Characterizing Gene Expression in Human Tissues to Better Understand Sex Differences in Health and Disease

Description
The regulation of gene expression, timing, location, and amount of a given project, ultimately affects the cellular structure and function. More broadly, gene regulation is the basis for cellular differentiation and development. However, gene expression is not uniform among individuals…

The regulation of gene expression, timing, location, and amount of a given project, ultimately affects the cellular structure and function. More broadly, gene regulation is the basis for cellular differentiation and development. However, gene expression is not uniform among individuals and varies greatly between genetic males and females. Males are hemizygous for the X chromosome, whereas females have two X chromosome copies. Contributing to the sex differences in gene expression between males and females are the sex chromosomes, X and Y. Gene expression differences on the autosomes and the X chromosome between males (46, XY) and females (46, XX) may help inform on the mechanisms of sex differences in human health and disease. For example, XX females are more likely to suffer from autoimmune diseases, and genetic XY males are more likely to develop cancer. Characterizing sex-specific gene expression among human tissues will help inform the molecular mechanisms driving sex differences in human health and disease. This dissertation covers a range of critical aspects in gene expression. In chapter 1, I will introduce a method to align RNA-Seq reads to a sex chromosome complement informed reference genome that considers the X and Y chromosomes' shared evolutionary history. Using this approach, I show that more genes are called as sex differentially expressed in several human adult tissues compared to a default reference alignment. In chapter 2, I characterize gene expression in an early formed tissue, the human placenta. The placenta is the DNA of the developing fetus and is typically XY male or XX female. There are well-documented sex differences in pregnancy complications, yet, surprisingly, there is no observable sex difference in expression of innate immune genes, suggesting expression of these genes is conserved. In chapter 3, I investigate gene expression in breast cancer cell lines. Cancer arises in part due to the disruption of gene expression. Here I show 19 tumor suppressor genes become upregulated in response to a synthetic protein treatment. In chapter 4, I discuss gene and allele-specific expression in Nasonia jewel wasp. Chapter 4 is a replication and extension study and discusses the importance of reproducibility.
Date Created
2021
Agent

Persistence of Weight Gain, Energy Intake, and Feed Efficiency in a Rat Population Inclusive of Obesity Prone and Obesity Resistant Male Sprague-Dawley Rats with Controlled Environmental Factors

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Description

Obesity has reached epidemic proportions all around the world, and it has doubled in prevalence in both adults and children in over 70 countries from 1980 to 2015 (Afshin et al., 2017). Excessive weight gain in this proportion has been…

Obesity has reached epidemic proportions all around the world, and it has doubled in prevalence in both adults and children in over 70 countries from 1980 to 2015 (Afshin et al., 2017). Excessive weight gain in this proportion has been shown to negatively affect human cognition, reward neurocircuitry, stress responsiveness, and quality of life (Morris et al., 2015). Obesity is an example of a complex interaction between the environment (i.e., high-fat diets) and heredity (i.e., polygenic patterns of inheritance). The overconsumption of a high-fat diet (HFD) is an environmental factor that commonly induces weight gain (Hariri & Thibault, 2010). Two dietary-induced phenotypes have been observed in rats as a bimodal distribution of weight gain: obesity-prone (OP) and obesity-resistant (OR). Levin et al. (1997) investigated male and female HFD-fed Sprague-Dawley rats designated as OR when their weight gains were less than the heaviest chow-fed controls, and OP when their weight gains were greater than the heaviest chow-fed controls. OP rats showed greater weight gain, similar energy intake (EI), and similar feed efficiency (FE) compared to OR rats. Pagliassotti et al. (1997) designated male HFD-fed Wistar rats as OP and OR based on upper and lower tertiles of weight gain. OP rats displayed greater weight gain and EI than OR rats. These investigations highlight a predicament regarding rodent research in obesity: independent variables such as rat age, gender, strain, distribution of dietary macronutrients, and fatty acid composition of HFD and chow vary considerably, making it challenging to generalize data. Our experiment utilized outbred male Sprague-Dawley rats (5-6 weeks) administered a chow diet (19% energy from fat; 3.1 kcal/g) and a lard-based HFD (60% energy from fat; 5.24 kcal/g) over eight weeks. Separate rat populations were examined over three consecutive years (2017-2020), and independent obesogenic environmental variables were controlled. We investigated the persistence of weight gain, EI, and FE in HFD-fed rats inclusive of a population of designated OP and OR rats based on tertiles of weight gain. We define persistence as being p > 0.05. We hypothesize that the profiles (periodic data) of the dependent variables (weight gain, EI, FE) will be similar and persistent throughout the three separate years, but the magnitudes (cumulative data) of the dependent variables will differ. Our findings demonstrate that HFD, OP, and OR groups were persistent for periodic and cumulative weight gain, along with FE across the three consecutive independent years. Our findings also demonstrate impersistence for periodic EI in all groups, along with impersistence in cumulative EI for CHOW, OP, and OR groups. Therefore, our results allude to an inconsistent relationship between EI and weight gain, indicating that EI does not completely explain weight gain. Thus, the weakness between EI and weight gain relationship may be attributed to a polygenic pattern of inheritance, possibly signaling a weight setpoint regardless of EI.

