Biology subjects

Giordano, E.

Publications and source records attributed to Giordano, E..

7 recordsLinked to original sources

bioRxiv2026

TREX2 component PCID2 scaffolds alternative SAC3-based subcomplexes with distinct RNA processing and export function

The TREX2 complex bridges transcription and RNA export. Its subunits show differences in expression, localization, and dynamics, suggesting distinct cellular roles. To understand the roles of individual TREX2 components, we characterized their interactomes. We identified novel, evolutionarily conserved SAC3(PCI-fold)-based subcomplexes with its PCID2 subunit. PCID2 acts as a scaffold for mutually exclusive yet structurally related subcomplexes with GANP, LENG8, and SAC3D1. These subcomplexes have alternative localization at the nuclear envelope, nuclear speckles and cytosol. LENG8 localizes in nuclear speckles and interacts extensively with the mRNA processing factors. LENG8 depletion alters mRNA processing and polyadenylation site usage. LENG8 thus acts upstream of the canonical TREX2 complex, in which PCID2 cooperates with GANP in mRNA export. Together, our findings reveal that TREX2 is not a uniform complex but a modular system, in which TREX2 subunits can assemble into functionally distinct subcomplexes through interacting partners that define their specificity and alternative functions. HIGHLIGHTSO_LITREX2 subunits play distinct roles in RNA retention and exhibit subunit-specific preference for interactions with different protein partners C_LIO_LIPCID2 forms mutually exclusive subcomplexes with GANP, LENG8, and SAC3D1 C_LIO_LIGANP, LENG8, and SAC3D1 alter PCID2 intracellular localization C_LIO_LILENG8 is a nuclear speckle protein that modulates alternative mRNA processing C_LI

molecular biology↗

bioRxiv2025

A novel cell indirect calorimetry method unveils the metabolic fluxomic signatures of human monocyte derived M(LPS+INF-γ) and M(IL-4) macrophages

Macrophages (M{Phi}) display distinct immunometabolic phenotypes upon polarization. While transcriptomic analyses have suggested divergent metabolic programs in human M(LPS+INF-{gamma}) and M(IL-4) M{Phi}, a comprehensive assessment of their metabolic fluxes is lacking. Aim of this study is to 1. develop and validate a novel indirect microcalorimetry method for quantifying cellular metabolic fluxes, and 2. exploit it to characterize fluxomic signatures of polarized human monocyte-derived macrophages. MethodsM{Phi} from healthy donors were differentiated into M0, M(LPS+INF-{gamma}), and M(IL-4) phenotypes and studied in four defined media: substrate-free, glucose, glycyl-glutamine, and glucose + glycyl-glutamine. A steady-state fluxomic model was constructed by integrating four independent measures - oxygen consumption and proton production (Seahorse XFp), lactate and ammonia release (microfluorimetry) - into stoichiometric equations of metabolism (SAAM II software). ResultsFluxes revealed that macrophages rely on glucose to sustain glycolysis, contributing [~]30% of citrate synthase flux, and predominantly on lipids for net citrate synthesis (first step of Krebs cycle). Upon polarization, M(LPS+INF-{gamma}) macrophages showed increased anaerobic glycolysis versus M0 and M(IL-4), with similar TCA fluxes to M0. In contrast, M(IL-4) macrophages exhibited higher TCA and malic enzyme fluxes, especially with glucose and glycyl-glutamine, and a trend toward enhanced lipid oxidation. ConclusionsThis novel method enables precise quantification of bioenergetic fluxes. In human M{Phi}, it reveals that M(LPS+INF-{gamma}) and M(IL-4) subsets exhibit distinct metabolic phenotypes, consistent with their immunological roles. These results resolve transcriptomic-metabolic discrepancies and provide a robust framework for assessing immunometabolism in primary human cells.

physiology↗

bioRxiv2025

Lamin A/C Deficiency Drives Genomic Instability and Poor Survival in Small-Cell Lung Cancer through Increased R-loop Accumulation

