scCT-DB, an omnibus for cancer patient-derived paired pre- and post-treatment single-cell transcriptomes

Sep 23, 2026

Uploaded by Rowan

Drug resistance remains a major barrier to effective cancer therapy, requiring detailed insight into cellular and molecular changes following treatment. Single-cell RNA sequencing of matched pre- and post-treatment patient samples offers high-resolution tracking of these dynamics, yet rapidly growing datasets hinder access, integration, and reuse. scCT-DB compiles 266 uniformly processed paired scRNA-seq datasets with structured metadata, spanning 6.19 million cells, 1142 patient samples, 27 cancer types, 96 regimens, and 102 drugs.

LanguageEnglish

CategoryHealthcare

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Pages18

Reading Time45 min

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scCT-DB, an omnibus for cancer patient-derived paired pre- and post-treatment single-cell transcriptomes

Abstract

Graphical abstract

Introduction

Nucleic Acids Research, 2026, 54, D1616–D1633 [https://doi.org/10.1093/nar/gkaf1065](https://doi.org/10.1093/nar/gkaf1065) Advance access publication date: 29 October 2025 Database issue scCT-DB, an omnibus for cancer patient-derived paired preand post-treatment single-cell transcriptomes to reveal drug perturbation and drug resistance mechanisms Shurui Ma1,2 ,†, Jianzhou Jiang2,3 ,†, Ruiyu Zhang4 ,†, Xinyi Ren 1,2 , Dan Li 1,2 , Xiangdong Li2,3 , Hong Mu5 , Peng Liu2,3 , Li Zuo1 , Tingting Zhao 1 , Anxin Gu4 ,* , Dong Li 1,2 ,* , Zhongyang Liu 1,2,3 ,* 1 School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China 2 State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Academy of Military Medical Sciences, Beijing 102206, China 3 School of Life Sciences, Hebei University, Baoding 071002, China 4 Department of Radiation Oncology, Harbin Medical University Cancer Hospital, Harbin 150040, China 5 Department of Emergency, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China ∗ To whom correspondence should be addressed. Email: [liuzy1984@163.com](liuzy1984@163.com) Correspondence may also be addressed to Dong Li. Email: [lidong.bprc@foxmail.com](lidong.bprc@foxmail.com) Correspondence may also be addressed to Anxin Gu. Email: [guanxin@hrbmu.edu.cn](guanxin@hrbmu.edu.cn) †The first three authors should be regarded as Joint First Authors. Abstract Drug resistance continues to be a major challenge in cancer treatment. Understanding cellular and molecular dynamics after treatment is crucial for elucidating resistance mechanisms. Single-cell RNA sequencing (scRNA-seq) of paired pre- and post-treatment patient samples enables high-resolution exploration of such dynamics, but rapidly accumulated relevant data bring challenges for easy data access, integration, andreuse. Therefore, we present the Cancer Treatment-related Single-Cell transcriptome DataBase (scCT-DB, [http://scctdb.ncpsb.org.cn](http://scctdb.ncpsb.org.cn)) . scCT-DB has comprehensively collected 266 patient-derived paired pre- and post-treatment scRNA-seq datasets processed by a uniform pipeline and with detailed and structured metadata, most of which simultaneously include information on primary/acquired drug response. scCT-DB includes 6.19 million cells from 1142 original patient samples, 27 major cancer types, 96 therapeutic regimens, and 102 drugs (involving chemotherapy, immunotherapy, hormone therapy, and targeted therapy) . scCT-DB also provides 48 dataset pairs with opposite primary response groupings and 41 longitudinal datasets with ≥3 sampling timepoints. Besides data browsing, download, and search, scCT-DB also supports single-dataset analysis (including cell abundance, gene, cell state, and intercellular communication perturbation analyses), dataset comparative and re-combination analyses, providing insights into drug perturbation mechanisms and their heterogeneity in patients, drug resistance mechanisms, and discovery of biomarkers predictive of treatment response, etc. Graphical abstract Received: August 15, 2025. Revised: September 16, 2025. Accepted: September 24, 2025 © The Author(s) 2025. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License ([https://creativecommons.org/licenses/by-nc/4.0/](https://creativecommons.org/licenses/by-nc/4.0/)), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact [reprints@oup.com](reprints@oup.com) for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact [journals.permissions@oup.com](journals.permissions@oup.com). Paired pre-and post-

FAQs

What is scCT-DB designed to address in cancer research?

scCT-DB addresses the difficulty of accessing, integrating, and reusing rapidly accumulated single-cell datasets needed to study treatment-induced drug perturbation and drug resistance mechanisms.

What data does scCT-DB include?

It provides 266 patient-derived paired pre- and post-treatment scRNA-seq datasets processed by a uniform pipeline, covering many cancer types, therapeutic regimens, and drugs, with structured metadata.

What analysis capabilities does scCT-DB support?

Beyond browsing, download, and search, it supports single-dataset analyses (e.g., cell abundance, gene, cell state, and communication perturbations) and comparative/re-combination analyses to explore resistance mechanisms and predictive biomarkers.

Sep 23, 2026

Uploaded by Rowan