Recent interesting non-SCSAP publications

April 8, 2022

. Single-cell RNA-seq reveals cell type–specific molecular and genetic associations to lupus

Abstract: Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease. Knowledge of circulating immune cell types and states associated with SLE remains incomplete. We profiled more than 1.2 million peripheral blood mononuclear cells (162 cases, 99 controls) with multiplexed single-cell RNA sequencing (mux-seq). …see Link for more information…

Also Highlighted in an article on Genomeweb. Find it HERE 

April 1, 2022

Research Techniques Made Simple: Spatial Transcriptomics

Arianna J Piñeiro 1Aubrey E Houser 1Andrew L Ji 2PMID: 35331388 PMCID: PMC8969263 (available on 2023-04-01)   DOI: 10.1016/j.jid.2021.12.014

Abstract: Transcriptome profiling of tissues and single cells facilitates interrogation of gene expression changes within diverse biological contexts. However, spatial information is often lost during tissue homogenization or dissociation. Recent advances in transcriptome profiling preserve the in situ spatial contexts…..Please see link for more information. 

March 22, 2022

Multiplexed droplet single-cell sequencing (Mux-Seq) of normal and transplant kidney.

Rashmi P, Sur S, Sigdel TK, Boada P, Schroeder AW, Damm I, Kretzler M, Hodgin J, Hartoularos G, Jimmie Ye C, Sarwal MM; Kidney Precision Medicine Project.Am J Transplant. 2022 Mar;22(3):876-885. doi: 10.1111/ajt.16871. Epub 2021 Dec 4.PMID: 34687145

Abstract: Maintenance of systemic homeostasis by kidney requires the coordinated response of diverse cell types. The use of single-cell RNA sequencing (scRNAseq) for patient tissue samples remains fraught with difficulties with cell isolation, purity, and experimental bias. The ability to characterize immune and parenchymal cells during transplant rejection will be invaluable…..Please see link for more information. 

March 15, 2022

Single-cell transcriptomics reveals distinct effector profiles of infiltrating T cells in lupus skin and kidney.

Dunlap GS, Billi AC, Xing X, Ma F, Maz MP, Tsoi LC, Wasikowski R, Hodgin JB, Gudjonsson JE, Kahlenberg JM, Rao DA.JCI Insight. 2022 Mar 15:e156341. doi: 10.1172/jci.insight.156341. Online ahead of print.PMID: 35290245
Abstract: Cutaneous lupus is commonly present in patients with systemic lupus erythematosus (SLE). T cells have been strongly suspected to contribute to the pathology of cutaneous lupus, yet our understanding of the relevant T cell phenotypes and functions remains incomplete. Here, we present a detailed single-cell RNA sequencing….Please see link for more information.

March 11, 2022

Single-Cell RNA Sequencing with Spatial Transcriptomics of Cancer Tissues.

Ahmed R, Zaman T, Chowdhury F, Mraiche F, Tariq M, Ahmad IS, Hasan A.Int J Mol Sci. 2022 Mar 11;23(6):3042. doi: 10.3390/ijms23063042.PMID: 35328458 

Abstract: Single-cell RNA sequencing (RNA-seq) techniques can perform analysis of transcriptome at the single-cell level and possess an unprecedented potential for exploring signatures involved in tumor development and progression. These techniques can perform sequence analysis of transcripts with a better resolution that could increase understanding of the cellular diversity found in the tumor microenvironment …Please see link for more information.

November 14, 2021

Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration
David W McKellar 1Lauren D Walter 2Leo T Song 1Madhav Mantri 3Michael F Z Wang 3Iwijn De Vlaminck # 4Benjamin D Cosgrove # 5

Skeletal muscle repair is driven by the coordinated self-renewal and fusion of myogenic stem and progenitor cells. Single-cell gene expression analyses of myogenesis have been hampered by the poor sampling of rare and transient cell states that are critical for muscle repair, and do not inform the spatial context that is important for myogenic differentiation. Here, we demonstrate how large-scale integration of single-cell and spatial transcriptomic data can overcome these limitations. ……Please see link for more information.

October 29, 2021

Single-Cell Proteomic Analysis Dissects the Complexity of Tumor Microenvironment in Muscle Invasive Bladder Cancer
Chao Feng 1 2 3Xi Wang 1 2 4Yuting Tao 1 2 3Yuanliang Xie 1 2 5Zhiyong Lai 1 2Zhijian Li 1 2Jiaxin Hu 1 2Shaomei Tang 1 2Lixin Pan 1 2Liangyu He 1 2 6 7Qiuyan Wang 1 2 4Tianyu Li 1 2 6 7Zengnan Mo 1 2 6 7

Muscle invasive bladder cancer (MIBC) is a malignancy with considerable heterogeneity. The MIBC tumor microenvironment (TME) is highly complex, comprising diverse phenotypes and spatial architectures. The complexity of the MIBC TME must be characterized to provide potential targets for precision therapy. Herein, an integrated combination of mass cytometry and imaging mass cytometry was used to analyze tumor cells, immune cells, and TME spatial characteristics of 44 MIBC patients. We detected tumor and immune cell clusters with abnormal phenotypes. ….Please see link for more information

Member publications – coming soon