2021 SURP Participants

Renal cancer is the sixth most common cancer in men and the eighth most common cancer in women. Renal cell carcinoma (RCC) is the most common and a highly aggressive type of malignant renal tumor, representing around 70% of all renal cancers. The World Health Organization (WHO) states that the most common sub-types of RCCs are clear cell RCCs (ccRCCs) and non-clear cell RCCs (nccRCC) including papillary RCCs (paRCCs) and chromophobe RCCs (chrRCCs), accounting for approximately 70%, 15%, and 5% of all RCCs, respectively. This taxonomy of RCCs is of immense importance as each sub-type has its own prognosis. Biopsy procedure, the gold standard, is the only technique that can provide a definite diagnosis for renal cancer. However, it is used as the last resort due to its high invasiveness, high cost, and turnaround and recovery times (approximately a week). Therefore, investigation of non-invasive imaging modalities to provide a reliable, accurate, less-expensive, and rapid diagnosis of renal tumors at an early stage is underway. In this research, we aim to identify and integrate the optimal discriminating morphological, textural, and functional markers that best describe the malignancy status of a given renal tumor. The integrated discriminating markers may lead to the development of a novel comprehensive renal cancer computer-aided diagnostic (RC-CAD) for accurate, fast, early, and inexpensive identification of renal cancer. The obtained preliminary results demonstrated an accuracy > 95% for differentiating between benign and malignant RCC renal tumors and identify the RCC sub-types for optimal medical management.

This project explores the application of modeling and simulation to understand disease progression and patient response to therapy. The goal is to provide clinicians with insight into tailoring treatment to individual patients. The student will be trained in machine learning techniques, as well as laboratory benchwork.

Central circuits that control swallow are located in dorsal medulla, and project to (pre-)motoneurons in ventral medulla. These circuits have not been characterized. The goal of this summer project is to cross index optical recordings and immunohistochemistry to identify the anatomical networks that mediate swallow, and to taxonomize their constituents based on their immunohistochemical profiles. 

We will use a transgenic mouse expressing the genetically-encoded Ca2+ indicator GCaMP6F in the germline to carry out optical recordings in vitro from these networks. To elicit orofacial behaviors, a stimulating electrode will be displaced along the dorsal half of the brainstem, and the effect of stimuli will be recorded optically from the sagittal face of the sectioned brainstem, while motor output will be recorded via suction electrodes sampling activity from ventral root C4 and the hypoglossal nerve (XIIn). Thereafter, brainstems will be fixed, and a 400 um thick section will be cut from the face from which optical recordings were made, and processed immunohistochemically, and then imaged using the confocal microscope in the microscopy core of the spinal cord injury center. We will screen for choline acetyltransferase (ChAT), somatostatin receptor (SST), and phox2b. The first is expressed in motoneurons, the second in constituents of respiratory rhythm-generating networks, and the third in visceral afferent pathways. 

Noah will shadow on the electrophysiology experiments, keeping notes on stimulus location and amplitude. He will then analyze the data using machine vision software developed in-house. He will be trained in the sectioning and immunoprocessing of tissue samples, and he will shadow on the confocal microscope.

From Dr. Fu: 

The analysis of human breath has a great potential to be developed as a powerful non-invasive tool for evaluating inhaled toxicants and diagnosis of diseases including cancers, chronic obstructive pulmonary disease (COPD), bacteria and virus infections. However, there are some critical challenges hindering breath analysis for clinical applications. These challenges include identifying trace volatile organic compounds (VOCs) related to disease biochemical processes and reducing interference of other VOCs in exhaled breath. We have developed a novel microreactor approach for chemoselective capture of carbonyl VOCs in exhaled breath. The innovations of this approach enable quantitative analysis of both aldehydes and ketones by ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS) and gas chromatography-mass spectrometry (GC-MS). The goal of this KY_INBRE summer project is to compare a new reagent 4-(2-aminooxyethyl)-morpholin-4-ium chloride (AMAH) coated micrchips with our current reagent 2-(aminooxy)ethyl-N,N,Ntrimethylammonium iodide (ATM) loaded microchips for capture of carbonyl compounds in exhaled breath. The obtained results will enable analysis of carbonyl compounds in exhaled breath by gas chromatography-mass spectrometry (GC-MS). The undergraduate research student Sarah Stasel from Western Kentucky University will focus on characterization of the new reagent (AMAH) for capture efficiencies of a few deuterated compounds including deuterated propanal, 2-butanone, pentanal using our current microchips. These compounds are found in exhaled breath. She will develop analytical methods for separation and detection of AMAH adducts of these compound by UHPLS-MS and GC-MS. The capture efficiencies will be compared with current reagent ATM loaded microchips. Finally, the AMAH loaded microchips will be used for analysis of exhaled breath samples. 

