Multiple neural bHLHs ensure the precision of a neuronal specification event in C. elegans

Neural bHLH transcription factors play a key role in the early steps of neuronal specification in many animals. We have previously observed that the Achaete-Scute HLH-3, the Olig HLH-16 and their binding partner the E protein HLH-2 activate the terminal differentiation program of a specific class of cholinergic neurons, AIY, in C. elegans. Here we identify a role for a fourth bHLH, the Neurogenin NGN-1, in this process, raising the question of why so many neural bHLHs are required for a single neuronal specification event. Using quantitative imaging we show that the combined action of different bHLHs is needed to activate the correct level of expression of the terminal selector transcription factors TTX-3 and CEH-10 that subsequently initiate and maintain the expression of a large battery of terminal differentiation genes. Surprisingly, the different bHLHs have an antagonistic effect on another target, the proapoptotic BH3-only factor EGL-1, normally not expressed in AIY and otherwise detrimental for its specification. We propose that the use of multiple neural bHLHs allows robust neuronal specification while, at the same time, preventing spurious activation of deleterious genes.

CRISPR/Cas-mediated chromosome engineering: opening up a new avenue for plant breeding

The advent of powerful site-specific nucleases, particularly the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system, which enables precise genome manipulation, has revolutionized plant breeding. Until recently, the main focus of researchers has been to simply knock-in or knock-out single genes, or to induce single base changes, but constant improvements of this technology have enabled more ambitious applications that aim to improve plant productivity or other desirable traits. One long-standing aim has been the induction of targeted chromosomal rearrangements (crossovers, inversions, or translocations). The feasibility of this technique has the potential to transform plant breeding, because natural rearrangements, like inversions, for example, typically present obstacles to the breeding process. In this way, genetic linkages between traits could be altered to combine or separate favorable and deleterious genes, respectively. In this review, we discuss recent breakthroughs in the field of chromosome engineering in plants and their potential applications in the field of plant breeding. In the future, these approaches might be applicable in shaping plant chromosomes in a directed manner, based on plant breeding needs.

Targeting uncoupling of copy number and gene expression in cancers

The high degree of aneuploidy in cancer is likely tolerated via extensive uncoupling of copy number (CN) and mRNA expression (UCNE) of deleterious genes located in copy number aberrations (CNAs). To test the extent and role of UCNE in cancer, we performed integrative analysis of multiomics data across The Cancer Genome Atlas (TCGA), encompassing ∼ 5000 individual tumors. We found many genes having UCNE, the degree of which are associated with increased oncogenic signaling, proliferation and immune-suppression. The occurrence of UCNE appears to be orchestrated by complex epigenetic and regulatory changes, with transcription factors (TFs) playing a prominent role. To further dissect the regulatory mechanisms, we developed a systems-biological approach to identify candidate TFs, which upon perturbation can offset UCNE and reduce tumor fitness. Applying our approach on TCGA data, we identified 20 putative targets, 45% of which were validated by independent sources. Among them are IRF1, which plays a prominent role in anti-tumor immunity and response to immune checkpoint therapy, ETS1, TRIM21 and GATA3, which are associated with anti-tumor immunity, tumor proliferation and metastasis. Together, our study indicates that UCNE is likely an important mechanism in cancer development that can be exploited therapeutically.

Simulation of Karyotype Evolution and Biodiversity in Asexual and Sexual Reproduction

Whether sexual reproduction increases biodiversity remains controversial. Traditionally, sex within a species has been thought to increase genetic diversity, inferring an acceleration of macro-evolution, promoting biodiversity. Recently, it was suggested that the main function of sex is to maintain genome integrity, rather than increase genetic diversity or purify deleterious genes within populations, as the karyotype encodes/safeguards the genomic blueprint. As such, the contribution of sex to biodiversity needs to be re-examined. Since many simulation studies focus only on gene-level selection, it is important to investigate how sexual and asexual reproduction differentially impact patterns of genome-level evolution and biodiversity. Based on the key difference between sexual and asexual reproduction, that sexual individuals are required to mate with a partner of the same genome for successful reproduction, we have performed a simulation to illustrate how such differences impact genome-mediated biodiversity. Asexual populations displayed high genome-level diversity whereas sexual populations evidenced low genome-level diversity. Further analysis demonstrated that the requirement of finding a partner possessing a compatible genome prevents new sexual species from emerging, which may explain why geographic isolation can promote speciation: by increasing mating and survival-domination opportunities. This study challenges the traditional concepts of speciation and the function of sex.

Synthesis and in vitro assessment of chemically modified siRNAs targeting BCL2 that contain 2′-ribose and triazole-linked backbone modifications

Short-interfering RNAs (siRNAs) are naturally occurring biomolecules used for post-transcriptional gene regulation, and therefore hold promise as a future therapeutic by silencing gene expression of overexpressed deleterious genes.

