Single Cell Spatial Analysis Program

Multi-omic single-cell velocity models epigenome-transcriptome interactions and improves cell fate prediction

Chen Li, Maria C Virgilio, Kathleen L Collins, Joshua D Welch

Abstract

Multi-omic single-cell datasets, in which multiple molecular modalities are profiled within the same cell, offer an opportunity to understand the temporal relationship between epigenome and transcriptome. To realize this potential, we developed MultiVelo, a differential equation model of gene expression that extends the RNA velocity framework to incorporate epigenomic data……

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Recording of cellular physiological histories along optically readable self-assembling protein chains.

Linghu C, An B, Shpokayte M, Celiker OT, Shmoel N, Zhang R, Zhang C, Park D, Park WM, Ramirez S, Boyden ES.Nat Biotechnol. 2023 Jan 2. doi: 10.1038/s41587-022-01586-7. Online ahead of print.PMID: 36593405

Abstract

Observing cellular physiological histories is key to understanding normal and disease-related processes. Here we describe expression recording islands-a fully genetically encoded approach that enables both continual digital recording of biological information within cells and subsequent high-throughput readout in fixed cells. Learn more

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SpaceX: gene co-expression network estimation for spatial transcriptomics

Acharyya S, Zhou X, Baladandayuthapani V.Bioinformatics. 2022 Nov 15;38(22):5033-5041. doi: 10.1093/bioinformatics/btac645.PMID: 36179087

Abstract

Motivation: The analysis of spatially resolved transcriptome enables the understanding of the spatial interactions between the cellular environment and transcriptional regulation. In particular, the characterization of the gene-gene co-expression at distinct spatial locations or cell types in the tissue enables delineation of spatial co-regulatory patterns as opposed to standard differential single gene analyses…….See publication for more….

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Integrated Workflow for the Label-Free Isolation and Genomic Analysis of Single Circulating Tumor Cells in Pancreatic Cancer

Rupp B, Owen S, Ball H, Smith KJ, Gunchick V, Keller ET, Sahai V, Nagrath S.
Abstract: As pancreatic cancer is the third deadliest cancer in the U.S., the ability to study genetic alterations is necessary to provide further insight into potentially targetable regions for cancer treatment. Circulating tumor cells (CTCs) represent an especially aggressive subset of cancer cells……

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Spatially aware dimension reduction for spatial transcriptomics.

Shang L, Zhou X.Nat Commun. 2022 Nov 23;13(1):7203. doi: 10.1038/s41467-022-34879-1.PMID: 36418351 Free PMC article.

Abstract

Spatial transcriptomics are a collection of genomic technologies that have enabled transcriptomic profiling on tissues with spatial localization information. Analyzing spatial transcriptomic data is computationally challenging, as the data collected from various spatial transcriptomic technologies are often noisy and display substantial spatial correlation across tissue locations. ….learn more

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March 2023

Multi-omic single-cell velocity models epigenome-transcriptome interactions and improves cell fate prediction.

Li C, Virgilio MC, Collins KL, Welch JD.Nat Biotechnol. 2023 Mar;41(3):387-398. doi: 10.1038/s41587-022-01476-y. Epub 2022 Oct 13.PMID: 36229609
Multi-omic single–cell datasets, in which multiple molecular modalities are profiled within the same cell, offer an opportunity to understand the temporal relationship between epigenome and transcriptome. …Application to multi-omic single–cell …
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February 2023

Subclonal evolution and expansion of spatially distinct THY1-positive cells is associated with recurrence in glioblastoma.

Al-Holou WN, Wang H, Ravikumar V, Shankar S, Oneka M, Fehmi Z, Verhaak RG, Kim H, Pratt D, Camelo-Piragua S, Speers C, Wahl DR, Hollon T, Sagher O, Heth JA, Muraszko KM, Lawrence TS, de Carvalho AC, Mikkelsen T, Rao A, Rehemtulla A.Neoplasia. 2023 Feb;36:100872. doi: 10.1016/j.neo.2022.100872. Epub 2023 Jan 6.PMID: 36621024 Free PMC article.
These specimens were evaluated for treatment response and to identify gene expression pathways driving treatment resistance. Findings were clinically validated using spatial transcriptomics of human GBMs. RESULTS: These studies reveal in replicate cohorts, a gene ex …
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February 2023

Bone marrow mesenchymal stem cells induce metabolic plasticity in estrogen receptor-positive breast cancer.