There are six objectives for the 10-weeks KY INBRE training and research project: 

1. Learn to do literature search and prepare a brief review of analysis of volatile organic compounds in exhaled breath 

2. Learn to use UHPLC-MS and GC-MS for analysis of VOCs 

3. Learn to operate microchips and preparing samples for quantitative analysis 

4. Characterize capture efficiencies of ATM and AMAH loaded microchips 

5. Learn to analyze exhaled breath samples using the microchips 

6. Learn to do data analysis and write a scientific report and manuscript for publication 

During the 10-weeks research, my PhD student Zhenzhen Xie supervises and trains the KY INBRE student. I will have one-to-one weekly meeting with the student to provide advice for the research project.

Background: Heart failure is often caused by loss of cardiomyocytes. To identify a combination of cell cycle regulators that can induce stable cytokinesis in adult post-mitotic cardiomyocytes, we screened a combination of cell-cycle regulators expressed in proliferating fetal cardiomyocytes. Overexpression of cyclin-dependent kinase 1 (CDK1), CDK4, cyclin B, and cyclin D efficiently induced cell division in post-mitotic mouse and human cardiomyocytes. In vivo, lineage tracing revealed that the four cell cycle regulators induced cardiomyocyte cell division of adult cardiomyocytes, resulting in significant improvement in cardiac function following acute or subacute myocardial infarction. These findings reveal a discrete combination of genes that can unlock the proliferative potential in cells that had exited the cell cycle (Mohamed et al., Cell, 2018). 

Goal: Achieve a cell cycle cocktail of genes/shRNA that fits in one cardiomyocyte-specific viral vector and generate >20% proliferating cardiomyocytes.

Spinal cord injury (SCI) is a devastating condition in which loss of neurons, their axons and axon myelinating oligodendrocytes (OLs) is a major driver of a long lasting functional deficits including disrupted sensation and locomotion. SCI causes immediate loss of neural tissue at the site of impact. In addition, delayed secondary damage broadens tissue loss enhancing deficits. Reducing the secondary injury is a clinically translatable neuroprotective strategy that could attenuate functional deficits and improve patients outcome after SCI. To identify new targets for neuroprotective therapies that could be relevant in SCI, we determined gene expression changes specifically in OLs at various times after SCI. We have identified several candidate genes that may regulate secondary injury-associated death of OLs. 

The summer research rotation student could help with further validation of the relevant targets. The following questions could be addressed: 

1. Which of the candidate genes are upregulated after experimental SCI at the protein level? 

2. Upon overexpression in rat OLs in cell culture, which of them are cytotoxic? 

Techniques that could be learned include: primary OL cultures, plasmid DNA preparation, transfection of primary OLs, immunofluorescence staining, epifluorescence and confocal microscopy, image analysis, tissue processing for histology. 

Suggested readings: 

Experimental approaches: 

• Kilanczyk E, S Saraswat Ohri, SR Whittemore, M. Hetman. (2016) Anti-oxidant protection of NADPH-depleted oligodendrocyte precursor cells is dependent on supply of reduced glutathione. ASN Neuro, 8(4). pii: 1759091416660404. doi:10.1177/1759091416660404. PubMed PMID: 27449129. 

• Slomnicki LP, SA Myers, S Saraswat Ohri, MV Parsch, KR Andres, JH Chariker, EC Rouchka, SR Whittemore, M Hetman. (2020) Improved locomotor recovery after contusive spinal cord injury in Bmal1-/- mice is associated with protection of the blood spinal cord barrier. Sci Rep. 10(1):14212. doi:10.1038/s41598-020-71131-6. PMID: 32848194. 

Review on pathogenesis of SCI: https://www.nature.com/articles/nrdp201718

Obesity is a serious health condition that can cause various disease such as heart disease, diabetes, and cancer (CDC 2021). According to the National Center for Health Statistics, more than 1 in 3 adults in the United States had obesity in 2013. Additionally, obesity has been associated with diets containing high sugar. Although environmental factors such as an unhealthy dietary regimen and insufficient exercise are well known to play roles in obesity, the biological and metabolic processes contributing to this condition have yet to be fully understood. Due to the polygenic aspect of obesity (as it is affected by many genes), one of the keys to understanding genetic susceptibility to obesity is the identification of DNA variations associated with this condition. In an effort to explore the biological pathways connected to obesity — such as finding specific genes responsible for obesity, we can potentially determine effective ways to treat this health condition. Using Drosophila (commonly known as fruit flies) as the model organism for this research, we investigated the phenotypic variations (body weight and food consumption) of various lines/strains of fruit flies under a low and high sugar diet. More specifically, this genome wide association study (GWAS) was done with the use of the Drosophila Genetic Reference Panel (DGRP). DGRP lines incorporate ~ 200 strains of inbred lines that have been genetically sequenced, allowing an in-depth genetic analysis. Preliminary analysis has suggested that some genes involved in the circadian clock system and the gustatory system are strongly associated with sugar-induced obesity. Upon completion of the GWAS, candidate genes that demonstrate an association with obesity will be tested a genetic mutagenesis approach. Overall, the results of this study will not only allow a better understanding of sugar mediated obesity, but have the potential to reveal certain genetic factors that may be connected to obesity in humans.

