Chemical & Biomolecular Engineering

Clemson University researchers help personalized medicine take a step forward

Clemson University researchers are helping lay the groundwork for computer simulations that could eventually be used to match cancer patients with the medicine that will help them get well.

A team of 11 researchers that included six from Clemson recently reported on its work in the journal Nature Communications. The research is a step forward for personalized medicine, helping raise hopes that clinicians will one day be able to plug patients’ data into a computer model to find the best possible medicine for each individual.

The paper’s authors built on previous work to develop a new way of creating and altering mechanistic models that bring together large datasets with minimal computer coding.

Marc Birtwistle, left, and Cemal Erdem are corresponding authors on a recent paper that helps advance personalized medicine

Cemal Erdem, a postdoctoral fellow in Clemson’s Department of Chemical and Biomolecular Engineering, said the paper will be of most interest to other researchers, especially those at pharmaceutical companies and those studying computational modeling or signaling networks.

“The impact of this paper is that we are trying to make it much, much easier to create these types of models,” he said. “We have this open-source tool now, with the code available on the internet. Researchers can take this code, create their own models and run simulations on their desktop computers or supercomputers.”

That code can be accessed here.

Marc Birtwistle, an associate professor of chemical and biomolecular engineering at Clemson, said his overarching goal in building models is to match drugs to patients. He said that his work is aimed at helping medical researchers answer design questions, similar to how an airplane manufacturer would run computer models of airplane designs before building an actual airplane.

“Medicine and pharma don’t have those types of design tools because they don’t exist yet,” Birtwistle said. “In a broad sense, that’s why this kind of work can be impactful. We’re trying to build that foundation so that those sorts of simulation models could help clinicians make decisions about patients.”

The team reported its findings in a paper titled, “A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling.”

“This work forms a foundational recipe for increased mechanistic model-based data integration on a single-cell level, an important building block for clinically-predictive mechanistic models,” researchers wrote in the abstract.

Most published mechanistic models are small in scale and limited in their abilities, and it can be a struggle to incorporate multiple datasets, researchers wrote. Large-scale models “can provide a more extensive representation of cellular interactions and are thus well-poised for data integration that complement shortcomings of machine learning approaches,” they wrote.

Birtwistle said that computational biology researchers now have a way to very easily build on the team’s work.

“The way the model is programmed and built is very simple and easy to use,” he said. “Before, it was very difficult and almost inaccessible, but now it’s accessible. I think we’re going to be able to recruit much more of a research community into building these sorts of approaches.”

Aurore Amrit, a fifth year pharmacy student at the University of Paris, was able to start running a model within days of starting her work as an exchange student in Birtwistle’s lab. Before the team developed its new system, it took a postdoctoral researcher six months to do the same work.

“I added some models for anti-cancer drugs,” Amrit said. “It’s very straightforward.”

David Bruce, chair of the Department of Chemical and Biomolecular Engineering, congratulated the team on publishing its work.

“This collaborative, multidisciplinary research helps keep Clemson at the forefront of health innovation,” Bruce said. “Thanks to the team’s work, the research community is better positioned to answer one of medicine’s most challenging questions– how to treat cancer as painlessly and effectively as possible.”

Corresponding authors on the paper were Erdem and Birtwistle. Co-authors from Clemson also included: Arnab Mutsuddy, a Ph.D. student in the Department of Chemical and Biomolecular Engineering; Ethan M. Bensman, who was an undergraduate in the School of Computing at the time of the research; William B. Dodd, an undergraduate in Clemson’s Department of Chemical and Biomolecular Engineering; and Alex Feltus, a professor in the Department of Genetics and Biochemistry.

Co-authors from other institutions were: Michael M. Saint-Antoine of the Center for Bioinformatics and Computational Biology at the University of Delaware; Mehdi Bouhaddou, of the Department of Cellular and Molecular Pharmacology at the University of California, San Francisco; Robert C. Blake of the Center for Applied Scientific Computing at Lawrence Livermore National Laboratory; and Sean M. Gross and Laura M. Heiser of the Department of Biomedical Engineering at Oregon Health & Science University.

Catalysis for Sustainable Energy is Fertilizing Student Growths

Graduate and undergraduate students showcase their teamwork at the Annual Research Forum of Creative Inquiry at Clemson University.
Clemson students team up with other college students from South Carolina in 10-week summer research.

In Dr. Ming Yang’s group, the current research projects in mitigating greenhouse gas emissions to value-added products through thermal and electrocatalysis are sponsored by NSF, NASA, and ACS. These research projects have become a fertile platform for graduate and undergraduate students to pursue their individual developments and to serve our community. In the past 2021-22 academic year, student researchers from Yang Lab received eleven awards from Clemson University and external organizations to elevate their research outcomes. These include the Undergraduate Research Awards of Clemson University to John Yeager and Nicolas Glisson, the Palmetto Academy Research Awards to Bridget Bruce and William Howl, the Undergraduate Research Award by NASA EPSCoR for Julia Wood, Graduate Student Travel Awards of Clemson University for Ewa Chukwu, Zehua Jin, and Alexander Adogwa, the Kokes’ Award by North American Catalysis Society for Ewa Chukwu,  1st Place Presentation at the Annual Postdoctoral Symposium of Clemson University for Dr. Manjeet Chhetri, and Advancing Science Grant by NOBCCHE for Ewa Chukwu. Congratulations to the team!

