Paaby AB et al. (2015) Elife "Wild worm embryogenesis harbors ubiquitous polygenic modifier variation."

Riccardi DD, Gunsalus KC, White AG, Rockman MV, Paaby AB, Piano F

[Elife, 2015]

Embryogenesis is an essential and stereotypic process that nevertheless evolves among species. Its essentiality may favor the accumulation of cryptic genetic variation (CGV) that has no effect in the wild-type but that enhances or suppresses the effects of rare disruptions to gene function. Here, we adapted a classical modifier screen to interrogate the alleles segregating in natural populations of Caenorhabditis elegans: we induced gene knockdowns and used quantitative genetic methodology to examine how segregating variants modify the penetrance of embryonic lethality. Each perturbation revealed CGV, indicating that wild-type genomes harbor myriad genetic modifiers that may have little effect individually but which in aggregate can dramatically influence penetrance. Phenotypes were mediated by many modifiers, indicating high polygenicity, but the alleles tend to act very specifically, indicating low pleiotropy. Our findings demonstrate the extent of conditional functionality in complex trait architecture.

Paaby, Annalise et al. (2011) International Worm Meeting "Uncovering cryptic genetic variation for C. elegans embryogenesis."

Gunsalus, Kris, Rockman, Matt, Piano, Fabio, White, Amelia, Paaby, Annalise

[International Worm Meeting, 2011]

Cryptic genetic variation (CGV) is allelic variation that affects phenotype, but only under certain conditions: when the system is "perturbed" by changes in the environment or genomic background. Such conditional effects are probably common in biological systems, but they pose barriers to the identification of causal alleles that underlie complex traits. In an to effort understand the nature of CGV, we are exploring the genetic architecture of early embryogenesis in C. elegans. Genome-wide screens have identified genes that affect embryogenesis in a single wild-type background (N2), providing a high degree of resolution in our understanding of the genetics underlying this process. We are utilizing this information to knock down embryonic genes in wild isolates, in order to identify natural allelic variants that affect early embryogenesis in perturbed animals. Embryogenesis is normally invariant, but using RNAi to silence critical embryonic genes reveals differences in embryonic lethality across strains. We have used high-throughput phenotyping methods to evaluate differences in hatching across 64 wild C. elegans strains, silenced at 43 different genes. The patterns of lethality indicate significant levels of CGV for embryogenesis. Some genes reveal high variance in lethality, suggesting that these loci are particularly good perturbation targets for revealing CGV elsewhere across the genome. We also observe significant variation in sensitivity to germline RNAi in these worms.

Paaby, Annalise B. et al. (2013) International Worm Meeting "C. elegans harbors pervasive cryptic genetic variation for embryogenesis."

Piano, Fabio, White, Amelia, Paaby, Annalise B., Gunsalus, Kris, Rockman, Matt

[International Worm Meeting, 2013]

To thoroughly explore the genetic architecture of early embryogenesis in C. elegans, we are searching for conditional relationships between embryonic genes. Genome-wide screens have identified genes that affect embryogenesis in a single wild-type background, providing a lot of information about the genetics underlying the process; we are leveraging this information to probe natural genetic variation across many wild C. elegans isolates. We have silenced a suite of 43 critical embryonic genes in 50 wild strains and characterized differences in lethality across strains. We observe pervasive "cryptic genetic variation" (CGV) for embryogenesis---that is, variation within the networks controlling early cell divisions that has functional consequences only under particular conditions. We find that disrupting genes responsible for polarizing the embryo in the first two cell divisions (PAR family members) uncover particularly high levels of CGV. Using association and linkage mapping, we find that very rarely are cryptic variants uncovered by different silenced genes, even among genes that interact closely and produce the same mutant phenotype. These results imply that CGV for embryogenesis has low pleiotropy, and likely point to new components in the embryogenesis gene network.

Chou, H. et al. (2017) International Worm Meeting "High-Throughput smFISH Analysis to Measure Natural Genetic Variation at Early Developmental Stages."

Deb, D., Paaby, A, Chou, H.

