Is Pharmacogenetic Panel Testing Applicable to Low-Dose Methotrexate in Rheumatoid Arthritis? – A Case Report

Figures & data

Table 1 Summary of the Genetic Variants of the Patient Determined with a Commercial PGx Panel Test for MTX

Gene, NE (Nucleotide Exchange); AE (Amino Acid Exchange)	Genotype of the Patient	Function in Pathway	Evidence for Polymorphism
ATP-binding cassette transporter B1 (ABCB1) aka P-glycoprotein, Efflux transporter →altered transport
ABCB1, g.2685+49T>C	rs2032583 CT	Active cellular efflux^Citation16	No studies in relation to low-dose MTX
ABCB1 c.3435T>C; p.I1145I	rs1045642 CC		T allele: a higher risk for ADRs,^Citation20 non-response,^Citation21 low disease activity;^Citation22 C allele: increased toxicity^Citation12,Citation23
ABCB1 c.1236T>C; p.G412G	rs1128503 CC		Conflicting evidence^Citation19,Citation24
ABCB1 c.2677G>A; p.A893T	rs2032582 GG		No studies in relation to low-dose MTX
ABCB1 c.2677G>T; p. A893S	rs2032582 GG		No studies in relation to low-dose MTX
ATP-binding cassette transporter G2 (ABCG2) aka Breast cancer resistance protein (BCRP), Efflux transporter →no alternation in transport
ABCG2 c.421C>A; p.Q141K	rs2231142 CC	Active cellular efflux^Citation16	A allele: adverse events^Citation47
ABCG2 g.1194+928A>G,	rs13120400 GG		G allele: reduced improvement or reduced severity^Citation48
ABCG2 g.89055379G>A,	rs17731538 GG		A allele: reduced improvement or reduced severity^Citation48
Glutathione transferase P1 (GSTP1), Detoxification of organic substances and protection of the organism from oxidative stress →no risk
GSTP1 c.313A>G; p.I105V	rs1695 AG	Detoxification of drugs	Conflicting evidence^Citation38,Citation39
Inosine triphosphate pyrophosphatase (ITPA), Adenosine pathway →no risk
ITPA c.94C>A; p. P32T	rs1127354 CC	Conversion of inosine triphosphate (ITP) to inosine monophosphate (IMP)	C allele: decreased risk of gastrointestinal toxicities and increased response to MTX^Citation32,Citation37
Organic anion transporting polypeptide 1B1 (SLCO1B1), Uptake transporter →no alteration in transport
SLCO1B1 c.521T>C; p.V174A	rs4149056 TT	Hepatic MTX excretion^Citation26	No studies in relation to low-dose MTX
SLCO1B1 c.463C>A; p.P155T	rs11045819 CC		No studies in relation to low-dose MTX
SLCO1B1 c.388A>G; p.N130D	rs2306283 AA		No studies in relation to low-dose MTX
SLCO1B1 c.-910G>A or g.4195G>A	rs4149015 GG		No studies in relation to low-dose MTX
Solute carrier 19A1 (SLC19A1), Uptake transporter → higher risk for toxic side effects; lower chance for remission
SLC19A1 (RFC1) c. 80G>A; p.H27R	rs1051266 GG	Entry in enterocytes^Citation10	G allele: gastrointestinal toxicity,^Citation10,Citation12 hepatotoxicity,^Citation12,Citation13 and alopecia;^Citation13 A allele: enhanced efficacy of MTX^Citation14

Notes: The subtitle consists of the gene name, the abbreviation, the pathway and the evaluation of the commercial PGx panel test for MTX.

Table 2 Summary of the Observed Genotypes Detected in Additional Genes Involved in the MTX Pathway

Gene, NE (Nucleotide Exchange); AE (Amino Acid Exchange)	Genotype of the Patient	Function in Pathway	Evidence for Polymorphism
5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase (AICAR)/ inosine monophosphate (IMP) cyclohydrolase (ATIC), De novo purine synthesis pathway →no risk
ATIC c.347C>G; p.Thr116Ser	rs2372536 CC	Conversion of AICAR into formyl aminoimidazole carboxamide ribonucleotide (FAICAR).^Citation36	G allele: increased risk of toxicity and better response.^Citation21,Citation36,Citation37
Gamma-glutamyl hydrolase (GGH), Polyglutamation →no risk
GGH−401 C>T	rs3758149 CC	Conversion of MTX-PG to MTX depends on the gamma-glutamyl hydrolase.^Citation49	T allele: decreased conversion of MTX to active metabolite and decreased MTX response^Citation28,Citation49
Methylenetetrahydrofolate reductase (MTHFR), Folate pathway → risk of higher toxicity and lower MTX response
MTHFR c.1298 A>C; p.Glu429Ala	rs1801131 AC	Conversion of 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate	C allele: central nervous system toxicity,^Citation32 hepatotoxicity,^Citation33 gastrointestinal ADRs^Citation34 or overall toxicity;^Citation25 A allele: better MTX response^Citation25,Citation35
MTHFR c.67765 C>T; p. p.Ala222Val	rs1801133 CT		T allele: increased risk for gastrointestinal ADRs,^Citation29,Citation30 hepatotoxicity,^Citation13,Citation30 and neurotoxicity^Citation31

Notes: The subtitle consists of the gene name, the abbreviation, the pathway and the evaluation for MTX.

Figure 1 Overview of the current understanding on enzymes and transporters involved in the pharmacokinetics and pharmacodynamics of methotrexate (MTX).

Abbreviations: ABCB1, ATP-binding cassette transporter B1 (aka P-glycoprotein); ABCC1–4, ATP-binding cassette transporter C1-C4 (aka multidrug resistance protein) (MRP1 to MRP4); ABCG2, ATP-binding cassette transporter G2 (aka breast cancer resistance protein BCRP); ATIC, 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase (AICAR)/inosine monophosphate (IMP) cyclohydrolase; DHFR, dihydrofolate reductase; FPGS, folylpolyglutamyl synthase; GGH, gamma-glutamyl hydrolase; GSTP1, glutathione transferase P1; ITPA, inosine triphosphate pyrophosphatase; MTHFR, methylenetetrahydrofolate reductase; MTX-PG, methotrexate polyglutamate; SLC19A1, solute carrier 19A1 (aka reduced folate carrier 1, RFC1); SLCO1B1/1B3, organic anion transporting polypeptide (OATP) 1B1 and OATP1B3; SLC22A6/A8, organic anion transporter (OAT)1 and OAT3; SLC46A1, proton-coupled folate transporter (PCFT); TYMS, thymidylate synthase.

Table 3 Medication of the Patient at the Time of Pharmacogenetic Panel Testing

Substance	Dosage	Indication
Tofacitinib 5 mg	1-0-1	Rheumatoid arthritis
Prednisone 5 mg	1-0-0	Rheumatoid arthritis
Diclofenac 150 mg	0-1-0	Influenza symptoms
Ibuprofen 200 mg	1-0-1 as necessary	Influenza symptoms
Dexlansoprazole 30 mg	0-1-0	as long as Ibuprofen
Vitamin D3 4500 IE/ml, 10ml	2 bottles per month	Vitamin D3 deficiency

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