A mouse brain stereotaxic topographic atlas with isotropic 1-μm resolution.

Multi-omics studies, represented by connectomes and spatial transcriptomes, have entered the era of single-cell resolution, necessitating a reference brain atlas with spatial localization capability at the single-cell level. However, such atlases are unavailable. Here we present a whole mouse brain dataset of Nissl-based cytoarchitecture with isotropic 1-μm resolution, achieved through continuous micro-optical sectioning tomography.

SlicesMapi: An Interactive Three-Dimensional Registration Method for Serial Histological Brain Slices.

Brain slicing is a commonly used technique in brain science research. In order to study the spatial distribution of labeled information, such as specific types of neurons and neuronal circuits, it is necessary to register the brain slice images to the 3D standard brain space defined by the reference atlas. However, the registration of 2D brain slice images to a 3D reference brain atlas still faces challenges in terms of accuracy, computational throughput, and applicability.

Electroacupuncture Ameliorates Knee Osteoarthritis By Rebalancing T Cell Homeostasis as Revealed By Immune Repertoire (IR) Sequencing.

Background: In this study, we used immune repertoire (IR) sequencing technology to profile the diversity of peripheral blood T cell receptors and used transcriptomics to profile the gene expression of peripheral blood neutrophil mRNA in patients with mild-moderate knee osteoarthritis (KOA) before and after electroacupuncture (EA) treatment.

Methods: An 8-week intervention with EA was performed on 3 subjects with KOA. IR sequencing of complementarity determining region 3 (CDR3) was performed using RNA extracted from peripheral blood T cells of KOA subjects prior to and at the end of the intervention, as well as healthy volunteers (controls) who matched the subjects in sex and age.

CASCC: a co-expression-assisted single-cell RNA-seq data clustering method.

Summary: Existing clustering methods for characterizing cell populations from single-cell RNA sequencing are constrained by several limitations stemming from the fact that clusters often cannot be homogeneous, particularly for transitioning populations. On the other hand, dominant cell populations within samples can be identified independently by their strong gene co-expression signatures using methods unrelated to partitioning. Here, we introduce a clustering method, CASCC (co-expression-assisted single-cell clustering), designed to improve biological accuracy using gene co-expression features identified using an unsupervised adaptive attractor algorithm.

The fibro-adipogenic progenitor APOD+DCN+LUM+ cell population in aggressive carcinomas.

We identified a progenitor cell population highly enriched in samples from invasive and chemo-resistant carcinomas, characterized by a well-defined multigene signature including APOD, DCN, and LUM. This cell population has previously been labeled as consisting of inflammatory cancer-associated fibroblasts (iCAFs). The same signature characterizes naturally occurring fibro-adipogenic progenitors (FAPs) as well as stromal cells abundant in normal adipose tissue.

Prognostic Factors in Philadelphia Chromosome-Positive Acute Myeloid Leukemia Using Fluorescence in Situ Hybridization.

Background: Philadelphia chromosome-positive acute myeloid leukemia (Ph+ AML) is a rare leukemia subtype first classified by the World Health Organization in 2016. The incidence of Ph+ AML is approximately 0.5 - 3%, and its prognosis is poor.

Bioinformatics Analysis of Neuroblastoma miRNA Based on GEO Data.

Objective: To analyze the changes in downstream genes, signaling pathways, and proteins based on the difference of microRNA (miRNA) expression in neuroblastoma (NB).

Methods: GSE128004 second-generation sequencing expression data were downloaded from GEO, and Limma package of R language was used to analyze differential expression, and a volcano map and heat map were drawn; the target genes corresponding to the differential miRNA were found using the miWalk web tool, and GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) were performed. The key genes were identified and verified in the TCGA database.

Single-cell analysis reveals the pan-cancer invasiveness-associated transition of adipose-derived stromal cells into COL11A1-expressing cancer-associated fibroblasts.

During the last ten years, many research results have been referring to a particular type of cancer-associated fibroblasts associated with poor prognosis, invasiveness, metastasis and resistance to therapy in multiple cancer types, characterized by a gene expression signature with prominent presence of genes COL11A1, THBS2 and INHBA. Identifying the underlying biological mechanisms responsible for their creation may facilitate the discovery of targets for potential pan-cancer therapeutics. Using a novel computational approach for single-cell gene expression data analysis identifying the dominant cell populations in a sequence of samples from patients at various stages, we conclude that these fibroblasts are produced by a pan-cancer cellular transition originating from a particular type of adipose-derived stromal cells naturally present in the stromal vascular fraction of normal adipose tissue, having a characteristic gene expression signature.

A novel ferroptosis-related gene signature for prognostic prediction of patients with lung adenocarcinoma.

Background: Lung adenocarcinoma (LUAD) is a heterogeneous disease characterized by high mortality and poor prognosis. Ferroptosis, a newly discovered iron-dependent type of cell death, has been found to play a crucial role in the development of cancers. However, little is known about the prognostic value of ferroptosis-related genes (FRGs) in LUAD.

Identification of prognostic alternative splicing events related to the immune microenvironment of hepatocellular carcinoma.

Background: Hepatocellular carcinoma (HCC) is one of the most common malignant tumors in the world, and its 5-year survival rate is less than 20%, despite various treatments being available. Increasing evidence indicates that alternative splicing (AS) plays a nonnegligible role in the formation and development of the tumor microenvironment (TME). However, the comprehensive analysis of the impact on prognostic AS events on immune-related perspectives in HCC is lacking but urgently needed.