Integrative Network Analysis of Pediatric AML Whole Genomes, cDNA Expression and Clinical Data Elements Reveals Shared As Well As t(8;21), Inv16 and MLL Specific Pathways; A Report From COG/NCI Target AML Initiative

Abstract 3519 Pediatric Acute Myeloid Leukemia (AML) offers a unique window into the genesis and progression of hematologic cancers because of its rapid progression and limited confounding factors. As part of the NCI TARGET AML initiative (target.cancer.gov), we report the initial integrative analysis of 58 pediatric AML whole-genome sequences [WGS, performed by Complete Genomics Inc. (CGI)] along with 225 Affymetrix microarrays, clinical cytogenetic and biomarker tests. WGS was performed on matched samples collected at diagnosis and remission from each patient. Candidate variants were identified by CGI and defined as being present only in tumor samples. To focus on the highest confidence variant calls, we developed stringent filters based on a set of 281 true-positive and 44 false-positive verified variants. We identified a total of 629 high-confidence variants in 58 cases (∼ 11 per patient). 99 of these variants occurred in 39 genes (2 to 8 per gene, up to 4 per sample). Analysis of the potential functional consequence of these variants identified 28 as deleterious impacting 17 genes in 21 of the 58 relapsed AMLs, including multiple mutations in AML-associated genes such as KIT, NRAS, PTPN11, and WT1, and several key hematopoietic genes (e.g. IKZF1, GATA2). Using microarray expression data, we identified 1,992 (1,051) genes that were differentially expressed in pediatric AML cases compared to 4 normal bone marrow samples [FDR-adjusted p-value = 0.05 (0.01)]. 249 differentially expressed genes were more than 6 standard deviations away from the control average in more than half of the samples (e.g. WT1, MYCN, miR155), suggesting the existence of a shared set of dysregulated processes across most pediatric AMLs. Network-oriented enrichment analysis using the Bioconductor (http://bioconductor.org) package DEGraph revealed differentially regulated interactions among 3,496 genes, including 1,437 cancer genes and highly enriched interactions involving growth factor/RTK signaling, down-regulated immune processes, and up-regulated transcription and translation. To pinpoint processes specific to AML subtypes, we used the Bioconductor package WGCNA to cluster the 225 microarray expression datasets and align them with clinically-identified cytogenetic and mutation data. We identified five distinct expression clusters. Three of these clusters corresponded to known cytogenetic abnormalities: MLL fusions, t(8;21), and Inv16. The other two clusters were cytogenetically normal, but all members of one cluster carry CEBPA mutations. The expression patterns of cases with t(8;21) and Inv16, while distinct, shared a number of features that distinguished them from samples with MLL abnormalities. For example, in both t(8;21) and Inv16 cases (but not in MLL cases) the fibroblast growth factor (FGF) receptor FGFR1 and the FGF ligand FGF11 were over-expressed compared to control samples. These differences may explain the higher rates of remission associated with Core Binding Factor (CBF) abnormalities. To identify potential relationships between sequence variants and differentially expressed genes, we used the Graphite Bioconductor package to search four publicly available databases (Reactome, NCI PID, KEGG, Biocarta) for known interactions of our candidate deleterious genes. Surprisingly, all but two of our candidate deleterious genes shared many interactors, suggesting they impacted shared processes. The core connected components of the mutation interaction network were all members of the set of dysregulated interactions that we identified by gene expression analysis and included multiple members of well-known pathways implicated in AML and other cancers (e.g. RTK/growth factor signaling, JAK/STAT signaling). Candidate mutations impacted both shared and distinct pathways. Furthermore, within shared pathways, the candidate mutations impacted shared and distinct targets. These findings have important implications for pathway-specific drug targeting. Comparing the interactions of candidate WGS mutations with those of clinically-identified chromosomal abnormalities, a further pattern emerges: CBF and MLL associated gene fusions appeared to impact a different set of genes and processes compared to WGS (presumably second-hit) variants, suggesting complementary roles. This finding has important implications for ongoing research and testing of targeted treatments. Disclosures: No relevant conflicts of interest to declare.

The coevolution of toxin and antitoxin genes drives the dynamics of bacterial addiction complexes and intragenomic conflict

Bacterial genomes commonly contain ‘addiction’ gene complexes that code for both a toxin and a corresponding antitoxin. As long as both genes are expressed, cells carrying the complex can remain healthy. However, loss of the complex (including segregational loss in daughter cells) can entail death of the cell. We develop a theoretical model to explore a number of evolutionary puzzles posed by toxin–antitoxin (TA) population biology. We first extend earlier results demonstrating that TA complexes can spread on plasmids, as an adaptation to plasmid competition in spatially structured environments, and highlight the role of kin selection. We then considered the emergence of TA complexes on plasmids from previously unlinked toxin and antitoxin genes. We find that one of these traits must offer at least initially a direct advantage in some but not all environments encountered by the evolving plasmid population. Finally, our study predicts non-transitive ‘rock-paper-scissors’ dynamics to be a feature of intragenomic conflict mediated by TA complexes. Intragenomic conflict could be sufficient to select deleterious genes on chromosomes and helps to explain the previously perplexing observation that many TA genes are found on bacterial chromosomes.

Human lifespan: what determines the intrinsic length of human lives?

SummaryHumans have an intrinsic lifespan of approximately 120 years. Classic evolutionary theories of ageing explain the limit as a response to inevitable cellular damage. The theories share the notion that natural selection acts less strongly to purge deleterious genes that are expressed after reproduction. Reproduction schedules are influenced by a species' ecology and so it is ecological factors which explain interspecies variation in lifespan. Human ecology has favoured the selection of an unusually large brain that both confers advantages that promote longevity and requires longevity to make it a worthwhile investment. The relatively long human lifespan therefore co-evolved with the large human brain.