The Benefits and Detriments of Aneuploidy in Cancer

Aneuploidy, defined as having a chromosome number that is not a multiple of the organism’s haploid number, is a hallmark of cancer. This creates an imbalanced karyotype, where the copy number of hundreds or thousands of genes is altered. About 90% of solid tumors and 70% of blood cancers are aneuploid. How does aneuploidy affect cancer cells? These copy number alterations affect expression at the RNA and protein level, which causes numerous problems for cells. Aneuploidy increases genomic instability, both through higher rates of DNA damage and causing more chromosome missegregation. The proteome is also significantly challenged; excess proteins aggregate or must be degraded and stress chaperones and the proteasome. These stresses culminate in slow proliferation, particularly through G1 of the cell cycle, relative to euploid cells. However, evidence is growing for the ways that aneuploidy benefits cancer cell fitness. Aneuploidy is associated with poor patient survival in cancer. In chapter 2, this dissertation describes another effect of aneuploidy: increased resistance to a wide variety of drugs. The slower proliferation of aneuploid cells is the predominant mechanism that protects them from some of the most common chemotherapeutics used today. When proliferation rate is equal between euploid and aneuploid cells, the chemotherapy resistance caused by aneuploidy mostly disappears; however, there is also some evidence for aneuploidy-induced-chemotherapeutic-resistance not explained by the cell cycle defects of aneuploidy. Beyond drug resistance, aneuploidy may benefit cancer cell fitness in other ways: there is growing, but still mixed, evidence that aneuploidy may promote immune-evasion of tumors and increase metastasis. This dissertation discusses the current evidence for how aneuploidy may provide advantages to a cancer cell. Outside of cancer, several chromosomal disorders exist, including Down syndrome, which may be better understood through aneuploidy. The appendix of this dissertation explores aneuploidy-tolerance and how trisomy 21 cells can relieve their proliferation deficit. A CRISPR screen for improved growth of trisomy 21 cells identified several genes of interest that may specifically contribute to proliferation of trisomy 21 cells. Ultimately, more work is needed to understand how these genes of interest interact with aneuploidy and trisomy 21 to affect proliferation.Ph.D

A <i>cis</i>-regulatory antisense RNA represses translation in <i>Vibrio cholerae</i> through extensive complementarity and proximity to the target locus

<div><p>As with all facultative pathogens, <i>Vibrio cholerae</i> must optimize its cellular processes to adapt to different environments with varying carbon sources and to environmental stresses. More specifically, in order to metabolize mannitol, <i>V. cholerae</i> must regulate the synthesis of MtlA, a mannitol transporter protein produced exclusively in the presence of mannitol. We previously showed that a <i>cis</i>-acting small RNA (sRNA) expressed by <i>V. cholerae,</i> MtlS, appears to post-transcriptionally downregulate the expression of <i>mtlA</i> and is produced in the absence of mannitol. We hypothesized that since it is complementary to the 5′ untranslated region (UTR) of <i>mtlA</i> mRNA, MtlS may affect synthesis of MtlA by forming an <i>mtlA</i>-MtlS complex that blocks translation of the mRNA through occlusion of its ribosome binding site. To test this hypothesis, we used in vitro translation assays in order to examine the role MtlS plays in <i>mtlA</i> regulation and found that MtlS is sufficient to suppress translation of transcripts harboring the 5′ UTR of <i>mtlA</i>. However, in a cellular context, the 5′ UTR of <i>mtlA</i> is not sufficient for targeted repression by endogenous MtlS; additional segments from the coding region of <i>mtlA</i> play a role in the ability of the sRNA to regulate translation of <i>mtlA</i> mRNA. Additionally, proximity of transcription sites between the sRNA and mRNA significantly affects the efficacy of MtlS.</p></div

Aneuploidy increases resistance to chemotherapeutics by antagonizing cell division

