Restoration of neuronal progenitors by partial reprogramming in the aged neurogenic niche

Partial reprogramming (pulsed expression of reprogramming transcription factors) improves the function of several tissues in old mice. However, it remains largely unknown how partial reprogramming impacts the old brain. Here we use single-cell transcriptomics to systematically examine how partial reprogramming influences the subventricular zone neurogenic niche in aged mouse brains. Whole-body partial reprogramming mainly improves neuroblasts (cells committed to give rise to new neurons) in the old neurogenic niche, restoring neuroblast proportion to more youthful levels. Interestingly, targeting partial reprogramming specifically to the neurogenic niche also boosts the proportion of neuroblasts and their precursors (neural stem cells) in old mice and improves several molecular signatures of aging, suggesting that the beneficial effects of reprogramming are niche intrinsic. In old neural stem cell cultures, partial reprogramming cell autonomously restores the proportion of neuroblasts during differentiation and blunts some age-related transcriptomic changes. Importantly, partial reprogramming improves the production of new neurons in vitro and in old brains. Our work suggests that partial reprogramming could be used to rejuvenate the neurogenic niche and counter brain decline in old individuals.

Rewiring of RNA methylation by the oncometabolite fumarate in renal cell carcinoma

Metabolic reprogramming is a hallmark of cancer that facilitates changes in many adaptive biological processes. Mutations in the tricarboxylic acid cycle enzyme fumarate hydratase (FH) lead to fumarate accumulation and cause hereditary leiomyomatosis and renal cell cancer (HLRCC). HLRCC is a rare, inherited disease characterized by the development of non-cancerous smooth muscle tumors of the uterus and skin, and an increased risk of an aggressive form of kidney cancer. Fumarate has been shown to inhibit 2-oxoglutarate-dependent dioxygenases (2OGDDs) involved in the hydroxylation of HIF1α, as well as in DNA and histone demethylation. However, the link between fumarate accumulation and changes in RNA post-transcriptional modifications has not been defined. Here, we determine the consequences of fumarate accumulation on the activity of different members of the 2OGDD family targeting RNA modifications. By evaluating multiple RNA modifications in patient-derived HLRCC cell lines, we show that mutation of FH selectively affects the levels of N6-methyladenosine (m6A), while the levels of 5-formylcytosine (f5C) in mitochondrial tRNA are unaffected. This supports the hypothesis of a differential impact of fumarate accumulation on distinct RNA demethylases. The observation that metabolites modulate specific subsets of RNA-modifying enzymes offers new insights into the intersection between metabolism and the epitranscriptome.

Abstract 4108: Understanding the role of telomere biology gene variation in cancer etiology

Telomere biology disorders (TBDs) are cancer-prone syndromes associated with increased risk of acute myeloid leukemia (AML), head and neck squamous cell carcinoma (HNSCC), bone marrow failure, pulmonary fibrosis, and liver disease. Germline variants in at least 15 different telomere biology genes have been implicated (ACD, CTC1, TERT, TERC, STN1, NAF1, NOP10, NHP2, TINF2, RTEL1, PARN, ZCCHC8, DKC1, WRAP53, POT1) with autosomal dominant (AD), autosomal recessive (AR), or X-linked (XLR) inheritance as well as de novo occurrence. We hypothesize that TBDs may be more common than the currently estimated 1:1,000,000.

We analyzed the prevalence of germline variants in the 15 TBD-associated genes using 1) The Genome Aggregation Database [gnomAD v2.1.1 non-cancer] and 2) The Cancer Genome Atlas (TCGA). Germline TCGA variants were called using HaplotypeCaller, Freebayes, and UnifiedGenotyper. All variants with minor allele frequency (MAF) <1% in gnomAD non-cancer were considered. They were classified as potentially deleterious based on ClinVar and/or loss of function classification and/or stringent in silico predictions utilizing REVEL, MetaSVM, CADD, BayesDel, Eigen for missense and a combination of spliceAI, spidex, and dbscSNV for splice site variants. For TERC (RNA telomerase template) variants in the pseudoknot/template region were considered deleterious. The known disease-causing inheritance pattern (AD, AR, XLR) for each gene was used to identify TCGA cases with a probable TBD.

There were 1215 potentially deleterious variants in TBD associated genes in the gnomAD v2.1.1 non-cancer dataset (n=134,187 samples) for a combined prevalence of 0.9%, without accounting for zygosity. In genes with AD/AR inheritance, variants were most common in: RTEL1 (249), TERT (104), and PARN (104). CTC1 and WRAP53, both associated with solely AR TBDs, also showed high variant frequencies (280 and 102, respectively). In the TCGA dataset, 9089 cancer cases (32 solid tumors and AML) were evaluated. We identified 227 cases (2.5%) with 161 mono- or biallelic rare, potentially deleterious variants in the 15 genes. Ninety-two cases had a probable underlying TBD [1% of total, 41 male, 51 female, median age at cancer diagnosis 46.5 (1-92) years]. Cancer diagnoses in these 92 cases included 24 solid tumors. The frequency of individuals with deleterious TBD-associated variants ranged from 0.4-2.8% in each of the 24 affected cancers. Notably, the heterozygous frequencies in lung squamous cell carcinoma and liver hepatocellular carcinoma were 1.6% and 2.2%, respectively. Our results show that the prevalence of TBDs may be noticeably higher than previously estimated, specifically in individuals with cancer. TBD-associated pathogenic germline variants may be implicated in the etiology of more solid tumor entities than previously recognized, warranting further studies.

Citation Format: Marena R. Niewisch, Jung Kim, Judith C. Lunger, Lisa J. McReynolds, Sharon A. Savage. Understanding the role of telomere biology gene variation in cancer etiology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4108.

You Get a Modification, and You Get a Modification… Everyone Gets a Modification!

In this issue of Molecular Cell,Sun et al. (2020) identify ERK-mediated phosphorylation of the m⁶A methyltransferase complex as a regulatory mechanism for m⁶A and pluripotency and highlight the potential of this interaction as a target for cancer therapy.