Single Cell Spatial Analysis Program

Publications of Interest

 

February 2024

Single–cell sequencing reveals Hippo signaling as a driver of fibrosis in hidradenitis suppurativa.

van Straalen KR, Ma F, Tsou PS, Plazyo O, Gharaee-Kermani M, Calbet M, Xing X, Sarkar MK, Uppala R, Harms PW, Wasikowski R, Nahlawi L, Nakamura M, Eshaq M, Wang C, Dobry C, Kozlow JH, Cherry-Bukowiec J, Brodie WD, Wolk K, Uluçkan Ö, Mattichak MN, Pellegrini M, Modlin RL, Maverakis E, Sabat R, Kahlenberg JM, Billi AC, Tsoi LC, Gudjonsson JE.J Clin Invest. 2024 Feb 1;134(3):e169225. doi: 10.1172/JCI169225.PMID: 38051587 Free PMC article.
Hidradenitis suppurativa (HS) is a chronic inflammatory disease characterized by abscesses, nodules, dissecting/draining tunnels, and extensive fibrosis. Here, we integrate single-cell RNA sequencing, spatial transcriptomics, and immunostaining to provide an …
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January 2024

SRT-Server: powering the analysis of spatial transcriptomic data.

Yang S, Zhou X.Genome Med. 2024 Jan 26;16(1):18. doi: 10.1186/s13073-024-01288-6.PMID: 38279156 Free PMC article.
BACKGROUND: Spatial resolved transcriptomics (SRT) encompasses a rapidly developing set of technologies that enable the measurement of gene expression in tissue while retaining spatiallocalization information. …As SRT technologies have advanced and an incr …
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July 2023

The promising application of cell–cell interaction analysis in cancer from single–cell and spatial transcriptomics.

Wang X, Almet AA, Nie Q.Semin Cancer Biol. 2023 Jul 15;95:42-51. doi: 10.1016/j.semcancer.2023.07.001. Online ahead of print.PMID: 37454878 Free article. Review.
Single–cell transcriptomics and spatial transcriptomics have become powerful new tools for researchers to profile the transcriptional landscape of cancer at unparalleled genetic depth. In this review, we discuss the rapidly growing array of computational tool …
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March 2023

Single–cell RNA sequencing and spatial transcriptomics reveal cancer-associated fibroblasts in glioblastoma with protumoral effects.

Jain S, Rick JW, Joshi RS, Beniwal A, Spatz J, Gill S, Chang AC, Choudhary N, Nguyen AT, Sudhir S, Chalif EJ, Chen JS, Chandra A, Haddad AF, Wadhwa H, Shah SS, Choi S, Hayes JL, Wang L, Yagnik G, Costello JF, Diaz A, Heiland DH, Aghi MK.J Clin Invest. 2023 Mar 1;133(5):e147087. doi: 10.1172/JCI147087.PMID: 36856115 Free PMC article.
Serial trypsinization of glioblastoma specimens yielded cells with CAF morphology and single–celltranscriptomic profiles based on their lack of copy number variations (CNVs) and elevated individual cell CAF probability scores derived from the expression of 9 …
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February 2023

Bacterial droplet-based single–cell RNA-seq reveals antibiotic-associated heterogeneous cellular states.

Ma P, Amemiya HM, He LL, Gandhi SJ, Nicol R, Bhattacharyya RP, Smillie CS, Hung DT.Cell. 2023 Feb 16;186(4):877-891.e14. doi: 10.1016/j.cell.2023.01.002. Epub 2023 Jan 27.PMID: 36708705
We introduce BacDrop, a highly scalable technology for bacterial single–cell RNA sequencing that has overcome many challenges hindering the development of scRNA-seq in bacteria. …
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February 2023

ASGARD is A Single–cell Guided Pipeline to Aid Repurposing of Drugs.

He B, Xiao Y, Liang H, Huang Q, Du Y, Li Y, Garmire D, Sun D, Garmire LX.Nat Commun. 2023 Feb 22;14(1):993. doi: 10.1038/s41467-023-36637-3.PMID: 36813801 Free PMC article.
Single–cell RNA sequencing technology has enabled in-depth analysis of intercellular heterogeneity in various diseases. …ASGARD shows significantly better average accuracy on single-drug therapy compared to two bulk-cell-based drug repurposing …
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February 2023

ScRNA-seq and ST-seq in liver research.

