Identification of genomic binding sites and direct target genes for the transcription factor DDIT3/CHOP

Increased chromatin accessibility underpins senescence

Senescence is a cellular state induced by various stressors or extracellular signals, but a universal pathway that triggers this process irrespective of the initial stressor has yet to be identified. Recent data indicate that chromatin opening, particularly in the noncoding genome, is a hallmark of cellular senescence. We propose a model in which this increased chromatin accessibility mediated by transcription factors downstream of the senescence-inducing stressors acts as a decisive factor to commit cells toward the senescence fate. Engagement toward senescence is then determined by the balance between mechanisms that increase or decrease chromatin accessibility and can be influenced by modulating the activity of specific histone-modifying complexes. Traits of senescent cells, such as increased nuclear and nucleolar size, the secretion of pro-inflammatory cytokines, reduced rRNA biogenesis, telomere dysfunction, expression of retrotransposons and endogenous retroviruses, as well as DNA damage, can all be attributed to increased chromatin accessibility. This concept suggests potential targets to tilt the balance toward the senescence response in the context of future therapies against cancer and age-related diseases.

Unveiling molecular secrets: Analysis of stable lentiviral packaging cell lines enables identification of novel viral gene functions

Lentiviral vectors (LVVs) are widely used in gene therapy due to their ability to infect both dividing and non-dividing cells. For LVV production, the creation of stable packaging cell lines with integrated genes necessary for viral replication offer a more consistent and scalable alternative to transient plasmid transfection approach. Although the development of such stable LVV packaging cell lines has been reported, the molecular changes induced by stable and inducible viral gene expression and the impact of genome integrated viral genes on cellular pathways remain poorly characterized. For better insight, we investigated the molecular characteristics of a stable LVV packaging cell line and its host cell line (HEK293T/17) by comparing differential expressed genes. This pathway analysis revealed significant changes in pathway usage between packaging and host cell lines, influenced by different viral transgenes. Gag-pol expression was found to suppress host translational machinery, while rev and VSV-G expression modulated mitochondrial pathways, including oxidative phosphorylation. HIV-1 tat expression, on the other hand, activated histone-related genes. These regulatory shifts suggest a strategic reprogramming of host cellular states to favor viral replication, curbing protein synthesis and energy production to levels that support viral assembly but impair the host's immune defense and the production of immune-related proteins. Our findings provide a deeper understanding of the molecular changes associated with stable viral gene expression, which can inform the optimization of LVV production in gene therapy applications.

Transcriptomic changes in oxidative stress, immunity, and cancer pathways caused by cannabis vapor on alveolar epithelial cells

As legalization of cannabis increases worldwide, vaping cannabis is gaining popularity due to the belief that it is less harmful than smoking cannabis. However, the safety of cannabis vaping remains untested. To address this, we developed a physiologically relevant method for in vitro assessment of cannabis vapor on alveolar epithelial cell cultures. We compared the transcriptional response in three in vitro models of cannabis vapor exposure using A549 epithelial cells in submerged culture, pseudo-air liquid interface (ALI) culture, and ALI culture coupled with the expoCube™ advanced exposure system. Baseline gene expression in ALI-maintained A549 cells showed higher expression of type 2 alveolar epithelial (AEC2) genes related to surfactant production, ion movement, and barrier integrity. Acute exposure to cannabis vapor significantly affected gene expression in AEC2 cells belonging to pathways related to cancer, oxidative stress, and the immune response without being associated with a DNA damage response. This study identifies potential risks of cannabis vaping and underscores the need for further exploration into its respiratory health implications.

