Hillmer, Axel - assoc. RG 09

Esophageal adenocarcinoma (EAC) incidence rose dramatically over the last decades. Since genomic analyses did not reveal common targets for therapies, treatment options are limited and prognosis is poor. EAC patients show large differences in response to neoadjuvant treatment but no biomarkers are known that predict initial and long term response to therapy.

It has been demonstrated for some solid tumors that cancer associated fibroblasts (CAFs) play an important role in tumor biology and for metastases. To investigate whether functional changes in CAFs are responsible for differences in treatment response and early metastases, cell type-specific transcriptome analyses are needed. It is now possible to perform single cell transcriptomics but this approach is still not scalable to investigate enough samples for clinical association. We have developed a protocol that combines fluorescence activated cell sorting with RNA-seq, allowing to analyse the transcriptomes of leukocytes, epithelial cells and fibroblasts separately.

We will apply this concept to treatment naïve EAC biopsies and normal tissues and will systematically identify cell-type specific alterations that correspond to treatment response and relapse. We will validate our findings using a large collection of EAC tissues for targeted assays and by experiments in tissue culture. Overall, we will be able to identify functional changes in CAFs and other tumor components that will help to explain the clinical course of an EAC patient and that provide new opportunities for intervention.

A better understanding of the tumor microenvironment with its different cell types is needed to clarify their roles for treatment response and disease progression of EAC.

We will define the transcriptomic profiles of leukocytes, fibroblasts and epithelial cells of EAC and normal tissue and will identify critical pathways in CAFs that correlate with treatment response and metastases. We will use this information to derive opportunities for new treatment concepts.

1. Chen J, Zhang T, Yang H, Teo ASM, Amer LB, Sherbaf FG, Tan CQ, Alvarez JJS, Lu B, Lim JQ, Takano A, Nahar R, Lee YY, Phua CZJ, Chua KP, Suteja L, Chen PJ, Chang MM, Koh TPT, Ong BH, Anantham D, Hsu AAL, Gogna A, Too CW, Aung ZW, Lee YF, Wang L, Lim TKH, Wilm A, Choi DPS, Ng PY, Toh CK, Lim WT, Ma S, Lim B, Liu J, Tam WL, Skanderup AMJ, Yeong JPS, Tan EH, Creasy C, Tan DSW*, Hillmer AM*, Zhai W*. (2020) Genomic landscape and ethnic specificity of lung adenocarcinoma in Asia. Nat Genet (accepted)
2. Wang Z, Yip LY, Lee JHJ, Wu Z, Chew HY, Chong PKW, Teo CC, Ang HY, Peh KLE, Yuan J, Ma S, Choo LSK, Basri N, Jiang X, Yu Q, Hillmer AM, Lim WT, Lim TKH, Takano A, Tan EH, Tan DSW, Ho YS, Lim B, Tam WL (2019) Methionine is a metabolic dependency of tumor-initiating cells. Nat Med 25:825-837
3. Kong SL, Li H, Tai JA, Courtois ET, Poh HM, Lau DP, Haw YX, Iyer NG, Tan DSW, Prabhakar S, Ruff D, Hillmer AM (2019) Concurrent Single-Cell RNA and Targeted DNA Sequencing on an Automated Platform for Comeasurement of Genomic and Transcriptomic Signatures. Clin Chem 65:272-281
4. Simoni Y, Becht E, Fehlings M, Loh CY, Koo S-L, Teng KWW, Yeong JPS, Nahar R, Zhang T, Kared H, Duan K, Ang N, Podinger M, Lee YY, Larbi A, Khng AJ, Tan E, Fu D, Mathew R, Teo M, Lim WT, Toh CK, Ong BH, Koh T, Hillmer AM, Takano A, Lim TKH, Tan EH, Weiwei Z, Tan ESW, Tan IB, Newell EW (2018) Bystander CD8+ T cells are abundant in human tumour infiltrates and lack expression of CD39. Nature 557:575-579
5. Nahar R, Zhai W, Zhang T, Takano A, Khng AJ, Lee YY, Liu X, Lim CH, Koh TPT, Aung Z, Lim TKH, Veeravalli L, Yuan J, Teo ASM, Chan CX, Poh HM, Chua IML, Liew AA, Lau DPX, Kwang XL, Toh CK, Lim WT, Lim B, Tam WL, Tan E-H, Hillmer AM#, Tan DSW# (2018) Elucidating the genomic architecture of Asian EGFR-mutant lung adenocarcinoma through multi-region exome sequencing. Nat Commun 9:216 (#corresponding author)
6. Li H, Courtois ET, Sengupta D, Tan Y, Chen KH, Goh JJL, Kong SL, Chua C, Hon LK, Tan WS, Wong M, Choi PJ, Wee LJK, Hillmer AM, Tan IB, Robson P, Prabhakar S (2017) Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors. Nat Genet 49:708-718
7. Cima I, Kong SL, Sengupta D, Tan IB, Phyo WM, Lee D, Hu M, Iliescu C, Alexander I, Goh WL, Rahmani M, Suhaimi N-AM, Vo JH, Tai JA, Tan JH, Chua C, Ten R, Lim WJ, Chew MH, Hauser CAE, van Dam RM, Lim W-Y, Prabhakar S, Lim B, Koh PK, Robson P, Ying JY, Hillmer AM, Tan MH (2016) Tumor-derived circulating endothelial cell clusters in colorectal cancer. Sci Transl Med 8:345ra89
8. Yao F*, Kausalya JP*, Sia YY, Teo ASM, Lee WH, Ong AGM, Zhang Z, Tan JHJ, Li G, Bertrand D, Liu X, Poh HM, Guan P, Zhu F, Pathiraja TN, Ariyaratne PN, Rao J, Woo XY, Cai S,  Mulawadi FH, Poh WT, Veeravalli L, Chan CS, Lim SS, Leong ST, Neo SC, Choi PSD, Chew EGY, Nagarajan N, Jacques P-E, So JBY, Ruan X, Yeoh KG, Tan P, Sung W-K, Hunziker W#, Ruan Y#, Hillmer AM# (2015) Recurrent fusion genes in gastric cancer: CLDN18-ARHGAP26 induces loss of epithelial integrity. Cell Rep 12:272-85 (*contributed equally, #corresponding author)