Life Sciences

Design of novel proteins targeting the PD-1/PD-L1 pathway

The PPI being analyzed is PD-1 to PD-L1. Programmed cell death 1 (PD-1) is a protein involved in regulating the immune system’s T-cell induced apoptosis system by suppressing T-cells. Therefore, PD-1 suppresses and prevents cell apoptosis. PD-1 performs this function in unison with PD-L1 or Programmed Death Ligand 1. The suppression of T-cells can only occur when PD-1 is bound to PD-L1, therefore, this a very important protein-protein interaction. Because this PPI is highly involved in cell cycle regulation it is a common target of cancer treatments. One common cancer treatment is a drug that blocks PD-1 and prevents it from complexing with PD-L1. By hindering this PPI, T-cells’ ability to kill possibly cancerous cells is increased. Using an evolutionary-profile based approach program called UniDesign, 300 possible different peptide sequences were created for PD-1 while keeping PD-L1 the same. Although results have not been obtained we hope to show through the experimental analysis that the designed sequences will have a stronger binding affinity to PD-L1 than PD-1. This research is important because better understanding this PPI plays a large role in cancer treatment research.

Computational design of protein binders to block the PD-1/PD-L1 pathway

The Programmed Cell Death Protein 1 (PD-1)/Programmed Cell Death Ligand 1 (PD-L1) pathway is crucial in the immune system’s response to cells in the human body. When PD-L1 binds to PD-1 it helps to prevent T-cells from killing other cells, including cancer cells which allows for tumor growth. We used an physics-based approach, EvoEF2, to create an artificial protein based on the structure of PD-1 to competitively bind to PD-L1. We are hoping to show through our binding experiment analyses that our designed proteins will have a stronger binding affinity to PD-L1 than PD-1. While PD-1 inhibitor drugs have been developed they are not completely effective, finding more effective ways to block this pathway could be an important step in future cancer drug research.

Design of cancer proteins

The goal of this research project is to develop a form of gene therapy for someone who has been diagnosed with cancer. In order to do so, it is essential that we change a protein protein interaction (PPI) between a cancerous cell and the protein it is interacting with so that the cancerous cell can cease to both mutate and produce even more cancerous proteins.

A Predictive Machine Learning Model for [18F] SnAr Radiofluorination

Positron Emission Tomography, commonly known as PET imaging, is a noninvasive, rapid, and accurate imaging system that tracks the distribution of a radioactive tracer. There are many strategies to incorporate radioactive nuclides into tracers for PET imaging, with the most prevalent approach being radiofluorination”” the incorporation of the radioactive nuclide 18F into a bioactive molecule. One of the most common ways of incorporating 18F into substrates is nucleophilic aromatic substitution (SNAr); however, this approach suffers from harsh conditions, exotic leaving groups, and unpredictability, thereby limiting the ease and broad use of this procedure. Herein, a predictive machine learning model will be developed for SNAr using nucleophilic 18F, allowing for prediction of radiochemical yields given a certain set of reaction conditions. An appropriate data structure for machine learning was constructed by encoding literature substrates and conditions. This involved DFT (density function theory) calculations using Gaussian09 to create an optimized structure and determine quantifiable properties, such as HOMO and LUMO energies, steric hindrance, and NMR data. However, due to the time requirements needed to assemble the data set, no concrete results have been produced as of yet. Using this data set, regression models will be generated via several machine learning algorithms in Python, ranging from simple linear models to more complex decision tree and neural network models. The project hopes to build a successful model that will allow for the prediction of radiochemical incorporation given a substrate and reaction conditions. This model may then be validated through further experimentation and generalized to a wider variety of substrates via strategic experiment selection.

Suppression of Heterotopic Ossification Using a TAK1 Inhibitor

Heterotopic ossification (or HO) is the abnormal growth of bone in soft tissues, such as muscles, tendons, and more which cause the subject to develop excruciating pain in their joints. After seeing how negatively HO affects a patient’s life, there is a clear need for prevention of the lesions to help improve the life of someone with HO. The host lab previously found that genetic or pharmacologic suppression of TGF-beta activated kinase 1 (TAK1) is efficient to mitigate HO. A next logical step of the study regarding HO is that the lowest possible dose of a TAK1 inhibitor, Takinib, with co-treatment of an anti-inflammatory drug, rapamycin, will suppress the growth of heterotopic ossification in mice. After induction of HO in our genetic mouse model for HO, a suboptimal dose of Takinib was orally administered with a range of rapamycin. Tissues with resulted HO were scanned by the micro-CT 500 microscopy scanner. CT scans of experimental mice with HO were investigated using a software called ITK Snap, which helps find the volume of the HO throughout the mice. The volumetric measurements revealed that combinations of suboptimal doses of Takinib and rapamycin effectively suppressed the growth of HO, or bone growth in soft tissues. Our findings suggest that co-treatment of TAK1 inhibitors with anti-inflammatory drugs, such as rapamycin, is the way to suppress the growth of heterotopic ossification with minimal side effects of each chemical. The study hopes to identify the lowest dose of the main anti-inflammatory chemical and how this dose will be effective in reducing the growth of HO. The identified chemical dose will ultimately serve as an efficient treatment for HO without adverse reactions not only in mice, but also in humans.

