A biomarker framework for liver aging: the Aging Biomarker Consortium consensus statement.

In human aging, liver aging per se not only increases susceptibility to liver diseases but also increases vulnerability of other organs given its central role in regulating metabolism. Total liver function tends to be well maintained in the healthy elderly, so liver aging is generally difficult to identify early. In response to this critical challenge, the Aging Biomarker Consortium of China has formulated an expert consensus on biomarkers of liver aging by synthesizing the latest scientific literature, comprising insights from both scientists and clinicians.

Global insights into aging: a multidisciplinary approach to understanding and addressing age-related challenges.

Aging has ascended to the forefront of scientific exploration, demanding a concerted global focus. The 2024 China Aging Science Conference and International Conference on Aging Biology hosted a panel discussion that brought international experts to delve into the complexities of aging research. The discussion underscores the imperative need for a multidisciplinary approach, integrating reductionist and holistic perspectives to unravel the molecular and epigenetic underpinnings of the aging process.

Single-cell transcriptomics identify a novel macrophage population associated with bone invasion in pituitary neuroendocrine tumors.

Background: Bone-invasive Pituitary Neuroendocrine Tumors (BI PitNETs) epitomize an aggressive subtype of pituitary tumors characterized by bone invasion, culminating in extensive skull base bone destruction and fragmentation. This infiltration poses a significant surgical risk due to potential damage to vital nerves and arteries. However, the mechanisms underlying bone invasion caused by PitNETs remain elusive, and effective interventions for PitNET-induced bone invasion are lacking in clinical practice.

Benzene-induced hematotoxicity enhances the self-renewal ability of HSPCs in Mll-Af9 mice.

Patients with benzene-induced leukemia undergo a continuous transformation from myelosuppression to malignant proliferation. However, the underlying mechanisms in this process remain unknown. Our previous studies have shown that the pathways involved in self-renewal capacity of bone marrow (BM) cells in Mll-Af9 mice exposed to benzene for life are significantly activated after severe blood toxicity.

Insights and Interventions in Age-Associated Inflammation.

Aging is a systemic, complex, and heterogeneous process characterized by a progressive decline in physiological functions, rendering it a major risk factor for various chronic diseases. Chronic inflammation has emerged as both a hallmark and a driver in this complicated process. This persistent inflammatory state arises from a spectrum of stimuli, ranging from external pathogens to internal cellular remnants, to metabolic dysregulation, and to chronic stress.

HapNetworkView: a tool for haplotype network exploration and visualization.

Background: Haplotype networks are useful for investigating the genealogical relationships among haplotypes and have been extensively used in molecular evolution and population genetic studies. However, existing tools for visualizing haplotype networks lack comprehensive functionalities for data exploration and layout adjustments. Therefore, there is a need for a useful tool capable of constructing and visualizing haplotype networks, facilitating the exploration of data, particularly with datasets with large sample sizes.

UDA-seq: universal droplet microfluidics-based combinatorial indexing for massive-scale multimodal single-cell sequencing.

The use of single-cell combinatorial indexing sequencing via droplet microfluidics presents an attractive approach for balancing cost, scalability, robustness and accessibility. However, existing methods often require tailored protocols for individual modalities, limiting their automation potential and clinical applicability. To address this, we introduce UDA-seq, a universal workflow that integrates a post-indexing step to enhance throughput and systematically adapt existing droplet-based single-cell multimodal methods.

Prognostic Significance of Computed Tomography-Derived Fractional Flow Reserve for Long-Term Outcomes in Individuals With Coronary Artery Disease.

Background: Data on the predictive value of coronary computed tomography angiography-derived fractional flow reserve (CT-FFR) for long-term outcomes are limited.

Methods And Results: A retrospective pooled analysis of individual patient data was performed. Deep-learning-based CT-FFR was calculated.

Mapping the chromothripsis landscape in urothelial carcinoma unravels great intratumoral and intertumoral heterogeneity.

Chromothripsis, a hallmark of cancer, is characterized by extensive and localized DNA rearrangements involving one or a few chromosomes. However, its genome-wide frequency and characteristics in urothelial carcinoma (UC) remain largely unknown. Here, by analyzing single-regional and multi-regional whole-genome sequencing (WGS), we present the chromothripsis blueprint in 488 UC patients.

From multi-omics to predictive biomarker: AI in tumor microenvironment.

In recent years, tumors have emerged as a major global health threat. An increasing number of studies indicate that the production, development, metastasis, and elimination of tumor cells are closely related to the tumor microenvironment (TME). Advances in artificial intelligence (AI) algorithms, particularly in large language models, have rapidly propelled research in the medical field.

Whole-genome sequencing identifies novel loci for keratoconus and facilitates risk stratification in a Han Chinese population.

Background: Keratoconus (KC) is a prevalent corneal condition with a modest genetic basis. Recent studies have reported significant genetic associations in multi-ethnic cohorts. However, the situation in the Chinese population remains unknown.

Metagenome-assembled genome of from urban bats in China.

We conducted metagenomic sequencing on a stool sample collected from urban-dwelling and obtained a metagenome-assembled genome of . Phylogenetic analysis revealed that this strain is closely related to the one isolated from dogs, forming a distinct clade separate from the reference genome.

