Symptom/Metabolome-Directed Genomics of ME/CFS by Dr Neil McGregor (2017)
GENOMICS FOR ME/CFS
NEIL R MCGREGOR PHD, CHRISTOPHER W ARMSTRONG BSC, PAUL GOOLEY PHD, HENRY BUTT PHD,
BIO21 INSTITUTE, UNIVERSITY OF MELBOURNE, AUSTRALIA.
JOHN WHITING MBBS, BCH, BAO, FRACP, SPECIALIST INFECTIOUS DISEASES AND INTERNAL MEDICINE, BRISBANE, AUSTRALIA
DON LEWIS MBBS, CFS DISCOVERY, DONCASTER VICTORIA, AUSTRALIA.
ME/CFS IS A HETEROGENEOUS SYNDROME
• Multiple studies have failed to find a single metabolic anomaly for ME/CFS.
• Multiple different definitions of ME/CFS have been assessed also without success.
• ME/CFS can only be concluded to be a heterogenous cluster of genetic/epigenetic events resulting in a
common set of host responses which form part of the definitions.
• Patients with similar onsets have different long term outcomes!!! Why???
• Patterns or clusters of sub-symptoms can be identified.
• Regression modelling of the symptoms/ metabolomes shows that:
• FATIGUE is best predicted by a change in glucose: a form of insulin resistance (Armstrong et al 2015).
• WIDE SPREAD PAIN is best predicted by changes in kidney handling of electrolytes and amino acids (McGregor et al 2016).
• Each of these symptom clusters must have an underlying genetic/epigenetic origin. Our approach is to use
Symptome/Metabolome directed assessments.
GENOME WIDE PILOT SNP STUDY DATA
• 56 CFS patients and 32 controls. 553,000 SNPs assessed of the 610,000 available. Excluded those with multiple misreads, and
uniform insertions and deletions.
• All patients had MECFS for >3-years and had not recovered.
• 316 SNPs were statistically significant with a z-score of ≥6.5.
• 162 (51%) SNPs were from 118 identifiable proteins/enzymes (Virtually all no coding regions).
• 49 (16%) SNPs were from 42 RNA genes.
• 142 (33%) were from intergenic sections of DNA without any known ability to produce a protein but may be promoters or
enhancers of other genes.
• To eliminate control sample aberrant distribution the data cross checked against 1000 genomes (Phase 3 May 2013).
• After 1000 genome cross check only 111 SNPs remained. Removed all with an odds ratio <2. Only 38 genes remained.
• A dataset was derived for all the SNPs associated with the 38 genes and any other gene that overlapped the gene which
may influence it expression.
GENETIC SUB CLUSTER ANALYSIS
1. Anomaly in G-protein coupled receptor protein.
2. Anomaly in G-protein coupled receptor protein and a STAT3 inflammation inhibitor gene.
3. Anomaly in G-protein coupled receptor protein and RNA helicase.
4. Anomaly in RNA helicase and Interleukin L-1 Kinase 3.
5. Anomaly in RNA Helicase and a viral adherence receptor.
6. Anomaly in RNA Helicase and Hedgehog Signalling.
7. Anomaly in RNA Helicase and Langerin (Dendritic cell pathogen receptor).
ODDS RATIOS OF MAJOR SNPS INCREASED IN ME/CFS
Gene SNP Heterozygote OR (95%CL) p Homozygote OR (95%CL) p
G-protein SNPs SNP a
5.4 (1.8-16.3) <.002
4.7 (1.6-14.1) <.005
RNA helicase SNPs SNP a
6.7 (2.4-18.4) <.0002
6.7 (2.4-18.4) <.0002
Langerin SNPs SNP a
3.6 (1.4-9.5) <.008
6.7 (1.8-25) <.004
DISTRIBUTION OF GENE SNPS: C V MECFS
2+ 0.06 0.48
1 0.52 0.33
0 0.42 0.19
9+ 0 0.13
5-8 0.22 0.4
1-4 0.47 0.45
0 0.31 0.02
4 0.14 0.32
3 0.28 0.32
2 0.24 0.26
1 0.1 0.1
0 0.24 0
RNA Helicase SNPs
Carriage of a mutated SNP within the ME/CFS and the controls.
Odds Ratios: 3.0 (95%CL 1.1-8.3) p<.02 21.5 (95%CL 2.5-185) p<.0002 12.6 (95%CL 3.5-45.0) p<.00001.
• Heterotrimeric receptor GTPase (G-Protein Coupled
• 3 Subunits
• The Alpha protein is highly mobile.
• The Beta and Gamma chains are tightly bound and
function as one.
• There are 20 alpha, 6 beta and 13 gamma proteins.
• Different combinations have different intracellular
RECEPTOR (GPCR) PATHWAYS
• Activation of the receptor binds GTP to the alpha
• The GTP-α and GTP-βγ proteins separate and perform
• Cytoplasmic viral RNA sensing
• These bind to the HMGB proteins and
remove viral RNA from the cytoplasm.
• Inhibited by Epidermal Growth Factor
• EGF receptor activated by Estrogen
receptor beta and by some viruses.
• Required for interferon production.
RH 1 RH2 RH3
• CD207 (AKA Langerin) is a protein largely
expressed in Dendritic (Langerhan) cells in skin,
the GUT and multilayered epithelium.
• Considered the first line of defense for viral and
non-commensal bacteria infections.
• It is a lectin detecting protein and is involved in
detection of multiple viruses and in presentation
of antigens from these pathogens to t-cells and the
LANGERIN AND HIV (VAN DER VLLIST AND GEIJTENBEEK 2010)
Normal response. Viral degradation
and presentation of antigens to the
Inhibition of Langerin. HIV binds to
CD4 receptor and invades the host.
LANGERIN AND VIRUSES
• Multiple viruses are able enter the cell through
a Langerin mediated process.
• Most of these viruses are associated with
exacerbation of the illness in MECFS patients.
HIV De Jong et al 2009
HSV1 De Jong et al 2010
HSV2 Puttur et al 2010
EBV Braz-Silva et al 2011
CMV Huang et al 2012
Influenza GeurtsvanKessel et al 2008
Measles Van der V et al 2011
HPV Bousarghin et al 2005
Dengue Limon-Flores et al 2005
• Only one mtDNA SNP was increased in MECFS. T456C (C=0% v ME=18%;
• Located in the hypervariable region it is a defining SNP for Haplogroup H5.
• Assessment of the autosomal genes carried by the H5 patients revealed they
all carried the CD207 (Langerin) SNP mutations.
• We found no evidence of a mitochondrial DNA anomaly.
• Using the symptom/ metabolome directed approach appears to have allowed us to delineated up to 7
underlying genetic cluster issues in the ME/CFS patient group.
• Anomalies in G-Protein coupled receptor proteins activity may be related to the increased prevalence
of orthostatic hypotension, photophobia, smell and taste hypersensitivity.
• Anomalies in RNA Helicases may be related to the Viral infection, viral induced onset and viral
reactivation events in MECFS patients.
• Anomalies in Langerin may relate to the increased pathogen related issues.
• No evidence of a mitochondrial genetic disorder.
• We need to very wary at this point in time.
• We need to be sure what we have found
DOES MATTER and is not DOESN’T MATTER.
• Members of the conference scientists aim to
do this confirmation.