Genome-Scale CRISPR-Cas9 Synthetic Lethal Screening of AML Cell Line Identified Functional Modulators of Etoposide Resistance Predictive of Clinical Outcome in AML Patients
Authors: Rafiee Roya , Sobh Amin , Elsayed Abdelrahman H. , Tagmount Abderrahmane , Vulpe Chris D , Lamba Jatinder K 
Published: November 2019

Despite the use of intensive chemotherapeutic regimens containing ara-C, daunorubicin and etoposide (ADE), in combination with stem cell transplantation for high-risk group patients, approximately significant patients experience relapse. Resistant and relapsed disease remains the most prevalent forms of clinical failure in treating this disease. The current scientific challenge is to identify candidate genes that are truly essential to drug resistance and thus may be pharmacologically targeted in a clinically effective manner. The development of the CRISPR/cas9 genome editing tool has dramatically improved the capabilities for functional screening in multiple systems including AML where genome-wide drop-out screens in AML cancer cell lines identified AML-essential genes. None of the studies have unfortunately integrated the CRISPR/cas9 screening tool with patient outcome data. In this study, we have successfully performed Genome scale Crispr knock out GeCKO -CRISPR/cas9 screening using Brunello library (targeting 19,114 genes) in K562 cell lines followed by treatments with etoposide, dauno and cytarabine. We performed a large-scale transduction into ~30 x 106 cells at a low multiplicity of infection (0.3). After puromycin selection the mutant cell library was exposed in triplicate to IC30 concentration of chemotherapeutic agents for up to 18 days with collection of samples at day 4 (ara-C, dauno, etoposide) days 12 and 18 (dauno and etoposide). A vehicle-only exposure was similarly carried out for 18 days. Direct sequencing of PCR amplified sgRNA guides from the pooled cells by short read sequencing (Illumina) was used to quantify the representation of each knockout clone in the pooled population (schema shown in Fig 1). The relative enrichment/depletion of each knockout clone was determined by ratio of the abundance of each clone between two samples. The FASTX-Toolkit, was used to extract the unique sgRNA sequences which were assembled into a Burrows-Wheeler index using the Bowtie build-index function and number of uniquely aligned reads for each sgRNA were calculated. The MaGeCK algorithms was used to analyze the read count data and perform statistical comparisons. The results for the etoposide screening are shown in Fig 2, overall 17 genes showed significant association with responsiveness to etoposide at all the three different time points (4, 12 and 18 days). Further investigation of these candidate genes in AML patients treated on AML02 trial demonstrated consistent and significant association between expression levels of several genes identified in CRISPR screening and clinical outcome. Fig 3 shows a representative result for 2 of the genes identified in etoposide screening, ABCC1and RAD54L2 both were associated with etoposide resistance in CRISPR screening and concordantly high expression was associated with greater induction 1 MRD, inferior event free survival (EFS, Fig 3) and overall survival (OS) in the AML02 cohort. ABCC1 is a drug efflux transporter that has been implicated in resistance to etoposide and daunorubicin as well as has been associated with poor prognosis in AML consistent with our results. RAD54L2, is a helicase involved in DNA damage repair response pathway. Other genes of interest identified in etoposide screening with significant association with clinical endpoints as MRD, EFS and OS included TKT, involved in pentose phosphate pathway and implicated in regulation of metabolic switch in cancer. A nucleotide excision repair gene, RAD23B, implicated in breast cancer progression as well as in CML and ALL. Similarly, for daunorubicin and cytarabine CRISPR/cas9 synthetic lethal screening identified target genes of clinical relevance that will be discussed in the presentation. Our approach shows that using CRISPR/cas9 targeted synthetic lethal screening as a reliable approach to not only identify and establish genes predictive of drug resistance and poor outcome but also potential targets for novel drug development that could be used in combination with currently approved agents.

Disclosures

No relevant conflicts of interest to declare.