Advancements in molecular characterization technologies have accelerated targeted cancer therapy research at unprecedented resolution and dimensionality. Integrating comprehensive multi-omic molecular profiling of a tumor, proteogenomics, marks a transformative milestone for preclinical cancer research. In this paper, we initially provided an overview of proteogenomics in cancer research, spanning genomics, transcriptomics, and proteomics. Subsequently, the applications were introduced and examined from different perspectives, including but not limited to genetic alterations, molecular quantifications, single-cell patterns, different post-translational modification levels, subtype signatures, and immune landscape. We also paid attention to the combined multi-omics data analysis and pan-cancer analysis. This paper highlights the crucial role of proteogenomics in preclinical targeted cancer therapy research, including but not limited to elucidating the mechanisms of tumorigenesis, discovering effective therapeutic targets and promising biomarkers, and developing subtype-specific therapies.

DNA double-strand breaks (DSBs) are the most severe form of DNA damage, primarily repaired by the non-homologous end joining (NHEJ) pathway. A critical step in this process is DNA synapsis, where the two broken ends are brought together to facilitate timely repair. Deficiencies in NHEJ synapsis can lead to improper DNA end configurations, potentially resulting in chromosomal translocations. NHEJ synapsis is a highly dynamic, multi-protein mediated assembly process. Recent advances in single-molecule techniques have led to significant progress in understanding the molecular mechanisms driving NHEJ synapsis. In this review, we summarize single-molecule methods developed for studying NHEJ synapsis, with a particular focus on the single-molecule fluorescence resonance energy transfer (smFRET) technique. We discuss the various molecular mechanisms of NHEJ synapsis uncovered through these studies and explore the coupling between synapsis and other steps in NHEJ. Additionally, we highlight the strategies, limitations, and future directions for single-molecule studies of NHEJ synapsis.

Viral epidemics pose major threats to global health and economies. A hallmark of viral infection is the reshaping of host cell membranes and cytoskeletons to form organelle-like structures, known as viral factories, which support viral genome replication. Viral infection in many cases induces the cytoskeletal network to form cage-like structures around viral factories, including actin rings, microtubule cages, and intermediate filament cages. Viruses hijack various organelles to create these replication factories, such as viroplasms, spherules, double-membrane vesicles, tubes, and nuclear viral factories. This review specifically examines the roles of cytoskeletal elements and the endomembrane system in material transport, structural support, and biochemical regulation during viral factory formation. Furthermore, we discuss the broader implications of these interactions for viral replication and highlight potential future research directions.

Chromatin contains not only heterochromatin (HC) and euchromatins (EC) but also facultative heterochromatin (fHC), which experience the dynamic remodeling between HCs and ECs by different regulators. The regulation of fHCs involves lots of different cell functions, like genomic stability and gene transcription. Heterochromatin protein 1 (HP1) recognizes methylated H3K9 and reshapes the chromatin into the fHCs through liquid–liquid phase separation (LLPS). Among the three members of the HP1 family, HP1α can condensate by itself and HP1β forms granules with the help of TRIM28, while the HP1γ cannot phase separation alone either and the coordinator is still unclear. So, in this study, we investigated the molecular mechanism of how HP1γ interacts with TRIM66 through PxVxL motif. Based on that, we examined the key regions that controlled the TRIM66-HP1γ co-phase separation behaviors both in vitro and in vivo. Furthermore, we proved that the liquid granules of TRIM66-HP1γ and chromatin highly correlated with H3K9me3 sites, which indicated the relationship with DNA damage response. Finally, combined with our previous study, we proposed the system for how TRIM66 remodeled the chromatin into compressed fHC through the TRIM66-HP1γ-H3K9me3 axis with liquid–liquid phase separation.

