Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disorder characterized by motor neuron degeneration. Although genetic contributions to both familial and sporadic ALS (sALS) cases are well established, a substantial portion of ALS heritability remains unexplained, suggesting the involvement of other genetic and epigenetic factors. To address this gap, we have devised a comprehensive multi-omics approach in a pair of Italian monozygotic twins discordant for ALS, performing DNA methylation, transcriptomic, and whole exome sequencing (WES). We then conducted a structured literature research on ALS-discordant monozygotic twins (n = 45) and on case-control sALS ( 7000 patients and 3000 controls), investigated for at least one of the omics approaches. Our exploratory analysis reveals distinct transcriptomic and epigenetic profiles underlying the discordant disease phenotypes in genetically identical individuals, particularly implicating immune system functions and brain development pathways. Notably, a comprehensive comparison of our results with existing literature underlined the involvement of pathways related to NK cell activation, chemokine production, and signal transduction, suggesting potential shared disease associated mechanisms across ALS cases. This hypothesis-generating study, although limited by the sample size, demonstrates the utility of multi-omics approaches in uncovering broader pathological insights into ALS, speculating on the possible contribution of innate immunity and epigenetic dysregulation in disease processes. This work provides a foundation for future research aimed at identifying disease-associated processes and biomarkers.

Background Lung cancer is characterized by wide genetic, molecular, and phenotypic alterations that may challenge diagnosis and clinical decision-making. This heterogeneity often leads to variable responses to therapies, resulting in suboptimal outcomes for many patients. Recent advancements in omics technologies have enabled a deeper exploration of mechanisms driving tumor behavior and identification of specific molecular signatures. Tumor metabolic reprogramming, one of the hallmarks of cancer development, progression, and recurrence, represents a promising field of research. Methods In this study, we developed a comprehensive metabolic signature using RNA-sequencing data from independent cohorts of patients diagnosed with stage I-III resectable lung adenocarcinoma (LUAD) to enhance patient stratification and prognostic accuracy. Results We identified a novel prognostic signature "LMetSig" consisting of 10 metabolic genes that significantly stratified LUAD patients into high- and low-risk subgroups for disease-free survival (DFS). Cox regression analysis demonstrated that LMetSig is an independent prognostic biomarker for DFS. Among the LMetSig, TK1 gene emerged as a promising LUAD-specific biomarker. It was undetectable in normal tissue, showed variable expression in tumor samples and correlated with shorter DFS when expressed at high levels. Conclusion Our findings suggest that LMetSig can significantly improve LUAD patients' stratification alongside conventional pathological and clinical parameters. By distinguishing high-risk patients from those with more favorable prognosis, this approach has the potential for informing personalized treatment strategies and improving clinical decision-making.

The maintenance of skeletal muscle is of pivotal importance, as its loss is often associated with progressive pathologies, generally worsening the prognosis. Increased levels of vitamin D binding protein (VDBP) were reported in diseases susceptible to muscle wasting, including several tumors. We hypothesized that VDBP might participate in muscle wasting and investigated its direct effects on skeletal muscle homeostasis. Here, we demonstrate that VDBP induces atrophy independently of vitamin D. In C2C12 myotubes, we identified intracellular actin dynamics perturbation and subsequent mitochondrial fragmentation as the main molecular mechanisms of VDBP-induced atrophy. Coherently, the ectopic introduction of VDBP in mice lacking the protein (Gc-knockout mice) induced muscle atrophy and decreased strength. Finally, we present proof-of-concept evidence that VDBP contributes to cancer-associated muscle wasting in Lewis lung carcinoma (LLC)-bearing male mice. Altogether, these findings provide novel insights into the biological function of VDBP as a pro-atrophic hormone with potential implications for the treatment of muscle wasting.