Sperm are perhaps the most highly specialized and modified cells in the animal world. They are specifically designed to be efficient couriers of the male’s genetic information. Animal sperm vary in shapes and sizes to carry out this task. Nonetheless, the general process of sperm production is largely similar from insects to mammals. Construction of a sperm is accomplished with the assistance of other cells in the testis. While many studies have uncovered genes that are active in sperm during their development, little is known about the genes and functions of the support cells in the testis. In the fruit fly, Drosophila melanogaster, each 64-spermatid cluster develops as an interconnected cyst and is encapsulated by a pair of somatic support cells, called cyst cells. Recent work in the lab has uncovered that communication between these somatic cyst cells and the spermatids is necessary to direct the separation of spermatids within a cyst during the late stages of spermatogenesis. To better understand the roles of the somatic support cells, this project will identify factors required in cyst cells to complete sperm development. For this project, we will specifically impair the functions of particular candidate genes only in the support cells of the testis to examine the impact on sperm formation. Because the process of spermatogenesis is similar across species, this work will not only aid in understanding cellular collaboration in Drosophila spermatogenesis, but it will contribute to our understanding of spermatogenesis in general.

Tumor suppressor genes are essential for cellular function in multicellular organisms, but many Tumor Suppressor Genes (TSGs) and tumor suppressing mechanisms remain unknown or their mechanisms poorly understood, particularly as they function in vivo. In the Duncan lab, we study planarian flatworms, which are best known for their remarkable regenerative abilities. In addition, they share many striking similarities to cancer cells, including genomic patterns that are known to mark TSGs in human cells, e.g. wide peaks of histone H3 K4 trimethylation (H3K4me3). We have analyzed the patterns of H3K4me3 signal across the planarian genome and identified many loci with this pattern. Moreover, we have identified the enzyme, Set1, that is largely responsible for creating this signature in planarian stem cells. Noteably, depletion of set1 in planarians induces stem cell phenotypes that suggest loss of TSG function, including hyperproliferation and an abnormal response to DNA damage. In his KBRIN project this summer, Zach is cloning genes we have identified as Set1 targets, i.e. potential TSGs. He is then creating dsRNA from these cloned constructs, delivering it to planarian animals, and assessing the effects. He is using both live animal imaging and immunofluorescence to screen for genes that cause phenotypes relevant to tumor suppression. This work will help discover new roles for known genes and uncover the functions of unknown planarian genes.

With tactile foraging ducks utilizing a bill to locate resources, research into mechanoreception is prevalent. The duck bill skin contains Herbst and Grandry corpuscles, which are multicellular non-neuronal structures, equivalent to Pacinian and Meisner corpuscles in human glabrous skin. As with mammalian corpuscles, in the duck bill sensory neurons interact with these corpuscles detect vibration and pressure. Various species of ducks have different foraging abilities, raising the question of whether this is reflected in the anatomy and/or function of structures that sense touch in the bill. The current study focuses on how densely populated the two types of corpuscles are in duck bills of seven species, to give insight as to whether the corpuscle density and size varies based upon foraging abilities. With results still underway, the goal is to be able to measure the density of corpuscles per/mm^2 in the bill skin and average corpuscle diameter, to correlate this with bone morphology and functional responses from trigeminal neurons from these species (Schneider et al., 2019). In addition, previous studies have recently shown that the lamellar cells of Herbst and Grandry corpuscles in late-stage embryos can be excited by mechanical stimulation (Nikolaev et al., 2020). Therefore, in parallel we are investigating the developmental time-course of expression of the force-gated ion channel piezo2 in these cells using in situ hybridization and qPCR. Understanding how these structures relate to tactile sensitivity can provide insight to how human mechanoreception forms and discriminates touch.

PRL-3 or PTP4A3 is an oncogenic phosphatase upregulated in a multitude of cancers with roles in tumorigenesis and metastasis. Despite the remarkable number of studies deciphering great insights into the physiological roles of PRL-3, structural challenges and high degree of homology between its family members remain challenging to therapeutically target PRL-3. Therefore, development of new tools to bypass these challenges are needed. Towards this end Nanobodies have emerged as an important research tool and has potential to be implemented in therapeutics as well. In the current project a bacterial immunotoxin PE38 will be fused to the nanobody that is highly specific to PRL-3 by the traditional insertional cloning into a bacterial expression construct pSKB3. The construct is then purified as a Immunotoxin fused to nanobody that has the ability to specifically bind to PRL-3 and potentially be toxic to the cancer cells. This strategy if successful can be used as a translational approach to therapeutically target PRL-3.

