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Wang, D.

Publications and source records attributed to Wang, D..

47 records · Page 3Linked to original sources

Genetic load and mutational meltdown in cancer cell populations

ABSRACTLarge and non-recombining genomes are prone to accumulating deleterious mutations faster than natural selection can purge (Mullers ratchet). A possible consequence would then be the extinction of small populations. Relative to most single-cell organisms, cancer cells, with large and non-recombining genomes, could be particularly susceptible to such \"mutational meltdown\". Curiously, deleterious mutations in cancer cells are rarely noticed despite the strong signals in cancer genome sequences. Here, by monitoring single-cell clones from HeLa cell lines, we characterize deleterious mutations that retard cell proliferation. The main mutational events are copy number variations (CNVs), which happen at an extraordinarily high rate of 0.29 events per cell division. The average fitness reduction, estimated to be 18% per mutation, is also very high. HeLa cell populations therefore have very substantial genetic load and, at this level, natural population would likely experience mutational meltdown. We suspect that HeLa cell populations may avoid extinction only after the population size becomes large. Because CNVs are common in most cell lines and cancer tissues, the observations hint at cancer cells vulnerability, which could be exploited by therapeutic strategies.

evolutionary biology

Spike-Timing Patterns Conform to Gamma Distribution with Regional and Cell Type-Specific Characteristics

Spike-timing patterns - crucial for synaptic plasticity and neural computation - are often modeled as Poisson-like random processes, log-normal distribution or gamma-distribution patterns, each with different underlying assumptions that may or may not be biologically true. However, it is not entirely clear whether (and how well) these different models would or would not capture spike-timing statistical patterns across different neurons, regions, animal species and cognitive states. Here, we examine statistical patterns of spike-timing irregularity in 13 different cortical and subcortical regions from mouse, hamster, cat and monkey brains. In contrast to the widely-assumed Poisson or log-normal distribution patterns, we show that spike-timing patterns of various projection neurons-including cortical excitatory principal cells, hippocampal pyramidal cells, inhibitory striatal medium spiny neurons and dopaminergic neurons, as well as fast-spiking interneurons - all invariantly conform to the gamma-distribution model. While higher regularity in spike-timing patterns are observed in a few cases, such as mouse DA neurons and monkey motor cortical neurons, there is no clear tendency in increased firing regularity from the sensory and subcortical neurons to prefrontal or motor cortices, as previously entertained. Moreover, gamma shapes of spike-timing patterns remain robust over various natural cognitive states, such as sleep, awake periods, or during fearful episodic experiences. Interestingly, ketamine-induced general anesthesia or unconsciousness is associated with the breakdown of forebrain spike patterns from a singular gamma distribution into two distinct subtypes of gamma distributions, suggesting the importance of this spike-timing pattern in supporting natural cognitive states. These results suggest that gamma-distribution patterns of spike timing reflect not only a fundamental property conserved across different neurons, regions and animal species, but also an operation crucial for supporting natural cognitive states. Such gamma-distribution-based spike-timing patterns can also have important implications for real-time neural coding and realistic neuromorphic computing.

neuroscience

An Intracellular Pathogen Response Pathway Promotes Proteostasis In C. elegans

Maintenance of proteostasis is critical for organismal health. Here we describe a novel pathway that promotes proteostasis, identified through the analysis of C. elegans genes upregulated by intracellular infection. We named this distinct transcriptional signature the Intracellular Pathogen Response (IPR), and it includes upregulation of several predicted ubiquitin ligase complex components such as the cullin cul-6. Through a forward genetic screen we found pals-22, a gene of previously unknown function, to be a repressor of the cul-6/Cullin gene and other IPR gene expression. Interestingly, pals-22 mutants have increased thermotolerance and reduced levels of stress-induced polyglutamine aggregates, likely due to upregulated IPR expression. We found the enhanced stress resistance of pals-22 mutants to be dependent on cul-6, suggesting that pals-22 mutants have increased activity of a CUL-6/Cullin-containing ubiquitin ligase complex. pals-22 mutant phenotypes are distinct from the well-studied heat shock and insulin signaling pathways, indicating that the IPR is a novel pathway that protects animals from proteotoxic stress.

