The small fluctuations in the CMB that WMAP detected (the 2007 article being about the "WMAP Cold Spot") are sensitive to the distribution of all matter -- including dark matter -- in the early universe.

Roughly, hot spots have more matter, get hotter as that matter collapses
into stars, hot gasses, and eventually black holes; cold spots have less matter, and because of the expansion they get colder, sparser, much bigger, and eventually become practically empty.

Early pockets of dark matter overdensity, similarly roughly, helps turn on the heat very early, and keeps the heat turned on longer than otherwise. Early pockets of dark matter underdensity makes it much harder for stars to light up in the first place.

Generally one simulates the introduction of non-uniformities in this distribution during Cosmic Inflation, and then the overdense areas collapse while the underdense areas experience the cosmological constant. At the time the universe has expanded enough that photons can free-stream (this marks the beginning of the CMB, see [1]) the density-differences in one part of the universe to another are very small, but over billions of years the collapsing dense regions become ever denser (and form stars and galaxies) while sparser regions simply become colder. (Both become emptier, relatively; collapsing a diffuse cloud into a dense cloud leaves behind a lot of space emptier than when the diffuse cloud was populating it).

Dark matter plays a crucial role here, because it collapses more slowly than visible matter by forming haloes and other structures, essentially suspending visible matter (gas) above the cores of galaxy clusters (where in later times you find really gargantuan black holes). It is also important that its underdensities and overdensities after Cosmic Inflation were roughly the same as that of what became the particles of the standard model, and it is this feature that appears to be crucial to structure formation : https://map.gsfc.nasa.gov/universe/bb_cosmo_struct.html

However, once the CMB has formed, those photons no longer interact appreciably with the dark matter of the universe -- the gravitational interaction is weak and gets weaker with the expansion of the universe.

So it is the early distribution of dark matter (before atoms, before protons) that is important in creating CMB cold and hot spots.

It would be odd to have a hot spot become anything but a matter structure (galaxy cluster) because of gravitational collapse. Likewise, it would be odd to have a VERY cold spot become anything but filled with a very sparse gas (e.g. hydrogen + photons + neutrinos). The WMAP Cold Spot is not THAT cold and so could have structures like galaxy clusters in it, but fewer of them than than in the filamentary structures. Indeed, we may live in someone else's cold spot. Galaxy surveys are trying to gather up evidence one way or another for the densities of galaxies and their ages along various lines of sight from here, which will help us determine how well WMAP cold and hot spots line up with galaxies. ALL galaxies are much more recent than the CMB.

Several ideas about how the WMAP Cold Spot could have been a WMAP Average Spot at the time the CMB was formed, but that (mostly new physics) events in the more modern universe present us with a relative cold spot. Some of these have the virtue that these more modern events are more amenable to study with our current level of technology than the distribution of gravitational waves after cosmic inflation and the detailed study of the cosmic neutrino background (which is similar to the cosmic microwave background, and so should have similar small temperature fluctuations; but measuring ultracold neutrinos is not something we can do today, nor can we yet look at the frequencies and amplitudes of primordial gravitational waves, however there may be indirect probes of both available before our descendants are able to observe them directly).

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[1] https://en.wikipedia.org/wiki/Decoupling_(cosmology)