A feature of neoplastic cells is that mutations in the key intermediates of TGF-β signaling contribute to the loss of sensitivity to its anti-tumor effects. The role of SMAD3 and SMAD4 germline mutations in breast cancer predisposition is currently unclear. To address this, mutation analysis of the Mad-Homology 2 domains in 408 breast cancer cases and 710 controls recruited by the Breast Cancer Family Registry (BCFR) was performed using Denaturing High-Pressure Liquid Chromatography. This study identified 23 distinct intronic variants, and three coding variants c.1214T>C, c.1478G>A, and c.1701A>G in SMAD4. No aberrant splicing was observed, but qPCR analysis and tissue expression data showed significantly elevated SMAD3 expression relative to controls (p<0.05). For SMAD4, c.1478G>A from a familial breast cancer case showed a 5-fold expression change. Taken together, inactivating alterations are not driving tumorigenesis. Rather, aberrant germline expression provides novel insight into SMAD3 and SMAD4’s roles in breast cancer predisposition.

A feature of neoplastic cells is that mutations in the key intermediates of TGF-β signaling contribute to the loss of sensitivity to its anti-tumor effects. The role of SMAD3 and SMAD4 germline mutations in breast cancer predisposition is currently unclear. To address this, mutation analysis of the Mad-Homology 2 domains in 408 breast cancer cases and 710 controls recruited by the Breast Cancer Family Registry (BCFR) was performed using Denaturing High-Pressure Liquid Chromatography. This study identified 23 distinct intronic variants, and three coding variants c.1214T>C, c.1478G>A, and c.1701A>G in SMAD4. No aberrant splicing was observed, but qPCR analysis and tissue expression data showed significantly elevated SMAD3 expression relative to controls (p<0.05). For SMAD4, c.1478G>A from a familial breast cancer case showed a 5-fold expression change. Taken together, inactivating alterations are not driving tumorigenesis. Rather, aberrant germline expression provides novel insight into SMAD3 and SMAD4’s roles in breast cancer predisposition.

No description available.

Gene regulation in C. elegans germ cells depend on transgenerational chromatin modification and small RNA pathways. Germline silencing mechanisms evolved to repress foreign DNA from compromising the transfer of genetic information to progeny. Effective genetic tools that circumvent the silencing machinery will facilitate studies using this model organism. Specifically, translation of heat-shock inducible transgenes is inhibited in the germline making it challenging to transiently express enzymes to modify the genome. Here, we describe a genetic screen design that can be used to identify pathways that prevent germline expression of heat-shock induced transgenes. We use split-GFP (GFP1-10 and GFP11) to confine a genetic screen to germ cells. Stable transgenic lines with germline expression of single-copy integrated GFP11 were produced using MosSCI. The insertion lines will be used in RNAi or chemical mutagenesis screens for the germline de-repression of GFP1-10 expressed under heat-shock promoters. The screen is likely to identify candidate RNAi or chromatin factors involved in repressing heat-shock expression in the germline, particularly from extrachromosomal arrays. Inducible high-level expression in the germline from extrachromosomal arrays would be a valuable tool for large-scale genome engineering.

Single nucleotide polymorphisms (SNPs) have great potential to serve as important biomarkers in the clinic to identify those at increased risk for developing cancer, progressing more rapidly, and not responding to therapies. However, the clinical application of cancer-associated SNPs has proven to be more complicated than expected. One of the necessary steps will certainly be the description of the molecular and cellular mechanisms behind the observed associations. The p53 tumour suppressor pathway harbours well-described SNPs that affect p53 signalling and cancer. The aim of the work presented in this thesis was to utilise this knowledge to more efficiently characterise cancer-associated SNPs. Firstly, cancer-associated SNPs in a p53 network gene, CD44, were studied. Specifically, based on CD44’s known roles in both p53-dependent and independent signalling, it was predicted that the cancer-associated SNPs could function as biomarkers for chronic lymphocytic leukaemia progression, and for the response to anti-EGFR therapy for colorectal cancer. Indeed, supportive data is presented. Next, a methodology is presented that aims to identify cancer-associated SNPs in functional p53 binding sites using genome-wide datasets. Interestingly, a SNP is identified that dramatically influences the ability of p53 to regulate transcription of the KITLG oncogene and that associates with one of the largest risks of cancer identified to date. Intriguingly, the SNP is also shown to have undergone positive selection throughout human evolution, signifying a selective advantage, but similar SNPs are demonstrated to be rare in the genome due to negative selection, indicating that polymorphisms in p53 binding sites have been primarily detrimental to humans. Lastly, and in order to begin to explore if other polymorphic transcription factor binding motifs could be found in cancer-associated SNPs, a methodology was designed to identify SNPs in E-box transcription factor binding motifs, as they are sensitive to single base pair changes and affect cancer. Taken together, the work presented in this thesis shows how the study of how SNPs associate with, and impact upon, cancer has great potential to improve both biological knowledge and clinical outcomes.

