Single-cell genetic analysis reveals the composition of initiating clones and phylogenetic patterns of branching and parallel evolution in myeloma.
Although intratumor heterogeneity has been inferred in multiple myeloma (MM), little is known about its subclonal phylogeny. To describe such phylogenetic trees in a series of patients with MM, we perform whole-exome sequencing and single-cell genetic analysis. Our results demonstrate that at presentation myeloma is composed of two to six different major clones, which are related by linear and branching phylogenies. Remarkably, the earliest myeloma-initiating clones, some of which only had the initiating t(11;14), were still present at low frequencies at the time of diagnosis. For the first time in myeloma, we demonstrate parallel evolution whereby two independent clones activate the RAS/MAPK pathway through RAS mutations and give rise subsequently to distinct subclonal lineages. We also report the co-occurrence of RAS and interferon regulatory factor 4 (IRF4) p.K123R mutations in 4% of myeloma patients. Lastly, we describe the fluctuations of myeloma subclonal architecture in a patient analyzed at presentation and relapse and in NOD/SCID-IL2Rγ(null) xenografts, revealing clonal extinction and the emergence of new clones that acquire additional mutations. This study confirms that myeloma subclones exhibit different survival properties during treatment or mouse engraftment. We conclude that clonal diversity combined with varying selective pressures is the essential foundation for tumor progression and treatment resistance in myeloma.
Centre for Myeloma Research, Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
L
L
Melchor
1] Centre for Myeloma Research, Division of Molecular Pathology, The Institute of Cancer Research, London, UK [2] Istituto di Ematologia Seràgnoli, Università degli Studi di Bologna, Policlinico S. Orsola-Malpighi, Bologna, Italy.
A
A
Brioli
Centre for Myeloma Research, Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
C P
CP
Wardell
Centre for Myeloma Research, Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
A
A
Murison
Molecular Haematology, Haemato-Oncology Research Unit, Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
N E
NE
Potter
Centre for Myeloma Research, Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
M F
MF
Kaiser
Centre for Myeloma Research, Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
R A
RA
Fryer
Centre for Myeloma Research, Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
D C
DC
Johnson
Centre for Myeloma Research, Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
D B
DB
Begum
Centre for Myeloma Research, Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
S
S
Hulkki Wilson
Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK.
G
G
Vijayaraghavan
Molecular Haematology, Haemato-Oncology Research Unit, Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
I
I
Titley
Istituto di Ematologia Seràgnoli, Università degli Studi di Bologna, Policlinico S. Orsola-Malpighi, Bologna, Italy.
M
M
Cavo
Centre for Myeloma Research, Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
F E
FE
Davies
Centre for Myeloma Research, Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
B A
BA
Walker
Centre for Myeloma Research, Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
G J
GJ
Morgan
D000368:Aged; D000818:Animals; D002880:Chromosomes, Human, Pair 11; D002883:Chromosomes, Human, Pair 14; D060965:Clonal Evolution; D005260:Female; D011905:Genes, ras; D006801:Humans; D050835:Interferon Regulatory Factors / Q000235:genetics; D008297:Male; D051379:Mice; D016513:Mice, SCID; D008875:Middle Aged; D009101:Multiple Myeloma / Q000235:genetics*; D009154:Mutation; D010802:Phylogeny; D012641:Selection, Genetic; D059010:Single-Cell Analysis; D014178:Translocation, Genetic; D000099218:Interferon Regulatory Factor-4
D050835:Interferon Regulatory Factors; D000099218:Interferon Regulatory Factor-4