Buschhaus JM, Rajendran S, Chen S, Wharram BL, Bevoor AS, Cutter AC, Humphries BA, Robison TH, Farfel AP, Luker GD.Mol Cancer Res. 2023 Feb 3:MCR-22-0451. doi: 10.1158/1541-7786.MCR-22-0451. Online ahead of print.PMID: 36735350
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January 2023

Two-sample test with g-modeling and its applications.

Zhai J, Jiang H.Stat Med. 2023 Jan 15;42(1):89-104. doi: 10.1002/sim.9603. Epub 2022 Nov 22.PMID: 36412978
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January 2023

SGLT2 inhibitors mitigate kidney tubular metabolic and mTORC1 perturbations in youth onset type 2 diabetes.

Schaub JA, AlAkwaa FM, McCown PJ, Naik AS, Nair V, Eddy S, Menon R, Otto EA, Demeke D, Hartman J, Fermin D, O’Connor C, Subramanian L, Bitzer M, Harned R, Ladd P, Pyle L, Pennathur S, Inoki K, Hodgin JB, Brosius FC, Nelson RG, Kretzler M, Bjornstad P.J Clin Invest. 2023 Jan 13:e164486. doi: 10.1172/JCI164486. Online ahead of print.PMID: 36637914 Free article.
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January 2023

Subclonal evolution and expansion of spatially distinct THY1-positive cells is associated with recurrence in glioblastoma.

Al-Holou WN, Wang H, Ravikumar V, Shankar S, Oneka M, Fehmi Z, Verhaak RG, Kim H, Pratt D, Camelo-Piragua S, Speers C, Wahl DR, Hollon T, Sagher O, Heth JA, Muraszko KM, Lawrence TS, de Carvalho AC, Mikkelsen T, Rao A, Rehemtulla A.Neoplasia. 2023 Feb;36:100872. doi: 10.1016/j.neo.2022.100872. Epub 2023 Jan 6.PMID: 36621024 Free PMC article.
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January 2023

Recording of cellular physiological histories along optically readable self-assembling protein chains.

Linghu C, An B, Shpokayte M, Celiker OT, Shmoel N, Zhang R, Zhang C, Park D, Park WM, Ramirez S, Boyden ES.Nat Biotechnol. 2023 Jan 2. doi: 10.1038/s41587-022-01586-7. Online ahead of print.PMID: 36593405
Link

January 2023

Single-cell transcriptomics reveals a mechanosensitive injury signaling pathway in early diabetic nephropathy.

Liu S, Zhao Y, Lu S, Zhang T, Lindenmeyer MT, Nair V, Gies SE, Wu G, Nelson RG, Czogalla J, Aypek H, Zielinski S, Liao Z, Schaper M, Fermin D, Cohen CD, Delic D, Krebs CF, Grahammer F, Wiech T, Kretzler M, Meyer-Schwesinger C, Bonn S, Huber TB.Genome Med. 2023 Jan 10;15(1):2. doi: 10.1186/s13073-022-01145-4.PMID: 36627643 Free PMC article.
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January 2023

WNT signaling in the tumor microenvironment promotes immunosuppression in murine pancreatic cancer.

Du W, Menjivar RE, Donahue KL, Kadiyala P, Velez-Delgado A, Brown KL, Watkoske HR, He X, Carpenter ES, Angeles CV, Zhang Y, Pasca di Magliano M.J Exp Med. 2023 Jan 2;220(1):e20220503. doi: 10.1084/jem.20220503. Epub 2022 Oct 14.PMID: 36239683 
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December 2022

Computational modeling implicates protein scaffolding in p38 regulation of Akt.

Kinnunen PC, Luker GD, Luker KE, Linderman JJ.J Theor Biol. 2022 Dec 21;555:111294. doi: 10.1016/j.jtbi.2022.111294. Epub 2022 Oct 1.PMID: 36195198
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December 2022

HIF1α lactylation enhances KIAA1199 transcription to promote angiogenesis and vasculogenic mimicry in prostate cancer.

