This research started me thinking about relatively small molecules we commonly ignore. I've mentioned peptide signalling and transcription factors above. A new idea surfaced yesterday, though this is not a direct implication of this research.
Another target of the antibodies found could be
protein kinases. While those are typically fairly large molecules, the regions which allow their activity are quite small. They are known to bind ATP to target molecules at sites characterized by a single amino-acid. Serine and threonine are the most common targets, but there are unusual kinases which bind at locations marked by tyrosine. These are now known to be important in the development of cancer, and there are cancer drugs using small molecules which block those binding sites. (Consider
Gleevec/imatinib, used against CML.)
From this point on my thoughts amount to speculation. I am thinking about the extraordinary range of evolution covered by organisms which enter a hypometabolic state in response to threats. There must be very general and important threats involved.
Cancer and viruses capable of inducing cancer would be such a threat. I will also note that it is extremely difficult to distinguish "CFS" from the prodromal phase of a number of cancers, particularly leukemias/lymphomas. Inhibiting activity of kinases would be a good response to slow the progression of cancer, it is what our most advanced cancer treatments now do when we know the particular kinase to target. We are only at the beginning of this work, with some 500 or so known kinases in humans. Nature might well have been doing this blindly much earlier.
In most paraneoplastic syndrome patients, where specific antibodies associated with cancer are found, there is no direct evidence of the associated cancer. (Some doctors deny this, but I believe this is a tautology requiring the presence of detectable cancer to qualify as a paraneoplastic disorder.) If the immune response, triggered by whatever cause, is the same as the immune response to an actual cancer several difficult puzzles about this disease would start to make sense.