Single-cell RNA sequencing in cancer: Applications, advances, and emerging challenges

Single cell genomic characterization reveals the cellular reprogramming of the gastric tumor microenvironment

(2020) Anuja Sathe et al.   CLINICAL CANCER RESEARCH

Peripheral T cell expansion predicts tumour infiltration and clinical response

(2020) Thomas D. Wu et al.   NATURE

Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas

(2020) Reuben Moncada et al.   NATURE BIOTECHNOLOGY

Transcriptional diversity and bioenergetic shift in human breast cancer metastasis revealed by single-cell RNA sequencing

(2020) Ryan T. Davis et al.   NATURE CELL BIOLOGY

Cytokeratin 5 alters β-catenin dynamics in breast cancer cells

(2020) Olivia McGinn et al.   ONCOGENE

Single-cell transcriptome analysis reveals TOX as a promoting factor for T cell exhaustion and a predictor for anti-PD-1 responses in human cancer

(2020) Kyungsoo Kim et al.   Genome Medicine

The Msi1-mTOR pathway drives the pathogenesis of mammary and extramammary Paget’s disease

(2020) Yongli Song et al.   CELL RESEARCH

Single-Cell RNA Sequencing of Tumor-Infiltrating NK Cells Reveals that Inhibition of Transcription Factor HIF-1α Unleashes NK Cell Activity

(2020) Jing Ni et al.   IMMUNITY

Unravelling the heterogeneity and dynamic relationships of tumor‐infiltrating T cells by single‐cell RNA sequencing analysis

(2020) Xin Yu et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Paracrine orchestration of intestinal tumorigenesis by a mesenchymal niche

(2020) Manolis Roulis et al.   NATURE

Tools for the analysis of high-dimensional single-cell RNA sequencing data

(2020) Yan Wu et al.   Nature Reviews Nephrology

Single-cell RNA sequencing demonstrates the molecular and cellular reprogramming of metastatic lung adenocarcinoma

(2020) Nayoung Kim et al.   Nature Communications

Dissecting the Single-Cell Transcriptome Network Underlying Gastric Premalignant Lesions and Early Gastric Cancer

(2020) Peng Zhang et al.   Cell Reports

Single-Cell RNA Sequencing Reveals a Dynamic Stromal Niche That Supports Tumor Growth

(2020) Sarah Davidson et al.   Cell Reports

Medulloblastoma Arises from the Persistence of a Rare and Transient Sox2+ Granule Neuron Precursor

(2020) Hayden J. Selvadurai et al.   Cell Reports

Single-cell RNA sequencing reveals the tumor microenvironment and facilitates strategic choices to circumvent treatment failure in a chemorefractory bladder cancer patient

(2020) Hye Won Lee et al.   Genome Medicine

Single-Cell Transcriptomic Analysis of Cardiac Progenitor Differentiation

(2020) Haiqing Xiong et al.   Current Cardiology Reports

Integrative Analysis and Machine Learning based Characterization of Single Circulating Tumor Cells

(2020) Arvind Iyer et al.   Journal of Clinical Medicine

Analysis of Dual Class I Histone Deacetylase and Lysine Demethylase Inhibitor Domatinostat (4SC-202) on Growth and Cellular and Genomic Landscape of Atypical Teratoid/Rhabdoid

(2020) Mariah M. Hoffman et al.   Cancers

Hybrid Stem Cell States: Insights Into the Relationship Between Mammary Development and Breast Cancer Using Single-Cell Transcriptomics

(2020) Tasha Thong et al.   Frontiers in Cell and Developmental Biology

Analysis of Gene Signatures of Tumor Microenvironment Yields Insight Into Mechanisms of Resistance to Immunotherapy

(2020) Ben Wang et al.   Frontiers in Bioengineering and Biotechnology

Dynamics of peripheral T cell clones during PD-1 blockade in non-small cell lung cancer

(2020) Fan Zhang et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

Immune cell infiltration features and related marker genes in lung cancer based on single-cell RNA-seq

