piRNAs Are Associated with Diverse Transgenerational Effects on Gene and Transposon Expression in a Hybrid Dysgenic Syndrome of D. virilis

Sexual reproduction allows transposable elements (TEs) to proliferate, leading to rapid divergence between populations and species. A significant outcome of divergence in the TE landscape is evident in hybrid dysgenic syndromes, a strong form of genomic incompatibility that can arise when (TE) family abundance differs between two parents. When TEs inherited from the father are absent in the mother's genome, TEs can become activated in the progeny, causing germline damage and sterility. Studies in Drosophila indicate that dysgenesis can occur when TEs inherited paternally are not matched with a pool of corresponding TE silencing PIWI-interacting RNAs (piRNAs) provisioned by the female germline. Using the D. virilis syndrome of hybrid dysgenesis as a model, we characterize the effects that divergence in TE profile between parents has on offspring. Overall, we show that divergence in the TE landscape is associated with persisting differences in germline TE expression when comparing genetically identical females of reciprocal crosses and these differences are transmitted to the next generation. Moreover, chronic and persisting TE expression coincides with increased levels of genic piRNAs associated with reduced gene expression. Combined with these effects, we further demonstrate that gene expression is idiosyncratically influenced by differences in the genic piRNA profile of the parents that arise though polymorphic TE insertions. Overall, these results support a model in which early germline events in dysgenesis establish a chronic, stable state of both TE and gene expression in the germline that is maintained through adulthood and transmitted to the next generation. This work demonstrates that divergence in the TE profile is associated with diverse piRNA-mediated transgenerational effects on gene expression within populations

Digital image analysis using video microscopy of human-derived prostate cancer vs normal prostate organoids to assess migratory behavior on extracellular matrix proteins

The advent of perpetuating living organoids derived from patient tissue is a promising avenue for cancer research but is limited by difficulties with precise characterization. In this brief communication, we demonstrate via time-lapse imaging distinct phenotypes of prostate organoids derived from patient material– without confirmation of cellular identity. We show that organoids derived from histologically normal tissue more readily spread on a physiologic extracellular matrix (ECM) than on pathologic ECM (p<0.0001), while tumor-derived organoids spread equally on either substrate (p=0.2406). This study is an important proof-of-concept to defer precise characterization of organoids and still glean information into disease pathology

Phenotype plasticity and altered sensitivity to chemotherapeutic agents in aggressive prostate cancer cells

In 2023, approximately 288,300 new diagnoses of prostate cancer will occur, with 34,700 disease-related deaths. Death from prostate cancer is associated with metastasis, enabled by progression of tumor phenotypes and successful extracapsular extension to reach Batson’s venous plexus, a specific route to the spine and brain. Using a mouse-human tumor xenograft model, we isolated an aggressive muscle invasive cell population of prostate cancer, called DU145J7 with a distinct biophysical phenotype, elevated histone H3K27, and increased matrix metalloproteinase 14 expression as compared to the non-aggressive parent cell population called DU145WT. Our goal was to determine the sensitivities to known chemotherapeutic agents of the aggressive cells as compared to the parent population. High-throughput screening was performed with 5,578 compounds, comprising of approved and investigational drugs for oncology. Eleven compounds were selected for additional testing, which revealed that vorinostat, 5-azacitidine, and fimepinostat (epigenetic inhibitors) showed 2.6-to-7.5-fold increases in lethality for the aggressive prostate cancer cell population as compared to the parent, as judged by the concentration of drug to inhibit 50% cell growth (IC50). On the other hand, the DU145J7 cells were 2.2-to-4.0-fold resistant to mitoxantrone, daunorubicin, and gimatecan (topoisomerase inhibitors) as compared to DU145WT. No differences in sensitivities between cell populations were found for docetaxel or pirarubicin. The increased sensitivity of DU145J7 prostate cancer cells to chromatin modifying agents suggests a therapeutic vulnerability occurs after tumor cells invade into and through muscle. Future work will determine which epigenetic modifiers and what combinations will be most effective to eradicate early aggressive tumor populations

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Alleviating and exacerbating foods in hidradenitis suppurativa

While dietary triggers have been investigated in acne and other inflammatory follicular dermatoses, there is a paucity of data on diet and hidradenitis suppurativa (HS). We sought to identify exacerbating and alleviating foods in HS patients. An anonymous survey was distributed via HS Facebook support groups and in person at HS specialty clinics. Participants were asked to select all that apply from a list to indicate foods that worsen and make HS better including sweet foods, breads and pasta, red meat, chicken, fish, canned foods, fruits, vegetables, dairy, high-fat foods, I do not know, and no. Only 12.0% (n = 89/744) identified alleviating foods while 32.6% (n = 237/728) identified HS-symptom-exacerbating foods. The most commonly reported exacerbating foods were sweets (67.9%), bread/pasta/rice (51.1%), dairy (50.6%), and high-fat foods (44.2%). The most commonly reported alleviating foods included vegetables (78.7%), fruit (56.2%), chicken (51.7%), and fish (42.7%). Further studies are required to evaluate the mechanistic links between diet and HS. HS patients may benefit from receiving dietary counseling as part of a comprehensive HS management plan.12 month embargo; first published: 29 August 2020This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Multiple transposable elements are associated with induction of hybrid dysgenesis.