NSUN2 lactylation drives cancer cell resistance to ferroptosis through enhancing GCLC-dependent glutathione synthesis.

Lactate-mediated lactylation on target proteins is recently identified as the novel posttranslational modification with profound biological functions. RNA 5-methylcytosine (mC) modification possesses dynamic and reversible nature, suggesting that activity of its methyltransferase NSUN2 is actively regulated. However, how NSUN2 activity is response to acidic condition in tumor microenvironment and then regulates cancer cell survival remain to be clarified.

Footprint-C reveals transcription factor modes in local clusters and long-range chromatin interactions.

The proximity ligation-based Hi-C and derivative methods are the mainstream tools to study genome-wide chromatin interactions. These methods often fragment the genome using enzymes functionally irrelevant to the interactions per se, restraining the efficiency in identifying structural features and the underlying regulatory elements. Here we present Footprint-C, which yields high-resolution chromatin contact maps built upon intact and genuine footprints protected by transcription factor (TF) binding.

"The COVID-19 pandemic in BRICS: Milestones, interventions, and molecular epidemiology".

Brazil, Russia, India, China, and South Africa (BRICS) are a group of developing countries with shared economic, healthcare, and scientific interests. These countries navigate multiple syndemics, and the COVID-19 pandemic placed severe strain on already burdened BRICS' healthcare systems, hampering effective pandemic interventions. Genomic surveillance and molecular epidemiology remain indispensable tools for facilitating informed pandemic intervention.

scGraph2Vec: a deep generative model for gene embedding augmented by graph neural network and single-cell omics data.

Background: Exploring the cellular processes of genes from the aspects of biological networks is of great interest to understanding the properties of complex diseases and biological systems. Biological networks, such as protein-protein interaction networks and gene regulatory networks, provide insights into the molecular basis of cellular processes and often form functional clusters in different tissue and disease contexts.

Results: We present scGraph2Vec, a deep learning framework for generating informative gene embeddings.

USP33 Regulates DNA Damage Response and Carcinogenesis Through Deubiquitylating and Stabilising p53.

The de-ubiquitinase USP33 has been shown to possess either tumour-promoting or inhibitory effect on human cancer cells. However, all these findings are mainly based on in vitro cell culture models, and the in vivo evidence, which is more plausible to digest the functional role of USP33 in carcinogenic process, is still lacking. Here, we demonstrate that USP33 modulates DNA damage responses including cell cycle arrest and apoptosis induction through associating with p53.

New insights into the mechanisms of red blood cell enucleation: From basics to clinical applications.

Background: Red blood cell (RBC) enucleation is a crucial step in the process of erythropoiesis. By removing the nucleus, RBCs gain greater flexibility, enabling them to traverse narrow capillaries with ease, thereby enhancing the efficiency of oxygen and carbon dioxide transport. This transformation underscores the intricate balance between cellular structure and function essential for maintaining homeostasis.

Quantification of multi-pathway metabolites related to folate metabolism and application in natural population with MTHFR C677T polymorphism.

Folate, serving as a crucial micronutrient, plays an important role in promoting human growth and supporting transformations to a variety of metabolic pathways including one-carbon, pyrimidine, purine, and homocysteine metabolism. The 5,10-methylenetetrahydrofolate reductase (MTHFR) enzyme is pivotal in the folate metabolic pathway. Polymorphism in the MTHFR gene, especially C677T, was associated with decreased enzyme activity and disturbance of folate metabolism, which is linked to various diseases including birth defects in newborns and neural tube abnormalities.

Microfluidic impedance flow cytometer leveraging virtual constriction microchannel and its application in leukocyte differential.

Microfluidic impedance flow cytometry has been widely used in leukocyte differential and counting, but it faces a bottleneck due to the trade-off between impedance detection throughput and sensitivity. In this study, a microfluidic impedance flow cytometer based on a virtual constriction microchannel was reported, in which the virtual constriction microchannel was constructed by crossflow of conductive sample and insulated sheath fluids with underneath micro-electrodes for impedance measurements. Compared to conventional mechanical constriction microchannels, this virtual counterpart could effectively avoid direct physical contact between cells and the microchannel walls to maintain high throughputs, and significantly reduce the volume of the impedance detection region for sensitivity improvements.

Immunosenescence Inventory-a multi-omics database for immune aging research.

The immune system is intricately interconnected with all other bodily systems. As individuals age, the immune system undergoes changes known as immunosenescence, increasing susceptibility to disease, and contributing significantly to the morbidity and mortality observed in older populations. Immunosenescence drives systemic aging and therefore represents a key therapeutic target to extend healthy aging.

Perspectives on biomarkers of reproductive aging for fertility and beyond.

Reproductive aging, spanning an age-related functional decline in the female and male reproductive systems, compromises fertility and leads to a range of health complications. In this Perspective, we first introduce a comprehensive framework for biomarkers applicable in clinical settings and discuss the existing repertoire of biomarkers used in practice. These encompass functional, imaging-based and biofluid-based biomarkers, all of which reflect the physiological characteristics of reproductive aging and help to determine the reproductive biological age.