(2020) R. Zhong et al.   Clinical & Translational Oncology

Stromal cell diversity associated with immune evasion in human triple‐negative breast cancer

(2020) Sunny Z Wu et al.   EMBO JOURNAL

IL22BP Mediates the Anti-Tumor Effects of Lymphotoxin Against Colorectal Tumors in Mice and Humans

(2020) Jan Kempski et al.   GASTROENTEROLOGY

Dissecting transcriptional heterogeneity in primary gastric adenocarcinoma by single cell RNA sequencing

(2020) Min Zhang et al.   GUT

Cellular heterogeneity landscape in laryngeal squamous cell carcinoma

(2020) Lianhao Song et al.   INTERNATIONAL JOURNAL OF CANCER

Single-cell transcriptomic architecture and intercellular crosstalk of human intrahepatic cholangiocarcinoma

(2020) Min Zhang et al.   JOURNAL OF HEPATOLOGY

Single-Cell Transcriptomics Analysis Identifies Nuclear Protein 1 as a Regulator of Docetaxel Resistance in Prostate Cancer Cells

(2020) Patricia M. Schnepp et al.   MOLECULAR CANCER RESEARCH

Discovery of New Targets to Control Metastasis in Pancreatic Cancer by Single-cell Transcriptomics Analysis of Circulating Tumor Cells

(2020) Spas Dimitrov-Markov et al.   MOLECULAR CANCER THERAPEUTICS

A single-cell landscape of high-grade serous ovarian cancer

(2020) Benjamin Izar et al.   NATURE MEDICINE

Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy

(2020) Charles P. Couturier et al.   Nature Communications

Chronic myelomonocytic leukaemia stem cell transcriptomes anticipate disease morphology and outcome

(2020) Daniel H Wiseman et al.   EBioMedicine

The use and limitations of single‐cell mass cytometry for studying human microglia function

(2020) Camila Fernández‐Zapata et al.   BRAIN PATHOLOGY

Single-Cell Characterization of Malignant Phenotypes and Developmental Trajectories of Adrenal Neuroblastoma

(2020) Rui Dong et al.   CANCER CELL

Therapy-Induced Evolution of Human Lung Cancer Revealed by Single-Cell RNA Sequencing

(2020) Ashley Maynard et al.   CELL

Organoids Model Transcriptional Hallmarks of Oncogenic KRAS Activation in Lung Epithelial Progenitor Cells

(2020) Antonella F.M. Dost et al.   Cell Stem Cell

The HDAC Inhibitor Domatinostat Promotes Cell Cycle Arrest, Induces Apoptosis and Increases Immunogenicity of Merkel Cell Carcinoma Cells

(2020) Lina Song et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Identification of a distinct luminal subgroup diagnosing and stratifying early stage prostate cancer by tissue-based single-cell RNA sequencing

(2020) Xiaoshi Ma et al.   Molecular Cancer

Analysis of circulating breast cancer cell heterogeneity and interactions with peripheral blood mononuclear cells

(2020) Heather M. Brechbuhl et al.   MOLECULAR CARCINOGENESIS

Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue

(2020) Daniel Gyllborg et al.   NUCLEIC ACIDS RESEARCH

A gene expression signature of TREM2hi macrophages and γδ T cells predicts immunotherapy response

(2020) Donghai Xiong et al.   Nature Communications

Single-cell RNA sequencing highlights the role of inflammatory cancer-associated fibroblasts in bladder urothelial carcinoma

(2020) Zhaohui Chen et al.   Nature Communications

AP-1 and TGFß cooperativity drives non-canonical Hedgehog signaling in resistant basal cell carcinoma

(2020) Catherine D. Yao et al.   Nature Communications

Baseline Frequency of Inflammatory Cxcl9-Expressing Tumor-Associated Macrophages Predicts Response to Avelumab Treatment

(2020) Yan Qu et al.   Cell Reports

Single-Cell Transcriptome Analysis of Colon Cancer Cell Response to 5-Fluorouracil-Induced DNA Damage

