Pathway level alterations rather than mutations in single genes predict response to HER2-targeted therapies in the neo-ALTTO trial.
We performed whole-exome sequencing of pretreatment biopsies and examined whether genome-wide metrics of overall mutational load, clonal heterogeneity or alterations at variant, gene, and pathway levels are associated with treatment response and survival.



Two hundred and three biopsies from the NeoALTTO trial were analyzed. Mutations were called with MuTect, and Strelka, using pooled normal DNA. Associations between DNA alterations and outcome were evaluated by logistic and Cox-proportional hazards regression.



There were no recurrent single gene mutations significantly associated with pathologic complete response (pCR), except PIK3CA [odds ratio (OR) = 0.42, P = 0.0185]. Mutations in 33 of 714 pathways were significantly associated with response, but different genes were affected in different individuals. PIK3CA was present in 23 of these pathways defining a ‘trastuzumab resistance-network’ of 459 genes. Cases with mutations in this network had low pCR rates to trastuzumab (2/50, 4%) compared with cases with no mutations (9/16, 56%), OR = 0.035; P < 0.001. Mutations in the ‘Regulation of RhoA activity’ pathway were associated with higher pCR rate to lapatinib (OR = 14.8, adjusted P = 0.001), lapatinib + trastuzumab (OR = 3.0, adjusted P = 0.09), and all arms combined (OR = 3.77, adjusted P = 0.02). Patients (n = 124) with mutations in the trastuzumab resistance network but intact RhoA pathway had 2% (1/41) pCR rate with trastuzumab alone (OR = 0.026, P = 0.001) but adding lapatinib increased pCR rate to 45% (17/38, OR = 1.68, P = 0.3). Patients (n = 46) who had no mutations in either gene set had 6% pCR rate (1/15) with lapatinib, but had the highest pCR rate, 52% (8/15) with trastuzumab alone.



Mutations in the RhoA pathway are associated with pCR to lapatinib and mutations in a PIK3CA-related network are associated with resistance to trastuzumab. The combined mutation status of these two pathways could define patients with very low response rate to trastuzumab alone that can be augmented by adding lapatinib or substituting trastuzumab with lapatinib.
Department of Breast Medical Oncology, Yale University, Yale Cancer Center, New Haven, USA.
W
W
Shi
Department of Breast Medical Oncology, Yale University, Yale Cancer Center, New Haven, USA.
T
T
Jiang
Vall d'Hebron Institute of Oncology, Barcelona, Spain.
P
P
Nuciforo
Department of Breast Medical Oncology, Yale University, Yale Cancer Center, New Haven, USA.
C
C
Hatzis
Frontier Science, Inverness, Scotland.
E
E
Holmes
Breast Center, Department of Obstetrics and Gynecology, University of Munich, Germany.
N
N
Harbeck
Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium.
C
C
Sotiriou
Spanish Breast Cancer Cooperative Group SOLTI, Barcelona, Spain.
L
L
Peña
Division of Research and Cancer Medicine, Peter MacCallum Cancer Centre, East Melbourne, Australia.
S
S
Loi
Hospital Moinhos de Vento, Porto Alegre, Brazil.
D D
DD
Rosa
Department of Medical Oncology, BC Cancer Agency, Vancouver, Canada.
S
S
Chia
The Christie/NIHR Clinical Research Facility, Manchester, UK.
A
A
Wardley
Department of Breast Surgery, Kyoto University Hospital, Kyoto, Japan.
T
T
Ueno
Hospital Moinhos de Vento, Porto Alegre, Brazil.
J
J
Rossari
Department of Obstetrics and Gynecology, Campus Kiel, University Hospital Kiel, Kiel, Germany.
H
H
Eidtmann
Novartis, Cambridge.
A
A
Armour
Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium.
M
M
Piccart-Gebhart
Department of Breast Medical Oncology, Yale University, Yale Cancer Center, New Haven, USA.
D L
DL
Rimm
Memorial Sloan-Kettering Cancer Center, Memorial Hospital, New York, USA.
J
J
Baselga
Department of Breast Medical Oncology, Yale University, Yale Cancer Center, New Haven, USA.
L
L
Pusztai
D000971:Antineoplastic Combined Chemotherapy Protocols / Q000627:therapeutic use*; D044963:Biopsy, Fine-Needle / Q000379:methods; D001943:Breast Neoplasms / Q000188:drug therapy* / Q000201:enzymology / Q000235:genetics*; D058534:Class I Phosphatidylinositol 3-Kinases / Q000235:genetics / Q000378:metabolism; D004273:DNA, Neoplasm / Q000235:genetics; D005260:Female; D006801:Humans; D000077341:Lapatinib; D058990:Molecular Targeted Therapy; D009154:Mutation; D016016:Proportional Hazards Models; D047428:Protein Kinase Inhibitors / Q000008:administration & dosage / Q000627:therapeutic use; D011799:Quinazolines / Q000008:administration & dosage / Q000627:therapeutic use*; D018719:Erb-b2 Receptor Tyrosine Kinases / Q000037:antagonists & inhibitors*; D000068878:Trastuzumab / Q000008:administration & dosage / Q000627:therapeutic use*; D000073359:Exome Sequencing; D020742:rhoA GTP-Binding Protein / Q000235:genetics / Q000378:metabolism
D058534:Class I Phosphatidylinositol 3-Kinases; D004273:DNA, Neoplasm; D000077341:Lapatinib; D047428:Protein Kinase Inhibitors; D011799:Quinazolines; D018719:Erb-b2 Receptor Tyrosine Kinases; D000068878:Trastuzumab; D020742:rhoA GTP-Binding Protein; C066737:RHOA protein, human; C484760:PIK3CA protein, human; C508053:ERBB2 protein, human