2024 Results

The UFlorida iGEM team is proud to annouce that we earned a Gold Medal distinction at the 2024 Grand Jamboree! A special thanks to our amazing PI, Dr. Jing Pan, and to our incredibly hard-working team, without whom this accomplishment would not be possible. UFlorida looks forward to competing in the iGEM in the future and continuing to grow as a lab through this experience!

Sepsis

Pathogenic infections occur when a bacteria, virus, or fungus enters and infects a human host cell. Typically, the presence of infected cells elicits an immune response to destroy both the infected cells and the pathogen. Sepsis is an abnormal and extreme immune response that leads to the destruction of healthy cells as well (Mayo Health Clinic, 2023). This autoimmune reaction can lead to tissue damage, organ failure, and in severe cases, death.

Sepsis is a public health crisis. Worldwide, there are over 48 million cases of sepsis leading to over 11 million sepsis-related deaths annually (World Health Organization, 2024). Cancer patients specifically have four times the incidence rate of developing sepsis, highlighting the increased severity as it impacts populations with already weakened immune systems (Sepsis Alliance, 2024). With its high overall prevalence and increased occurrence in immunocompromised populations, sepsis is the leading cause of hospital deaths, costs, and readmissions. The lack of a simple diagnosis and treatment for sepsis contributes to the severity of these issues. Understanding sepsis progression and how it affects the body are crucial components to the development of sepsis management tools.

The severity of a sepsis diagnosis alongside the lack of understanding associated with sepsis progression, diagnosis, and treatment creates objectives for sepsis research; however, studying sepsis is difficult and requires a reliable model for experimentation. Upon discovering this need, the UFlorida iGEM team decided to develop a new model to study sepsis response via bone marrow organoid.

Current Models

Studying sepsis in patients presents significant challenges due to the complexity and variability of the condition. The diagnosis of sepsis is particularly challenging since the condition's symptoms commonly coexist with other inflammatory illnesses, and blood cultures which are essential for diagnosing infections typically return negative results and take days to produce results (Kuye & Rhee, 2018). The identification and monitoring of sepsis are further complicated by the non-specific character of the dysregulated host response and the absence of a universally accepted clinical definition. It is difficult to improve outcomes for septic patients due to these factors, which also lead to delays in diagnosis and treatment (Kuye & Rhee, 2018).

Animal models are the current standard for sepsis research. Various animal models have been implemented, specifically utilizing rodent models to develop an understanding of sepsis infection (Cai et al., 2023). Current models have attempted to induce a sepsis-like response through bacterial infection, fungal infection, cecal slurry, endotoxemia, intraperitoneal models, bacterial clot implantation, and cecal ligation and puncture (Cai et al., 2023). The conclusions drawn from animal studies are not always clinically relevant (Nandi et al., 2020). For example, the animal model utilizing bacterial or fungal infection may convey differing results compared to the clinical effects of sepsis infection in a human (Cai et al., 2023). Endotoxemia models, which function by introducing endotoxins to cause inflammation, do not manifest the sepsis symptoms the same way clinical sepsis infection would (Cai et al., 2023). With sepsis infection having such a broad range of possible clinical manifestations and impacts on each individual patient, the modeling of the infection in an animal can be difficult to apply to clinical cases (Nandi et al., 2020).

Hematopoiesis

Hematopoiesis is the formation of the cellular components of blood, derived from hematopoietic stem cells (Jagannathan-Bogdan & Zon, 2013). During sepsis, the body often undergoes “emergency hematopoiesis,” a rapid production of blood cells in response to infection. Cytokines and other signaling molecules propel this process by encouraging the bone marrow to create more immune cells to combat the infection (Olisaemeka Ogbue et al., 2023).