© 2020 National Academy of Sciences. All rights reserved. Aneuploidy, defined as whole chromosome gains and losses, is associated with poor patient prognosis in many cancer types. However, the condition causes cellular stress and cell cycle delays, foremost in G1 and S phase. Here, we investigate how aneuploidy causes both slow proliferation and poor disease outcome. We test the hypothesis that aneuploidy brings about resistance to chemotherapies because of a general feature of the aneuploid condition—G1 delays. We show that single chromosome gains lead to increased resistance to the frontline chemotherapeutics cisplatin and paclitaxel. Furthermore, G1 cell cycle delays are sufficient to increase chemotherapeutic resistance in euploid cells. Mechanistically, G1 delays increase drug resistance to cisplatin and paclitaxel by reducing their ability to damage DNA and microtubules, respectively. Finally, we show that our findings are clinically relevant. Aneuploidy correlates with slowed proliferation and drug resistance in the Cancer Cell Line Encyclopedia (CCLE) dataset. We conclude that a general and seemingly detrimental effect of aneuploidy, slowed proliferation, provides a selective benefit to cancer cells during chemotherapy treatment

Multiple sclerosis genomic map implicates peripheral immune cells and microglia in susceptibility

INTRODUCTION: Multiple sclerosis (MS) is an inflammatory and degenerative disease of the central nervous system (CNS) that often presents in young adults. Over the past decade, certain elements of the genetic architecture of susceptibility have gradually emerged, but most of the genetic risk for MS remained unknown. RATIONALE: Earlier versions of the MS genetic map had highlighted the role of the adaptive arm of the immune system, implicating multiple different T cell subsets. We expanded our knowledge of MS susceptibility by performing a genetic association study in MS that leveraged genotype data from 47,429 MS cases and 68,374 control subjects. We enhanced this analysis with an in-depth and comprehensive evaluation of the functional impact of the susceptibility variants that we uncovered. RESULTS: We identified 233 statistically independent associations with MS susceptibility that are genome-wide significant. The major histocompatibility complex (MHC) contains 32 of these associations, and one, the first MS locus on a sex chromosome, is found in chromosome X. The remaining 200 associations are found in the autosomal non-MHC genome. Our genome-wide partitioning approach and large-scale replication effort allowed the evaluation of other variants that did not meet our strict threshold of significance, such as 416 variants that had evidence of statistical replication but did not reach the level of genome-wide statistical significance. Many of these loci are likely to be true susceptibility loci. The genome-wide and suggestive effects jointly explain ~48% of the estimated heritability for MS. Using atlases of gene expression patterns and epigenomic features, we documented that enrichment for MS susceptibility loci was apparent in many different immune cell types and tissues, whereas there was an absence of enrichment in tissue-level brain profiles. We extended the annotation analyses by analyzing new data generated from human induced pluripotent stem cell–derived neurons as well as from purified primary human astrocytes and microglia, observing that enrichment for MS genes is seen in human microglia, the resident immune cells of the brain, but not in astrocytes or neurons. Further, we have characterized the functional consequences of many MS susceptibility variants by identifying those that influence the expression of nearby genes in immune cells or brain. Last, we applied an ensemble of methods to prioritize 551 putative MS susceptibility genes that may be the target of the MS variants that meet a threshold of genome-wide significance. This extensive list of MS susceptibility genes expands our knowledge more than twofold and highlights processes relating to the development, maturation, and terminal differentiation of B, T, natural killer, and myeloid cells that may contribute to the onset of MS. These analyses focus our attention on a number of different cells in which the function of MS variants should be further investigated. Using reference protein-protein interaction maps, these MS genes can also be assembled into 13 communities of genes encoding proteins that interact with one another; this higher-order architecture begins to assemble groups of susceptibility variants whose functional consequences may converge on certain protein complexes that can be prioritized for further evaluation as targets for MS prevention strategies. CONCLUSION: We report a detailed genetic and genomic map of MS susceptibility, one that explains almost half of this disease’s heritability. We highlight the importance of several cells of the peripheral and brain resident immune systems—implicating both the adaptive and innate arms—in the translation of MS genetic risk into an auto-immune inflammatory process that targets the CNS and triggers a neurodegenerative cascade. In particular, the myeloid component highlights a possible role for microglia that requires further investigation, and the B cell component connects to the narrative of effective B cell–directed therapies in MS. These insights set the stage for a new generation of functional studies to uncover the sequence of molecular events that lead to disease onset. This perspective on the trajectory of disease onset will lay the foundation for developing primary prevention strategies that mitigate the risk of developing MS