An atlas of transcribed enhancers across helper T cell diversity for decoding human diseases

Oguchi et al. introduced a technique to investigate the precise position of the RNA 5′-ends in single cells, enabling simultaneous profiling of gene expression and enhancer activity.

Key findings
✔ Rare and uncharacterized cell types, including GPR25-expressing regulatory T cells
✔ 62,803 bidirectionally transcribed candidate enhancers (btcEnhs) and 218,508 accessible chromatin regions active across diverse CD4+ T cells
✔ Higher cell type specificity for RNA transcription than for chromatin accessibility both at promoters and enhancers
✔ The heritability of immune-mediated diseases enriched more in btcEnhs than in open chromatin regions
✔ Interpretation of genetic variants associated with a range of immune-mediated diseases
✔ Frequent activity of btcEnhs harboring disease SNPs in specific subsets of CD4+ T cells
✔ Fine-scale chromatin contact maps derived from ultradeep Micro-C data.

#singlecellnews

Unveiling major histocompatibility complex-mediated pan-cancer immune features

Feng et al. integrated scRNA-seq, bulk RNA-seq, and spatial transcriptomic analyses to unveil pan-cancer immune characteristics governed by the MHC transcriptional feature (MHC.sig).

Key findings
✅ MHC.sig as a potential universal pan-cancer marker for anti-tumor immunity
✅ Potential genes for immune therapy synergy
✅ Predictive efficacy for responsiveness of immune checkpoint inhibitors across diverse datasets and cancer types
✅ Interactions between C1QC+macrophages and malignant cells, providing insights into potential therapeutic agents and their sensitivity characteristics. #singlecellnews

Mitochondrial genetics through the lens of single-cell multi-omics

Nitsch et al. highlight emerging strategies designed to capture mitochondrial genetic variation across individual cells for lineage tracing and studying mitochondrial genetics in primary human cells and clinical specimens.

Key points
?Recent advances surrounding single-cell mitochondrial genome sequencing
?Integration with functional genomic readouts
?Somatic mitochondrial DNA mutations as clonal markers of cellular population dynamics in complex human tissues
?Opportunities of single-cell whole mitochondrial genome sequencing in mitochondrial genetics and deciphering cellular heterogeneity and disease.

#singlecellnews

A dataset for spatial transcriptomics and histology image analysis

Jaume et al. introduced HEST-1k, a collection of 1,108 spatial transcriptomic profiles, each linked to a hematoxylin and eosin-stained whole slide image and metadata.

Key points
☑ 131 public and internal cohorts encompassing 25 organs, two species (Homo Sapiens and Mus Musculus), and 320 cancer samples from 25 cancer types
☑ The identification of 1.5 million expression-morphology pairs and 60 million nuclei
☑ Testing on benchmarking foundation models for histopathology, biomarker identification, and multimodal representation learning
☑ Available at https://github.com/mahmoodlab/hest

#singlecellnews

*⚡ASCA unites 237 members from 43 countries*

Our community on Telegram includes over 1300 members, and we have about 3400 subscribers on LinkedIn.

We encourage researchers to contact each other and perform joint projects focusing on the application of single-cell techniques.

We believe that such a dynamic field as single-cell analysis allows finding new positions, colleagues, and friends. We invite you to plunge into the amazing world of single-cell science together!

?ASCA membership is free.

➡Join ASCA: https://ascanet.org/registration/

#ASCAinfo

Immune system compartmentalization under symbiosis in the stony coral Oculina arbuscula

Valadez-Ingersoll et al. used a multiomic approach to characterize symbiotic states of the facultatively symbiotic coral Oculina arbuscula by generating genotype-controlled fragments of symbiotic and aposymbiotic tissue.

Key findings
?No difference in bacterial communities between symbiotic states
?Differential abundance of proteins related to immunity, consistent with immune suppression during symbiosis
?Diverse cell clusters within six cell types across symbiotic states
?High expression of nitrogen cycling and sugar transport genes in the gastrodermal cell cluster containing algal-hosting cells from symbiotic tissue
?Low expression of genes involved in immune regulation in gastrodermal cells from symbiotic tissue.

#singlecellnews

Structure and dynamics of enterovirus genotype networks

Dabilla and Dolan established SEARCHLIGHT, a facile method to recover viral genotypes from infected samples by leveraging existing single-cell platforms to partition individual infected cells.

Key findings
✔Capturing and assembling hundreds of complete, and near-complete, viral haplotypes from individual infected cells
✔Link of host cell transcriptional phenotypes to the genetic structures underlying virus adaptation
✔The common evolutionary dynamics of enterovirus populations
✔Illustrating how viral populations reach through mutational “tunnels” to span evolutionary landscapes and maintain connection with multiple adaptive genotypes simultaneously. #singlecellnews

Human transcription factor combinations mapped by footprinting with deaminase

He et al. reported a novel technique to measure human transcription factors (TFs)' binding sites genome-wide with single-base resolution by footprinting with deaminase (FOODIE).

Key points
?Requiring only thousands of cells, significantly fewer than required for ChIP-seq or DNase-seq
?Demonstrating site-specific TF binding fractions and the cooperativity among adjacent TFs
?Cell-type-specific TF footprinting in heterogeneous tissues. #singlecellnews

Dear colleagues!

We kindly inform you that 8 days left till the registration for the ASCA Workshop 2024 (26-30 August, Tomsk) closes.

Participation: free (no registration fee).

➡️ https://ascanet.org/events/registration/?ID=398

#ASCAinfo

Integrated platform for multiscale molecular imaging and phenotyping of the human brain

Park et al. developed a platform that simultaneously extracts spatial, molecular, morphological, and connectivity information of individual cells from the same human brain.

Key points of the platform:
✅ A vibrating microtome for ultraprecision slicing of large-scale tissues without losing cellular connectivity (MEGAtome)
✅ A polymer hydrogel-based tissue processing technology for multiplexed multiscale imaging of human organ–scale tissues (mELAST)
✅ A computational pipeline for reconstructing three-dimensional connectivity across multiple brain slabs (UNSLICE)
✅ Analyzing human Alzheimer’s disease pathology at multiple scales and demonstrating scalable neural connectivity mapping in the human brain.

#singlecellnews