Journal Club: Anaerobic metabolism is very important factor during cochlear development

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Today's journal article

Wu M, Jia G, Liu Y, Lou Y, Li Y, Xia M, Li H, Li W. PKM2 controls cochlear development through lactate-dependent transcriptional regulation. 

Why I picked this article

The life of a cell is dependent on energy. Glycolysis is a process by which cells produce energy. Glycolysis does not require oxygen, and energy molecule, ATP, can be produced by a series of enzymes that break down sugar. This is in contrast to another method for cells to produce energy through "oxidative phosphorylation" where oxygen is used to extract energy from sugar in the mitochondria. While oxidative phosphorylation is much more efficient in terms of producing a lot of energy per sugar, glycolysis is a quick process. In many cells, during development, when cells need a lot of energy for growth, they tend to rely more on glycolysis.

One of the important enzymes in glycolysis is pyruvate kinase. There are multiple types of pyruvate kinase. Of those, Pyruvate Kinase M2 (PKM2) is the type often found in developing/growing cells. 

This research uses a combination of cultured organoids, genetically modified mice and genetic manipulation to investigate the implications of having/not having enough PKM2 in the cochlea. 

Some of the research findings

Model:

  • 3-dimensional (3D) cochlear organoids:
    • Prepared from mouse pup (transgenic mice where the developing inner ear is easy to isolate)
    • Culture condition EFI- CL (EFI, CHIR99021, and LPA) 
    • RNA-seq data = Sequence Read Archive (SRA) ID codes: PRJNA1107354 and PRJNA1107371
  • PKM2 conditional knockout animal:
    • Crossed between Sox9-CreER mice, tdTomato mice and PKM2 floxed mice. 
    • The end result is conditional knockout (depletion) of PKM2 protein in non-sensory epithelial cells of the inner ear.
  • Viral transfection - AAV with the PKM2 gene was used to produce more PKM2 in the developing cochlea in culture (prepared from 2-day-old mouse pups, or human foetus cochlea). 
    • Alternatively, cochlear in culture was treated with lactate. 

Findings: 

  • Looking for mRNA expression in organoids suggested that proteins related to glycolysis were being produced more than oxidative phosphorylation-related proteins in the developing inner ear. One of the key glycolysis proteins being produced in the developing inner ear was PKM2. 
  • In PKM2 conditional knockout mice, cell division and growth were impaired compared to controls. 
Part of Figure 2K. Organoids with (top) or without PKM2 (bottom). Wu et al. 2025
  • PKM2 conditional knockout leads to the development of a smaller cochlea with fewer sensory cells. 
  • PKM2 enzyme generates a by-product of glycolysis called "pyruvate" which subsequently becomes lactate. In search of how PKM2 deficiency impacts cochlear development, researchers hypothesised that lactate may regulate protein synthesis in cells by lactate-dependent modification in the DNA molecule, called "lysine lactylation". Indeed, they found signs of lactylation on a part of DNA called H3K9 and speculate that this is how PKM2 and lactate may regulate cochlear development. 
  • The authors then tested to see if they could regulate the regeneration capability of cochlear cells by modulating glycosylation-related proteins. Researchers used a viral vector to manipulate cochlear cells such that they produce more than the usual amount of PKM2. 
  • Having more PKM2 in developing cells produced more pyruvate and lactate as predicted, and it promoted more cell division and growth. Having more PKM2 or lactate during early development in culture produced more sensory cells. 

Haruna's takeaway

Overall, this research showed the importance of the glycosylation process in developing the cochlea, and showed that simply having more lactate and PKM2, cells can reproduce more. I have actually previously heard about this "metabolic shift" from glycosylation as the main source of energy in stem cells to more oxidative phosphorylation-dependent metabolism in more mature cells, as a concept in neurons in some publications. In immature cells, or stem cells, mitochondria, which are the key organelle for oxidative phosphorylation, are also often different in shape and have different capabilities. So I would imagine the developmental shift from glycosylation to oxidative phosphorylation to be matched with a developmental change in mitochondrial capability, in terms of timing. 

What is interesting is the regulation of cells by products of glycosylation, like lactate. Is this a part of some kind of feedback to fine-tune the timing and number of cell divisions, so that we don't under- or overproduce cells? There are many studies trying to convert cochlear cells to acquire "stem-like" properties so they can start dividing and regenerate the cochlea. This publication points to a metabolic shift to glycosylation as a key, relevant factor. 

Methodologically, this study was highly technical because it had both organoids and cochlear culture. And cochlear cultures were prepared from not only mice, but also from human foetal tissues. The type of work is very challenging to establish both ethically and technically. 

On the final note, I find the common theme of life and metabolism very interesting; between new/immature cells and more mature cells, the main metabolism modes change, and cells become less flexible later in life.... This sounds just like what happens at the whole organism level. 

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This is Haruna's 19/100 of the 100-day challenge to post a science blog article every day! I love inner ear biology & cochlear physiology.