Al‐Zahrani, Khalid N.

Abstract BACKGROUND IDH-mutant gliomas are diffusely infiltrating, slow-growing brain tumors that inevitably undergo malignant progression to grade IV astrocytoma - a highly aggressive and uniformly fatal disease with dismal prognosis. Despite extensive research, the molecular mechanisms underlying this transformation remain poorly understood. While alterations in canonical driver genes such as CDKN2A, PTEN, and PDGFRA have been implicated, the broader landscape of genetic drivers involved in IDH-mutant glioma progression is largely uncharacterized. In contrast to many other malignancies, IDH-mutant gliomas acquire relatively few somatic point mutations during progression - typically in the range of 30 to 40 - suggesting that alternative mechanisms may be driving tumor evolution. Notably, these tumors exhibit widespread chromosomal instability, resulting in a heterogeneous and highly prevalent pattern of copy number alterations (CNAs). This observation raises the possibility that gene dosage changes due to CNAs play a critical role in tumor progression. MATERIAL AND METHODS To investigate this hypothesis, we performed integrative analysis of IDH-mutant glioma cohorts from the Mayo Clinic and TCGA datasets (~1,500 patients), identifying twelve highly recurrent CNAs significantly associated with patient outcomes. We refer to these as malignant IDH-associated CNAs (mIDH CNAs). We hypothesized that these recurrent CNAs harbor driver genes that confer selective growth advantages, thereby contributing to their recurrence and prognostic relevance. To systematically assess the functional impact of genes within these regions, we developed a novel in vivo CRISPR-based screening platform, termed CRISPR-Knock Out and Activation Linked Assay (CRISPR-KOALA). This approach utilizes stereotaxic delivery of lentiviral gRNA libraries - targeting mouse orthologs of ~1,800 genes within recurrently deleted regions and ~1,200 genes within amplified regions - into the brains of a genetically engineered mouse model of IDH-mutant glioma (rs557mut;IDHmut;P53KO;AtrxKO;Cas9GFP: Yanchus et. al Science 2022). RESULTS Mice injected with mIDH CNA-targeting libraries developed tumors significantly more rapidly than control cohorts. Deconvolution of the CRISPR-KOALA screen identified several putative driver genes, including regulators of the NOTCH signaling pathway, lipid metabolism modulators such as THEM6, and the NMDA receptor modulator GRINA - implicating dysregulation of metabolism, immune response, and glutamatergic signaling in the malignant transformation of IDH-mutant gliomas. CONCLUSION Together, these findings provide critical insights into the genetic mechanisms driving the progression of IDH-mutant gliomas and identify new candidate genes and pathways for potential therapeutic targeting.

Abstract Low-grade gliomas (LGG) are slowly growing brain cancers that ultimately undergo a malignant progression to lethal secondary glioblastomas with a dismal prognosis. Despite intensive research, very little progress has been made in our understanding of this transformation. Hence, outside of known alternations in well-characterized driver genes CDKN2A, PTEN and PDGFRA, genetic drivers that underlie LGG transformation are largely unknown. Contrary to other types of cancer, LGGs exhibit very few driver mutations (30-40 mutations) as they progress. Interestingly, LGGs also exhibit a highly prevalent and heterogenous pattern of copy-number-alterations (CNAs) suggesting that they might be driven by changes in gene dosages that result from widespread chromosomal instability observed within these tumors. Through analysis of the human Mayo Clinic and TCGA LGG datasets (~1500 patients), we have identified eleven highly recurrent CNAs affecting LGG patients, many of which correlate with patient survival. We hypothesized that these CNAs contain driver genes that confer a growth advantage resulting in the highly recurrent CNA pattern and prognostic associations. To investigate the tumor suppressive potential of the ~1800 genes located in recurrently deleted regions and the oncogenic potential of the ~1200 genes located in recurrently amplified regions, our lab developed a novel in vivo ‘CRISPR-Knock Out and Activation Linked Assay’ (CRISPR-KOALA). Stereotaxic delivery of arm-level CNA lentiviral gRNA libraries targeting the mouse orthologs of genes in CNAs into the brain of our animal model (rs557mut;IDHmut;P53KO;AtrxKO;Cas9GFP: Yanchus et. al Science 2022) resulted in rapid formation of tumors compared to animals injected with control libraries. Deconvoluting the screen revealed enrichment of immune modulators such as Them6 as well as a modulator of NMDA receptors (Grina) implicating immune system and glutamate dysregulation in LGG malignant transformation. Taken together, our study provides insights into mechanisms underlying LGG progression which may serve to inform intervention strategies for this lethal disease.

Establishing causal links between inherited polymorphisms and cancer risk is challenging. Here, we focus on the single-nucleotide polymorphism rs55705857, which confers a sixfold greater risk of isocitrate dehydrogenase ( IDH) –mutant low-grade glioma (LGG). We reveal that rs55705857 itself is the causal variant and is associated with molecular pathways that drive LGG. Mechanistically, we show that rs55705857 resides within a brain-specific enhancer, where the risk allele disrupts OCT2/4 binding, allowing increased interaction with the Myc promoter and increased Myc expression. Mutating the orthologous mouse rs55705857 locus accelerated tumor development in an Idh1 R132H -driven LGG mouse model from 472 to 172 days and increased penetrance from 30% to 75%. Our work reveals mechanisms of the heritable predisposition to lethal glioma in ~40% of LGG patients.

Abstract Low-grade glioma (LGG) are generally slowly growing brain cancers, that frequently undergo malignant progression to aggressive, secondary glioblastoma with a dismal prognosis. By combining genetically engineered Idh1-mutant mice with in vivo CRISPR gene editing we generated a mouse model faithfully recapitulating the founder mutations of LGG. Clonal activation of the neomorphic Idh1 R132H mutation cooperates with Trp53 and Atrx mutations to trigger development of brain tumors but only with ~30% penetrance and very long latency. To elucidate the molecular mechanisms underlying the malignant progression of IDH1-mutant LGG, we devised and deployed a direct in vivo CRISPR screen targeting genes commonly mutated in human IDH-mutant secondary glioblastoma. Stereotaxic delivery of a lentiviral sgRNA library targeting the mouse orthologs of these genes into the brain of Idh1 R132H ;Trp53;Atrx;Cas9 and control Idh1 wt ;Trp53;Atrx;Cas9 compound mutant mice resulted in rapid formation of tumors that recapitulate human Idh1-mutant glioblastoma. Deconvoluting the screen showed that PI3K pathway members Pten and Pik3ca as well as Notch1, Smarca4 and Fat1 are preferentially enriched in Idh1 R132H-tumors, while Rb1 and NF2 were enriched in Idh1 wt tumors. Co-mutation analysis further identified additional co-occurring driver combinations such as Bcor-Met, Olig2-Met, Olig2-Med12 or Bcor-Olig2. We validated the tumor suppressive function of Notch1 and Pten using conventional floxed knock-out alleles and found that Notch1 functions in a haploinsufficient manner. Interestingly, Idh1 R132H did not alter tumor latency or pathology in a high grade p53;Pten;Rb1 mutant background, indicating that the neomorphic IDH-mutations can drive low but not high grade glioma development. Our study provides a functional landscape of gliomagenesis suppressors in vivo.