Clonality in Multiple Myeloma

DANA‐FARBER CANCER INSTITUTE

Nikhil C. Munshi, MD

Professor of Medicine Harvard Medical School

Director Basic and Correlative SciencesJerome Lipper Myeloma Center

Dana-Farber Cancer Institute

John Shaughnessy, Jr et al. Blood 2000;96:1505-1511©2000 by American Society of Hematology

• Bone marrow cells simultaneously hybridized with probes for D13S272 (red) and D13S31 (green).

• 5% cells were normal (i)• 48% cells demonstrated

monosomy (ii)• 12% cells showed

monosomy for D13S272 and complete loss of the D13S31 signal (iii)

• 23% of the cells had no signal for either probe (iv).

Clonal heterogeneity and dispersed interstitial deletions in myeloma

More than 60% sub clonality in 17p predicts for poor outcome

PFS OS

Avet-loiseau et al. Blood 2013

Neha Korde et al. Blood 2011;117:5573-5581

©2011 by American Society of Hematology

Evolution of Multiple Myeloma –Genomic Changes

Normal Plasma Cells

Myeloma Cells

ExtramedullaryDisease

MGUSCells

Spontaneous Evolution• Inherent• Microenvironmental• Immune effects

Spontaneous Evolution• Inherent• Microenvironmental• Immune effects

Therapy Effects• Clonal selection• Clonal induction• Mutation promotion• Effcet on repair

Clonal progression in cancer

Normal Preclinical Overtmalignan cy

Frequent Subclonal Variants in MM

Complex Landscape of Rearrangements and clonal evolution in Smoldering and Multiple Myeloma Revealed By Whole‐

Genome Sequencing 

WGS of 100 matched paired myeloma samples (SMM, ND, relapse/normal) in a cohort of 30 patients:

Complex Genomic

Changes Even at Early stage

Disease

Bolli et al. Nature Comm In Press

Branching Evolution may Drive Subset of SMM progression into symptomatic MM

Bolli et al. Nature Comm In Press

Two Types of SMM Associated with Distinct Evolution and Pattern of Progression to

symptomatic MM

Bolli et al. Nature Comm In Press

Complex landscape of chromosome rearrangements in MM

Del

Gain

ITD

inversion

translocation

% of p

atients

coordinnates

Chr 1

Chr 6

Chr 16

Chr 15

Chromosomal changes occur over the time in MM

HD1q+Del Xt(8p12;Xq23)

CN‐LOH X8p‐3q‐

Xq27‐

NDMM4

HD1q+Del Xt(8p12;Xq23)

CN‐LOH Xt(8q11.21;Xq25) 

8p‐

t(8q11.21;Xq25)delXq25*5q‐3q‐

RMM4

HD1q+Del X

t(8p12;Xq23)8p‐CN‐LOH X

SMM4

Multiple genetically distinct subclones occur in multiple myeloma

• Multiple genetically distinct subclones are present at diagnosis, increase during the course of disease1–4

– These evolve over time due to selective pressures from treatment and factors in the microenvironment1,4

– This clonal evolution can result in disease progression and treatment resistance5

1. Bahlis N et al. Blood 2012;120:927–282. Keats JJ et al. Blood 2012;120:1067–763. Bianchi G, Ghobrial IM. Curr Cancer Ther Rev 2014;10:70–9

4. Bolli N et al. Nat Commun 2014;5:29975. Brioli A et al. Br J Haematol 2014;165:441–54.

Marc S. Raab et al. Blood 2016;127:2155-2157

©2016 by American Society of Hematology

The clinical course and management of a patient with BRAFV600E-mutant MM developing resistance to treatment

with vemurafenib.

RAS‐RAF mutations often late and convergent

Bolli et al. Nature Comms, 2014

Trametinib +Dabrafenib for BRAF/NRAS/KRAS mutant MM

Determine if mutation in BRAF, KRAS, NRAS

Braf mutated Braf with KRASOr NRAS mutated

KRAS or NRAS mutated

Treat with Dabrafenib

Treat with Dabrafenib+ Trametinib

Treat with Trametinib

Conclusion & Clinical Implications• Clonal heterogenity and sub clonal evolution are

fundamental to malignant cells – myeloma no exception

• Different patterns of disease evolution over time across patients ‐ Need for repeated genomic analysis

• So what are the mechanisms driving early versus late clones may be different

From Whole Exome Sequencing NNMF extracted 2 main mutational 

signatures in myeloma

AID May Drive MGUS/SMM While  APOBEC May Act at A Later Time During MM Evolution

Deeper WGS Identifies Additional Mutational Processes

In Myeloma Transcribed Region is Under Pressure of DNA Repair Related Mutational Processes:

Composite Analysis Using RNA‐seq, ATAC‐seq and WGS

Whole Genome Sequencing

ATACseq

RNAseq

Transcribed Region is Under Pressure of DNA Repair Related Mutational Processes in

Multiple Myeloma

Subclonal Mutations Shows >85% Contribution from DNA Repair Signatures

in The Coding Region

APOBEC is An Important Mutational Processes in Myeloma

Walker et al Nat Comm 2015 Bolli et al. Leukemia 2018

Elevated Functional Deaminase Activity in MM

Impact of elevated APOBEC 3 G expression on genomic instability in MM cells

APOBECs may be a good target for therapy !!

Conclusion & Clinical Implications• Clonal heterogeneity and sub clonal evolution

are fundamental to malignant cells – myeloma no exception

• Different patterns of disease evolution over time across patients ‐ Need for repeated genomic analysis

• Mechanisms driving early versus late clones may be different

• Number of factors determine clonal selection and therapy may have significant impact on genome -need to consider types of agents and combinations used and lengthy of therapy

WGS at diagnosis

WGS at relapse

WGS at diagnosis andrelapse – Significant increase in complexity

Conclusion & Clinical Implications• Sub clonal variants and clonal evolution

o A moving Target

oTry and eliminate the clones aggressively

oA sensitive clone mat remerge

o Is Targeted therapy really possible?

oNeed for multi target therapy

oRise of immunotherapy!

Masood Shammas, PhDPrabhala Rao, PhDMariateresa Fulciniti, PhDWeihua Song, MDJagannath Pal, MD, PhDPuru Nanjappa, PhDJianhong Lin, MDMaria Gkotzamanidou , MD, PhDAdan Soerling, MD, PhDWeihong Zhang, MDTeresa Calimari, MDAriel Kwart, BSSophia Adamia, PhDRajya Bandi, MSYuTzu Tai, MDJooeun Bae, PhD

Kenneth Anderson, MD

Giovanni Parmigiani, PhDMehmet Samur, PhDYi Li, PhDNaim Rashid, PhD and Bioinformatics Group

Dr. Herve Avet-LousieuDr Stephane Miniville, Dr. Philippe MoreauDr. Florence MAGRANGEASDr. Michel Attal and IFM

Peter CampbellAndy FutrealGraham BignellNiccolo BoliDavid Wage

DANA-FARBER CANCER INSTITUTE