Single cell and Spatial Multi-Omics

A central direction of the lab is methodology development for single-cell and spatial multi-omics, including Xenium spatial transcriptomics and related imaging-based platforms. We build scalable algorithms for cell segmentation, tissue architecture analysis, cell-state mapping, and cell-cell interaction inference, with applications in cancer, immune biology, and immune-mediated disease research. A recent spatial transcriptomics study illustrates how these approaches can connect tissue organization with disease mechanisms (Qin et al., 2025).

Prior work on integrative single-cell regulome analysis (Wang et al., 2020) and stem-cell hierarchies in cancer (Wei et al., 2022) forms part of the methodological foundation for this direction. We also apply single-cell transcriptomics to study non-genetic, transcriptomic mechanisms of therapy response and resistance in pediatric cancer models (Yang et al., 2025).

References

2025

bioRxiv

Spatial Transcriptomics Identify T Cell-Driven Mechanisms of Kidney Damage in Immune Checkpoint Inhibitor-Associated Acute Interstitial Nephritis

Qian Qin, Lennard Ostendorf, Sophia L Wells, and 24 more authors

bioRxiv, Oct 2025

DOI Bib HTML

@article{Qin2025ICIAIN,
  title = {Spatial Transcriptomics Identify {T} Cell-Driven Mechanisms of Kidney Damage in Immune Checkpoint Inhibitor-Associated Acute Interstitial Nephritis},
  author = {Qin, Qian and Ostendorf, Lennard and Wells, Sophia L and Gao, Ce and Tran, Miles and Alikhan, Firasat M and Zhang, Xiwen and Chewcharat, Api and Rider, Robert S and Prell, Sean A and Chowdhury, Raad B and Weins, Astrid and Shah, Sujal I and Mistry, Kavita and Bowman, Teresa and Villani, Alexandra-Chloe and LeBoeuf, Nicole R and Selamet, Umut and Ravi, Katherine Scovner and Sharon, Elad and Leaf, David E and Moledina, Dennis G and Sise, Meghan E and De Vlaminck, Iwijn and Rao, Deepak A and Wei, Kevin and Gupta, Shruti},
  journal = {bioRxiv},
  pages = {2025.10.31.685702},
  month = oct,
  year = {2025},
  doi = {10.1101/2025.10.31.685702},
}

Nat Commun

The PIK3CA/AKT pathway drives therapy resistance in rhabdomyosarcoma

Q Yang, Y Wang, L A Corchete Sanchez, and 13 more authors

Nature Communications, Dec 2025

DOI Bib HTML

@article{Yang2025RMSResistance,
  title = {The {PIK3CA/AKT} pathway drives therapy resistance in rhabdomyosarcoma},
  author = {Yang, Q and Wang, Y and Corchete Sanchez, L A and Mathavarajah, S and Qin, Qian and Wei, Y and Alpert, E and Whelton, L and Sharma, P and Strom, S and Oultache, I and Iafrate, A J and Pinello, L and Rheinbay, E and Yan, C and Langenau, D M},
  journal = {Nature Communications},
  volume = {17},
  number = {1},
  pages = {65},
  month = dec,
  year = {2025},
  doi = {10.1038/s41467-025-66632-9},
}

2022

Nat Cancer

Single-cell analysis and functional characterization uncover the stem cell hierarchies and developmental origins of rhabdomyosarcoma

Y Wei, Qian Qin, C Yan, and 1 more author

Nature Cancer*Co-first authors , 2022

DOI Bib

@article{Wei2022Rhabdomyosarcoma,
  title = {Single-cell analysis and functional characterization uncover the stem cell hierarchies and developmental origins of rhabdomyosarcoma},
  author = {Wei, Y and Qin, Qian and Yan, C and others},
  journal = {Nature Cancer},
  year = {2022},
  doi = {10.1038/s43018-022-00414-w},
}

2020

Genome Biol

Integrative analyses of single-cell transcriptome and regulome using MAESTRO

C Wang, D Sun, X Huang, and 13 more authors

Genome Biology, 2020

Bib HTML

@article{Wang2020MAESTRO,
  title = {Integrative analyses of single-cell transcriptome and regulome using {MAESTRO}},
  author = {Wang, C and Sun, D and Huang, X and Wan, C and Li, Z and Han, Y and Qin, Qian and Fan, J and Qiu, X and Xie, Y and Meyer, C A and Brown, M and Tang, M and Long, H and Liu, T and Liu, X S},
  journal = {Genome Biology},
  volume = {21},
  number = {1},
  pages = {198},
  year = {2020},
}