Assessing Heat Resistance and Selecting Heat-Resistant Individuals of Largemouth Bass (Micropterus salmoides) with Tiered Thermal Exposure

Largemouth bass (LMB, Micropterus salmoides), a commercially important farmed fish, is vulnerable to heat stress. Breeding heat-resistant LMB is highly desirable in the face of global warming. However, we still lack an efficient method to assess the heat resistance of LMB. In this study, the critical thermal maximum (CTmax) and static exposure methods were first performed to assess the heat resistance of LMB juveniles. The CTmax values of the experimental fish (average body weight 9.87 ± 3.14 g) ranged from 39 to 40 °C but were too close together to differentiate the individual heat resistance. Static exposure experiments with varying temperatures and fish groups also did not provide a clear method for determining the heat resistance. To address these limitations, we developed a tiered exposure method, where the temperature was increased step-wise, starting from 28 to 34 °C at 2 °C increments and then at 0.5 °C increments above 34 °C, with each step lasting one day. The heat resistance of the fish was quantified as the lethal cumulative temperature (LCT), allowing for the classification of fish as sensitive or resistant to heat stress based on their LCT values. To correlate the changes in tissue structure and gene expression with the heat resistance, a new batch of LMB juveniles (average body weight 23.66 ± 6.98 g) were subjected to tiered heat exposure. Brain and liver tissues were collected from the control (without heat exposure), resistant and sensitive (still alive but demonstrated abnormal symptoms) individuals when the temperature was maintained at 35.5 °C for 24 h. The liver tissues of the heat-sensitive individuals showed significant damage and increased cell apoptosis (p < 0.05) relative to those of the resistant ones. The ddit3/chop, bax and casp3 genes demonstrated differential expressions in the liver of the sensitive and resistant fish. Additionally, the LMB juveniles (average body weight 84.06 ± 20.95 g) were found to be more heat resistant than the adults from different sources (average body weight 364.29 ± 84.43 g and 545.71 ± 184.56 g). Through the tiered exposure method, extremely heat-resistant individuals were successfully selected from the population (average body weight 22.69 ± 6.89 g). These findings provide valuable insights into the thermal biology of LMB and the potential for breeding heat-resistant LMB varieties.

Differential enrichment of retinal ganglion cells underlies proposed core neurodegenerative transcription programs

In a published Correction 1 , a revised analysis updated two "core transcription programs" proposed to underlie axon injury-induced retinal ganglion cell (RGC) neurodegeneration. Though extensive, the Correction purported to leave the two principal conclusions of its parent study 2 unaltered. The first of those findings was that a core program mediated by the Activating Transcription Factor-4 (ATF4) and its likely heterodimeric partner does not include numerous canonical ATF4 target genes stimulated by RGC axon injury. The second was that the Activating Transcription Factor-3 (ATF3) and C/EBP Homologous Protein (CHOP) function with unprecedented coordination in a parallel program regulating innate immunity pathways. Here those unexpected findings are revealed to instead reflect insufficient knockout coupled with differences in RGC enrichment across conditions. This analysis expands on the published Correction's redefinition of the purported transcription programs to raise foundational questions about the proposed functions and relationships of these transcription factors in neurodegeneration.

FUS::DDIT3 Fusion Protein in the Development of Myxoid Liposarcoma and Possible Implications for Therapy

The FUS::DDIT3 fusion protein, formed by the chromosomal translocation t (12;16) (q13;p11), is found in over 90% of myxoid liposarcoma (MLS) cases and is a crucial protein in its development. Many studies have explored the role of FUS::DDIT3 in MLS, and the prevailing view is that FUS::DDIT3 inhibits adipocyte differentiation and promotes MLS growth and invasive migration by functioning as an aberrant transcription factor that affects gene expression and regulates its downstream molecules. As fusion proteins are gradually showing their potential as targets for precision cancer therapy, FUS::DDIT3 has also been investigated as a therapeutic target. Drugs that target FUS::DDIT3 and its downstream molecules for treating MLS are widely utilized in both clinical practice and experimental studies, and some of them have demonstrated promising results. This article reviews the findings of relevant research, providing an overview of the oncogenic mechanisms of the FUS::DDIT3 fusion protein in MLS, as well as recent advancements in its therapy.

