Biology subjects

Olney, K. C.

Publications and source records attributed to Olney, K. C..

7 recordsLinked to original sources

bioRxiv2024

Psilocybin causes sex, time, and dose dependent alterations in brain signaling pathways

Psilocybin is a psychedelic tryptamine that has emerged as a potential candidate for the treatment of a variety of conditions, including treatment resistant depression and post-traumatic stress disorder. Clinical trials which have assessed the efficacy of psilocybin for these conditions report a rapid and sustained improvement in patient- and clinician-rated depression scores. The established mechanism of action for psychedelics such as psilocybin is agonism of the serotonin 2A receptor (5HT2AR), however, the downstream events that mediate their therapeutic effects remain uncertain. As high doses of psychedelics are known to induce strong perceptual alterations, an additional outstanding question is whether subperceptual doses induce similar molecular effects as psychoactive dosages. Here, we report the first analysis of dose- and sex-dependent transcriptional changes in forebrains of female and male mice at 3 timepoints (8 hours, 24 hours, and 7 days) following a single administration of psilocybin at low (0.25 mg/kg) or high (1 mg/kg) doses. Grouped analysis of both sexes reveals dose- and time-dependent transcriptomic alterations. We report more rapid transcriptional changes and attenuation of such changes in females following a single low-dose relative to males treated identically. Females also responded more robustly to high-dose administration relative to males at 8 and 24 hours, with signal attenuation in both sexes by 7 days. A notable observation was the persistent transcriptional effect of low-dose psilocybin at 7 days, which outlasted high-dose changes, and which suggests that low doses may have prolonged biological effects. A myriad of pathways were altered depending on sex and timepoint, but common features included functions related to neuronal differentiation, neurogenesis, and changes in receptor signaling. These data reveal dose- and sex-dependent molecular effects of psilocybin and support previous studies demonstrating its effect on dendritogenesis. Given ongoing clinical interest in psilocybin for treating mental health disorders, our results suggest that these sexually divergent changes should be considered when weighing treatment strategies. Additional consideration should be given to temporal effects of low vs high dosages on gene transcription, especially when timing psilocybin with adjuvant cognitive behavioral therapy.

neuroscience↗

bioRxiv2022

Sex differences in early and term placenta are conserved in adult tissues

BackgroundPregnancy complications vary based on the fetuss genetic sex, which may, in part, be modulated by the placenta. Further, developmental differences early in life can have lifelong health outcomes. Yet, sex differences in gene expression within the placenta at different time points throughout pregnancy and comparisons to adult tissues remains poorly characterized. MethodsHere, we collect and characterize sex differences in gene expression in term placentas ( [≥] 36.6 weeks; 23 male XY and 27 female XX). These are compared with sex differences in previously collected first trimester placenta samples and 42 non-reproductive adult tissues from GTEx. ResultsWe identify 268 and 53 sex differentially expressed genes in the uncomplicated late first trimester and term placentas, respectively. Of the 53 sex differentially expressed genes observed in the term placentas, 31 are also sex differentially expressed genes in the late first trimester placentas. Furthermore, sex differences in gene expression in term placentas are highly correlated with sex differences in the late first trimester placentas. We found that sex differential gene expression in the term placenta is significantly correlated with sex differences in gene expression in 42 non-reproductive adult tissues (correlation coefficient ranged from 0.892 to 0.957), with the highest correlation in brain tissues. Sex differences in gene expression were largely driven by gene expression on the sex chromosomes. We further show that some gametologous genes (genes with functional copies on X and Y) will have different inferred sex differences if the X-linked gene expression in females is compared to the sum of the X-linked and Y-linked gene expression in males. ConclusionsWe find that sex differences in gene expression are conserved in late first trimester and term placentas and that these sex differences are conserved in adult tissues. We demonstrate that there are sex differences associated with innate immune response in late first trimester placentas but there is no significant difference in gene expression of innate immune genes between sexes in healthy full term placentas. Finally, sex differences are predominantly driven by expression from sex-linked genes. HighlightsO_LISex differences in gene expression in late first trimester placentas are positively correlated with sex differences in gene expression in full term placentas; sex differences develop early and are maintained. C_LIO_LISex differences in gene expression on the sex chromosomes in the placenta are correlated to sex differences in adult tissues. C_LIO_LISex-linked gametolog genes require additional methodological approaches for accurate quantification. C_LI

genomics↗

bioRxiv2021

Lack of parent-of-origin effects in Nasonia jewel wasp: a replication and extension study

