Lung cancer is one of the most frequent and deadly disease. This presentation summarizes the systematic genomics profiling efforts of lung adenocarcinoma patients of Indian origin, as published in Chandrani, P., Prabhash, K., Prasad, R., Sethunath, V., Ranjan, M., Iyer, P., Aich, J., Dhamne, H., Iyer, D. N., Upadhyay, P., Mohanty, B., Chandna, P., Kumar, R., Joshi, A., Noronha, V., Patil, V., Ramaswamy, A., Karpe, A., Thorat, R., Chaudhari, P., Ingle, A., Choughule, A., Dutt, A. (2017). "Drug-sensitive FGFR3 mutations in lung adenocarcinoma.“ Annals of Oncology 28(3): 597-603. The study uses lung adenocarcinoma primary tumor samples (FFPE blocks) for Illumina next-generation sequencing (NGS) and microfluidics (RainDance) based discovery of therapeutically relevant alterations followed by validation in 363 patient samples using mass-spectrometry based Sequenom MassArray. The study identifies novel FGFR3 mutations in addition to well known EGFR, KRAS, EML4-ALK, AKT, PIK3CA, FGFR4, ERBB2 (HER2) etc. The novel FGFR3 mutations detected in lung adenocarcinoma were further characterized using in-vitro and in-vivo experiments to confirm their transforming capability and drug sensitivity against tyrosine kinase inhibitor (TKI - BGJ398). This study provides first glance of actionable alterations in Indian lung adenocarcinoma patients and establish base for further development of precision medicine options tailored for the patients of Indian origin as well as for global population.

1. Pratik Chandrani, PhD
Medical Oncology Department, TMH
Computational Biology Centre, ACTREC
Tata Memorial Centre, Mumbai
pratikchandrani@gmail.com
Landscape/Mutation Profile of Driver
Genes in Lung Adenocarcinoma of
Indian Ethnicity
Chandrani, P., Prabhash, K., Prasad, R., Sethunath, V., Ranjan, M., Iyer, P., Aich, J., Dhamne,
H., Iyer, D. N., Upadhyay, P., Mohanty, B., Chandna, P., Kumar, R., Joshi, A., Noronha, V., Patil,
V., Ramaswamy, A., Karpe, A., Thorat, R., Chaudhari, P., Ingle, A., Choughule, A., Dutt, A.
(2017). "Drug-sensitive FGFR3 mutations in lung adenocarcinoma.“
Annals of Oncology 28(3): 597-603.

2. What is The Incidence of Driver Mutations in Lung Adenocarcinoma?
In Caucasian Population
(1007 patients)
In Indian Population
(before this study, 2017)
?
Adapted from Lung Cancer Mutation Consortium

3. EGFR & KRAS Profiling of Lung Cancer in India
EGFR is mutated at intermediate frequency of 23% in Indian NSCLC patients
EGFR positive
EGFR negative
Months
Probabilityof
OverallSurvival(OS)
Improved survival of EGFR positive patients
KRAS mutant
KRAS wild-type
KRAS mutation in Indian NSCLC
Chougule et. al. 2013 PLoS ONE
Noronha et. al. 2013 PLoS ONE Chougule et. al. 2014 Br J Cancer

4. 676 hot-spots in 196
genes using RainDance
micro-fluidics + NGS
Discovery of FGFR3 –
a novel oncogene
125 Patients
Discovery
49 mutations in 23
genes using Mass-
spectrometry
Landscape of
alterations
~ 400 Patients
Validation
Soft agar + kinase
inhibitor + xenograft +
IHC
Potential novel
therapeutics
NIH/3T3 & NOD-SCID
Pre-Clinical
Chandrani et al. Ann Oncol. 2017 Mar 1;28(3):597-603.
Profiling of Therapeutically Relevant Alterations in Lung Cancer of Indian Origin

5. Recurrent Novel FGFR3 Mutations in Lung Adenocarcinoma
Microfluidics + NGS Generates High Quality Data from FFPE Tissues
Read pairs
Percent
reads on
target
Normalised
Coverage
Number of
coding
variants
Number of
known SNPs
Expected EGFR
Mutations
EGFR
Mutations
Found by NGS
5XA 51,18,296 92 1573.9 837 111 L858R, Del 19 Del 19
5XB 63,77,317 94 1547.1 2145 214 L858R, Del 19 L858R
10XA 68,92,629 94 1547.0 756 94 Del 19 Del 19
10XB 52,00,746 95 1550.6 795 115 Del 19 Found in UNK
15X 83,30,714 75 1481.6 1110 125 Del 19 Del 19
Unk 72,95,420 20 1516.6 1607 191 L858R, Del 19 L858R, Del 19

6. Spectrum of Mutations Validated by Mass-spectrometry in 363 Samples
* TaqMan and SNaPshot assays were performed in addition to MassArray. # FISH was performed on total 76 samples for EML4-ALK.

7. First Landscape of Targetable Alterations in Indian Lung Adenocarcinoma
* TaqMan and SNaPshot assay were performed in addition to MassArray. # FISH was performed on total 76 samples for EML4-ALK.

8. Is Mutant FGFR3 Oncogenic and Sensitive to Pharmacological Inhibition?

9. FGFR3 Mutations are Activating and Transforming
Experiments performed with Vidya, Ratnam, Malika

10. FGFR3 Mutations are Sensitive to Pharmacological Inhibition

11. FGFR3 Mutations are More Frequent in Younger Lung Cancer Patients
Clinicopathological
features
Variables
N (% along
column)
FGFR3 status (N=363)
(% along row)
P-value*
Mutant
(N=20)
Wild-type
(N=323)
Age
< 45 years 95 (26%) 9 (9.5%) 86 (90.5%)
0.048
> 45 years 269 (74%) 11 (4%) 258 (96%)
Gender
Male 226 (62%) 9 (4%) 217 (96%)
0.102
Female 137 (38%) 11 (8%) 126 (92%)
Smoking
Smoker 73 (20%) 2 (3%) 71 (97%)
0.199
Non-smoker 268 (80%) 18 (7%) 250 (93%)
Highlighted P-value is marginally significant. * Chi squared test.

12. FGFR3 Mutant Lung Cancer Patient Responds Better to Standard Therapy

13. FGFR3 Mutations are Associated with Clinical Outcome in Human Cancers

14. 2 weeks
Pazopanib
Liao R. et al., Cancer Res 2013;73:5195-5205
Oral SCC patient harboring FGFR2 mutation shows partial response to
Pazopanib -- FGFRs are potential therapeutic targets in human cancers!

15. Summary & Future Prospect
 First spectrum of actionable alterations in Indian lung cancer genome has been
established, including: EGFR, KRAS, FGFR3, EML4-ALK, AKT1, PIK3CA, FGFR4
and HER2 genes.
 Novel mutations in FGFR3 gene are discovered and observed to be oncogenic &
sensitive to pharmacological inhibition by in-vitro and in-vivo assays.
 FGFR3 mutations are more frequent in younger lung cancer patients and
responds better to standard therapy.
 Systematic clinical trial should be designed for establishing targeted therapy
against discovered genes for Indian lung adenocarcinoma patients.