bims-ginsta 2023-08-13 papers

Issue of 2023‒08‒13
six papers selected by
Jinrong Hu, National University of Singapore

Chromosome Res. 2023 Aug 10. 31(3): 19

Chromosomal instability and inflammation: a catch-22 for cancer cells.

Anouk van den Brink, Maria F Suárez Peredo Rodríguez, Floris Foijer.

Chromosomal instability (CIN), an increased rate of chromosomal segregation abnormalities, drives intratumor heterogeneity and affects most human cancers. In addition to chromosome copy number alterations, CIN results in chromosome(s) (fragments) being mislocalized into the cytoplasm in the form of micronuclei. Micronuclei can be detected by cGAS, a double-strand nucleic acid sensor, which will lead to the production of the second messenger 2'3'-cGAMP, activation of an inflammatory response, and downstream immune cell activation. However, the molecular network underlying the CIN-induced inflammatory response is still poorly understood. Furthermore, there is emerging evidence that cancers that display CIN circumvent this CIN-induced inflammatory response, and thus immune surveillance. The STAT1, STAT3, and NF-κB signaling cascades appear to play an important role in the CIN-induced inflammatory response. In this review, we discuss how these pathways are involved in signaling CIN in cells and how they are intertwined. A better understanding of how CIN is being signaled in cells and how cancer cells circumvent this is of the utmost importance for better and more selective cancer treatment.

Keywords: Aneuploidy; CIN-induced inflammation; Chromosomal instability

DOI: https://doi.org/10.1007/s10577-023-09730-y

Proc Natl Acad Sci U S A. 2023 08 15. 120(33): e2305002120

Partial cytological diploidization of neoautotetraploid meiosis by induced cross-over rate reduction.

Adrián Gonzalo, Pablo Parra-Nunez, Andreas L Bachmann, Eugenio Sanchez-Moran, Kirsten Bomblies.

Polyploids, which arise from whole-genome duplication events, have contributed to genome evolution throughout eukaryotes. Among plants, novel features of neopolyploids include traits that can be evolutionarily or agriculturally beneficial, such as increased abiotic stress tolerance. Thus, in addition to being interesting from an evolutionary perspective, genome duplication is also increasingly recognized as a promising crop improvement tool. However, newly formed (neo)polyploids commonly suffer from fertility problems, which have been attributed to abnormal associations among the multiple homologous chromosome copies during meiosis (multivalents). Here, we test the long-standing hypothesis that reducing meiotic cross-over number may be sufficient to limit multivalent formation, favoring diploid-like bivalent associations (cytological diploidization). To do so, we developed Arabidopsis thaliana lines with low cross-over rates by combining mutations for HEI10 and TAF4b. Double mutants showed a reduction of ~33% in cross-over numbers in diploids without compromising meiotic stability. Neopolyploids derived from the double mutant show a cross-over rate reduction of about 40% relative to wild-type neotetraploids, and groups of four homologs indeed formed fewer multivalents and more bivalents. However, we also show that the reduction in multivalents comes with the cost of a slightly increased frequency of univalents and that it does not rescue neopolyploid fertility. Thus, while our results do show that reducing cross-over rates can reduce multivalent frequency in neopolyploids, they also emphasize that there are additional factors affecting both meiotic stability and neopolyploid fertility that will need to be considered in solving the neopolyploid fertility challenge.

Keywords: autotetraploid; multivalent; polyploidy; recombination rate

DOI: https://doi.org/10.1073/pnas.2305002120

Nat Struct Mol Biol. 2023 Aug 10.

Replication dynamics identifies the folding principles of the inactive X chromosome.

Rawin Poonperm, Saya Ichihara, Hisashi Miura, Akie Tanigawa, Koji Nagao, Chikashi Obuse, Takashi Sado, Ichiro Hiratani.

Chromosome-wide late replication is an enigmatic hallmark of the inactive X chromosome (Xi). How it is established and what it represents remains obscure. By single-cell DNA replication sequencing, here we show that the entire Xi is reorganized to replicate rapidly and uniformly in late S-phase during X-chromosome inactivation (XCI), reflecting its relatively uniform structure revealed by 4C-seq. Despite this uniformity, only a subset of the Xi became earlier replicating in SmcHD1-mutant cells. In the mutant, these domains protruded out of the Xi core, contacted each other and became transcriptionally reactivated. 4C-seq suggested that they constituted the outermost layer of the Xi even before XCI and were rich in escape genes. We propose that this default positioning forms the basis for their inherent heterochromatin instability in cells lacking the Xi-binding protein SmcHD1 or exhibiting XCI escape. These observations underscore the importance of 3D genome organization for heterochromatin stability and gene regulation.

