New twist on an 80-year-old biochemical pathway

Date:
March 9, 2022
Source:
Memorial Sloan Kettering Cancer Center
Summary:
With the resurgence of interest in cancer metabolism, researchers
are coming to realize that there is more to a cell's biochemistry
than once thought.



FULL STORY ========================================================================== Every year, thousands of biochemistry majors and medical students
around the world learn to memorize the major biochemical pathways that
allow cells to function. How these 10 or so pathways are described in
textbooks hasn't changed much since the early 20th century, when they
were first discovered.


==========================================================================
But with the resurgence of interest in cancer metabolism in the past
decade, researchers are coming to realize that there is more to a cell's biochemistry than once thought.

The latest plot twist comes from a team of scientists at the Sloan
Kettering Institute who report that they have discovered a previously unappreciated metabolic pathway -- an alternate version of the famous
Krebs cycle, also known as the tricarboxylic acid (TCA) cycle.

The TCA or Krebs cycle -- named after Hans Krebs, the German-born
biochemist who discovered it in 1937 -- is a central hub of cellular metabolism. It is a core part of the process by which cells "burn" sugars
to make ATP, the cell's energy-carrying molecule. In its standard form,
the cycle occurs entirely in a cell's mitochondria.

"We and other scientists have recognized for a while that there is
variation in the degree to which cells use parts of the TCA cycle,
suggesting that cells may have multiple ways to meet their fundamental metabolic needs," says Lydia Finley, a cell biologist in SKI who led the
team. "Now, with this latest research, we can say there is a complete alternative to the canonical TCA cycle, and we explain how it works." Implications for Understanding Cancer Cell Metabolism Through several converging lines of evidence, Dr. Finley's team showed that an alternate version of the TCA cycle takes place partly in the mitochondria and partly
in the cytosol. Rather than burning sugar for energy, this alternate
version of the TCA cycle allows cells to use the carbons in sugar to
build important molecules such as lipids for cell membranes.



==========================================================================
Not only that, but a cell's use of one or the other version of the TCA
cycle is associated with changes in its identity, the team showed.

These findings, which were reported on March 9, 2022, in Nature, have
broad implications for understanding how cells adapt their metabolism
to meet changing needs. They also may suggest additional avenues for
cancer therapies geared at targeting a tumor's metabolism.

Putting Together the Puzzle Pieces The new results came out of a
productive collaboration in the Finley lab between Gerstner Sloan
Kettering graduate student Paige Arnold and Tri- Institutional MD-PhD
student Benjamin Jackson.

Arnold had been using carbon-tracing techniques to study the flow of
carbons through the TCA cycle in different cell types. She had noticed,
for example, that there seemed to be variation in the extent to which
cells put their carbons into the TCA cycle versus skipping one part of it.



========================================================================== Around the same time, Jackson was using computational methods to analyze publicly available data from experiments in which the genome-editing
tool CRISPR had been used to systematically knock out genes for various enzymes, one at a time, to see what effect this had on cells.

"You would hypothesize that if the TCA cycle were one functional module,
then any one of those enzymes should have a relatively similar effect when
you remove it," Dr. Finley points out. "What Ben noticed is that's not
actually the case." "The metabolic enzymes seemed to form two separate modules," Jackson says.

"This backed up the anecdotal evidence that we were accumulating that
there were different parts of the TCA cycle that cells could use or
not use." The CRISPR studies Jackson analyzed were performed in cancer
cell lines -- in other words, cells that aren't "normal." Arnold wanted to
know if normal also engage in this alternative or noncanonical cycle. The Finley lab often works with embryonic stem cells, so Arnold had easy
access to these normal cells.

Arnold traced the flow of carbons through them and found that they also
engaged in the noncanonical TCA cycle.