 

What are our undergraduates working on this summer?

Dr. Jessica Larsen’s Research Lab –
Grace Anderson, junior undergraduate researcher

Grace Anderson, a junior undergraduate researcher for Dr. Jessica Larsen, is working on an SC BioCRAFT funded project this summer. The overarching goal of Grace’s project is to improve the current standard of care for brain tumors.

Cancerous cells left adjacent to the removed tumor account for 96% of recurrent tumors, providing motivation for immediate local drug delivery to that area while helping the tissue to heal. Preventing tumor resurgence and healing the brain tissue post-surgery can be performed simultaneously using thermally responsive hydrogels.

Grace is working to create polymers that are liquid at room temperature and gel up at body temperature, encapsulating and delivering a drug slowly over time.

Dr. Eric Davis’s Research Lab –

This summer, undergraduate researchers Jaden Stutts and Alana LeSuer are working in Prof. Davis’s lab on highly interdisciplinary projects encompassing polymer science, energy storage and delivery, and membrane-based aqueous separations.

Jaden Stutts, undergraduate researcher

Jaden, a rising Junior who joined the lab in Spring 2020, is currently working towards completing her Departmental Honors Thesis on a project centered around the fabrication and characterization of poly(hydroxyethylmethacrylate) (pHEMA) and lignin soft composites (i.e., composite hydrogels), which have potential applications in biotechnologies such as wound dressing and drug delivery.

While prevalent in biomedical research, hydrogels comprised primarily of pHEMA are not mechanically robust and suffer from degradation issues, limiting their implementation in many applications. With the introduction of lignin, an abundant biopolymer that is a byproduct of the pulping and paper industry, we are able to tune both the mechanical and transport properties of the soft composites, creating materials with tailored functionality. Along with altering various synthesis parameters, Jaden will also investigate how the properties of the composite hydrogels change depending the source of the lignin – e.g., hardwood or softwood.

Alana Lesuer, undergraduate researcher, and Xueting Wang, Ph.D. student

Alana, a rising Senior in the program, is working with one of the graduate students in Prof. Davis’s lab on a project involving ionomer (i.e., polymers containing a fixed charge along the backbone) nanocomposites for use in vanadium redox flow batteries. Redox flow batteries, which can be thought of as large car batteries, have emerged as a promising electrical grid-scale energy storage technology due to their scalability.

However, the current state-of-the-art ionomer used to separate the liquid electrolytes in the battery suffers from issues related to electrolyte crossover, reducing the efficiency and lifetime of the battery. To address this issue, Alana will work to fabricate and characterize ionomers containing functionalized nanoparticles that have shown promise at addressing issues related to electrolyte crossover without compromising the attractive properties of these ionomer membranes.

Specifically, Alana will be synthesizing sulfonated poly(ether ether ketone) membranes containing silica nanoparticles with a wide range of surface functionalities. By varying the concentration and surface functionalization of the nanoparticles, the ion transport properties of the membranes can be significantly altered, ultimately leading to membranes with better performance properties than the current benchmark ionomers.

Both Jaden’s and Alana’s work are funded by a summer research grant through the Clemson University Creative Inquiry Program, as well as through an external grant from the Materials Assembly and Design Excellence in South Carolina (MADE in SC) Program titled, “Closing the Gap of Underrepresented Minorities and Women in Polymer-Related Research”.

Student researchers in catalysis to tackle greenhouse gas emissions and to produce clean energy

Case Sandor and John Yeagar are working on the project entitled “Catalysis for Carbon-Neutral space Exploration”, to produce propulsion fuel molecules through cathode reactions and life-supply O2 through anode reactions in separated streams.

Four student researchers engaged in catalytic materials and reaction engineering research at Dr. Ming Yang’s group have been recently recognized by the university and external funding agencies for their ongoing research work that aims to tackle climate change and to harvest clean energies.

Luis Morales and John Yeager, junior undergraduate students, were recently accepted into Clemson’s 2021 Summer Creative Inquiry program and given the accompanying Undergraduate Research Award (CI & UR Award). Luis and John, through both thermocatalytic and electrocatalytic approaches, will investigate how chemical engineers can significantly cut CO2 greenhouse gas emissions by turning the CO2 into value-added products through cost-effective environmentally benign catalytic reactions.

Case Sandor, senior undergraduate student, is a recipient of the Undergraduate Student Award from South Carolina NASA Space Grant Consortium. The agency funded Case for 400 hours of research to develop catalytic materials and electrochemical reactors that can convert CO2 in space and cabin into renewable fuels so as to empower deep space exploration. Case will also participate in outreach/public engagement activities during his award period to advocate research and science to public.

Ewa Chukwu and Luis Morales are undertaking a thermocatalytic approach in the project entitled “Catalysis for Clean Manufacturing”. Their research seeks to optimize the selective reduction of CO2 to value-added carbon-based chemicals as building blocks for various industrial processes.

Ewa Chukwu, a first-year international PhD student, has been selected to participate in the Student Program at the 2021 ARPA-E Energy Innovation Summit sponsored by the US Department of Energy. The 2021 Student Program will include the top graduate-level students, an engaging panel discussion regarding a career in energy, a Meet & Greet to speak with energy industries, and many opportunities to learn about cutting-edge energy initiatives.

Congratulations Case, Ewa, John, and Luis! Full speed ahead!