DOI: https://doi.org/10.1038/s41594-023-01052-1

Trends Mol Med. 2023 Aug 07. pii: S1471-4914(23)00158-2. [Epub ahead of print]

The NRF2/Keap1 pathway as a therapeutic target in inflammatory bowel disease.

Sem Geertsema, Arno R Bourgonje, Raphael R Fagundes, Ranko Gacesa, Rinse K Weersma, Harry van Goor, Giovanni E Mann, Gerard Dijkstra, Klaas N Faber.

Oxidative stress (OS) is an important pathophysiological mechanism in inflammatory bowel disease (IBD). However, clinical trials investigating compounds directly targeting OS in IBD yielded mixed results. The NRF2 (nuclear factor erythroid 2-related factor 2)/Keap1 (Kelch-like ECH-associated protein 1) pathway orchestrates cellular responses to OS, and dysregulation of this pathway has been implicated in IBD. Activation of the NRF2/Keap1 pathway may enhance antioxidant responses. Although this approach could help to attenuate OS and potentially improve clinical outcomes, an overview of human evidence for modulating the NRF2/Keap1 axis and more recent developments in IBD is lacking. This review explores the NRF2/Keap1 pathway as potential therapeutic target in IBD and presents compounds activating this pathway for future clinical applications.

Keywords: NRF2/Keap1 pathway; inflammatory bowel disease; oxidative stress; personalized medicine; redox medicine

DOI: https://doi.org/10.1016/j.molmed.2023.07.008

medRxiv. 2023 Jul 24. pii: 2023.07.22.23292618. [Epub ahead of print]

Identifying risk genes for embryo aneuploidy using ultra-low coverage whole-genome sequencing.

Siqi Sun, Mansour Aboelenain, Daniel Ariad, Mary E Haywood, Charles R Wageman, Marlena Duke, Aishee Bag, Manuel Viotti, Mandy Katz-Jaffe, Rajiv C McCoy, Karen Schindler, Jinchuan Xing.

Background: Aneuploidy, the state of a cell containing extra or missing chromosomes, frequently arises during human meiosis and is the primary cause of early miscarriage and maternal age-related in vitro fertilization (IVF) failure. IVF patients exhibit significant variability in aneuploidy rates, although the exact genetic causes of the variability in aneuploid egg production remain unclear. Preimplantation genetic testing for aneuploidy (PGT-A) using ultra-low coverage whole-genome sequencing (ulc-WGS) is a standard test for identifying and selecting IVF-derived embryos with a normal chromosome complement. The wealth of embryo aneuploidy data and ulc-WGS data from PGT-A has potential for discovering variants in paternal genomes that are associated with aneuploidy risk in their embryos.Methods: Using ulc-WGS data from ∼10,000 PGT-A biopsies, we imputed genotype likelihoods of genetic variants in parental genomes. We then used the imputed variants and aneuploidy calls from the embryos to perform a genome-wide association study of aneuploidy incidence. Finally, we carried out functional evaluation of the identified candidate gene in a mouse oocyte system.
Results: We identified one locus on chromosome 3 that is significantly associated with maternal meiotic aneuploidy risk. One candidate gene, CCDC66, encompassed by this locus, is involved in chromosome segregation during meiosis. Using mouse oocytes, we showed that CCDC66 regulates meiotic progression and chromosome segregation fidelity, especially in older mice.
Conclusions: Our work extended the research utility of PGT-A ulc-WGS data by allowing robust association testing and improved the understanding of the genetic contribution to maternal meiotic aneuploidy risk. Importantly, we introduce a generalizable method that can be leveraged for similar association studies using ulc-WGS data.

DOI: https://doi.org/10.1101/2023.07.22.23292618

Curr Opin Physiol. 2023 Aug;34 None

Spatiotemporal regulation of Rho GTPase signaling during endothelial barrier remodeling.

Jeffrey Ma van der Krogt, Ivanka Je van der Meulen, Jaap D van Buul.

The vasculature is characterized by a thin cell layer that comprises the inner wall of all blood vessels, the continuous endothelium. Endothelial cells can also be found in the eye's cornea. And even though cornea and vascular endothelial (VE) cells differ from each other in structure, they both function as barriers and express similar junctional proteins such as the adherens junction VE-cadherin and tight-junction member claudin-5. How these barriers are controlled to maintain the barrier and thereby its integrity is of major interest in the development of potential therapeutic targets. An important target of endothelial barrier remodeling is the actin cytoskeleton, which is centrally coordinated by Rho GTPases that are in turn regulated by Rho-regulatory proteins. In this review, we give a brief overview of how Rho-regulatory proteins themselves are spatiotemporally regulated during the process of endothelial barrier remodeling. Additionally, we propose a roadmap for the comprehensive dissection of the Rho GTPase signaling network in its entirety.

DOI: https://doi.org/10.1016/j.cophys.2023.100676