FOXA2 Promotes Metastatic Competence in Small Cell Lung Cancer

Authors:
Kenta Kawasaki^1,2, Sohrab Salehi³, Yingqian A. Zhan⁴, Kevin Chen⁵, Jun Ho Lee¹, Eralda Salataj⁴, Hong Zhong², Parvathy Manoj², Dennis Kinyua², Barbara P. Mello², Harsha Sridhar², Sam E. Tischfield⁶, Irina Linkov⁷, Nicholas Ceglia³, Matthew Zatzman³, Eli Havasov³, Neil Shah², Fanli Meng⁶, Brian Loomis⁶, Umesh K. Bhanot⁷, Esther Redin², Elisa de Stanchina⁵, Pierre-Jacques Hamard⁴, Richard P. Koche⁴, Andrew McPherson³, Álvaro Quintanal-Villalonga², Sohrab P. Shah³, Joan Massagué^1,8,* Charles M. Rudin^2,8,*

---

^*Corresponding authors
¹ Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
² Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
³ Computational Oncology Program, Memorial Sloan Kettering Cancer Center, New York NY, USA
⁴ Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
⁵ Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York NY, USA
⁶ Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, NY, USA
⁷ Pathology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
⁸ Weill Cornell Medicine Graduate School of Medical Sciences, New York, NY, USA

Organization

The repository is organized as follows.

src/Notebooks contains the notebooks to reproduce figures in the study. The directory contains the following files.

- common_utils.py
- preprocessing.ipynb
- FOXA2_compartments.ipynb
- integration_harmony.ipynb
- integration_scvi.ipynb
- co_expression.ipynb
- fetal_scores.ipynb
- FOXA2_expression.ipynb
- tmb_comparison.ipynb

Here we describe each file.

common_utils.py: Utility functions that are shared across the notebooks.

preprocessing.ipynb Functions for dublet detection.

FOXA2_compartments.ipynb: Generates figures related to tissue compartment expressing FOXA2.

integration_harmony.ipynb: Generates figures related to batch correction using harmony.

integration_scvi.ipynb: Generates figures related to batch correction using scVI.

co_expression.ipynb: Generates figures related to co-expression of FOXA2 and select TFs.

fetal_scores.ipynb: Generates figures related to fetal scores in FOXA2+ and FOXA2- cells.

FOXA2_expression.ipynb: Generates figures related to genes correlated with FOXA2's expression.

tmb_comparison.ipynb: Generates figures related to the study of the tumor mutation burden.