The purpose of this study was to examine the secretion of inflammatory cytokines by cultured monocytes/macrophages in patients with premature coronary artery disease (CAD). The study included 38 patients with premature CAD and 35 patients without CAD. A primary culture of CD14+ monocytes was obtained by immunomagnetic separation. The inflammatory response was induced by incubation of a cell culture with lipopolysaccharide (LPS) for 24 hours on Days 1 and 6. Basal and LPS-stimulated secretion of the cytokines, tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), interleukin-6 (IL-6), interleukin-8 (IL-8) and monocyte chemotactic protein-1 (MCP-1) was assessed by enzyme immunoassay on Days 2 and 7 of cultivation. The level of basal secretion of TNF-α, IL-1β, IL-6, MCP-1 was higher in patients with CAD compared to patients in the control group. The levels of re-stimulated TNF-α secretion and the levels of LPS-stimulated and re-stimulated IL-1β secretion on the second and sixth days were also higher in patients with CAD. LPS-stimulated MCP-1 secretion on the second day did not differ in patients of both groups, but re-stimulated MCP-1 secretion was higher in patients with CAD. The results of logistic regression analysis showed that the basal secretion levels of IL-1β and IL-6 were independently associated with premature CAD, along with smoking, body mass index and serum HDL-cholesterol levels.

Some microbes are referred to as model organisms because they are easy to study in the laboratory and hold the ability to retain their characteristics during DNA replication, DNA transcription, and other fundamental processes. Studying these microbes in living cells via single-molecule imaging allows us to better understand these processes at highly improved spatiotemporal resolution. Single particle tracking photoactivated localization microscopy (sptPALM) is a robust tool for detecting the positions and motions of individual molecules with tens of nanometers of spatial and millisecond temporal resolution in vivo, providing insights into intricate intracellular environments that traditional ensemble methods cannot. With this approach, the fluorophores are photoactivated stochastically, a series of images are recorded, and the positions of fluorophores are identified in these images, and ultimately the locations are linked together to yield trajectories of individual molecules. Quantitative kinetic and spatial information, such as reaction rates, diffusion coefficients, and localization maps, can be obtained by further analysis. Here, we present a single-molecule tracking protocol that includes sample preparation, data acquisition and brief data processing. This protocol will enable researchers to directly unveil molecular and cellular mechanisms underlying the essential biological processes.

Acute myeloid leukemia (AML) is a rare tumor that invades the blood and bone marrow, it is rapidly progressive, highly aggressive, and difficult to cure. Studies have shown that long non-coding RNA (lncRNA) and ferroptosis play important roles in AML. However, few studies have been done on ferroptosis-related lncRNA for AML. To investigate the role of ferroptosis-related lncRNA in AML prognosis, we screened the differentially expressed genes related to ferroptosis and lncRNA. Ferroptosis-related lncRNA associated with AML prognosis was obtained by Pearson correlation analysis. By using univariate Cox analysis, least absolute shrinkage and selection operator (LASSO) analysis, and multivariate Cox analysis, the ten prognostic genes were used for constructing the prognostic model. The model was then validated using a Kaplan-Meier analysis and Cox regression analysis. The ROC results have shown that the model could better predict AML survival. We identified some mutated genes that may affect the poor prognosis based on the somatic mutation analysis. The enrichment pathway analysis of prognostic genes revealed that these genes were mainly enriched in some immune pathways and cancer pathways. By immune infiltration analysis, we found that high-risk patients may respond better to immunotherapy.

Research using the model organism nematode C. elegans has greatly facilitated our understanding of sensory biology, including touch, olfaction, taste, vision and proprioception. While hearing had long been considered to be restricted to vertebrates and some arthropods, we recently discovered that C. elegans is capable of sensing and responding to airborne sound in a frequency and sound source-size-dependent manner. C. elegans auditory sensation occurs when airborne sound physically vibrates their external cuticle (skin) to activate the sound-sensitive mechanosensory FLP/PVD neurons via nicotinic acetylcholine receptors (nAChRs), triggering aversive phonotaxis behavior. Here, we report stepwise methods to characterize these three features of C. elegans auditory sensation, including sound-evoked skin vibration, neuronal activation, and behavior. This approach provides an accessible platform to investigate the cellular and molecular mechanisms underlying auditory sensation and mechanotransduction mechanisms in C. elegans.