Lessons From 80 Years Ago These two sets of experiments seemed to confirm
that there really was an alternate way to perform the TCA cycle, one that
is not in textbooks. But why had Krebs missed it? To try to answer that question, Arnold decided to review Krebs' original papers from the 1930s
and 40s. She found, to her surprise, that Krebs had made his pivotal discoveries in one particular type of tissue: pigeon breast muscle.

"Nobody really talks about that," Arnold says. "But it made us wonder if
maybe different cell types have distinct preferences for whether they
use the traditional TCA cycle or this alternate version." She decided
to reconstruct Krebs' original experiments, only in a dish rather than
in pigeon muscle. She used mouse stem-like muscle cells to grow a muscle
fiber precursor called a myotube and then traced the carbons. When she
did this, she saw something interesting: "When the cells were still in a
more stem- like stage, they seemed to be doing a lot of this noncanonical
TCA cycle, similar to embryonic stem cells and cancer cells," Arnold
says. "But as soon as the cells had differentiated into myotubes,
they immediately switched to the more traditional TCA cycle. This is
in keeping with what Krebs saw in pigeon muscle tissue." To the team,
this result suggested a clear link between changes in cell identity and
usage of particular biochemical pathways. To test whether the changes
in cell fate required use of the different pathways, the team performed additional experiments in which they chemically or genetically blocked
certain enzymes in the cycles and asked whether the cells could still
change their fate. They could not. This finding implied that changes in
cell fate required different biochemical pathways.

To Burn or To Build Why would a cell opt for a different form of the
TCA cycle at all? According to Dr. Finley, the Krebs cycle is really
good at maximizing ATP production. It helps cells combust all their
nutrients down to carbon dioxide.

"That's great if what you really care about is making ATP," Dr. Finley
says.

"But if you want to grow, ATP is actually not the limiting reagent. You actually need to retain those carbons to make new biomass. That's what
the noncanonical TCA cycle does: It allows you to take carbons from
glucose and export them to the cytosol, where they can be used to build
other molecules.

So, instead of burning the carbon, you get to keep it." This
growth-oriented cycle may have particular relevance to cancer, whose
signature characteristic is unlimited growth.

Dr. Finley cautions that their laboratory experiments were all done
in a dish rather than in animals. The team is keenly interested in understanding whether and when it occurs in vivo, both in normal animals
and in tumors.

"That will help us know whether it might be a good cancer drug target,"
Dr.

Finley says.

An Unexpected Opportunity due to the COVID Pandemic Dr. Finley thinks
that the more researchers begin to look for alternative biochemical
pathways, the more they might find. In some ways, their discovery of a noncanonical TCA cycle was facilitated by unplanned downtime in the lab,
owing to the COVID-19 pandemic.

As Jackson explains: "I was at home, and we could not come into the lab
because of the pandemic. So it became a very fortuitous time to work on
this project, to work out all the bugs of the code." For Arnold, too,
the pandemic-related downtime provided a chance to really delve into
the historical literature and mull over other labs' data in which she
thought she could see evidence of this other cycle operating.

"In the end, the computational work that I did and the model Paige was
building came together, and it became a really satisfying collaboration," Jackson says.

There is a fitting endnote to this story. When Krebs submitted his
original paper on the TCA cycle to Nature, it was rejected. At the time,
the editors didn't have space. This time, thankfully, they do.


========================================================================== Story Source: Materials provided by
Memorial_Sloan_Kettering_Cancer_Center. Note: Content may be edited for
style and length.


========================================================================== Journal Reference:
1. Paige K. Arnold, Benjamin T. Jackson, Katrina I. Paras, Julia
S. Brunner,
Madeleine L. Hart, Oliver J. Newsom, Sydney P. Alibeckoff, Jennifer
Endress, Esther Drill, Lucas B. Sullivan, Lydia W. S. Finley. A
non- canonical tricarboxylic acid cycle underlies cellular
identity. Nature, 2022; DOI: 10.1038/s41586-022-04475-w ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2022/03/220309131858.htm

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