(2020) Sung Rye Park et al.   Cell Reports

Single-cell transcriptome analysis of tumor and stromal compartments of pancreatic ductal adenocarcinoma primary tumors and metastatic lesions

(2020) Wei Lin et al.   Genome Medicine

Single-cell RNA-sequencing reveals distinct patterns of cell state heterogeneity in mouse models of breast cancer

(2020) Syn Kok Yeo et al.   eLife

Hypoxia Promotes Syndecan-3 Expression in the Tumor Microenvironment

(2020) Endika Prieto-Fernández et al.   Frontiers in Immunology

Single-Cell RNA-Sequencing Shift in the Interaction Pattern Between Glioma Stem Cells and Immune Cells During Tumorigenesis

(2020) You Zhai et al.   Frontiers in Immunology

A map of tumor–host interactions in glioma at single-cell resolution

(2020) Francesca Pia Caruso et al.   GigaScience

A Systems Biology Approach to Identifying a Master Regulator That Can Transform the Fast Growing Cellular State to a Slowly Growing One in Early Colorectal Cancer Development Model

(2020) Jihye Choi et al.   Frontiers in Genetics

Single-cell transcriptome atlas of lung adenocarcinoma featured with ground glass nodules

(2020) Tao Lu et al.   Cell Discovery

Dynamic single-cell RNA sequencing identifies immunotherapy persister cells following PD-1 blockade

(2020) Kartik Sehgal et al.   JOURNAL OF CLINICAL INVESTIGATION

Defining HPV-specific B cell responses in patients with head and neck cancer

(2020) Andreas Wieland et al.   NATURE

A `one-two punch' therapy strategy to target chemoresistance in estrogen receptor positive breast cancer

(2020) Feng Chi et al.   Translational Oncology

Single cell characterization of B-lymphoid differentiation and leukemic cell states during chemotherapy in ETV6-RUNX1-positive pediatric leukemia identifies drug-targetable transcription factor activities

(2020) Juha Mehtonen et al.   Genome Medicine

Reshaping the Immune Microenvironment by Oncolytic Herpes Simplex Virus in Murine Pancreatic Ductal Adenocarcinoma

(2020) Liming Zhang et al.   MOLECULAR THERAPY

Optofluidic real-time cell sorter for longitudinal CTC studies in mouse models of cancer

(2019) Bashar Hamza et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Neutrophils escort circulating tumour cells to enable cell cycle progression

(2019) Barbara Maria Szczerba et al.   NATURE

KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance

(2019) Kunihiko Hinohara et al.   CANCER CELL

Tissue-infiltrating immune cells as prognostic markers in oral squamous cell carcinoma: a systematic review and meta-analysis

(2019) Elin Hadler-Olsen et al.   BRITISH JOURNAL OF CANCER

Adaptive Immune Resistance Emerges from Tumor-Initiating Stem Cells

(2019) Yuxuan Miao et al.   CELL

A Cellular Taxonomy of the Bone Marrow Stroma in Homeostasis and Leukemia

(2019) Ninib Baryawno et al.   CELL

Identification of Breast Cancer Stem Cell Related Genes Using Functional Cellular Assays Combined With Single-Cell RNA Sequencing in MDA-MB-231 Cells

(2019) Emma Jonasson et al.   Frontiers in Genetics

Single-cell RNA sequencing reveals the impact of chromosomal instability on glioblastoma cancer stem cells

(2019) Yanding Zhao et al.   BMC Medical Genomics

Neutrophils Driving Unconventional T Cells Mediate Resistance against Murine Sarcomas and Selected Human Tumors

(2019) Andrea Ponzetta et al.   CELL

Single cell RNA-sequencing: replicability of cell types

(2019) Megan Crow et al.   CURRENT OPINION IN NEUROBIOLOGY

Application of single-cell RNA sequencing methodologies in understanding haematopoiesis and immunology

