Detection of SARS-CoV-2 RNA using RT-LAMP and molecular beacons

BACKGROUND

Rapid spread of SARS-CoV-2 has led to a global pandemic, resulting in the need for rapid assays to allow diagnosis and prevention of transmission. Reverse transcription-polymerase chain reaction (RT-PCR) provides a gold standard assay for SARS-CoV-2 RNA, but instrument costs are high and supply chains are potentially fragile, motivating interest in additional assay methods. Reverse transcription and loop-mediated isothermal amplification (RT-LAMP) provides an alternative that uses orthogonal and often less expensive reagents without the need for thermocyclers. The presence of SARS-CoV-2 RNA is typically detected using dyes to report bulk amplification of DNA; however, a common artifact is nonspecific DNA amplification, which complicates detection.

RESULTS

Here we describe the design and testing of molecular beacons, which allow sequence-specific detection of SARS-CoV-2 genomes with improved discrimination in simple reaction mixtures. To optimize beacons for RT-LAMP, multiple locked nucleic acid monomers were incorporated to elevate melting temperatures. We also show how beacons with different fluorescent labels can allow convenient multiplex detection of several amplicons in "single pot" reactions, including incorporation of a human RNA LAMP-BEAC assay to confirm sample integrity. Comparison of LAMP-BEAC and RT-qPCR on clinical saliva samples showed good concordance between assays. To facilitate implementation, we developed custom polymerases for LAMP-BEAC and inexpensive purification procedures, which also facilitates increasing sensitivity by increasing reaction volumes.

CONCLUSIONS

LAMP-BEAC thus provides an affordable and simple SARS-CoV-2 RNA assay suitable for population screening; implementation of the assay has allowed robust screening of thousands of saliva samples per week.

MMB-FOXM1-driven premature mitosis is required for CHK1 inhibitor sensitivity

To identify genes whose loss confers resistance to CHK1 inhibitors, we perform genome-wide CRISPR-Cas9 screens in non-small-cell lung cancer (NSCLC) cell lines treated with the CHK1 inhibitor prexasertib (CHK1i). Five of the top six hits of the screens, MYBL2 (B-MYB), LIN54, FOXM1, cyclin A2 (CCNA2), and CDC25B, are cell-cycle-regulated genes that contribute to entry into mitosis. Knockout of MMB-FOXM1 complex components LIN54 and FOXM1 reduce CHK1i-induced DNA replication stress markers and premature mitosis during Late S phase. Activation of a feedback loop between the MMB-FOXM1 complex and CDK1 is required for CHK1i-induced premature mitosis in Late S phase and subsequent replication catastrophe, indicating that dysregulation of the S to M transition is necessary for CHK1 inhibitor sensitivity. These findings provide mechanistic insights into small molecule inhibitors currently studied in clinical trials and provide rationale for combination therapies.

Branigan et al., by using genome-wide CRISPR screens, identify the MMB-FOXM1 complex as being required for CHK1 inhibitor (CHK1i) sensitivity. Their study shows that CHK1i-induced premature activation of the G2/M transcriptional program by this complex triggers a breakdown in the separation of DNA synthesis and mitosis, leading to replication catastrophe.

CHK1 Inhibitor Blocks Phosphorylation of FAM122A and Promotes Replication Stress

While effective anti-cancer drugs targeting the CHK1 kinase are advancing in the clinic, drug resistance is rapidly emerging. Here, we demonstrate that CRISPR-mediated knockout of the little-known gene FAM122A/PABIR1 confers cellular resistance to CHK1 inhibitors (CHK1is) and cross-resistance to ATR inhibitors. Knockout of FAM122A results in activation of PP2A-B55α, a phosphatase that dephosphorylates the WEE1 protein and rescues WEE1 from ubiquitin-mediated degradation. The resulting increase in WEE1 protein expression reduces replication stress, activates the G2/M checkpoint, and confers cellular resistance to CHK1is. Interestingly, in tumor cells with oncogene-driven replication stress, CHK1 can directly phosphorylate FAM122A, leading to activation of the PP2A-B55α phosphatase and increased WEE1 expression. A combination of a CHK1i plus a WEE1 inhibitor can overcome CHK1i resistance of these tumor cells, thereby enhancing anti-cancer activity. The FAM122A expression level in a tumor cell can serve as a useful biomarker for predicting CHK1i sensitivity or resistance.

Abstract 4287: Whole-genome CRISPR/Cas9 screen of the CHK1 inhibitor prexasertib implicates FAM122A loss as a potential resistance mechanism

Introduction: Phase I clinical trials of the CHK1 inhibitor prexasertib have been completed in non-small cell lung cancer (NSCLC) and other cancers and several Phase I-II trials are currently recruiting. By inhibiting the G2/M and S-phase checkpoints, prexasertib has been shown to cause increased replication stress, DNA damage and premature entry into mitosis, resulting in mitotic catastrophe and cell death. While the inhibitor is showing therapeutic promise, acquired resistance is of concern. Little is known about how cancer cells may become resistant to CHK1 inhibitors. Understanding potential resistance mechanisms may help predict patient responses, design CHK1 therapy combinations and implement means of re-sensitization.