genetics

Epigenetic Reprogramming of Tissue-Specific Transcription Promotes Metastasis

Tumor metastasis is the cause of death for 90% of cancer patients, and no currently-available therapies target this multi-step process in which cancer cells spread from the local tissue of a primary tumor to distant organs where they establish secondary tumors1. Although epithelial-to-mesenchymal transition2, tumor-secreted exosomes3, epigenetic regulators as well as other genes4-8 have been implicated in metastasis, little is known about how cells adapt to and colonize new tissue environments. Here, we show that the epigenetics-mediated reprogramming of tissue-specific gene transcription in cancer cells promotes metastasis. Using colorectal cancer (CRC) as a model, we found in both clinical and cell line studies that metastatic CRC cells lose their colon-specific gene transcription program and gain a liver-specific gene transcription program as they metastasize in the liver. Further, we found this transcription reprogramming is driven by a reshaped epigenetic landscape of both typical and super-enhancers. Chemical inhibition of enhancer activity disrupts the ability of cells to execute altered transcription programs and consequently inhibits metastasis. Binding motif analysis of the enhancers in liver metastatic CRC cells identified the liver-specific transcription factor FOXA2 as a key regulator, and knocking down of FOXA2 expression prevents the colonization of metastatic CRC cells in the liver of a mice xenograft model. These results, together with additional observations of similar reprogramming in several cohorts of clinical CRC tumor samples and in multiple other forms of metastatic cancers, indicate that this reprogramming may be a common feature of metastasis in multiple cancers and suggest the targeted disruption of this epigenetic reprogramming as a strategy for the development of therapies to treat metastasis, the leading cause of cancer-related mortality.

cancer biology

Members of the abscisic acid co-receptor PP2C protein family mediate salicylic acid-abscisic acid crosstalk

The interplay between abscisic acid (ABA) and salicylic acid (SA) influences plant responses to various (a)biotic stresses; however, the underlying mechanism(s) for this crosstalk is largely unknown. Here we report that type 2C protein phosphatases (PP2Cs), some of which are negative regulators of ABA signaling, bind SA. SA binding suppressed the ABA-enhanced interaction between these PP2Cs and various ABA receptors belonging to the PYR/PYL/RCAR protein family. Additionally, SA suppressed ABA-enhanced degradation of PP2Cs and ABA-induced stabilization of SnRK2s. Supporting SAs role as a negative regulator of ABA signaling, exogenous SA suppressed ABA-induced gene expression, whereas SA-deficient sid2-1 mutants displayed heightened PP2C degradation and hypersensitivity to ABA-induced suppression of seed germination. Together, these results suggest a new molecular mechanism through which SA antagonizes ABA signaling. A better understanding of the crosstalk between these hormones is important for improving the sustainability of agriculture in the face of climate change.

plant biology

Dynamic response to initial stage blindness in visual system development

Sensitive periods and experience-dependent plasticity have become core issues in visual system development. Converging evidence indicates that visual experience is an indispensable factor in establishing mature visual system circuitry during sensitive periods and the visual system exhibits substantial plasticity when facing deprivation. The mechanisms that underlie the environmental regulation of visual system development and plasticity are of great interest but need further exploration. Here, we investigated a unique sample of human infants who experienced initial stage blindness (beginning at birth and lasting 2 to 8 months) before the removal of bilateral cataracts. Retinal thickness, axial length, refractive status, visual grating acuity and genetic integrity were recorded during the preoperative period or at surgery, and then during follow-up. The results showed that the development of the retina is malleable and associated with external environment influences. Our work supported that the retina might play critical roles in the development of the experience-dependent visual system and its malleability might partly contribute to the sensitive period plasticity.\n\nSUMMARY STATEMENTThe follow-up investigation of a group of human infants, who experienced initial stage blindness before the removal of bilateral cataracts, revealed that retinal development is associated with environment influences and its malleability might be a potential basis of plasticity.

developmental biology

Adaptation of the FADS gene family in Europe: Variation across time, geography and subsistence

Fatty acid desaturase (FADS) genes encode rate-limiting enzymes for the biosynthesis of omega-6 and omega-3 long chain polyunsaturated fatty acids (LCPUFAs). This biosynthesis is essential for individuals subsisting on LCPUFAs-poor, plant-based diets. Positive selection on FADS genes has been reported in multiple populations, but its presence and pattern in Europeans remain elusive. Here, with analyses of ancient and modern DNA, we demonstrated that positive selection acted on the same FADS variants both before and after the advent of farming in Europe, but on opposite alleles. Selection in recent farmers also varied geographically, with the strongest signal in Southern Europe. These varying selection patterns concur with anthropological evidence of differences in diets, and with the association of recently-adaptive alleles with higher FADS1 expression and enhanced LCPUFAs biosynthesis. Genome-wide association studies revealed associations of recently-adaptive alleles with not only LCPUFAs, but also other lipids and decreased risk of several inflammation-related diseases.

genomics

A Multi-Parameter Analysis of Cellular Coordination of Multiple Transcriptome Regulation Mechanisms