He J, Deng C, Krall L, Shan Z.Cell Regen. 2023 Feb 3;12(1):11. doi: 10.1186/s13619-022-00152-5.PMID: 36732412 Review.
Spatial transcriptomics, which combine gene expression data with spatial information, has quickly expanded in recent years. …Methods like single-cell RNA sequencing (scRNA-seq) are usually used together with spatial transcriptome sequencing (ST-seq) …
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February 2023

From ‘Omics to Multi–omics Technologies: the Discovery of Novel Causal Mediators.

Mohammadi-Shemirani P, Sood T, Paré G.Curr Atheroscler Rep. 2023 Feb;25(2):55-65. doi: 10.1007/s11883-022-01078-8. Epub 2023 Jan 3.PMID: 36595202 Free PMC article. Review.
RECENT FINDINGS: Multi–omics approaches are growing in adoption as they provide orthogonal evidence and overcome the limitations of individual types of ‘omics data. …The intrinsically unbiased nature of ‘omics data is well-suited to exploratory analy …
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January 2023

Single–cell spatial explorer: easy exploration of spatial and multimodal transcriptomics.

Pont F, Cerapio JP, Gravelle P, Ligat L, Valle C, Sarot E, Perrier M, Lopez F, Laurent C, Fournié JJ, Tosolini M.BMC Bioinformatics. 2023 Jan 27;24(1):30. doi: 10.1186/s12859-023-05150-1.PMID: 36707753 Free PMC article.
BACKGROUND: The development of single–cell technologies yields large datasets of information as diverse and multimodal as transcriptomes, immunophenotypes, and spatial position from tissue sections in the so-called ‘spatial transcriptomics‘. … …
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January 2023

Screening cell–cell communication in spatial transcriptomics via collective optimal transport.

Cang Z, Zhao Y, Almet AA, Stabell A, Ramos R, Plikus MV, Atwood SX, Nie Q.Nat Methods. 2023 Jan 23. doi: 10.1038/s41592-022-01728-4. Online ahead of print.PMID: 36690742
Spatial transcriptomic technologies and spatially annotated single–cell RNA sequencing datasets provide unprecedented opportunities to dissect cell–cell communication (CCC). …Here, we present COMMOT (COMMunication analysis by Optimal Tr …
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January 2023

RNA methylation influences TDP43 binding and disease pathogenesis in models of amyotrophic lateral sclerosis and frontotemporal dementia.

McMillan M, Gomez N, Hsieh C, Bekier M, Li X, Miguez R, Tank EMH, Barmada SJ.Mol Cell. 2023 Jan 19;83(2):219-236.e7. doi: 10.1016/j.molcel.2022.12.019. Epub 2023 Jan 11.PMID: 36634675
Emphasizing the importance of m6A for TDP43 binding and function, we identified several m6A factors that enhance or suppress TDP43-mediated toxicity via single–cell CRISPR-Cas9 in primary neurons. The most promising modifier-the canonical m6A reader YTHDF2-accumulat …
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January 2023

Spatial and single–cell transcriptomics decipher the cellular environment containing HLA-G+ cancer cells and SPP1+ macrophages in colorectal cancer.

Ozato Y, Kojima Y, Kobayashi Y, Hisamatsu Y, Toshima T, Yonemura Y, Masuda T, Kagawa K, Goto Y, Utou M, Fukunaga M, Gamachi A, Imamura K, Kuze Y, Zenkoh J, Suzuki A, Niida A, Hirose H, Hayashi S, Koseki J, Oki E, Fukuchi S, Murakami K, Tobo T, Nagayama S, Uemura M, Sakamoto T, Oshima M, Doki Y, Eguchi H, Mori M, Iwasaki T, Oda Y, Shibata T, Suzuki Y, Shimamura T, Mimori K.Cell Rep. 2023 Jan 17;42(1):111929. doi: 10.1016/j.celrep.2022.111929. Online ahead of print.PMID: 36656712 Free article.
In the current study, we investigate whether events occurring at the invasion front are of particular importance for CRC treatment strategies. To this end, we analyze CRC tissues by combining spatialtranscriptomics from patients with a public single–cell …
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January 2023

Lineage-specific regulatory changes in hypertrophic cardiomyopathy unraveled by single-nucleus RNA-seq and spatial transcriptomics.

