Promises and Obstacles in Lipidomics Research

Following the advancements in genomic and proteomic biomarker development, scientists are now looking for something more versatile that changes throughout the course of a disease and represents the physiological environment at a given moment. This kind of biomarker holds strong promises for quick and non-invasive liquid biopsy development and can be a great complementation to genetic profiling of patients. The lipidome is gaining more traction among scientists in this field of research, and in this article, we explore why.

Neurology is leading the way

Neurology is the pioneer field when it comes to lipidomics. “The central nervous system is highly enriched in lipids, not only in terms of quantity, but also diversity of lipid structures. Characterizing this diversity and how lipids are modulated during aging and neurodegenerative diseases is key to clarify their role in pathology,” says Sayuri Miyamoto, Professor at the University of São Paulo. Her recent research¹ is focused on the lipidomic alterations in the spinal cord of a rat model of Amyotrophic Lateral Sclerosis (ALS). The work greatly illustrates how the lipidome can be applied for diagnostic and disease follow-up in neurodegenerative disorders. “We primarily sought to identify diagnostic lipids reflecting disease progression,” Miyamoto and the leading scientists on the project explain. Their results suggest important roles for the lipidome beyond the central nervous system. “So far, our data suggest major alterations in the lipidome of all tissues and fluids that might be helpful to understand disease progression.”

A major finding of the team is the observation of an increase in cholesteryl esters in the spinal cords of ALS rats. “This data alone suggest that blockage of cholesterol synthesis or esterification specifically in the central nervous system may help attenuating the progression of ALS.” Understanding the molecular mechanisms driving the lipidome alterations in the context of ALS and validating their results in ALS patients is the next envisioned step for the team. “Since lipids are a major pool of metabolites, not only can they be used as biomarkers, but also in personalized medicine and serve as potential targets for therapies,” Miyamoto envisions.

Multidisciplinary interest towards the lipidome

Lipidomics research is quickly moving beyond neurology. An illustration of this is the work of Professor Ronan Quéré and team from the University of Burgundy-Franche-Comté who are analyzing a particular lipid conformation at the plasma membrane: the lipid rafts (LRs)². LRs are particular membrane domains composed of lipids and glycoproteins and are involved in membrane fluidity and signaling events. LRs are highly important for cell types characterized with high level of signal transduction passing through the plasma membrane. Quéré and colleagues have focused their attention on hematopoietic stem cells (HSC) and how a high-fat diet (HFD) modulates TGF-β1 signaling through the lipid rafts.

“LRs need perfect ratio between cholesterol and sphingolipids for homeostasis. Our hypothesis was that changes in diet (…) would modify LRs and the localization of receptors proteins within LRs. We discovered that LRs become clustered after HFD and the TGF-β1 receptor was found clustered among LRs, which inhibit its function involved in retention/maintenance of HSC in an organism,” Quéré explains. The team is planning on continuing their work in the pathological context of Acute Myeloid Leukemia (AML) using a well-established mouse model. “We would like to know if a HFD during a feeding of four weeks would accelerate the development of hematological malignancies such as leukemia.”

Membrane receptors of tumor cells are a main target of a number of anti-cancer therapies. It is, therefore, crucial to understand the mechanisms regulating their activation and signal transduction.

Can we regulate the lipidome through diet?

An important feature of all metabolomic entities, including lipids, is that their concentrations and profiles are precisely regulated by anabolism and catabolism. This therefore suggests that lipids can be modulated through dietary control, and diet could become a treatment for lipid-related disorders.“For treatment of cancer, yes, I think it would be possible to use diet as a therapy, but only associated (in combination) with chemical compounds already used in therapy (such as chemotherapy). A specific diet by itself would not have effect on cancer, but would maybe ameliorate efficiency of a therapy,” Quéré explains.

Miyamoto’s team reflects on the need for further research on the topic: “We believe that a precise quantification of molecular species of lipids is crucial for determining lipidome alterations in response to diet. (…) Nevertheless, there is only a few lipidomics studies focused on diet in clinical trials or large cohorts!"

What are the technologies being used and what are their limitations?

The lipidome offers great potential for basic and translational research, however, it simultaneously confronts scientists with many technological challenges, arising mainly from the biochemical nature of lipids.

The method of choice when studying lipids is mass spectrometry (MS). “Among the modern methods for lipid profiling, MS has definitely changed paradigms of what is possible to quantify as far as the diversity of lipid compounds,” the team of Miyamoto explains. There are many MS approaches for scientists to choose from: tandem MS, shotgun, MS coupled to liquid chromatography, and various ionization methods. Although these methods have enabled researchers to reach milestone discoveries in lipidomics, there is a persistent need for more technological achievements. “Lipidomics as well as metabolomics by MS are both just scratching the surface in terms of scientific discoveries, but several robust research outcomes have been already demonstrating their effectiveness in clinical studies,” Miyamoto says.

When it comes to studying a very specific cell population and a small lipid pool such as the LRs there are alternative approaches that can be adopted outside of MS. “Another technology is immunostaining and confocal microscopy on purified cells (HSC purified by cell sorting with a Fluorescence Activated Cell Sorting (FACS)). LRs can easily be stained with the Cholera Toxin Subunit B (CTB) conjugated with a fluorochrome. (…) This is to me the best technology today, but it is time consuming and not a high throughput technique. There is unfortunately today, in my knowledge, no prominent technologies to analyze further samples on rare populations,” Quéré says.

This approach also does not allow one to correlate expression of LRs with a certain receptor and their direct interaction. “If one day a technology can associate performance of FACS and microscopy, we will be able to do a lot of new high throughput work,” Quéré concludes. Development of high throughput methods is an important limitation as well as standardization of methods and controls across laboratories. “The number one challenge of any MS method is reproducibility,” Miyamoto is convinced.

How is the lipidome complementing genomic and proteomic data?

Today more than ever it is clear that a combination of multiomics data is the key to understanding the complexity of cell physiology. For the work of Quéré’s team it is essential to combine proteomics and lipidomics in order to decipher a receptor’s localization within the LRs. Miyamoto and her colleagues' work in a parallel fashion: “We believe that any phenotype of a given individual is a result of life-long environmental factors shaping hierarchical domains of the genome, transcriptome, proteome and finally the metabolome. The latter ultimately reflects the individual phenotype. (...) We believe that the combination of omics sciences has a great potential to elucidate metabolic pathways that lead to disease progression and thus offers excellent opportunities for targeted therapies development,” they conclude.

The promising perspective of using lipids as biomarkers and therapy targets drives the increased interest in the field. Moreover, it looks set to motivate the development of novel technologies that will enable scientists to dive deeper into understanding the complex nature of lipids.

References:

1.       Chaves-Filho, A. B. et al. Alterations in lipid metabolism of spinal cord linked to amyotrophic lateral sclerosis. Sci. Rep. 9, 11642 (2019).

2.       Hermetet, F. et al. High-fat diet disturbs lipid raft/TGF-β signaling-mediated maintenance of hematopoietic stem cells in mouse bone marrow. Nat. Commun. 10, 1–11 (2019).

Prof. Ronan Quéré and Prof. Sayuri Miyamoto and her team members Marcos Yoshinaga and Adriano Chaves-Filho spoke to Maya Chergova, Ph.D. for Technology Networks.