(2019) Anna M. Ranzoni et al.   Essays in Biochemistry

Current best practices in single‐cell RNA‐seq analysis: a tutorial

(2019) Malte D Luecken et al.   Molecular Systems Biology

Hydro-Seq enables contamination-free high-throughput single-cell RNA-sequencing for circulating tumor cells

(2019) Yu-Heng Cheng et al.   Nature Communications

Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts

(2019) Ela Elyada et al.   Cancer Discovery

Molecular and Kinetic Analyses of Circulating Tumor Cells as Predictive Markers of Treatment Response in Locally Advanced Rectal Cancer Patients

(2019) Bianca C. Troncarelli Flores et al.   Cells

New Challenges in Tumor Mutation Heterogeneity in Advanced Ovarian Cancer by a Targeted Next-Generation Sequencing (NGS) Approach

(2019) Marica Garziera et al.   Cells

Single-cell transcriptomics reveals the landscape of intra-tumoral heterogeneity and stemness-related subpopulations in liver cancer

(2019) Daniel Wai-Hung Ho et al.   CANCER LETTERS

Single‐cell RNA‐seq reveals the invasive trajectory and molecular cascades underlying glioblastoma progression

(2019) Bo Pang et al.   Molecular Oncology

Single-cell RNA sequencing reveals compartmental remodeling of tumor-infiltrating immune cells induced by anti-CD47 targeting in pancreatic cancer

(2019) Yu Pan et al.   Journal of Hematology & Oncology

Single-cell transcriptomics reveals multi-step adaptations to endocrine therapy

(2019) Sung Pil Hong et al.   Nature Communications

Single-cell RNA sequencing reveals stromal evolution into LRRC15+ myofibroblasts as a determinant of patient response to cancer immunotherapy

(2019) Claudia X Dominguez et al.   Cancer Discovery

A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart

(2019) Michaela Asp et al.   CELL

Cancer stem cells (CSCs): metabolic strategies for their identification and eradication

(2018) Ernestina M. De Francesco et al.   BIOCHEMICAL JOURNAL

Recent Developments in Single-Cell RNA-Seq of Microorganisms

(2018) Yi Zhang et al.   BIOPHYSICAL JOURNAL

Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing

(2018) Charissa Kim et al.   CELL

Cancer-associated fibroblasts in tumor microenvironment – Accomplices in tumor malignancy

(2018) Zehuan Liao et al.   CELLULAR IMMUNOLOGY

AR Expression in Breast Cancer CTCs Associates with Bone Metastases

(2018) Nicola Aceto et al.   MOLECULAR CANCER RESEARCH

Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis

(2018) Peter Savas et al.   NATURE MEDICINE

Phenotype molding of stromal cells in the lung tumor microenvironment

(2018) Diether Lambrechts et al.   NATURE MEDICINE

Single-cell RNA sequencing for the study of development, physiology and disease

(2018) S. Steven Potter   Nature Reviews Nephrology

Profiling human breast epithelial cells using single cell RNA sequencing identifies cell diversity

(2018) Quy H. Nguyen et al.   Nature Communications

Cancer Stem Cells (CSCs) in Drug Resistance and their Therapeutic Implications in Cancer Treatment

(2018) Lan Thi Hanh Phi et al.   Stem Cells International

Single-cell RNA sequencing reveals diverse intratumoral heterogeneities and gene signatures of two types of esophageal cancers

(2018) Hongjin Wu et al.   CANCER LETTERS

Acquired cancer resistance to combination immunotherapy from transcriptional loss of class I HLA

(2018) K. G. Paulson et al.   Nature Communications

Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq

(2018) Mihriban Karaayvaz et al.   Nature Communications

High-density single cell mRNA sequencing to characterize circulating tumor cells in hepatocellular carcinoma

(2018) Delia D’Avola et al.   Scientific Reports

A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade

(2018) Livnat Jerby-Arnon et al.   CELL

Detection of Apoptotic Circulating Tumor Cells Using in vivo Fluorescence Flow Cytometry