Adipose tissue macrophage infiltration and hepatocyte stress increase GDF-15 throughout development of obesity to MASH

Plasma growth differentiation factor-15 (GDF-15) levels increase with obesity and metabolic dysfunction-associated steatotic liver disease (MASLD) but the underlying mechanism remains poorly defined. Using male mouse models of obesity and MASLD, and biopsies from carefully-characterized patients regarding obesity, type 2 diabetes (T2D) and MASLD status, we identify adipose tissue (AT) as the key source of GDF-15 at onset of obesity and T2D, followed by liver during the progression towards metabolic dysfunction-associated steatohepatitis (MASH). Obesity and T2D increase GDF15 expression in AT through the accumulation of macrophages, which are the main immune cells expressing GDF15. Inactivation of Gdf15 in macrophages reduces plasma GDF-15 concentrations and exacerbates obesity in mice. During MASH development, Gdf15 expression additionally increases in hepatocytes through stress-induced TFEB and DDIT3 signaling. Together, these results demonstrate a dual contribution of AT and liver to GDF-15 production in metabolic diseases and identify potential therapeutic targets to raise endogenous GDF-15 levels.

Transcriptomic analysis identifies dysregulated pathways and therapeutic targets in PMM2-CDG

PMM2-CDG (MIM # 212065), the most common congenital disorder of glycosylation, is caused by the deficiency of phosphomannomutase 2 (PMM2). It is a multisystemic disease of variable severity that particularly affects the nervous system; however, its molecular pathophysiology remains poorly understood. Currently, there is no effective treatment. We performed an RNA-seq based transcriptomic study using patient-derived fibroblasts to gain insight into the mechanisms underlying the clinical symptomatology and to identify druggable targets. Systems biology methods were used to identify cellular pathways potentially affected by PMM2 deficiency, including Senescence, Bone regulation, Cell adhesion and Extracellular Matrix (ECM) and Response to cytokines. Functional validation assays using patients' fibroblasts revealed defects related to cell proliferation, cell cycle, the composition of the ECM and cell migration, and showed a potential role of the inflammatory response in the pathophysiology of the disease. Furthermore, treatment with a previously described pharmacological chaperone reverted the differential expression of some of the dysregulated genes. The results presented from transcriptomic data might serve as a platform for identifying therapeutic targets for PMM2-CDG, as well as for monitoring the effectiveness of therapeutic strategies, including pharmacological candidates and mannose-1-P, drug repurposing.

Gene of the month: DDIT3

DNA damage-inducible transcript 3 (DDIT3) gene, mapped to the human chromosome 12q13.3, encodes a protein that belongs to the CCAAT/enhancer-binding protein family of transcription factors. DDIT3 is involved in the proliferative control that responds to endoplasmic reticulum stress in normal conditions, dimerising other transcription factors with basic leucine zipper (bZIP) structural motifs. DDIT3 plays a significant role during cell differentiation, especially adipogenesis, arresting the maturation of adipoblasts. In disease, FUS/EWSR1::DDIT3 fusion is the pathogenic event that drives the development of myxoid liposarcoma. The amplification of DDIT3 in other adipocytic neoplasms mediates the presence of adipoblast-like elements. Another fusion, GLI1::DDIT3, has rarely been documented in other tumours. This paper reviews the structure and function of DDIT3, its role in disease-particularly cancer-and its use and pitfalls in diagnostic testing, including immunohistochemistry as a tissue-based marker.

Transcriptional landscape of mitochondrial electron transport chain inhibition in renal cells

Analysis of the transcriptomic alterations upon chemical challenge, provides in depth mechanistic information on the compound's toxic mode of action, by revealing specific pathway activation and other transcriptional modulations. Mapping changes in cellular behaviour to chemical insult, facilitates the characterisation of chemical hazard. In this study, we assessed the transcriptional landscape of mitochondrial impairment through the inhibition of the electron transport chain (ETC) in a human renal proximal tubular cell line (RPTEC/TERT1). We identified the unfolded protein response pathway (UPR), particularly the PERK/ATF4 branch as a common cellular response across ETC I, II and III inhibitions. This finding and the specific genes elaborated may aid the identification of mitochondrial liabilities of chemicals in both legacy data and prospective transcriptomic studies.