Brain metastases from breast cancer (BCBM) are fatal and lack effective treatments. Their cellular and molecular drivers remain poorly understood, partly due to limited preclinical models that fail to capture patient tumor heterogeneity. Cancer stem-like cells (CSCs) are implicated in metastatic dissemination; however, their specific role in brain metastasis remains unclear. In this study, CSCs are isolated from human BCBM specimens and characterized for stem-like properties, including CD44 and ALDH1 expression, sphere formation, tumorigenicity, and in vitro and in vivo self-renewal. Intra-nipple and intra-cardiac xenograft models demonstrate CSC ability to generate brain and bone metastases that recapitulate patient-specific dissemination patterns. Transcriptomic and functional analyses reveal cellular heterogeneity and identify a metastasis-initiating cell (MIC) subpopulation enriched in stemness and adhesion-related pathways. These MICs exhibit enhanced adhesion to brain endothelium and undergo brain-specific transcriptomic reprogramming that enables vascular co-option, resistance to stromal stress, and survival-promoting interactions with brain-resident cells. High-throughput drug screening indicates broad therapeutic resistance within the CSC compartment. Through the comprehensive characterization of BCBM-derived CSCs, this study establishes a clinically relevant model that identifies CSCs and the MIC subpopulation as key drivers of brain metastatic progression and as promising targets for the development of effective therapeutic strategies.

During the COVID-19 pandemic, healthcare systems experienced significant disruption, increasing the risk of multidrug-resistant (MDR) pathogen transmission. Acinetobacter baumannii, a critical-priority MDR pathogen, is known for its ability to persist in hospital environments and rapidly acquire resistance. To investigate the genomic characteristics, antimicrobial resistance determinants, and phylogenetic relationships of outbreak-associated Acinetobacter baumannii isolates, whole-genome sequencing (WGS) and comparative genomic analyses on 24 clinical and environmental strains collected during the COVID-19 period were performed. Twenty-four A. baumannii isolates collected between August 2020 and February 2021 from clinical and environmental samples were analyzed by WGS. All isolates displayed an MDR phenotype, with uniform resistance to carbapenems and aminoglycosides, and preserved colistin susceptibility. One environmental strain showed extreme drug resistance. WGS confirmed medium-quality genome assemblies and the clonal spread of a single A. baumannii lineage. Most resistance genes, including OXA-23, ADC-type β-lactamases, and ade efflux pumps, were chromosomally encoded and shared across all isolates. Plasmid-mediated resistance genes were variably distributed. This outbreak of MDR A. baumannii was driven by the clonal dissemination of a genomically stable lineage. Combined genomic and epidemiological analyses underscore the importance of integrated surveillance and environmental decontamination to prevent the spread of MDR pathogens.

Understanding the biosynthetic potential of the human microbiome remains a significant challenge with far-reaching scientific and translational implications. Analyses of human-associated (meta)genomic sequencing data undeniably show that the biosynthetic diversity encoded in these genomes is largely underexplored. A crucial step in studying specialized metabolites involves the sequence-based identification of genes encoding biosynthetic pathways, typically organized into biosynthetic gene clusters (BGCs). In this review, we provide a concise and updated overview of the widening range of computational approaches that have effectively addressed the sequence-based identification of BGCs across both isolated genomes and complex microbial communities. These advancements are set to deepen our understanding of the biosynthetic potential and diversity of microorganisms residing in different human body sites.

Lysine-specific histone demethylase 1A (LSD1) is an epigenetic regulator involved in various biological processes, including metabolic pathways. We demonstrated the therapeutic potential of its pharmacological inhibition in glioblastoma using DDP_38003 (LSD1i), which selectively targets tumor-initiating cells (TICs) by hampering their adaptability to stress. Through biological, metabolic, and omic approaches, we now show that LSD1i acts as an endoplasmic reticulum (ER) stressor, activating the integrated stress response and altering mitochondrial structure and function. These effects impair TICs’ oxidative metabolism and generate reactive oxygen species, further amplifying cellular stress. LSD1i also impairs TICs’ glycolytic activity, causing their metabolic decline. TICs with enhanced glycolysis benefit from LSD1-directed therapy. Conversely, metabolically silent TICs mantain ER and mitochondrial homeostasis, adapting to stress conditions, including LSD1i treatment. A dropout short hairpin RNA screening identifies postglycosylphosphatidylinositol attachment to proteins inositol deacylase 1 (PGAP1) as a mediator of resistance to LSD1i. Disruptions in ER and mitochondrial balance holds promise for improving LSD1-targeted therapy efficacy and overcoming treatment resistance.