In diploid cells, the paternal and maternal alleles are, on average, equally expressed. There are exceptions from this: a small number of genes express the maternal or paternal allele copy exclusively. This phenomenon, known as genomic imprinting, is common among eutherian mammals and some plant species; however, genomic imprinting in species with haplodiploid sex determination is not well characterized. Previous work reported no parent-of-origin effects in the hybrids of closely related haplodiploid Nasonia vitripennis and Nasonia giraulti jewel wasps, suggesting a lack of epigenetic reprogramming during embryogenesis in these species. Here, we replicate the gene expression dataset and observations using different individuals and sequencing technology, as well as reproduce these findings using the previously published RNA sequence data following our data analysis strategy. The major difference from the previous dataset is that they used an introgression strain as one of the parents and we found several loci that resisted introgression in that strain. Our results from both datasets demonstrate a species-of-origin effect, rather than a parent-of-origin effect. We present a reproducible workflow that others may use for replicating the results. Overall, we reproduced the original report of no parent-of-origin effects in the haplodiploid Nasonia using the original data with our new processing and analysis pipeline and replicated these results with our newly generated data.

genomics↗

bioRxiv2019

Patchy, incomplete, and heterogeneous X-inactivation in the human placenta

One of the X chromosomes in genetic females is silenced by a process called X chromosome inactivation (XCI). Variation in XCI across the placenta may contribute to observed sex differences and variability in pregnancy outcomes. However, XCI has predominantly been studied in human adult tissues. Here we sequenced and analyzed DNA and RNA from two locations from 30 full-term pregnancies. Implementing an allele specific approach to examine XCI, we report evidence that XCI in the human placenta is patchy, with large patches of either silenced maternal or paternal X chromosomes. Further, using similar measurements, we show that this is in contrast to adult tissues, which generally exhibit mosaic X-inactivation, where bulk samples exhibit both maternal and paternal X chromosome expression. Further, by comparing skewed samples in placenta and adult tissues, we identify genes that are uniquely silenced or expressed in the placenta compared to adult tissues highlighting the need for tissue-specific maps of XCI.

genomics↗

bioRxiv2019

Aligning RNA-Seq reads to a sex chromosome complement informed reference genome increases ability to detect sex differences in gene expression

BackgroundHuman X and Y chromosomes share an evolutionary origin and, as a consequence, sequence similarity. We investigated whether sequence homology between the X and Y chromosomes affects alignment of RNA-Seq reads and estimates of differential expression. We tested the effects of using reference genomes and reference transcriptomes informed by the sex chromosome complement of the samples genome on measurements of RNA-Seq abundance and sex differences in expression. ResultsThe default genome includes the entire human reference genome (GRCh38), including the entire sequence of the X and Y chromosomes. We created two sex chromosome complement informed reference genomes. One sex chromosome complement informed reference genome was used for samples that lacked a Y chromosome; for this reference genome version, we hard-masked the entire Y chromosome. For the other sex chromosome complement informed reference genome, to be used for samples with a Y chromosome, we hard-masked only the pseudoautosomal regions of the Y chromosome, because these regions are duplicated identically in the reference genome on the X chromosome. We analyzed transcript abundance in the whole blood, brain cortex, breast, liver, and thyroid tissues from 20 genetic female (46, XX) and 20 genetic male (46, XY) samples. Each sample was aligned twice; once to the default reference genome and then independently aligned to a reference genome informed by the sex chromosome complement of the sample, repeated using two different read aligners, HISAT and STAR. We then quantified sex differences in gene expression using featureCounts to get the raw count estimates followed by Limma/Voom for normalization and differential expression. We additionally created sex chromosome complement informed transcriptome references for use in pseudo-alignment using Salmon. Transcript abundance was quantified twice for each sample; once to the default target transcripts and then independently to target transcripts informed by the sex chromosome complement of the sample. ConclusionsWe show that regardless of the choice of read aligner, using an alignment protocol informed by the sex chromosome complement of the sample results in higher expression estimates on the pseudoautosomal regions of the X chromosome in both genetic male and genetic female samples, as well as an increased number of unique genes being called as differentially expressed between the sexes. We additionally show that using a pseudo-alignment approach informed on the sex chromosome complement of the sample eliminates Y-linked expression in female XX samples. Author summaryThe human X and Y chromosomes share an evolutionary origin and sequence homology, including regions of 100% identity; this sequence homology can result in reads misaligning between the sex chromosomes, X and Y. We hypothesized that misalignment of reads on the sex chromosomes would confound estimates of transcript abundance if the sex chromosome complement of the sample is not accounted for during the alignment step. For example, because of shared sequence similarity, X-linked reads could misalign to the Y chromosome. This is expected to result in reduced expression for regions between X and Y that share high levels of homology. For this reason, we tested the effect of using a default reference genome versus a reference genome informed by the sex chromosome complement of the sample on estimates of transcript abundance in human RNA-Seq samples from whole blood, brain cortex, breast, liver, and thyroid tissues of 20 genetic female (46, XX) and 20 genetic male (46, XY) samples. We found that using a reference genome with the sex chromosome complement of the sample resulted in higher measurements of X-linked gene transcription for both male and female samples and more differentially expressed genes on the X and Y chromosomes. We additionally investigated the use of a sex chromosome complement informed transcriptome reference index for alignment free quantification protocols. We observed no Y-linked expression in female XX samples only when the transcript quantification was performed using a transcriptome reference index informed on the sex chromosome complement of the sample. We recommend that future studies requiring aligning RNA-Seq reads to a reference genome or pseudo-alignment with a transcriptome reference should consider the sex chromosome complement of their samples prior to running default pipelines.