Midfacial Defects with Ectopic Cartilages through Ectopic X Chromosome Inactivation by Enhanced Bone Morphogenic Protein Signaling

Craniofacial defects have affected some humans from birth, running rampant without many methods to lessen the impact. We aim to explore potential solutions to the phenomenon using model mice. We recently reported that transgenic mice with enhanced bone morphogenic protein (BMP) signaling in neural crest cells induced midfacial defects along with ectopic cartilages in the face but not in trunk neural crest cells (NCCs). Here, we hypothesized that enhanced BMP signaling in NCCs formed ectopic cartilages, resulting in midfacial defects. Single-cell RNA sequencing identified candidate genes that may be involved in the ectopic cartilage formation. Among them, Xist, a central component of X chromosome inactivation, is our focus because it was significantly increased in cranial NCCs from mutant mice but not in trunk NCCs from mutant mice. That led us to the idea that ectopic X chromosome inactivation by increased Xist is responsible for the ectopic cartilages in the face since Xist is not increased in trunk NCCs, and ectopic cartilages did not form in the trunk. To analyze that, we counted inactivated X chromosomes of cranial and trunk NCCs, allowing us to analyze how they impacted ectopic cartilage formation. Female cells normally inactivate one of two X chromosomes in a nucleus. Here, we showed that some of the cranial NCCs from mutant mice have two inactivated X chromosomes in a nucleus, which means ectopic X chromosome inactivation. Moreover, trunk NCCs from both control and mutant mice did not have two inactivated X chromosomes in a nucleus as we expected. Our preliminary results indicated that cranial NCCs from mutant mice have ectopic X chromosome inactivation, and trunk NCCs from mutant mice did not have ectopic X chromosome inactivation. That outcome supports that ectopic X chromosome inactivation in the cranial region is partially responsible for ectopic cartilage formation. That area could be a target for clinical treatment of the ailment. Considering the increased Xist in mutant mice, an inhibitor would be ideal for treatment, allowing X chromosome inactivation.

Effects of temporomandibular joint disorder in chewing cycle

Temporomandibular joint disorders (TMJD) are a series of disorders that affect the joint articulating the mandible and the skull, which is responsible for jaw movement. Abnormal jaw movement and abnormal temporomandibular joint (TMJ) shape are typical symptoms in TMJD patients. It is yet unknown whether abnormal TMJ movement is a result of the alterations in the TMJ in TMJD. In this study, we will use Evc2 mutant mice, which bears TMJ in abnormal shape, to understand if abnormal joint shape may lead to abnormal jaw movement. Currently, video of one mutant mouse, which has its Evc2 gene deleted in neural crest derived tissues, and one control mouse were taken to analyze jaw movement. After tracking fiducial markers planted in the mice with a program called XMALab onto a 3D coordinate plane for four consistent chews, we discovered a difference in chewing pattern between the mutant mouse and the control mouse by looking at the distance between the mandible and the skull in the duration of its chewing. We found that while the control mouse clearly had two types of chewing patterns, the mutant mouse only had a scattered chewing pattern with one noticeable type of chewing pattern. The chewing range of the mutant mouse was approximately half of that of the chewing range of the control mouse. Possible explanations of this is that the mutant mouse possibly is not physically capable of moving the jaw to do two cycles or the mouse could be in possible pain, preventing the two chewing patterns we saw in control. There is a notable difference in the chewing patterns between the control mouse and the mutant mouse, indicating that abnormal TMJ impacts chewing cycle.

Development of PROTAC-based degrader of ERG transcription factor in prostate cancer

Victoria Zeng Pronouns: she/her/hers Research Mentor(s): Xiaoju Wang, Associate Research Scientist Research Mentor School/College/Department: Pathology-Michigan Center for Translational Pathology, Michigan Medicine Presentation Date: Thursday, April 22, 2021 Session: Session 3 (1pm-1:50pm) Breakout Room: Room 11 Presenter: 5 Event Link Abstract For privacy concerns this abstract cannot be published at this time. Authors: Xiaoju Wang, Victoria …

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Use of Novel Small-Molecule PP2A Activators in Prostate Cancer Cell Lines

Dysregulation of kinases and phosphatases in the signal-transduction-pathway disrupts cellular homeostasis and can result in serious diseases and a variety of cancers. The dysregulation of phosphatases in cancer have received little attention by the scientific community and thus additional knowledge of their role in carcinogenesis is needed to better understand cancer progression and to explore their potential as drug targets (Leonard, 2020). Specifically, I have been helping two staff scientists in the Narla lab study the post-translational modifications of protein-phosphatase PP2A in prostate cancer using molecular biology assays and to test novel small-molecule PP2A activators the Narla lab is developing. These novel small-molecule PP2A activators are expected to prompt downregulation of oncogenic transcription factors and modulate post-translational changes.

Epigenetic Mechanisms of X-chromosome Inactivation

X chromosome inactivation (XCI) is a dosage compensation method thought to equalize gene expression between males and females through the silencing of one of two X chromosomes in eutherian mammals. This process is carried out by the long non-coding RNA Xist, which is expressed from the prospective inactive X. Xist then recruits polycomb group proteins to help mediate gene silencing. One such protein, EED, which is a part of the polycomb repressive complex 2 (PRC2), has been shown to help deposit and maintain histone H3 lysine 27 trimethylation (H3K27me3) on the inactive X. This epigenetic tag is commonly associated with gene silencing and thought to play an integral role in XCI. However other components of the PRC2 complex, specifically the roles of the catalytic proteins EZH1 and EZH2 are less known and this project seeks to better understand their impact on XCI.