PAS domain containing protein kinase (Pask) is essential in the detection of and respective response regarding environmental signals from within the stem cell niche. The ability to phosphorylate Wdr5, a strictly nuclear protein and eventual epigenetic activator of transcription, is key to the function of Pask. However, in normal cell conditions, Pask remains in the cytosol of the cell, waiting to perform its function. Here, we examine some of the possible mechanisms by which Pask is able to migrate to the nucleus. Without the migration back into the cytosol, stem cells keep differentiating and this has detrimental effects on homeostasis of the cell, therefore making this mechanism incredibly critical to the function of PasK and by extension, the differentiation of stem cells.

Neural crest cells are responsible for forming multiple tissues in the body. The periocular mesenchyme is a subgroup of neural crest cells that forms the anterior segment of the eye, which includes the lens, cornea, and the iris. In the Famulski lab, zebrafish were used as the model organism to study these periocular mesenchyme cells on the molecular level. The periocular mesenchyme cells were isolated and a single cell transcriptome analysis identified the genes highly expressed by the cells. Si:ch211-251b21.1 and hgd were two of these upregulated genes. Si:ch211-251b21.1 is suspected to be a glutamate receptor of the kainate family, while hgd is involved in pigment synthesis. Knocking out both genes with the CRISPR Cas9 system resulted in a particular phenotype that included maldevelopment of the anterior segment. My project will focus on the role of the potential glutamate receptor si:ch211-251b21.1 for eye development. The subgroup of glutamate receptors in zebrafish embryos will be inhibited with drugs known from previous studies. These drugs include CNQX, UBP 302, Kainate acid, and sym2081. CNQX and UBP 302 are Kainate receptor antagonists, that will block the glutamate receptor function. Kainate acid and sym2081 are Kainate receptor agonist which could produce an enhanced effect of the kainate receptor on the cell. After drug exposure, in situ hybridization and antibody stainings will be performed to examine if the drugs had an impact on the expression and function of si:ch211-251b21.1. The expected result includes a similar phenotype from the CRISPR Cas9 knockout and changes in expression of the si:ch211-251b21.1 gene.

Sperm are perhaps the most highly specialized and modified cells in the animal world. They are specifically designed to be efficient couriers of the male’s genetic information. Animal sperm vary in shapes and sizes to carry out this task. Nonetheless, the general process of sperm production is largely similar from insects to mammals. Construction of a sperm is accomplished with the assistance of other cells in the testis. While many studies have uncovered genes that are active in sperm during their development, little is known about the genes and functions of the support cells in the testis. In the fruit fly, Drosophila melanogaster, each 64-spermatid cluster develops as an interconnected cyst and is encapsulated by a pair of somatic support cells, called cyst cells. Recent work in the lab has uncovered that communication between these somatic cyst cells and the spermatids is necessary to direct the separation of spermatids within a cyst during the late stages of spermatogenesis. To better understand the roles of the somatic support cells, this project will identify factors required in cyst cells to complete sperm development. For this project, we will specifically impair the functions of particular candidate genes only in the support cells of the testis to examine the impact on sperm formation. Because the process of spermatogenesis is similar across species, this work will not only aid in understanding cellular collaboration in Drosophila spermatogenesis, but it will contribute to our understanding of spermatogenesis in general.

The channels for transmitting electrical activity along neurons is similar from squid to humans with sodium currents accounting for the upstroke of an action potential and potassium channels for the rapid and delayed ionic flux for the repolarization. Pharmacological agents tetraethylammonium chloride (TEA) and 4-aminopyridine (4-AP) block different subsets of voltage gated potassium (K+) channels. The chordotonal organs in crab limbs are a model of proprioceptive sensation and have rapidly- and slowly-adapting sensory neurons. Since 4-AP is used clinically for amyotrophic lateral sclerosis (ALS) and Multiple sclerosis (MS) treatments, a better understanding of its action on proprioceptive models can aid in understanding the potential effects in mammalian systems. To assess the action of these blockers on the function of proprioceptive sensory neurons, the neurons were evoked by movements associated with the joint while applying these compounds individually as well as in combination. Both 4-AP and TEA decreased activity individually, as well as when combined together. Full function was not returned in most preparations after the 4-AP and TEA were washed out individually or from the cocktail exposure. Thus, the potassium channels are sensitive to both blockers in this marine crustacean model. It appears the action is on electrical induction and conduction within the axons. This crab crustacean proprioceptive model can be used for future intensive investigations, building on the results presented, in the pharmacology of the mechanosensitive channels and neuronal activity.