Materials and Methods: NSCLC cell lines A549 and NCI-H460 stably expressing the Cas9 endonuclease were obtained from the Genetic Perturbation Platform at the Broad Institute. Cells were infected with the Brunello v2 lentiviral sgRNA library and grown for 15 days in prexasertib-treated media. Cells were collected pre- and post-drug selection, genomic DNA was extracted, and sgRNA sequences were PCR amplified and Illumina sequenced. Top hits among knockouts that conferred drug resistance were identified by the STARS gene-ranking algorithm. Hit validation was performed with sgRNAs and pooled siRNAs (Qiagen). Prexasertib IC50s were assessed by colony formation and CellTiter-Glo cell viability assays. Cell cycle analysis was performed by propidium iodide flow cytometry. PP2A activity was measured using Ser/Thr phosphatase assay kits (Upstate Biotechnology). Dinaciclib and LB-100 were obtained from Selleck and Apexbio, respectively.

Results: CRISPR knockouts of several individual genes were found to promote resistance of both cell lines to prexasertib with false discovery rates < 0.01%. One top hit codes for a little-known but highly conserved protein FAM122A, which has been shown to inhibit PP2A, which dephosphorylates the Chk1 target protein CDC25C. SiRNA knockdown or sgRNA knockout of FAM122A conferred prexasertib resistance. Similarly, prexasertib-mediated G2/M accumulation was inhibited by FAM122A knockdown. FAM122A silencing increased PP2A activity. FAM122A knockdown mediated resistance was reversed with PP2A B subunit α siRNA knockdown or the PP2A inhibitor LB-100. Dinaciclib, an inhibitor of the CDC25C kinase CDK2, increased prexasertib resistance.

Conclusion: Although CHK1 inhibitors like prexasertib show promise, one mechanism of resistance may be through other cell-cycle regulating compensatory pathways. Identification of FAM122A loss as a potential mechanism for resistance suggests a predictive biomarker and means for re-sensitization of cancer cells to CHK1 inhibitors.

Citation Format: Peter Deraska, Hunter Reavis, Shelby Labe, Alan D'Andrea, David Kozono. Whole-genome CRISPR/Cas9 screen of the CHK1 inhibitor prexasertib implicates FAM122A loss as a potential resistance mechanism [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4287.

Abstract 1650: Whole-genome RNAi screen identified BCAS1 as a novel modifier of non-small cell lung carcinoma radioresistance

Introduction: Despite optimal chemotherapy, radiotherapy and/or surgery, non-small cell lung carcinoma (NSCLC) remains the leading cause of cancer-related death in the United States. Therefore, there is a need for agents, such as radiosensitizers, that can improve the efficacy of current therapies. Using a whole-genome shRNA screen, we sought to identify and characterize novel gene products that may be involved in NSCLC radioresistance. We hypothesize that these proteins may represent novel targets for NSCLC radiosensitization.

Materials and Methods: A whole-genome pooled retroviral shRNA screen was performed using the Hannon-Elledge library of 74,705 distinct shRNAs directed against over 18,000 genes, to identify gene knockdowns that showed cytotoxicity only in cells treated with fractionated radiation given daily Monday-Friday. To confirm targets identified in the whole-genome screen, we treated A549 and NCI-H460 NSCLC cells with siRNAs targeted against the genes of interest and assessed cell viability following irradiation using the CellTiter-Glo assay and clonogenic survival assays.

Results: We identified six novel genes (BCAS1, c7orf24, CDC45L, KIAA0101, TCN1 and TNC) whose knockdown sensitized NSCLC cells to radiation. Of the six genes, siRNA knockdown of BCAS1 showed the most consistent increases in sensitivity to ionizing radiation. Analysis of cell viability following radiation revealed that BCAS1 knockdown resulted in a 50% additional decrease in cell viability in A549 and NCI-H460 cells following 8 and 4 Gy of ionizing radiation, respectively. We confirmed these results by clonogenic survival assays. To assess for tumor-specific expression in NSCLC, we compared expression data between matched normal tissue and NSCLC biopsy samples and found that BCAS1 is substantially more highly expressed in tumor tissues. Examination of affinity capture-mass spectroscopy data suggested that BCAS1 interacts with RUVBL2, a RuvB-like AAA ATPase, which has known functions in DNA damage and repair.

Conclusions: BCAS1 emerged from a whole-genome RNAi screen as a potential target for improving the efficacy of radiotherapy in NSCLC. We demonstrated that BCAS1 is overexpressed in tumor tissues compared to normal lung, and that its knockdown consistently sensitizes NSCLC cell lines to radiation, validating the screen hit. Ongoing work suggests that BCAS1 may modulate DNA damage repair. Further studies to understand the mechanism by which BCAS1 is involved in radioresistance are necessary.

