The triumphs and limitations of computational methods for scRNA-seq

PV Kharchenko - Nature methods, 2021 - nature.com
The rapid progress of protocols for sequencing single-cell transcriptomes over the past
decade has been accompanied by equally impressive advances in the computational …

CCR8-targeted specific depletion of clonally expanded Treg cells in tumor tissues evokes potent tumor immunity with long-lasting memory

Y Kidani, W Nogami, Y Yasumizu… - Proceedings of the …, 2022 - National Acad Sciences
Foxp3-expressing CD25+ CD4+ regulatory T cells (Tregs) are abundant in tumor tissues.
Here, hypothesizing that tumor Tregs would clonally expand after they are activated by …

A single‐cell RNA expression atlas of normal, preneoplastic and tumorigenic states in the human breast

B Pal, Y Chen, F Vaillant, BD Capaldo, R Joyce… - The EMBO …, 2021 - embopress.org
To examine global changes in breast heterogeneity across different states, we determined
the single‐cell transcriptomes of> 340,000 cells encompassing normal breast, preneoplastic …

Single-cell immune landscape of human atherosclerotic plaques

DM Fernandez, AH Rahman, NF Fernandez… - Nature medicine, 2019 - nature.com
Atherosclerosis is driven by multifaceted contributions of the immune system within the
circulation and at vascular focal sites. However, specific characteristics of dysregulated …

Clonal replacement of tumor-specific T cells following PD-1 blockade

KE Yost, AT Satpathy, DK Wells, Y Qi, C Wang… - Nature medicine, 2019 - nature.com
Immunotherapies that block inhibitory checkpoint receptors on T cells have transformed the
clinical care of patients with cancer. However, whether the T cell response to checkpoint …

Single-cell RNA-seq highlights intra-tumoral heterogeneity and malignant progression in pancreatic ductal adenocarcinoma

J Peng, BF Sun, CY Chen, JY Zhou, YS Chen, H Chen… - Cell research, 2019 - nature.com
Pancreatic ductal adenocarcinoma (PDAC) is the most common type of pancreatic cancer
featured with high intra-tumoral heterogeneity and poor prognosis. To comprehensively …

CD8+ T cell differentiation and dysfunction in cancer

M Philip, A Schietinger - Nature Reviews Immunology, 2022 - nature.com
CD8+ T cells specific for cancer cells are detected within tumours. However, despite their
presence, tumours progress. The clinical success of immune checkpoint blockade and …

Insights gained from single-cell analysis of immune cells in the tumor microenvironment

X Ren, L Zhang, Y Zhang, Z Li… - Annual review of …, 2021 - annualreviews.org
Understanding tumor immune microenvironments is critical for identifying immune modifiers
of cancer progression and developing cancer immunotherapies. Recent applications of …

[HTML][HTML] Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease

PA Szabo, HM Levitin, M Miron, ME Snyder… - Nature …, 2019 - nature.com
Human T cells coordinate adaptive immunity in diverse anatomic compartments through
production of cytokines and effector molecules, but it is unclear how tissue site influences T …

Single-cell analyses of renal cell cancers reveal insights into tumor microenvironment, cell of origin, and therapy response

Y Zhang, SP Narayanan, R Mannan… - Proceedings of the …, 2021 - National Acad Sciences
Diverse subtypes of renal cell carcinomas (RCCs) display a wide spectrum of
histomorphologies, proteogenomic alterations, immune cell infiltration patterns, and clinical …