Liu X, Yin K, Chen L, Chen W, Li W, Zhang T, Sun Y, Yuan M, Wang H, Song Y, Wang S, Hu S, Zhou Z.Cell Discov. 2023 Jan 17;9(1):6. doi: 10.1038/s41421-022-00490-3.PMID: 36646705 Free PMC article.
An in-depth elucidation of the lineage-specific changes in pathological cardiac remodeling of HCM is pivotal for the development of therapies to mitigate the progression. Here, we performed single-nucleus RNA-seq of the cardiac tissues from HCM patients or healthy donors a …

 

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January 2023

Fan Z, Luo Y, Lu H, Wang T, Feng Y, Zhao W, Kim P, Zhou X.Nucleic Acids Res. 2023 Jan 6;51(D1):D1138-D1149. doi: 10.1093/nar/gkac889.PMID: 36243975 Free PMC article.
SPASCER contains datasets from 43 studies, including 1082 sub-datasets from 16 organ types across four species. scRNA-seq was integrated to deconvolve/map spatial transcriptomics, and processed with spatial cell–cell interaction, gene pattern an …

 

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December, 2022

spaCI: deciphering spatial cellular communications through adaptive graph model.

Tang Z, Zhang T, Yang B, Su J, Song Q.Brief Bioinform. 2022 Dec 21:bbac563. doi: 10.1093/bib/bbac563. Online ahead of print.PMID: 36545790
Cell–cell communications are vital for biological signalling and play important roles in complex diseases. Recent advances in single–cell spatial transcriptomics (SCST) technologies allow examining the spatial cell communication la …

 

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December, 2022

scCapsNet-mask: an updated version of scCapsNet with extended applicability in functional analysis related to scRNA-seq data.

Wang L, Nie R, Zhang J, Cai J.BMC Bioinformatics. 2022 Dec 12;23(1):539. doi: 10.1186/s12859-022-05098-8.PMID: 36510124
In another example, the scCapsNet-mask was trained on scRNA-seq data, and then used to assign cell type in spatial transcriptomics that may contain non-standard sample of doublets. …Therefore, it can extend its applicability in functional analysis, such as …

 

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December, 2022

Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging.
Haase C, Gustafsson K, Mei S, Yeh SC, Richter D, Milosevic J, Turcotte R, Kharchenko PV, Sykes DB, Scadden DT, Lin CP.Nat Methods. 2022 Dec;19(12):1622-1633. doi: 10.1038/s41592-022-01673-2. Epub 2022 Nov 24.PMID: 36424441 Free PMC article.

While the properties of individual cells are increasingly being deciphered using powerful single-cell sequencing technologies, understanding their spatial organization and temporal evolution remains a major challenge. Here, we present Image-seq, a technology that provides …LEARN MORE

 

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December, 2022

Comprehensive visualization of cell-cell interactions in single-cell and spatial transcriptomics with NICHES.

Raredon MSB, Yang J, Kothapalli N, Lewis W, Kaminski N, Niklason LE, Kluger Y.Bioinformatics. 2022 Dec 2:btac775. doi: 10.1093/bioinformatics/btac775. Online ahead of print.PMID: 36458905
RESULTS: NICHES allows embedding of ligand-receptor signal proxies to visualize heterogeneous signaling archetypes within cell clusters, between cell clusters, and across experimental conditions. When applied to spatial transcriptomic data, NICHES can be used to ref …LEARN MORE 
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November, 2022

A spatiotemporally resolved single-cell atlas of the Plasmodium liver stage.

Afriat A, Zuzarte-Luís V, Bahar Halpern K, Buchauer L, Marques S, Chora ÂF, Lahree A, Amit I, Mota MM, Itzkovitz S.Nature. 2022 Nov;611(7936):563-569. doi: 10.1038/s41586-022-05406-5. Epub 2022 Nov 9.PMID: 36352220

Abstract: Malaria infection involves an obligatory, yet clinically silent liver stage<sup>1,2</sup>. Hepatocytes operate in repeating units termed lobules, exhibiting heterogeneous gene expression patterns along the lobule axis<sup>3</sup>, but the effects of hepatocyte zonation on parasite development at the molecular level remain unknown. Here we combine single-cell RNA sequencing<sup>4</sup> and single-molecule transcript imaging<sup>5</sup> to characterize the host and parasite temporal expression programmes….LEARN MORE

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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 

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April 1, 2022

Research Techniques Made Simple: Spatial Transcriptomics

Arianna J Piñeiro 1, Aubrey E Houser 1, Andrew 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. 

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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. 

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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.
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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.

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November 14, 2021

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

Abstract
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.

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October 29, 2021

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

Abstract
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

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Member publications – coming soon