[International Worm Meeting, 2017]

The development of C. elegans is precise and stereotyped, including patterns of cell division in early embryogenesis. Nevertheless, natural genetic variation in wild-type isolates can cause dramatic differences in phenotype following single-gene perturbations, indicating that different wild-type genotypes harbor functional variation in critical gene networks1. These same wild isolates also show extreme variation in the efficacy of germline RNAi1. What are the genetic, molecular and cellular mechanisms that govern these differences? And how do they evolve when stabilizing selection ensures that phenotypic development remains stable and stereotyped? Here we use single-molecule FISH to quantitatively measure the gene expression at specific locations and time points in early development. By characterizing the temporal and spatial heterogeneities of mRNA transcript numbers in the first few cell divisions, we can connect sub-cellular phenotypes to known variations in early embryonic pathway function and germline RNAi. We use a high-throughput, semi-automated pipeline to acquire precise transcript counts at precisely staged embryos, including implementation of the machine learning spot-counting software Aro2. Despite near-invariant cell division phenotypes, wild isolates show significant differences in transcript abundance for critical embryonic genes. These differences in gene expression do not fully explain differences in embryonic lethality following gene knockdown, as neither wild-type gene expression nor transcript abundance following RNAi correlates perfectly with patterns of embryonic lethality. Notably, we observe significant difference in transcript abundance variance following RNAi among wild-type isolates, suggesting inefficiency of RNAi may be controlled by stochastic thresholds. Currently, we are scaling up the experiments using a microfluidic chip specifically designed for worm embryos in order to test hypotheses with high statistical rigor. References: 1- Wild worm embryogenesis harbors ubiquitous polygenic modifier variation. A.B. Paaby, A.G. White, D.D. Riccardi, K.C. Gunsalus, F. Piano, M.V. Rockman. Elife (2015), p. 4 2- Aro: a machine learning approach to identifying single molecules and estimating classification error in fluorescence microscopy images. A.C. Wu and S.A. Rifkin. BMC Bioinformatics (2015), 16:102

Kaul, S. et al. (2019) International Worm Meeting "Using polarity establishment through par genes as a model to study the evolution of complex processes."

Kaul, S., Paaby, A.

[International Worm Meeting, 2019]

The relationship between a genotype and its corresponding phenotype is often very complex. One reason for this complexity is that for any polygenic trait, the participating genes may interact with each other non-additively in determination of the phenotype. An example of this is genetic background effects, wherein allelic variation across the genome can mediate the affect of a focal allele on phenotype. Interactions between genes may also influence how genes, traits and complex processes evolve over time. The purpose of this project is to interrogate how genetic dependencies affect natural genetic and functional variation in a well-defined process, the establishment of polarity in the C. elegans early embryo. The first cell division is a critical developmental step and exhibits stereotyped precision both within natural populations and across nematode phylogeny-its developmental function is highly conserved. Yet, we observe significant natural genetic variation in pathway genes and substantial variation in apparent levels of purifying selection. We are combining gene-specific functional tests and whole genome sequencing analysis to uncover genetic relationships that mediate the expression of natural genetic variation and potentially constrain evolution. We find that the par-2 locus harbors significant variation within C. elegans populations and between Caenorhabditis species, and may have consequential influence on micro-evolutionary trajectories.

White A et al. (2013) IEEE Trans Med Imaging "DevStaR: high-throughput quantification of C. elegans developmental stages."

Gunsalus K, Paaby A, Geiger D, Sontag E, Lees B, White A, Piano F, Kao HL, Erickson K, Cipriani G

[IEEE Trans Med Imaging, 2013]

We present DevStaR, an automated computer vision and machine learning system that provides rapid, accurate, and quantitative measurements of C. elegans embryonic viability in high-throughput (HTP) applications. A leading genetic model organism for the study of animal development and behavior, C. elegans is particularly amenable to HTP functional genomic analysis due to its small size and ease of cultivation, but the lack of efficient and quantitative methods to score phenotypes has become a major bottleneck. DevStaR addresses this challenge using a novel hierarchical object recognition machine that rapidly segments, classifies, and counts animals at each developmental stage in images of mixed-stage populations of C. elegans. Here, we describe the algorithmic design of the DevStaR system and demonstrate its performance in scoring image data acquired in HTP screens.

Quartey MO et al. (2021) Sci Rep "The A(1-38) peptide is a negative regulator of the A(1-42) peptide implicated in Alzheimer disease progression."