(2018) Jacqueline Nolan et al.   CYTOMETRY PART A

Cancer stem cells (CSCs) in cancer progression and therapy

(2018) Masoud Najafi et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Longitudinal single-cell RNA sequencing of patient-derived primary cells reveals drug-induced infidelity in stem cell hierarchy

(2018) Ankur Sharma et al.   Nature Communications

Spatially and functionally distinct subclasses of breast cancer-associated fibroblasts revealed by single cell RNA sequencing

(2018) Michael Bartoschek et al.   Nature Communications

Single-cell RNA-sequencing reveals transcriptional dynamics of estrogen-induced dysplasia in the ovarian surface epithelium

(2018) Nhung H. Vuong et al.   PLoS Genetics

Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types

(2017) Santiago J. Carmona et al.   GENOME RESEARCH

Comparative Analysis of Single-Cell RNA Sequencing Methods

(2017) Christoph Ziegenhain et al.   MOLECULAR CELL

APE1/Ref-1 knockdown in pancreatic ductal adenocarcinoma - characterizing gene expression changes and identifying novel pathways using single-cell RNA sequencing

(2017) Fenil Shah et al.   Molecular Oncology

Single-cell transcriptomics uncovers distinct molecular signatures of stem cells in chronic myeloid leukemia

(2017) Alice Giustacchini et al.   NATURE MEDICINE

Aging increases cell-to-cell transcriptional variability upon immune stimulation

(2017) Celia Pilar Martinez-Jimenez et al.   SCIENCE

Combating subclonal evolution of resistant cancer phenotypes

(2017) Samuel W. Brady et al.   Nature Communications

Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer

(2017) Woosung Chung et al.   Nature Communications

Size-based detection of sarcoma circulating tumor cells and cell clusters

(2017) Masanori Hayashi et al.   Oncotarget

A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications

(2017) Ashraful Haque et al.   Genome Medicine

A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation

(2016) S. Nestorowa et al.   BLOOD

Single cell genomics reveals activation signatures of endogenous SCAR's networks in aneuploid human embryos and clinically intractable malignant tumors

(2016) Gennadi V. Glinsky   CANCER LETTERS

T cell fate and clonality inference from single-cell transcriptomes

(2016) Michael J T Stubbington et al.   NATURE METHODS

Genetic interrogation of circulating multiple myeloma cells at single-cell resolution

(2016) J. G. Lohr et al.   Science Translational Medicine

Transcriptome sequencing of HER2-positive breast cancer stem cells identifies potential prognostic marker

(2016) Bo Lei et al.   TUMOR BIOLOGY

Laser capture microscopy coupled with Smart-seq2 for precise spatial transcriptomic profiling

(2016) Susanne Nichterwitz et al.   Nature Communications

p53 Regulates Progenitor Cell Quiescence and Differentiation in the Airway

(2016) Alicia M. McConnell et al.   Cell Reports

RNA-Seq of single prostate CTCs implicates noncanonical Wnt signaling in antiandrogen resistance

(2015) D. T. Miyamoto et al.   SCIENCE

Single-cell analysis of lung adenocarcinoma cell lines reveals diverse expression patterns of individual cells invoked by a molecular target drug treatment

(2015) Ayako Suzuki et al.   GENOME BIOLOGY

Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells

(2015) Kyu-Tae Kim et al.   GENOME BIOLOGY

Circulating Tumor Cell Clusters Are Oligoclonal Precursors of Breast Cancer Metastasis

(2014) Nicola Aceto et al.   CELL

Single-Cell RNA Sequencing Identifies Extracellular Matrix Gene Expression by Pancreatic Circulating Tumor Cells

(2014) David T. Ting et al.   Cell Reports

Tumor adaptation and resistance to RAF inhibitors

(2013) Piro Lito et al.   NATURE MEDICINE

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

mRNA-Seq of Single Prostate Cancer Circulating Tumor Cells Reveals Recapitulation of Gene Expression and Pathways Found in Prostate Cancer

(2012) Gordon M. Cann et al.   PLoS One

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS