Conundrums of Choice of 'Normal' Kidney Tissue for Single Cell Studies

Jain S.

The review discusses choices and challenges to be considered in each of the steps in planning omics experiments with a detailed discussion about strengths and weaknesses of various "healthy" tissue sources for omics and atlas studies.

Spatial epigenome-transcriptome co-profiling of mammalian tissues

Zhang D, Deng Y, Kukanja P, Agirre E, Bartosovic M, Dong M, Ma C, Ma S, Su G, Bao S, Liu Y, Xiao Y, Rosoklija GB, Dwork AJ, Mann JJ, Leong KW, Boldrini M, Wang L, Haeussler M, Raphael BJ, Kluger Y, Castelo-Branco G, Fan R.

Ten Years of Extracellular Matrix Proteomics: Accomplishments, Challenges, and Future Perspectives

Naba A.

Additional resources

• The Matrisome Project

The HRA Organ Gallery Affords Immersive Superpowers for Building and Exploring the Human Reference Atlas with Virtual Reality

Bueckle A, Qing C, Luley S, Kumar Y, Pandey N, Börner K.

This paper introduces ongoing research and development of the Human Reference Atlas (HRA) Organ Gallery, a virtual reality application offering an immersive view on the organs and tissue blocks of the HRA, and includes a description of use cases and current as well as planned features.

Additional resources

• 3D models of the HRA v1.4
• Tissue blocks are served via the CCF

Senescent cell population with ZEB1 transcription factor as its main regulator promotes osteoarthritis in cartilage and meniscus

Swahn H, Li K, Duffy T, Olmer M, D'Lima DD, Mondala TS, Natarajan P, Head SR, Lotz MK.

We present a detailed single cell map of healthy human cartilage and meniscus describing markers, phenotypes, differentiation, regulation, and organization of cells, serving as reference for the analysis of joint diseases, such as osteoarthritis.

Additional resources

• Datasets in the GEO repository

Super-resolution SRS microscopy with A-PoD

Jang H, Li Y, Fung AA, Bagheri P, Hoang K, Skowronska-Krawczyk D, Chen X, Wu JY, Bintu B, Shi L.

We present software tools for achieving super resolution (~60nm resolution) multiplex imaging of human organ tissues and cells, mapping spatial heterogeneity of metabolites and macromolecules relatively large scale tissue area to small cellular organelles.

Additional resources

• All data are available within the paper and and its supplementary information.

Computational Pathology Fusing Spatial Technologies

Border S, Lucarelli N, Eadon MT, El-Achkar TM, Jain S, Sarder P.

Perspective on spatial technologies in biology, and fusing/ correlating such data using computational AI for inference.

Spatially Resolved Top-Down Proteomics of Tissue Sections Based on a Microfluidic Nanodroplet Sample Preparation Platform

Liao YC, Fulcher JM, Degnan DJ, Williams SM, Bramer LM, Veličković D, Zemaitis KJ, Veličković M, Sontag RL, Moore RJ, Paša-Tolić L, Zhu Y, Zhou M.

We highlight an integrated informatics workflow for regiospecific quantitation of hundreds of proteofroms from small dissected portions of tissue with nanodroplet processing in one pot for trace samples by top-down proteomics (nanoPOTS-TDP),

Additional resources

• Dataset

193 nm Ultraviolet Photodissociation for the Characterization of Singly Charged Proteoforms Generated by MALDI

Zemaitis KJ, Zhou M, Kew W, Paša-Tolić L.

We outline the implementation of ultraviolet photodissociation (UVPD) for the confident characterization of proteoforms desorbed and ionized by MALDI for tandem mass spectrometry.

Additional resources

• Data files

A streamlined tandem tip-based workflow for sensitive nanoscale phosphoproteomics

Tsai CF, Wang YT, Hsu CC, Kitata RB, Chu RK, Velickovic M, Zhao R, Williams SM, Chrisler WB, Jorgensen ML, Moore RJ, Zhu Y, Rodland KD, Smith RD, Wasserfall CH, Shi T, Liu T.

A streamlined nanoscale phosphoproteomics method for robust, sensitive, spatially resolved phosphoproteomics.

Real-time spatial registration for 3D human atlas

Chen L, Teng D, Zhu T, Kong J, Herr BW, Bueckle A, Börner K, Wang F.

Enhanced Spatial Mapping of Histone Proteoforms in Human Kidney Through MALDI-MSI by High-Field UHMR-Orbitrap Detection

Zemaitis KJ, Veličković D, Kew W, Fort KL, Reinhardt-Szyba M, Pamreddy A, Ding Y, Kaushik D, Sharma K, Makarov AA, Zhou M, Paša-Tolić L.

We demonstrate the first use of a custom ultrahigh mass range (UHMR) Orbitrap for the characterization of intact proteoforms up to 16.5 kDa directly from tissue with high mass resolving power and near cellular spatial resolution (20 μm) at high-throughput.

Additional resources

• All supplemental info is linked to in the paper.

Spatial profiling of chromatin accessibility in mouse and human tissues

Deng Y, Bartosovic M, Ma S, Zhang D, Kukanja P, Xiao Y, Su G, Liu Y, Qin X, Rosoklija GB, Dwork AJ, Mann JJ, Xu ML, Halene S, Craft JE, Leong KW, Boldrini M, Castelo-Branco G, Fan R.

We present spatially resolved chromatin accessibility profiling of tissue sections via next-generation sequencing by combining in situ ATAC-seq chemistry and microfluidic deterministic barcoding.

Additional resources

• Datasets in the GEO repository

Highly multiplexed, label-free proteoform imaging of tissues by individual ion mass spectrometry

Su P, McGee JP, Durbin KR, Hollas MAR, Yang M, Neumann EK, Allen JL, Drown BS, Butun FA, Greer JB, Early BP, Fellers RT, Spraggins JM, Laskin J, Camarillo JM, Kafader JO, Kelleher NL.

Additional resources

• Supplementary materials
• Tables S1 to S4

Integrated single cell sequencing and histopathological analyses reveal diverse injury and repair responses in a participant with acute kidney injury: A clinical-molecular-pathologic correlation.

Menon R, Bomback AS, Lake BB, Stutzke C, Grewenow SM, Menez S, D'Agati VD, Jain S.

We applied single cell and single nucleus RNAseq analysis and clinicopathological correlations using a biopsy from a single patient to delineate molecular features of acute kidney injury and insights into recovery.

Additional resources

• Supplemental materials
• Metadata file for single-cell RNA sequencing (scRNAseq) from tissue acquisition to sequencing and analysis
• Metadata file for single-nucleus RNA sequencing (snRNA-seq) from tissue acquisition to sequencing and analysis

Viv: multiscale visualization of high-resolution multiplexed bioimaging data on the web

Manz T, Gold I, Patterson NH, McCallum C, Keller MS, Herr BW 2nd, Börner K, Spraggins JM, Gehlenborg N.

Additional resources

• Viv API

PHGDH expression increases with progression of Alzheimer’s disease pathology and symptoms

Chen X, Calandrelli R, Girardini J, Yan Z, Tan Z, Xu X, Hiniker A, Zhong S.

Additional resources

• GEO profiles
• Gene
• Gene (GeneRIF)
• MedGen
• Nucleotide
• Nucleotide
• Nucleotide (RefSeq)
• Nucleotide (RefSeq)
• Nucleotide (weighted)
• Protein
• Protein (RefSeq)

Membrane marker selection for segmenting single cell spatial proteomics data

Dayao MT, Brusko M, Wasserfall C, Bar-Joseph Z.

Additional resources

• HBM869.VZJM.366
• HBM432.LLCF.677
• HBM588.FHDS.363
• HBM279.TQRS.775
• HBM337.FSXL.564
• HBM376.QCCJ.269
• HBM754.WKLP.262
• HBM556.KSFB.592
• HBM288.XSQZ.633

Mapping the Proteoform Landscape of Five Human Tissues

Drown BS, Jooß K, Melani RD, Lloyd-Jones C, Camarillo JM, Kelleher NL.

Additional resources

• Raw files, mzIdentMl, and tdReport files in Massive
• Link to TDViewer freeware from Northwestern University to view search results in tdReport format

Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging

Hickey JW, Neumann EK, Radtke AJ, Camarillo JM, Beuschel RT, Albanese A, McDonough E, Hatler J, Wiblin AE, Fisher J, Croteau J, Small EC, Sood A, Caprioli RM, Angelo RM, Nolan GP, Chung K, Hewitt SM, Germain RN, Spraggins JM, Lundberg E, Snyder MP, Kelleher NL, Saka SK.

We provide essential resources and key considerations for obtaining robust and reproducible multiplexed imaging data for antibody-based approaches.

Additional resources

• NCI CPTC Antibody Characterization Program