Date Created
2021-12
Agent

Persistence of Weight Gain, Energy Intake, and Feed Efficiency in a Rat Population Inclusive of Obesity Prone and Obesity Resistant Male Sprague-Dawley Rats with Controlled Environmental Factors

161071-Thumbnail Image.png
Description

Obesity has reached epidemic proportions all around the world, and it has doubled in prevalence in both adults and children in over 70 countries from 1980 to 2015 (Afshin et al., 2017). Excessive weight gain in this proportion has been…

Obesity has reached epidemic proportions all around the world, and it has doubled in prevalence in both adults and children in over 70 countries from 1980 to 2015 (Afshin et al., 2017). Excessive weight gain in this proportion has been shown to negatively affect human cognition, reward neurocircuitry, stress responsiveness, and quality of life (Morris et al., 2015). Obesity is an example of a complex interaction between the environment (i.e., high fat diets) and heredity (i.e., polygenic patterns of inheritance). The overconsumption of a high-fat diet (HFD) is an environmental factor that commonly induces weight gain (Hariri & Thibault, 2010). Two dietary-induced phenotypes have been observed in rats as a bimodal distribution of weight gain: obesity-prone (OP) and obesity-resistant (OR). Levin et al. (1997) investigated male and female HFD-fed Sprague-Dawley rats designated as OR when their weight gains were less than the heaviest chow-fed controls, and OP when their weight gains were greater than the heaviest chow-fed controls. OP rats showed greater weight gain, similar energy intake (EI), and similar feed efficiency (FE) compared to OR rats. Pagliassotti et al. (1997) designated male HFD-fed Wistar rats as OP and OR based on upper and lower tertiles of weight gain. OP rats displayed greater weight gain and EI than OR rats. These investigations highlight a predicament regarding rodent research in obesity: independent variables such as rat age, gender, strain, distribution of dietary macronutrients, and fatty acid composition of HFD and chow vary considerably, making it challenging to generalize data. Our experiment utilized outbred male Sprague-Dawley rats (5-6 weeks) administered a chow diet (19% energy from fat; 3.1 kcal/g) and a lard-based HFD (60% energy from fat; 5.24 kcal/g) over eight weeks. Separate rat populations were examined over three consecutive years (2017-2020), and independent obesogenic environmental variables were controlled. We investigated the persistence of weight gain, EI, and FE in HFD-fed rats inclusive of a population of designated OP and OR rats based on tertiles of weight gain. We define persistence as being p > 0.05. We hypothesize that the profiles (periodic data) of the dependent variables (weight gain, EI, FE) will be similar and persistent throughout the three separate years, but the magnitudes (cumulative data) of the dependent variables will differ. Our findings demonstrate that HFD, OP, and OR groups were persistent for periodic and cumulative weight gain, along with FE across the three consecutive independent years. Our findings also demonstrate impersistence for periodic EI in all groups, along with impersistence in cumulative EI for CHOW, OP, and OR groups. Therefore, our results allude to an inconsistent relationship between EI and weight gain, indicating that EI does not completely explain weight gain. Thus, the weakness between EI and weight gain relationship may be attributed to a polygenic pattern of inheritance, possibly signaling a weight setpoint regardless of EI.