Citation Format: Colin O’Leary, Peter Deraska, Alan D’Andrea, David Kozono. Whole-genome RNAi screen identified BCAS1 as a novel modifier of non-small cell lung carcinoma radioresistance. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1650.

USP9X inhibition promotes radiation-induced apoptosis in non-small cell lung cancer cells expressing mid-to-high MCL1

BACKGROUND AND PURPOSE

Radiotherapy (RT) is vital for the treatment of locally advanced non-small cell lung cancer (NSCLC), yet its delivery is limited by tolerances of adjacent organs. We sought therefore to identify and characterize gene targets whose inhibition may improve RT.

MATERIALS AND METHODS

Whole genome pooled shRNA cytotoxicity screens were performed in A549 and NCI-H460 using a retroviral library of 74,705 sequences. Cells were propagated with or without daily radiation Monday-Friday. Radiosensitization by top differential dropout hits was assessed by clonogenic assays. Apoptosis was assessed using a caspase 3/7 cell-based activity assay and by annexin V-FITC and PI staining. MCL1 expression was assessed by qPCR and Western blotting.

RESULTS

USP9X, a deubiquitinase, was a top hit among druggable gene products. WP1130, a small molecule USP9X inhibitor, showed synergistic cytotoxicity with IR. MCL1, an anti-apoptotic protein deubiquitinated by USP9X, decreased with USP9X inhibition and IR. This was accompanied by increases in caspase 3/7 activity and apoptosis. In a panel of NSCLC lines, MCL1 and USP9X protein and gene expression levels were highly correlated. Lines showing high levels of MCL1 expression were the most sensitive to USP9X inhibition.

CONCLUSIONS

These data support the use of MCL1 expression as a predictive biomarker for USP9X inhibitors in NSCLC therapy.

Abstract 3336: NF-κB inhibition by DMAPT radiosensitizes non-small cell lung carcinoma by impairing DNA double strand break repair

Background: Despite optimal radiation therapy (RT), chemotherapy and/or surgery, non-small cell lung carcinoma (NSCLC) remains the leading cause of cancer-related death in the United States. Previously, we demonstrated that proteasome inhibition blocks the expression of Fanconi anemia/homologous recombination (FA/HR) genes via inhibition of the NF-κB pathway. Dimethylaminoparthenolide (DMAPT) is a water-soluble analog of parthenolide that has been shown to decrease p65/p50 heterodimer DNA binding. We hypothesized that DMAPT may radiosensitize NSCLC cells by impairing NF-κB-mediated expression of DNA double strand break (DSB) repair genes.

Materials and Methods: Cytotoxicity and radiosensitivity were assessed using clonogenic assays. IκB kinase (IKK) activity was measured using a substrate phosphorylation assay. HR and canonical non-homologous end joining (cNHEJ) were measured using A549 cells stably expressing reporter constructs that express GFP upon repair of I-SceI-induced DNA DSBs. DNA damage and DSB repair biomarker foci were assessed by immunofluorescence. For in vivo studies, 1×106 A549 cells were injected subcutaneously into the flanks of NCr nude mice. Once tumors reached an average size of 200 mm3, mice were treated concurrently with vehicle or DMAPT (100 mg/kg) ± focal ionizing radiation (4 Gy x 5) using a small animal radiation research platform (SAARP). Tumor growth was followed for three months following treatment.

Results: Radiation and NF-κB inhibition with DMAPT showed synergistic cytotoxicity. Treatment of A549 cells with DMAPT resulted in a decrease in constitutive IκBα phosphorylation by IKK. NF-κB inhibition via DMAPT resulted in a 60-70% decrease in HR. In addition, treatment with DMAPT resulted in ≥80% loss of IR-induced BRCA1, FANCD2, and RAD51 foci. NF-κB inhibition with either DMAPT or overexpression of the NF-κB super-repressor IκBα(S32A, S36A) resulted in a 50-70% decrease in cNHEJ. Treatment with DMAPT resulted in the loss of IR-induced phosphoDNA-PKS2056 foci. Further, treatment with DMAPT resulted in the persistence of radiation-induced γH2AX foci over a 24 hour period (100% of DMAPT treated cells showing foci compared to 30% of vehicle treated cells). Compared to either single agent DMAPT or IR alone, combined treatment of A549 xenografts with DMAPT and IR prevented tumor growth over three months (p < 0.0001).

Conclusions: DMAPT inhibits NF-κB signaling by inhibiting IKK. This in turn inhibits HR and cNHEJ by preventing the recruitment of DNA repair proteins to sites of IR-induced DNA damage. Both in vitro and in vivo experiments show support for further evaluation of DMAPT as a NSCLC radiosensitizer.

Citation Format: Colin O'Leary, Peter Deraska, Christopher Sweeney, Alan D'Andrea, David Kozono. NF-κB inhibition by DMAPT radiosensitizes non-small cell lung carcinoma by impairing DNA double strand break repair. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3336. doi:10.1158/1538-7445.AM2015-3336