Luo Y, Yang Z, Yu Y, Zhang P.Int J Biol Macromol. 2022 Dec 1;222(Pt B):2225-2243. doi: 10.1016/j.ijbiomac.2022.10.014. Epub 2022 Oct 6.PMID: 36209908
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December 2022

Single-cell RNA-sequencing identifies anti-cancer immune phenotypes in the early lung metastatic niche during breast cancer.

Orbach SM, Brooks MD, Zhang Y, Campit SE, Bushnell GG, Decker JT, Rebernick RJ, Chandrasekaran S, Wicha MS, Jeruss JS, Shea LD.Clin Exp Metastasis. 2022 Dec;39(6):865-881. doi: 10.1007/s10585-022-10185-4. Epub 2022 Aug 24.PMID: 36002598
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November 2022

Spatially aware dimension reduction for spatial transcriptomics.

Shang L, Zhou X.Nat Commun. 2022 Nov 23;13(1):7203. doi: 10.1038/s41467-022-34879-1.PMID: 36418351 Free PMC article.
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November 2022

The fate of early perichondrial cells in developing bones.

Matsushita Y, Chu AKY, Tsutsumi-Arai C, Orikasa S, Nagata M, Wong SY, Welch JD, Ono W, Ono N.Nat Commun. 2022 Nov 28;13(1):7319. doi: 10.1038/s41467-022-34804-6.PMID: 36443296 Free PMC article.
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September 2022

Keap1 moderates the transcription of virus induced genes through G9a-GLPand NFκB p50 recruitment.

Burns VE, Kerppola TK.Immunology. 2022 Sep;167(1):105-121. doi: 10.1111/imm.13527. Epub 2022 Jul 7.PMID: 35751391
 
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August 2022

BASS: multi-scale and multi-sample analysis enables accurate cell type clustering and spatial domain detection in spatial transcriptomic studies.

Li Z, Zhou X.
Genome Biol. 2022 Aug 4;23(1):168. doi: 10.1186/s13059-022-02734-7.

PMID: 35927760

 
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August 2022

Dissecting the Heterogeneity of Human Thoracic Aortic Aneurysms Using Single-Cell Transcriptomics.

Mizrak D, Feng H, Yang B.
Arterioscler Thromb Vasc Biol. 2022 Aug;42(8):919-930. doi: 10.1161/ATVBAHA.122.317484. Epub 2022 Jun 16.

PMID: 35708028 Review.

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July 2022

Integrated Workflow for the Label-Free Isolation and Genomic Analysis of Single Circulating Tumor Cells in Pancreatic Cancer.

Rupp B, Owen S, Ball H, Smith KJ, Gunchick V, Keller ET, Sahai V, Nagrath S.
Int J Mol Sci. 2022 Jul 16;23(14):7852. doi: 10.3390/ijms23147852.

PMID: 35887203 Free PMC article.

 
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July 2022

Spatial Transcriptomics as a Novel Approach to Redefine Electrical Stimulation Safety.

Whitsitt QA, Koo B, Celik ME, Evans BM, Weiland JD, Purcell EK.
Front Neurosci. 2022 Jul 19;16:937923. doi: 10.3389/fnins.2022.937923. eCollection 2022.

PMID: 35928007 Free PMC article.

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July 2022

Statistical analysis of spatially resolved transcriptomic data by incorporating multiomics auxiliary information

Li Y, Zhou X, Cao H.
Genetics. 2022 Jul 30;221(4):iyac095. doi: 10.1093/genetics/iyac095.

PMID: 35731210

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July 2022

Joint dimension reduction and clustering analysis of single-cell RNA-seq and spatial transcriptomics data.

Liu W, Liao X, Yang Y, Lin H, Yeong J, Zhou X, Shi X, Liu J.
Nucleic Acids Res. 2022 Jul 8;50(12):e72. doi: 10.1093/nar/gkac219.

PMID: 35349708 Free PMC article.

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September 2021

Virus Infection Induces Keap1 Binding to Cytokine Genes, Which Recruits NF-κB p50 and G9a-GLP and Represses Cytokine Transcriptition.

Burns VE, Kerppola TK.J Immunol. 2021 Sep 1;207(5):1437-1447. doi: 10.4049/jimmunol.2100355. Epub 2021 Aug 16.PMID: 34400522 Free PMC article.
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