Date Created
2021-12
Agent

A review of pathway-based visualization and quantification analysis tools using microarray data

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Description
Pathway analysis helps researchers gain insight into the biology behind gene expression-based data. By applying this data to known biological pathways, we can learn about mutations or other changes in cellular function, such as those seen in cancer. There are…

Pathway analysis helps researchers gain insight into the biology behind gene expression-based data. By applying this data to known biological pathways, we can learn about mutations or other changes in cellular function, such as those seen in cancer. There are many tools that can be used to analyze pathways; however, it can be difficult to find and learn about the which tool is optimal for use in a certain experiment. This thesis aims to comprehensively review four tools, Cytoscape, PaxtoolsR, PathOlogist, and Reactome, and their role in pathway analysis. This is done by applying a known microarray data set to each tool and testing their different functions. The functions of these programs will then be analyzed to determine their roles in learning about biology and assisting new researchers with their experiments. It was found that each tools holds a very unique and important role in pathway analysis. Visualization pathways have the role of exploring individual pathways and interpreting genomic results. Quantification pathways use statistical tests to determine pathway significance. Together one can find pathways of interest and then explore areas of interest.
Date Created
2020-05
Agent

Hepatitis C Prevention Measures in Pakistan

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Description
Hepatitis C virus (HCV) is endemic in Pakistan, with 5% of the population suffering from the disease. A unique aspect about HCV in Pakistan is the major role that healthcare workers play in its transmission, by reusing needles and giving…

Hepatitis C virus (HCV) is endemic in Pakistan, with 5% of the population suffering from the disease. A unique aspect about HCV in Pakistan is the major role that healthcare workers play in its transmission, by reusing needles and giving therapeutic injections when they are not needed. This issue is furthered by patients’ misconceptions that invasive treatments, like injections, are more effective than oral medicines. The purpose of this project was to create a short video that addressed this inaccurate and dangerous perception, by educating Pakistanis about HCV and how to prevent infection and reinfection. In addition to disease transmission, accessibility to treatment options in Pakistan were also discussed. The video featured Pakistani physicians and some young adults. There were several limitations that delimited the project, including time, budget, the sudden death of a project participant, and the current COVID-19 epidemic as well as cultural, language, and physical barriers that come from filming a video about Pakistan as Americans. In the future, this video can serve as a framework for future efforts.
Date Created
2020-05
Agent

A search for parent-of-origin effects in the parasitoid jewel wasp Nasonia vitripennis

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Description
In most diploid cells, autosomal genes are equally expressed from the paternal and maternal alleles resulting in biallelic expression. However, as an exception, there exists a small number of genes that show a pattern of monoallelic or biased-allele expression based…

In most diploid cells, autosomal genes are equally expressed from the paternal and maternal alleles resulting in biallelic expression. However, as an exception, there exists a small number of genes that show a pattern of monoallelic or biased-allele expression based on the allele’s parent-of-origin. This phenomenon is termed genomic imprinting and is an evolutionary paradox. The best explanation for imprinting is David Haig's kinship theory, which hypothesizes that monoallelic gene expression is largely the result of evolutionary conflict between males and females over maternal involvement in their offspring. One previous RNAseq study has investigated the presence of parent-of-origin effects, or imprinting, in the parasitic jewel wasp Nasonia vitripennis (N. vitripennis) and its sister species Nasonia giraulti (N. giraulti) to test the predictions of kinship theory in a non-eusocial species for comparison to a eusocial one. In order to continue to tease apart the connection between social and eusocial Hymenoptera, this study proposed a similar RNAseq study that attempted to reproduce these results in unique samples of reciprocal F1 Nasonia hybrids. Building a pseudo N. giraulti reference genome, differences were observed when aligning RNAseq reads to a N. vitripennis reference genome compared to aligning reads to a pseudo N. giraulti reference. As well, no evidence for parent-of-origin or imprinting patterns in adult Nasonia were found. These results demonstrated a species-of-origin effect. Importantly, the study continued to build a repository of support with the aim to elucidate the mechanisms behind imprinting in an excellent epigenetic model species, as it can also help with understanding the phenomenon of imprinting in complex human diseases.
Date Created
2019
Agent

Isoform Variation across Triple Negative Breast Cancer and Prostate Cancer

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Description
Cancer is a disease in which abnormal cells divide uncontrollably and destroy body tissue, and currently plagues today’s world. Carcinomas are cancers derived from epithelial cells and include breast and prostate cancer. Breast cancer is a type of carcinoma that…