To understand cellular coordination of multiple transcriptome regulation mechanisms, we simultaneously measured transcription rate (TR), mRNA abundance (RA) and translation activity (TA). This revealed multiple quantitative insights. First, the genomic profiles of the three parameters are systematically different in key statistical features. Sequentially more genes exhibit extreme low or high expression values from TR to RA, then to TA. That is, because of cellular coordination of these regulatory mechanisms, sequentially higher levels of gene expression selectivity are achieved as genetic information flow from the genome to the proteome. Second, the contribution of the stabilization-by-translation regulatory mechanism to the cellular coordination process was assessed. The data enabled an estimation of mRNA stability, revealing a moderate but significant positive correlation between the estimated mRNA stability and translation activity. Third, the proportion of a mRNA occupied by un-translated regions (UTR) exhibits a negative relationship with the level of this correlation, and is thus a major determinant of the mode of regulation of the mRNA. High-UTR-proportion mRNAs tend to defy the stabilization-by-translation regulatory mechanism, staying out of the polysome but remaining stable; mRNAs with little UTRs largely follow this regulation. In summary, we quantitatively delineated the relationship among multiple transcriptome regulation parameters, i.e., cellular coordination of corresponding regulatory mechanisms.

systems biology

Modern human origins: multiregional evolution of autosomes and East Asia origin of Y and mtDNA

The neutral theory has been used as a null model for interpreting nature and produced the Recent Out of Africa model of anatomically modern humans. Recent studies, however, have established that genetic diversities are mostly at maximum saturation levels maintained by selection, therefore challenging the explanatory power of the neutral theory and rendering the present molecular model of human origins untenable. Using improved methods and public data, we have revisited human evolution and found sharing of genetic variations among racial groups to be largely a result of parallel mutations rather than recent common ancestry and admixture as commonly assumed. We derived an age of 1.86-1.92 million years for the first split in modern human populations based on autosomal diversity data. We found evidence of modern Y and mtDNA originating in East Asia and dispersing via hybridization with archaic humans. Analyses of autosomes, Y and mtDNA all suggest that Denisovan and Neanderthal were archaic Africans with Eurasian admixtures and ancestors of South Asia Negritos and Aboriginal Australians. Verifying our model, we found more ancestry of Southern Chinese from Hunan in Africans relative to other East Asian groups examined. These results suggest multiregional evolution of autosomes and replacements of archaic Y and mtDNA by modern ones originating in East Asia, thereby leading to a coherent account of modern human origins.

evolutionary biology

Genetic footprint of population fragmentation and contemporary collapse in a freshwater cetacean

Understanding demographic trends and patterns of gene flow in an endangered species is crucial for devising conservation strategies. Here, we examined the extent of population structure and recent evolution of the critically endangered Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis). By analysing genetic variation at the mitochondrial and nuclear microsatellite loci for 148 individuals, we identified three populations along the Yangtze River, each one connected to a group of admixed ancestry. Each population displayed extremely low genetic diversity, consistent with extremely small effective size ([≤]92 individuals). Habitat degradation and distribution gaps correlated with highly asymmetric gene-flow that was inefficient in maintaining connectivity between populations. Genetic inferences of historical demography revealed that the populations in the Yangtze descended from a small number of founders colonizing the river from the sea during the last Ice Age. The colonization was followed by a rapid population split during the last millennium predating the Chinese Modern Economy Development. However, genetic diversity showed a clear footprint of population contraction over the last 50 years leaving only ~2% of the pre-collapsed size, consistent with the population collapses reported from field studies. This genetic perspective provides background information for devising mitigation strategies to prevent this species from extinction.

evolutionary biology

Evaluation on Efficient Detection of Structural Variants at Low Coverage by Long-Read Sequencing

BackgroundStructural variants (SVs) in human genomes are implicated in a variety of human diseases. Long-read sequencing delivers much longer read lengths than short-read sequencing and may greatly improve SV detection. However, due to the relatively high cost of long-read sequencing, it is unclear what coverage is needed and how to optimally use the aligners and SV callers.\n\nResultsIn this study, we developed NextSV, a meta-caller to perform SV calling from low coverage long-read sequencing data. NextSV integrates three aligners and three SV callers and generates two integrated call sets (sensitive/stringent) for different analysis purposes. We evaluated SV calling performance of NextSV under different PacBio coverages on two personal genomes, NA12878 and HX1. Our results showed that, compared with running any single SV caller, NextSV stringent call set had higher precision and balanced accuracy (F1 score) while NextSV sensitive call set had a higher recall. At 10X coverage, the recall of NextSV sensitive call set was 93.5% to 94.1% for deletions and 87.9% to 93.2% for insertions, indicating that ~10X coverage might be an optimal coverage to use in practice, considering the balance between the sequencing costs and the recall rates. We further evaluated the Mendelian errors on an Ashkenazi Jewish trio dataset.\n\nConclusionsOur results provide useful guidelines for SV detection from low coverage whole-genome PacBio data and we expect that NextSV will facilitate the analysis of SVs on long-read sequencing data.

genomics