Current research suggests that understanding how sepsis affects hematopoiesis may be the key to understanding sepsis progression (Wang et al., 2021). Unfortunately, changes in hematopoiesis during sepsis progression are not clearly understood (Olisaemeka Ogbue et al., 2023). Currently, research on hematopoiesis in the bone marrow is limited by the fact that hematopoiesis in rodents and humans is quite different. In initial embryonic development, humans and rodents both start hematopoiesis in the yolk sac, then move to the liver, spleen, and finally, the bone marrow, but the timing and complexity differ (Zambidis, 2005). Additionally, the regulatory mechanisms for stem cell maintenance, gene expression, and bone marrow structure vary between humans and rodents, making it difficult to model human hematopoietic pathophysiology (Parekh & Crooks, 2012).

Bioethics

Ethical concerns arise when considering the use of animal subjects in sepsis research (Nandi et al., 2020). The harm done to animal subjects must be weighed in comparison to what is gained through the research. The possibility of subject death due to sepsis infection brings into question the morality of utilizing live animals to study sepsis. Furthermore, more accurate representations of sepsis infection in animal models might include the presence of comorbidities in the research subjects (Guillon et al., 2019). The incorporation of additional diseases in the subjects for the purpose of producing better experimental results raises ethical dilemmas regarding the subjects’ well-being.

A bone marrow aspiration or biopsy would be needed to study the cellular composition of a human patient’s bone marrow, which are highly invasive procedures (Nagaraju et al., 2023). In a bone marrow biopsy, a small core of bone marrow tissue is removed using a special needle (Mayo Clinic, 2018). Patients in septic shock may not be able to withstand an invasive procedure and the principle of maleficence bars physicians from worsening a patient’s prognosis (Nagaraju et al., 2023). Additionally, sepsis can impair patients’ consciousness, which inhibits their ability to consent to studies (Polito et al., 2015). Sepsis is a rapidly fluctuating condition, and to fully understand the changes in the bone marrow, these changes need to be monitored over time (Nagaraju et al., 2023). The limited accessibility of the bone marrow, the critical state of sepsis patients, and issues of inhibited consciousness bar the possibility of collecting samples at multiple time points in human subjects. Overall, studying bone marrow pathophysiology in sepsis patients is not feasible due to significant bioethical and medical considerations.

Organoids

Organoids are 3D structures most commonly derived from induced pluripotent stem cells (iPSCs) (Zhao et al., 2022). iPSCs are cells of the body reprogrammed to a pluripotent state, able to differentiate into the majority of somatic cells (Cerneckis et al., 2024). A patient’s cells can be collected, reprogrammed, and made into new cell types. Organoid models present key biological, morphological, and functional characteristics of an organ or tissue (Zhao et al., 2022). Organoids serve as miniature, isolated platforms to study tissues ex vivo, eliminating many ethical issues associated with the use of animal models. Additionally, their separation from a living being enables greater manipulation and examination of the modeled structure in a controlled environment.

Existing organoids include models of the brain, kidney, lung, intestine, stomach, and liver. These “mini-organs” have facilitated groundbreaking research on the microbiome, neurological processes, cancer, regenerative medicine, developmental biology, drug discovery, and disease mechanisms. In 2023, Khan et al. published an article detailing the differentiation protocol to create bone marrow organoids, which can provide key insights into the body’s center for blood cell production. The UFlorida iGEM team adapted this protocol for our project to study the immune response in depth ex vivo.

Our Solution

The UFlorida iGEM team is developing in vitro and in silico human iPSC-derived bone marrow organoids to study sepsis response. This year, our team focused on optimizing organoid production procedures and developing an in silico model to predict cellular behavior to investigate bone marrow pathophysiology. Our in silico model unveils the cellular changes that occur in the bone marrow when a sepsis-like inflammatory response is introduced and provides insight into behaviors we may see in the wet laboratory.

Our research findings bring our team a step closer to creating a fully isolated and manipulatable in vitro bone marrow organoid. By establishing this model, the UFlorida iGEM team seeks to bring scientists and physicians one step closer to understanding bone marrow pathophysiology caused by sepsis. A bone marrow organoid exposed to sepsis-like conditions can be studied in depth over time without requiring an invasive collection procedure or confounding factors present in rodent biology. By deepening our understanding of the complex biological response, we will enhance sepsis diagnosis, characterization, and treatment.