Acute myeloid leukemia (AML) is a heterogeneous disease with an unmet need for novel therapeutic drugs. Previous studies have reported the upregulation of diacylglycerol kinases (DGKs) in AML. This study investigated the effects of ritanserin, a DGKα-specific inhibitor, and DGKζ-IN4 or BAY 2965501, DGKζ-selective inhibitors, on a panel of AML cell lines. Ritanserin induced apoptotic cell death across all tested models, whereas DGKζ inhibitors triggered both apoptosis and necrosis to variable extents, with HL-60 cells being the most responsive to both compounds. Drug sensitivity did not correlate with DGKα or DGKζ expression levels, indicating that additional factors may influence cellular susceptibility. THP-1 proteomic profiling revealed that ritanserin broadly downregulated proteins involved in antigen presentation, cell cycle and metabolism, while BAY 2965501 affected a smaller and distinct but functionally similar protein subset, implying different mechanisms of action. Gene silencing confirmed AML cell line-specific dependence on DGK isoforms: HEL cells were sensitive to DGKα knockdown, HL-60 to DGKζ silencing, whereas K562 and THP-1 were resistant to both. These findings indicate that DGKs targeting can effectively reduce AML cell viability. However, AML heterogeneity and the limited selectivity of current inhibitors underscore the need for predictive biomarkers and combinatorial strategies to translate DGK inhibition into effective therapy.

Skeletal muscle wasting is a defining feature of cancer cachexia, a multifactorial syndrome that drastically compromises patient quality of life and treatment outcomes. Mitochondrial dysfunction is a major contributor to skeletal muscle wasting in cancer cachexia, yet the upstream molecular drivers remain elusive. Here we show that cancer impairs the activity of cAMP-dependent protein kinase A (PKA) and of its transcriptional effector CREB1 in skeletal muscle, ultimately contributing to the downregulation of a core transcriptional network that supports mitochondrial integrity and function. The restoration of cAMP-PKA-CREB1 signalling through pharmacological inhibition of the cAMP-hydrolysing phosphodiesterase 4 (PDE4) rescues the expression of mitochondrial-related genes, improves mitochondrial function and mitigates skeletal muscle wasting in male mice. Altogether, our data identify tumour-induced suppression of the cAMP-PKA-CREB1 axis as a central mechanism contributing to mitochondrial dysfunction in skeletal muscle during cancer cachexia. Furthermore, these findings highlight PDE4, particularly the PDE4D isoform, as a potential therapeutic target to preserve muscle mitochondrial function and counteract muscle wasting in cancer cachexia.

Abstract Introduction: Non-small cell lung cancer (NSCLC) is a highly heterogenous disease with the largest number of cancer-related mortality worldwide, one of the reasons for this is the complex and diverse tumor microenvironment (TME) comprising of numerous cell types. Several studies have already highlighted the importance of TME in dictating progression steps and response to therapies; however, a transcriptome-based molecular subtyping of patients in lung adenocarcinomas (LUADs) and lung squamous cell carcinomas (LUSCs) can further determine the distinct tumor immune microenvironment (TiME), which can eventually provide a systematic overview to improve the diagnosis and prognosis of patients. Material and method: To elucidate such nature of interactions between tumor cells and cells comprising the TME, we exploited the transcriptome of 300 early stages (Ib-IIIa) NSCLC recruited in the prospective observational clinical trial PROMOLE. With the help of a clustering approach, initially we performed a molecular-based virtual stratification/dissection on the NSCLC patients. Next, to elucidate the relative cell-type abundance, a deconvolution approach was applied to identify the possibility of tumor infiltrating immune cells within these subgroups. Immunohistochemistry (IHC) was then used to substantiate these predictions on tumor cells. Results and discussion: The resulting subgroups of LUADs and LUSCs are biologically well-characterized by mutational and gene expression profiles. Cell-type abundance approach identified samples which are enriched with tumor infiltrating immune cells like Neutrophils, Tcells, macrophages, etc. These findings were positively confirmed by IHC with multiple cell markers such as MPO, CD4, CD8, CD68, etc. Integrating these two results highlighted the proportion of TiME in the two different sub-populations along with shedding some light on the crosstalk happening between different cancer-/immune- cell lines. Conclusion: The in-silico predictions on bulk RNA data by virtual micro-dissection, distinguished the two distinct NSCLC subtypes, each associated with clinical and molecular features. Furthermore, the immune cells infiltration suggests a possible role of infiltrating tumor immune cells with the prognosis of patients. Our analysis successfully performed an intra-sample and inter-sample comparison, which can unveil new prognostic markers that can provide relevant information for cancer immunotherapy. Citation Format: Sushant Parab, Francesca Napoli, Davide Corà, Gabriella Doronzo, Valentina Communanza, Luisella Righi, Luca Primo, Valentina Monica, Lorenzo Manganaro, Bianco Selene, Paolo Bironzo, Giorgio Scagliotti, Federico Bussolino. Deciphering the crosstalk within the tumor microenvironment of NSCLC by a virtual microdissection approach [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1536.