With the discovery and development of CRISPR, the technology that might allow us to modify the human germline is at our fingertips, and, consequently, serious practical and ethical consideration is warranted. In the following paper, I examine the ethics of using CRISPR in this way and argue that modifying the human germline for the purpose of preventing serious genetic disease is, in principle, ethically acceptable and ought to be allowed. I present several arguments to this effect including arguments that rely on the principles of beneficence and autonomy. I also examine the larger societal implications of human germline modification. I then respond to six of the most prominent objections that have been raised against CRISPR and germline gene modification before concluding with a brief discussion of the biggest challenge that we face as we move forward with CRISPR, that of limiting the use of this promising and incredibly versatile technology.

lin-11 and let-711 are early-developmental gene expression regulators with no previously known roles in aging regulation. Yet, they show strong aging-correlated expression profiles (Lund, Tedesco et al. 2002). lin-11 is strongly upregulated in very old worm populations, and let-711 is progressively downregulated in aging worm populations. Microarray studies were performed to identify their genome-wide targets, which were then subjected to further lifespan and genetic analysis to investigate their role in C. elegans aging. The results indicate that the target pools of both lin-11 and let-711 are enriched for aging genes, since a significant number of tested genes increased lifespan. This enrichment of aging genes in their target pools provides strong evidence that lin-11 and let-711 are indeed regulating the expression of aging genes in adult C. elegans. The data suggests that increased lin-11 expression as well as reduced let-711 expression may be promoting longevity by downregulating the insulin/IGF-1 pathway. Decreasing let-711 may also be contributing to longevity by downregulating the germline signaling pathway. K11E4.2, R53.5, C49A9.2 and Y82E9BR.5 are four genes from the lin-11 target pool, whose knockdown produced increases inlifespan. These are unannotated genes, and the details of their roles in aging regulation are not known at this point. ins-3 expression was downregulated two-fold upon knockdown of lin-11, suggesting the possible involvement of lin-11 in regulation of the insulin/IGF-1 pathway. An RNAi construct for ins-3 was not available and it is not known whether loss of ins-3 leads to lifespan extension. let-711 knockdown resulted in an almost four-fold reduction in pdk-1 expression. pdk-1 is an integral part of the insulin/IGF-1 pathway and its knockdown by RNAi extended lifespan. Four other genes from the let-711 target pool that increased lifespan, cdc-25.1, gna-2, meg-1 and ooc-3, all have germline specific functions. The extensions in lifespan generated by these genes were completely dependent on DAF-16. Furthermore, for gna-2, meg-1 or ooc-3, they were independent of DAF-2. These results agree with previously established mechanisms for germline regulation of aging, suggesting the involvement of let-711 in regulating the germline-signaling pathway.

Maintaining cells in an undifferentiated totipotent state is essential for initiating developmental programs that lead to a fully formed organism in each generation and for maintaining immortal germ cells across generations. Caenorhabditis elegans is a powerful genetic model organism to study early germ cell development due to the animal’s transparency and the ability to screen for mutant phenotypes. However, our ability to use standard techniques to study gene expression using fluorescent reporter genes has been limited due to germline-specific silencing mechanisms that repress transgenes. Therefore, we lack even basic knowledge of how expression is regulated in C. elegans germ cells. In this study, we develop methods to overcome these silencing mechanisms by using a class of noncoding DNA, called Periodic An/Tn Clusters (PATCs), to prevent transgene silencing in the germline. We use these improved tools to test the proposed role of putative germline-specific regulatory DNA motifs and the role a periodic TT signal within germline promoters. We fused GFP to the promoter of a germline expressed gene (pcn-1), which is enriched for PATCs and contains a germline-specific motif (TTAAAG). Our results show that despite enrichment and phylogenetic conservation, the TTAAAG motif is not required for germline expression. To test additional motifs and periodic TTs, we have designed a system that will allow us to test synthetic gene fragments for bi-directional germline expression. These tools will allow us to rapidly test motif redundancy, motif spacing, and TT periodicity using gfp and rfp signals in the germline and will enable experiments aimed at understanding the role of germline regulatory elements.

KIF1A is a molecular motor for membrane-bound cargo important to the development and survival of sensory neurons. KIF1A dysfunction has been associated with several Mendelian disorders with a spectrum of overlapping phenotypes, ranging from spastic paraplegia to intellectual disability. We present a novel pathogenic in-frame deletion in the KIF1A molecular motor domain inherited by two affected siblings from an unaffected mother with apparent germline mosaicism. We identified eight additional cases with heterozygous, pathogenic KIF1A variants ascertained from a local data lake. Our data provide evidence for the expansion of KIF1A-associated phenotypes to include hip subluxation and dystonia as well as phenotypes observed in only a single case: gelastic cataplexy, coxa valga, and double collecting system. We review the literature and suggest that KIF1A dysfunction is better understood as a single neuromuscular disorder with variable involvement of other organ systems than a set of discrete disorders converging at a single locus. / National Institutes of Health / Revisión por pares

No description available.