evolutionary biology↗

bioRxiv2017

Activation of tumor suppressor genes in breast cancer cells by a synthetic chromatin effector

Mounting evidence from genome-wide studies of cancer show that chromatin-mediated epigenetic silencing at large cohorts of genes is strongly linked to a poor prognosis. This mechanism is thought to prevent cell differentiation and enable evasion of the immune system. Drugging the cancer epigenome with small molecule inhibitors to release silenced genes from the repressed state has emerged as a powerful approach for cancer research and drug development. Targets of these inhibitors include chromatin-modifying enzymes that can acquire drug-resistant mutations. In order to directly target a generally conserved feature, elevated trimethyl-lysine 27 on histone H3 (H3K27me3), we developed the Polycomb-based Transcription Factor (PcTF), a fusion activator that targets methyl-histone marks via its N-terminal H3K27me3-binding motif, and co-regulates sets of silenced genes. Here, we report transcriptome profiling analyses of PcTF-treated breast cancer model cell lines. We identified a set of 19 PcTF-upregulated genes, or PUGs, that were consistent across three distinct breast cancer cell lines. These genes are associated with the interferon response pathway. Our results demonstrate for the first time a chromatin-mediated interferon-related transcriptional response driven by an engineered fusion protein that physically links repressive histone marks with active transcription.

synthetic biology↗

bioRxiv2017

Bioinformatics Core Competencies for Undergraduate Life Sciences Education

Bioinformatics is becoming increasingly central to research in the life sciences. However, despite its importance, bioinformatics skills and knowledge are not well integrated in undergraduate biology education. This curricular gap prevents biology students from harnessing the full potential of their education, limiting their career opportunities and slowing genomic research innovation. To advance the integration of bioinformatics into life sciences education, a framework of core bioinformatics competencies is needed. To that end, we here report the results of a survey of life sciences faculty in the United States about teaching bioinformatics to undergraduate life scientists. Responses were received from 1,260 faculty representing institutions in all fifty states with a combined capacity to educate hundreds of thousands of students every year. Results indicate strong, widespread agreement that bioinformatics knowledge and skills are critical for undergraduate life scientists, as well as considerable agreement about which skills are necessary. Perceptions of the importance of some skills varied with the respondents degree of training, time since degree earned, and/or the Carnegie classification of the respondents institution. To assess which skills are currently being taught, we analyzed syllabi of courses with bioinformatics content submitted by survey respondents. Finally, we used the survey results, the analysis of syllabi, and our collective research and teaching expertise to develop a set of bioinformatics core competencies for undergraduate life sciences students. These core competencies are intended to serve as a guide for institutions as they work to integrate bioinformatics into their life sciences curricula.\n\nSignificance StatementBioinformatics, an interdisciplinary field that uses techniques from computer science and mathematics to store, manage, and analyze biological data, is becoming increasingly central to modern biology research. Given the widespread use of bioinformatics and its impacts on societal problem-solving (e.g., in healthcare, agriculture, and natural resources management), there is a growing need for the integration of bioinformatics competencies into undergraduate life sciences education. Here, we present a set of bioinformatics core competencies for undergraduate life scientists developed using the results of a large national survey and the expertise of our working group of bioinformaticians and educators. We also present results from the survey on the importance of bioinformatics skills and the current state of integration of bioinformatics into biology education.

bioinformatics↗