Cancer is a disease in which abnormal cells divide uncontrollably and destroy body tissue, and currently plagues today’s world. Carcinomas are cancers derived from epithelial cells and include breast and prostate cancer. Breast cancer is a type of carcinoma that forms in breast tissue cells. The tumor cells can be further categorized after testing the cells for the presence of certain molecules. Hormone receptor positive breast cancer includes the tumor cells with receptors that respond to the steroid hormones, estrogen and progesterone, or the peptide hormone, HER2. These forms of cancer respond well to chemotherapy and endocrine therapy. On the other hand, triple negative breast cancer (TNBC) is characterized by the lack of hormone receptor expression and tends to have a worse prognosis in women. Prostate cancer forms in the cells of the prostate gland and has been attributed to mutations in androgen receptor ligand specificity. In a subset of triple negative breast cancer, genetic expression profiling has found a luminal androgen receptor that is dependent on androgen signaling. TNBC has also been found to respond well to enzalutamide, a an androgen receptor inhibitor. As the gene of the androgen receptor, AR, is located on the X chromosome and expressed in a variety of tissues, the responsiveness of TNBC to androgen receptor inhibition could be due to the differential usage of isoforms - different gene mRNA transcripts that produce different proteins. Thus, this study analyzed differential gene expression and differential isoform usage between TNBC cancers – that do and do not express the androgen receptor – and prostate cancer in order to better understand the underlying mechanism behind the effectiveness of androgen receptor inhibition in TNBC. Through the analysis of differential gene expression between the TNBC AR+ and AR- conditions, it was found that seven genes are significantly differentially expressed between the two types of tissues. Genes of significance are AR and EN1, which was found to be a potential prognostic marker in a subtype of TNBC. While some genes are differentially expressed between the TNBC AR+ and AR- tissues, the differences in isoform expression between the two tissues do not reflect the difference in gene expression. We discovered 11 genes that exhibited significant isoform switching between AR+ and AR- TNBC and have been found to contribute to cancer characteristics. The genes CLIC1 and RGS5 have been found to help the rapid, uncontrolled growth of cancer cells. HSD11B2, IRAK1, and COL1Al have been found to contribute to general cancer characteristics and metastasis in breast cancer. PSMA7 has been found to play a role in androgen receptor activation. Finally, SIDT1 and GLYATL1 are both associated with breast and prostate cancers. Overall, through the analysis of differential isoform usage between AR+ and AR- samples, we uncovered differences that were not detected by a gene level differential expression analysis. Thus, future work will focus on analyzing differential gene and isoform expression across all types of breast cancer and prostate cancer to better understand the responsiveness of TNBC to androgen receptor inhibition.
Date Created
2019-05
Agent

The Effects of Sex Chromosome Complement Aware Read Mapping on Variant Calling in Hepatocellular Carcinoma

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Description
Hepatocellular carcinoma (HCC) is a type of liver cancer common in Sub-Saharan Africa and South East Asian countries. Each year more than 700,000 new cases and more than 600,000 deaths are recorded worldwide due to HCC. According to the American…

Hepatocellular carcinoma (HCC) is a type of liver cancer common in Sub-Saharan Africa and South East Asian countries. Each year more than 700,000 new cases and more than 600,000 deaths are recorded worldwide due to HCC. According to the American Cancer Society HCC is ranked the 5th most common cancer worldwide with a male:female susceptibility ratio ranging between 2:1 and 8:1. HCC risk factors include lifestyle behaviors, such as persistent alcohol abuse and smoking, prolonged exposure to aflatoxins, chronic viral hepatitis infections, inherited metabolic diseases and non-alcoholic fatty liver diseases. To understand the genetic effects underlying sex-bias in HCC, it is necessary to include the sex chromosomes in genomics analyses. X and Y chromosomes are often discluded in genomics studies because of the technical and analytical challenges: sequence homology. The purpose of this thesis is to analyze the effects of sex chromosome complement aware read mapping to germline variant calling. 10 male and 10 female tumor adjacent samples from The Cancer Genome Atlas Liver Hepatocellular Carcinoma (TCGA LIHC) cohort were processed using sex-aware and default reference and the concordance of the two approaches was examined. We detected a higher disconcordance of 0.69% on variants called on the X chromosome and a disconcordance of 0.51% on variants called on the Y chromosomes for the reference and alternative alleles respectively compared to autosomes. Variants called on the REF/ALT genotypes had a disconcordances of 1.00%, 1.05%, 1.35% and 12.34% for the autosomes, chromosome 7, the X, and the Y chromosome, respectively. At the end of the project we concluded that the generated datasets showed the effect of sex-aware read mapping on variant calling. Though the data did not show the sites that can be called as variants in one dataset but not in the other, rather the concordance looked at sites that were called as variants in both data sets.
Date Created
2019-05
Agent