Various human diseases are triggered by molecular alterations influencing the fine-tuned expression and activity of transcription factors, usually due to imbalances in targets including protein-coding genes and non-coding RNAs, such as microRNAs (miRNAs). The transcription factor EB (TFEB) modulates human cellular networks, overseeing lysosomal biogenesis and function, plasma–membrane trafficking, autophagic flux, and cell cycle progression. In endothelial cells (ECs), TFEB is essential for the maintenance of endothelial integrity and function, ensuring vascular health. However, the comprehensive regulatory network orchestrated by TFEB remains poorly understood. Here, we provide novel mechanistic insights into how TFEB regulates the transcriptional landscape in primary human umbilical vein ECs (HUVECs), using an integrated approach combining high-throughput experimental data with dedicated bioinformatics analysis. By analyzing HUVECs ectopically expressing TFEB using ChIP-seq and examining both polyadenylated mRNA and small RNA sequencing data from TFEB-silenced HUVECs, we have developed a bioinformatics pipeline mapping the different gene regulatory interactions driven by TFEB. We show that TFEB directly regulates multiple miRNAs, which in turn post-transcriptionally modulate a broad network of target genes, significantly expanding the repertoire of gene programs influenced by this transcription factor. These insights may have significant implications for vascular biology and the development of novel therapeutics for vascular disease.

The maintenance of skeletal muscle is of pivotal importance, as its loss is often associated with progressive pathologies, generally worsening the prognosis. Increased levels of vitamin D binding protein (VDBP) were reported in diseases susceptible to muscle wasting, including several tumors. We hypothesized that VDBP might participate in muscle wasting and investigated its direct effects on skeletal muscle homeostasis. Here we demonstrate that VDBP induces atrophy independently of vitamin D. In C2C12 myotubes, we identified intracellular actin dynamics perturbation and subsequent mitochondrial dysfunction as the main molecular mechanisms of VDBP-induced atrophy. Coherently, the ectopic introduction of VDBP in mice lacking the protein (Gc-knockout mice) induced muscle atrophy and decreased strength. Finally, we present proof-of-concept evidence that VDBP contributes to cancer-associated muscle wasting. Altogether, these findings provide novel insights into the biological function of VDBP as a pro-atrophic hormone with potential implications for the treatment of muscle wasting.

Human cytomegalovirus (HCMV) is an opportunistic pathogen causing severe diseases in immunosuppressed individuals. To replicate its double-stranded DNA genome, HCMV induces profound changes in cellular homeostasis that may resemble senescence. However, it remains to be determined whether HCMV-induced senescence contributes to organ-specific pathogenesis. Here, we show a direct cytopathic effect of HCMV on primary renal proximal tubular epithelial cells (RPTECs), a natural setting of HCMV disease. We find that RPTECs are fully permissive for HCMV replication, which endows them with an inflammatory gene signature resembling the senescence-associated secretory phenotype (SASP), as confirmed by the presence of the recently established SenMayo gene set, which is not observed in retina-derived epithelial (ARPE-19) cells. Although HCMV-induced senescence is not cell-type specific, as it can be observed in both RPTECs and human fibroblasts (HFFs), only infected RPTECs show downregulation of LAMINB1 and KI67 mRNAs, and enhanced secretion of IL-6 and IL-8, which are well-established hallmarks of senescence. Finally, HCMV-infected RPTECs have the ability to trigger a senescence/inflammatory loop in an IL-6-dependent manner, leading to the development of a similar senescence/inflammatory phenotype in neighboring uninfected cells. Overall, our findings raise the intriguing possibility that this unique inflammatory loop contributes to HCMV-related pathogenesis in the kidney.