<p>(A) Relative mapping abundance of single-end, 100 bp reads from strain 9 and strain 160 (normalized by reads mapping to the genome), to a consolidated repeat library. Eleven elements are in 3-fold excess in strain 160 and are indicated here and throughout with red. TART elements are about 1.7-fold in excess and are indicated here and throughout with blue. No apparent TEs were found in excess in strain 9. (B) Using piledriver (<a href="https://github.com/arq5x/piledriver" target="_blank">https://github.com/arq5x/piledriver</a>) we assessed homogeneity within reads mapping to the TE library by determining the average frequency of the major variant in both strains. TEs in excess in strain 160 are either more homogenous in strain 160 or similarly aged between strains, with the exception of element 1069 which shows slightly more homogeneity in strain 9.</p

Increased TE expression in the dysgenic germline persists through adulthood.

<p>(A) RPKM+0.01 (log 10, average across both ages) for TEs, Dysgenic vs. Non-dysgenic germline. TEs that are in excess in 160 are more highly expressed, as well as many TEs that are not in excess. (B) Fold excess in expression (RPKM+0.01, log 2, average across both ages) vs. fold excess in abundance in strain 160. Nearly all TEs that are in excess in 160 show increased expression in the dysgenic germline (11/12). But multiple TEs that are equivalent in abundance between strains are also increased in expression. (C,D) Increased expression in the dysgenic germline is maintained as flies age. Note: Log scale obscures magnitude of difference for some TEs that demonstrate significant differences in expression identified due to low variation across replicates.</p

Properties of TEs significantly more expressed in the dysgenic germline by at last 2-fold (FDR<0.1).

<p>160:9 Abundance, 160:9 total piRNA, Expression: D (Dysgenic, RPKM), Expression: ND (Non-dysgenic, RPKM), Ping-pong pair density: D (Dysgenic, per Million piRNAs mapped), Ping-pong pair density: ND (Non-Dysgenic, per Million piRNAs mapped). Type I: Higher in copy number in 160, higher in piRNA abundance in 160, F1 piRNA ping-pong pair density defined by maternal loading. Type II: Higher in copy number in 160, higher in piRNA abundance in 160, F1 piRNA ping-pong density equilibrated. Type III. Higher in copy number in 160, higher in piRNA abundance in 160, F1 piRNA ping-pong density higher in dysgenic. Type IV: Higher in copy number in 9, higher in piRNA abundance in 160, F1 piRNA ping-pong pair density defined by maternal loading. Type V: Higher in copy number in 9, higher in piRNA abundance in 160, no ping-pong pairs detected. Type VI: Higher in copy number in 9, equivalent piRNA abundance in 9 and 160, F1 piRNA ping-pong density higher in non-dysgenic.</p><p>Properties of TEs significantly more expressed in the dysgenic germline by at last 2-fold (FDR<0.1).</p

Genic piRNA targeting is increased in the dysgenic germline.

<p>(A) log10 Z-score heat map of genic (CDS) piRNA density for <i>D</i>. <i>melanogaster</i> orthologs (above a threshold of 5 piRNAs per CDS per 1 million mapped in at least one of four columns). Of these 105 genes, there is an excess of genic piRNAs in the dysgenic germline (89 genes with greatest genic targeting in dysgenesis, P<0.001) (B) Sense vs. Anti-sense abundance for piRNAs in genic piRNA class for one library (Sample 1). Some CDS regions are predominantly the source of anti-sense piRNAs, but the majority are biased as a source of sense strand piRNA (C) Distribution of expression levels (log 10 RPKM+0.01) for all genes in the genome and piRNA target genes (expression levels from non-dysgenic germline). Genic piRNA targets are derived from more highly expressed genes (p < 0.001). (D) Of 105 genes, the 89 that show excess genic piRNA in dysgenesis are also more lowly expressed in dysgenesis. Shown is the distribution of expression ratios (dysgenic:non-dysgenic) for all genes and genes that are increased as a source of genic piRNAs in dysgenesis (p < 0.001).</p

Germline and ovary genic cluster behavior across generations for <i>D</i>. <i>virilis</i> orthologs of <i>center divider</i> and <i>oysgedart</i> from <i>D</i>. <i>melanogaster</i>.

<p>piRNA mapping densities are indicated. mRNA-seq RPKM for germline (0–2 H embryo) is also indicated. Allelism was determined by counting mRNA-seq reads based on SNPs that distinguish strain 9 and 160. Strain 160 cluster identity is maintained for <i>cdi</i> in non-dysgenic progeny in which strain 160 is the mother. This is correlated with silencing of both alleles in the non-dysgenic germline. In contrast, the cluster is not maintained in the dysgenic germline and both alleles are expressed. Somatic expression is not affected. Germline cluster identity for <i>oysgedart</i> (which in the germline is predominantly sense) is lost in progeny. In this case, expression is even between reciprocal progeny, but germline expression is lower from the 9 allele in both directions of the cross. For cluster behavior in F3 backcrosses, heterozygosity or homozygosity of the respective allele is indicated. Notice how cluster identity is maintained for <i>cdi</i> to varying degrees in individuals homozygous for the 9 allele. In contrast, cluster activity is absent in all progeny for <i>oysgedart</i>.</p