Patterns of Sex-Biased Gene Expression in the Human Brain

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Description
Schizophrenia is a disease that affects 15.2/100,000 US citizens, with about 0.6-1.9% of the total population being afflicted with some range of severity of the disease. A lot of research has been done on the progression of the disease and…

Schizophrenia is a disease that affects 15.2/100,000 US citizens, with about 0.6-1.9% of the total population being afflicted with some range of severity of the disease. A lot of research has been done on the progression of the disease and its differences between males and females; however, the true underlying cause of the disease remains unknown. In the literature, however, there is a lot of indication that a genetic cause for schizophrenia is the primary origin for the disorder. In order to establish a foundation in differential gene expression and isoform expression between males and females, we utilized the Genotype-Tissue Expression Project data set (which contains samples from healthy individuals at their time of death) for the amygdala, anterior cingulate cortex, and frontal cortex. We performed quality control on the data with Trimmomatic and visualized it with FastQC and MultiQC. We then aligned to a sex-specific reference genome with Hisat2. Finally, we performed a differential expression analysis dthrough the limma/voom package with inputs from featureCounts. An isoform level analysis was run on the anterior cingulate cortex with the IsoformSwitchAnalyzeR package. We were able to identify a few differentially expressed genes in the three tissue sites, which included XIST and other highly conserved, Y-linked genes. As for the isoform level analysis, we were able to identify 13 genes with significant levels of differential isoform usage and expression, two of which have clinical relevance (DAB1 and PACRG). These findings will allow for a comparison to be made by future studies on gene expression in brain tissue samples from patients that had been diagnosed with schizophrenia in their life. By identifying any unique genes in these patients, gene therapies can be developed to target and correct any misexpression that may be occurring.
Date Created
2019-05
Agent

Systematic Analysis of the Factors Contributing to the Variation and Change of the Microbiome

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Description
Understanding changes and trends in biomedical knowledge is crucial for individuals, groups, and institutions as biomedicine improves people’s lives, supports national economies, and facilitates innovation. However, as knowledge changes what evidence illustrates knowledge changes? In the case of microbiome, a…

Understanding changes and trends in biomedical knowledge is crucial for individuals, groups, and institutions as biomedicine improves people’s lives, supports national economies, and facilitates innovation. However, as knowledge changes what evidence illustrates knowledge changes? In the case of microbiome, a multi-dimensional concept from biomedicine, there are significant increases in publications, citations, funding, collaborations, and other explanatory variables or contextual factors. What is observed in the microbiome, or any historical evolution of a scientific field or scientific knowledge, is that these changes are related to changes in knowledge, but what is not understood is how to measure and track changes in knowledge. This investigation highlights how contextual factors from the language and social context of the microbiome are related to changes in the usage, meaning, and scientific knowledge on the microbiome. Two interconnected studies integrating qualitative and quantitative evidence examine the variation and change of the microbiome evidence are presented. First, the concepts microbiome, metagenome, and metabolome are compared to determine the boundaries of the microbiome concept in relation to other concepts where the conceptual boundaries have been cited as overlapping. A collection of publications for each concept or corpus is presented, with a focus on how to create, collect, curate, and analyze large data collections. This study concludes with suggestions on how to analyze biomedical concepts using a hybrid approach that combines results from the larger language context and individual words. Second, the results of a systematic review that describes the variation and change of microbiome research, funding, and knowledge are examined. A corpus of approximately 28,000 articles on the microbiome are characterized, and a spectrum of microbiome interpretations are suggested based on differences related to context. The collective results suggest the microbiome is a separate concept from the metagenome and metabolome, and the variation and change to the microbiome concept was influenced by contextual factors. These results provide insight into how concepts with extensive resources behave within biomedicine and suggest the microbiome is possibly representative of conceptual change or a preview of new dynamics within science that are expected in the future.
Date Created
2018
Agent
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