulators of the UPR. Using a lentiviral genome-wide CRISPR-Cas9 knockout library, we identified over-represented sgRNAs (associated with pro-apoptotic genes) and underrepresented sgRNAs (associated with pro-survival genes) following ER stress induced by Thapsigargin and Tunicamycin. One of the top candidates identified was Survivin/BIRC5, a protein with anti-apoptotic and cell cycle regulatory activities and which is overexpressed in tumor cells compared to healthy tissues. Functional studies revealed that genetic or pharmacological inhibition of Survivin expression enhanced ER stress-induced apoptosis, but not apoptosis in response to other forms of stress. These findings were validated in multiple cancer cell lines, ruling out off-target effects. Mechanistically, ER stress led to PERK-dependent downregulation of Survivin, and overexpression of Survivin blocked Thapsigargin-induced apoptosis. In vivo xenograft models showed that combining Survivin ablation with PERK inhibition significantly delayed tumor growth and improved overall survival. Through a combination of bioinformatics analysis and loss-of-function studies, we identified the transcription factor KLF4 as a mediator of PERK-dependent effects on Survivin repression. Notably, CRISPR-mediated KLF4 knockout successfully rescued Survivin levels post-ER stress. Additionally, an analysis of TCGA data across various tumor types provided supporting evidence of a negative correlation between KLF4 and Survivin expression. In summary, this study unveils a novel regulatory axis, PERK-KLF4-Survivin, as a key determinant of cell fate in the cellular responses to ER stress. Targeting Survivin in conjunction with PERK inhibition showed promising antitumor effects in vivo. The growth and spread of tumors involve intricate interactions with the surrounding tissue microenvironment. As a tumor develops, it faces various stresses from its microenvironment, including hypoxia, nutrient deficiency, and acidosis. In response to these challenges, cancer cells can hijack existing cytoprotective mechanisms, such as the Unfolded Protein Response (UPR). The UPR activates signaling pathways at the translational and later transcriptional levels to alleviate cellular stress and prevent cell death. However, under unresolved or chronic endoplasmic reticulum (ER) stress, the UPR may paradoxically promote cell death. The precise mechanisms through which the UPR influences cellular fate during ER stress remain poorly understood. To address this knowledge gap, we employed a functional CRISPR-based genetic knockout screen to identify novel regulators of the UPR. Using a lentiviral genome-wide CRISPR-Cas9 knockout library, we identified over-represented sgRNAs (associated with pro-apoptotic genes) and underrepresented sgRNAs (associated with pro-survival genes) following ER stress induced by Thapsigargin and Tunicamycin. One of the top candidates identified was Survivin/BIRC5, a protein with anti-apoptotic and cell cycle regulatory activities and which is overexpressed in tumor cells compared to healthy tissues. Functional studies revealed that genetic or pharmacological inhibition of Survivin expression enhanced ER stress-induced apoptosis, but not apoptosis in response to other forms of stress. These findings were validated in multiple cancer cell lines, ruling out off-target effects. Mechanistically, ER stress led to PERK-dependent downregulation of Survivin, and overexpression of Survivin blocked Thapsigargin-induced apoptosis. In vivo xenograft models showed that combining Survivin ablation with PERK inhibition significantly delayed tumor growth and improved overall survival. Through a combination of bioinformatics analysis and loss-of-function studies, we identified the transcription factor KLF4 as a mediator of PERK-dependent effects on Survivin repression. Notably, CRISPR-mediated KLF4 knockout successfully rescued Survivin levels post-ER stress. Additionally, an analysis of TCGA data across various tumor types provided supporting evidence of a negative correlation between KLF4 and Survivin expression. In summary, this study unveils a novel regulatory axis, PERK-KLF4-Survivin, as a key determinant of cell fate in the cellular responses to ER stress. Targeting Survivin in conjunction with PERK inhibition showed promising antitumor effects in vivo. Functional knockout CRISPR/Cas9-based screens were performed in SQ20B and A375 cells to identify new mediators of Endoplasmic Reticulum (ER) stress. The Human GeCKO_v2 sgRNA libraries (AddGene Pooled Library #1000000048, #1000000049) were utilized. 10^8 A375 or SQ20B cells were transduced in 60-well plates both with A and B half-libraries at a MOI of 0.3. After 48h, cells were selected with puromycin for 3 days and an initial pool of 40 million cells was harvested (Qiagen Blood and Tissue extraction kit) for genomic DNA extraction (UT samples). After puromycin selection, cells were left to repopulate the plates and were treated for 24h with 0.5uM of Thapsigargin or Tunicamycin, two ER stress imitators. After 50% of the cells died due to ER stress, the remaining cells were left to grow and treatment with Thapsigargin or Tunicamycin was repeated once more to increase the resistance to ER stress population. Cells were collected for lysing and DNA isolation. After a 72h recovery and expansion, their genomic DNA was extracted and PCR-amplified. A second step PCR was performed to add a specific adaptor sequence to each sample, forming the sgRNA fragment libraries. Next-generation sequencing was performed on an Illumina HiSeq 2500 system to quantify the presence of each sgRNA. After demultiplexing, QC and adapter removal, MAGeCK v0.5.7 was applied to assess gene importance.