ANA's are negative in approximately 5% with lupus. Other antibody markers of lupus include cardiolipin antibody, anti-smith antibody, DNA antibodies, SS-A and SS-B antibodies.
I had a butterfly redness across my cheeks and nose and suspected this symptom might be due to Lupus but after many tests my rheumatologist ruled that out. Many years later I finally figured out this symptom was from bouts of hyperthyroidism from Hashimoto's thyroiditis (autoimmune hypothyroidism).
There are many possible causes of a redness across the cheeks but your condition looks to be immune related since you noted the redness disappear taking the chemotherapy drug methotrexate (may cause very serious, life-threatening side effects however). There is a drug called LDN (low dose naltrexone) and the side effects, if you should have any, are usually mild.
Excerpt from the website - Low Dose Naltrexone...
"In human cancer, research by Zagon over many years has demonstrated inhibition of a number of different human tumors in laboratory studies by using endorphins and low dose naltrexone. It is suggested that the increased endorphin and enkephalin levels, induced by LDN, work directly on the tumors' opioid receptors — and, perhaps, induce cancer cell death (apoptosis). In addition, it is believed that they act to increase natural killer cells and other healthy immune defenses against cancer.
In general, in people with diseases that are partially or largely triggered by a deficiency of endorphins (including cancer and autoimmune diseases), or are accelerated by a deficiency of endorphins (such as HIV/AIDS), restoration of the body's normal production of endorphins is the major therapeutic action of LDN."