Microbial communities exert a profound influence on various facets of animal behavior and physiology, making the comprehension of their interactions with hosts or the environment essential. Drosophila melanogaster, a widely recognized model organism, has been pivotal in elucidating host-microbe interactions. Despite the existence of several protocols for generating germ-free (GF) Drosophila, their reproducibility has been constrained by the technical difficulty of maintaining airtight conditions in centrifuge tubes. In this study, we introduce a refined method for the production of GF Drosophila, complemented by a straightforward verification process to ascertain its efficacy. We propose an innovative strategy employing bio-reaction tubes equipped with a 0.22 μm filter membrane cap, which facilitates the rearing and maintenance of GF flies, thereby streamlining the procedure and enhancing the efficiency of model construction.

Membrane proteins often need to be inserted into or attached to the cell membrane to perform their functions. Understanding their transmembrane topology and conformational dynamics during insertion is crucial for elucidating their roles. However, it remains challenging to monitor nanoscale changes in the insertion depth of individual proteins in membranes. Here, we introduce two single-molecule imaging methods, SIFA and LipoFRET, designed for in vitro observation of the nanoscale architecture of membrane proteins within membranes. These methods have demonstrated their efficacy in studying biomolecules interacting with bio-membranes with sub-nanometer precision.

Fibroblast activation protein (FAP) is a key molecule in the field of oncology, with significant impacts on tumor diagnosis and treatment. Importantly, it has paved the way for the development of radiotracers for quinoline-based FAP inhibitors (FAPIs), which are currently among the most promising radiotracers for PET imaging in cancer. We performed a bibliometric analysis of scientific publications related to FAP and FAPI-based radiotracers, which included the quantification and visualization of current research trends and prospects based on various bibliometric indicators. In our survey of FAP-related studies in the Web of Science Core Collection databases, R and VOSviewer were used for visualization and bibliometric analyses based on country, institute, author, journal, and keywords. We also examined the methodology, radionuclide type, imaging instruments, and major diseases associated with studies on FAPI-based radiotracers. The results revealed 2,664 FAP-related publications from 1992 to the present. Germany, the USA, and China dominated paper publications, multinational collaborations, and societal impacts on FAP research. Southwest Medical University was the most productive institute, while Haberkorn Uwe authored the most cited papers and the highest H-index. The European Journal of Nuclear Medicine and Molecular Imaging and the Journal of Nuclear Medicine were the most influential periodicals. Keywords "FAP", "⁶⁸Ga-FAPI", and "PET/CT" emerged as the most significant in this field. This study may help elucidate current research trends, hotspots, and directions for future research.

Mesenchymal stem cells (MSCs) show significant promise in treating immune diseases due to their ability to differentiate into various cell types and their immunomodulatory properties. However, the mechanisms by which MSCs regulate CD4⁺T cells, essential for immune responses, are not yet fully understood. This study aims to provide a comprehensive overview of how MSCs and their secreted extracellular vesicles (EVs) modulate CD4⁺T cells in immune diseases. We begin by discussing the immunomodulatory properties of MSCs and the factors contributing to their effectiveness. Following this, we explore how MSCs interact with CD4⁺T cells through various pathways, including the secretion of soluble factors, direct cell-cell contact, and EV-mediated communication. A key focus is on the therapeutic potential of MSC-derived EVs, which are rich in bioactive molecules such as proteins, lipids, and nucleic acids. These molecules can regulate the phenotype and function of CD4⁺T cells. The challenges and future perspectives in utilizing MSCs and EVs for immune-disease therapy are also addressed. Overall, this research aims to enhance our understanding of the mechanisms behind MSC-mediated regulation of CD4⁺T cells and provide insights into the potential use of MSCs and EVs as therapeutic tools in immune diseases. In summary, understanding how MSCs and their EVs control CD4⁺T cells can offer valuable perspectives for developing innovative immunotherapeutic approaches. Leveraging the immunomodulatory capacity of MSCs and EVs holds promise for managing immune-related disorders.