Pennington PR, Heistad RM, Nyarko JNK, Barnes JR, Bolanos MAC, Parsons MP, Knudsen KJ, De Carvalho CE, Leary SC, Mousseau DD, Buttigieg J, Maley JM, Quartey MO

[Sci Rep, 2021]

The pool of -Amyloid (A) length variants detected in preclinical and clinical Alzheimer disease (AD) samples suggests a diversity of roles for A peptides. We examined how a naturally occurring variant, e.g. A(1-38), interacts with the AD-related variant, A(1-42), and the predominant physiological variant, A(1-40). Atomic force microscopy, Thioflavin T fluorescence, circular dichroism, dynamic light scattering, and surface plasmon resonance reveal that A(1-38) interacts differently with A(1-40) and A(1-42) and, in general, A(1-38) interferes with the conversion of A(1-42) to a -sheet-rich aggregate. Functionally, A(1-38) reverses the negative impact of A(1-42) on long-term potentiation in acute hippocampal slices and on membrane conductance in primary neurons, and mitigates an A(1-42) phenotype in Caenorhabditis elegans. A(1-38) also reverses any loss of MTT conversion induced by A(1-40) and A(1-42) in HT-22 hippocampal neurons and APOE 4-positive human fibroblasts, although the combination of A(1-38) and A(1-42) inhibits MTT conversion in APOE 4-negative fibroblasts. A greater ratio of soluble A(1-42)/A(1-38) [and A(1-42)/A(1-40)] in autopsied brain extracts correlates with an earlier age-at-death in males (but not females) with a diagnosis of AD. These results suggest that A(1-38) is capable of physically counteracting, potentially in a sex-dependent manner, the neuropathological effects of the AD-relevant A(1-42).

Danielle Thierry-Mieg et al. (2003) Worm Breeder's Gazette "www.wormgenes.org , a new gene centered database"

Vahan Simonyan, Michel Potdevin, Mark Sienkiewicz, Yuji KOHARA, Jean Thierry-Mieg, Danielle Thierry-Mieg, Tadasu SHIN-I

[Worm Breeder's Gazette, 2003]

Wormgenes is a new resource for C.elegans offering a detailed summary about each gene and a powerful query system.

Tangrodchanapong T et al. (2020) Front Pharmacol "Frondoside A Attenuates Amyloid- Proteotoxicity in Transgenic Caenorhabditis elegans by Suppressing Its Formation."

Tangrodchanapong T, Sobhon P, Meemon K

[Front Pharmacol, 2020]

Oligomeric assembly of Amyloid- (A) is the main toxic species that contribute to early cognitive impairment in Alzheimer's patients. Therefore, drugs that reduce the formation of A oligomers could halt the disease progression. In this study, by using transgenic <i>Caenorhabditis elegans</i> model of Alzheimer's disease, we investigated the effects of frondoside A, a well-known sea cucumber <i>Cucumaria frondosa</i> saponin with anti-cancer activity, on A aggregation and proteotoxicity. The results showed that frondoside A at a low concentration of 1 M significantly delayed the worm paralysis caused by A aggregation as compared with control group. In addition, the number of A plaque deposits in transgenic worm tissues was significantly decreased. Frondoside A was more effective in these activities than ginsenoside-Rg3, a comparable ginseng saponin. Immunoblot analysis revealed that the level of small oligomers as well as various high molecular weights of A species in the transgenic <i>C. elegans</i> were significantly reduced upon treatment with frondoside A, whereas the level of A monomers was not altered. This suggested that frondoside A may primarily reduce the level of small oligomeric forms, the most toxic species of A. Frondoside A also protected the worms from oxidative stress and rescued chemotaxis dysfunction in a transgenic strain whose neurons express A. Taken together, these data suggested that low dose of frondoside A could protect against A-induced toxicity by primarily suppressing the formation of A oligomers. Thus, the molecular mechanism of how frondoside A exerts its anti-A aggregation should be studied and elucidated in the future.

Hodgkin JA (1998) International Journal of Developmental Biology "Seven types of pleiotropy."

Hodgkin JA

[International Journal of Developmental Biology, 1998]

Pleiotropy , a situation in which a single gene influences multiple phenotypic tra its, can arise in a variety of ways. This paper discusses possible underlying mechanisms and proposes a classification of the various phenomena involved.