Lamin A/C (LMNA), a key component of the nuclear envelope, is essential for maintaining nuclear integrity and genome organization [1]. While LMNA dysregulation has been implicated in genomic instability across cancer and aging, the underlying mechanisms remain poorly understood [2]. Here, we investigate LMNAs role in small-cell lung cancer (SCLC), a highly aggressive malignancy characterized by extreme genomic instability [3, 4]. We demonstrate that LMNA depletion promotes R-loop accumulation, transcription-replication conflicts, replication stress, DNA breaks, and micronuclei formation. Mechanistically, LMNA loss disrupts nuclear pore complex distribution, reducing phenylalanine-glycine (FG)-nucleoporin incorporation and impairing RNA export efficiency. Furthermore, we show that LMNA expression is epigenetically repressed by EZH2 during SCLC differentiation from neuroendocrine (NE) to non-NE states. Clinically, low LMNA levels correlate with significantly worse survival in SCLC patients. These findings uncover a novel role for LMNA in safeguarding genome integrity and shaping tumor heterogeneity, with broad implications for cancer and aging. Significance StatementLamin A/C, a key structural component of the nuclear envelope, is frequently lost or mutated in cancer, laminopathies, and aging-related disorders. Lamin A/C loss is associated with genomic instability, but the underlying mechanisms remain incompletely understood. We demonstrate that LMNA loss drives genomic instability by promoting R-loop accumulation through disrupted nuclear pore dynamics and impaired RNA export. These findings reveal a previously unrecognized link between LMNA loss, nuclear envelope dysfunction, and genome instability. Targeting this pathway could help mitigate genomic instability in aging and laminopathies, while leveraging R-loop accumulation may enhance the efficacy of DNA-damaging therapies in cancer.

cancer biology↗

bioRxiv2024

Development and validation of a computational tool to predict treatment outcomes in cells from High-Grade Serous Ovarian Cancer patients

Treatment of High-Grade Serous Ovarian Cancer (HGSOC) is often ineffective due to frequent late-stage diagnosis and development of resistance to therapy. Timely selection of the most effective (combination of) drug(s) for each patient would improve outcomes, however the tools currently available to clinicians are poorly suited to the task. We here present a computational simulator capable of recapitulating cell response to treatment in ovarian cancer. The technical development of the in silico framework is described, together with its validation on both cell lines and patient-derived laboratory models. A calibration procedure to identify the parameters that best recapitulate each patients response is also presented. Our results support the use of this tool in preclinical research, to provide relevant insights into HGSOC behaviour and progression. They also provide a proof of concept for its use as a personalised medicine tool and support disease monitoring and treatment selection.

bioengineering↗

bioRxiv2024

Simultaneous silencing of gut nucleases and a vital target gene by adult dsRNA feeding enhances RNAi efficiency and mortality in Ceratitis capitata adults.

Ceratitis capitata, known as Mediterranean fruit fly (Medfly), is a major dipteran pest significantly impacting fruit and vegetable farming. Currently, its control heavily relies mainly on chemical insecticides, which pose health risks and have effects on pollinators. A friendly and species-specific alternative strategy involves providing double-stranded RNA (dsRNA) through feeding to disrupt essential functions in pest insects, which is poorly explored in dipteran species. Previous reports in Orthoptera and Coleoptera species suggested that dsRNA degradation by two specific nucleases in the intestinal lumen is among the major obstacle to feeding-mediated RNAi in insects. In our study, we experimented with three-day adult feeding using a combination of dsRNA molecules that target the expression of the ATPase vital gene and two intestinal dsRNA nucleases. These dsRNA molecules were recently tested separately in two Tephritidae species, showing limited effectiveness [1,2]. In contrast, we observed 79% mortality over seven days, which was associated with a decrease in mRNA levels of the three targeted genes. As expected, we also observed a reduction in dsRNA degradation following RNAi against nucleases. This research illustrates the potential of utilizing molecules as pesticides to achieve mortality rates in Medfly adults by targeting crucial genes and intestinal nucleases. Furthermore, it underscores the importance of exploring RNAi-based approaches for pest management Simple SummaryThe control of insect pest species, mainly belonging to Orthoptera, Hemiptera, and Coleoptera species, can be based on novel emerging species-specific pesticides. These consist of dsRNA molecules delivered by feeding to insect larvae or adults, which suppress vital gene functions by RNA-RNA sequence complementarity and RNA interference. However, fewer studies of dsRNA feeding have been performed in dipteran pest insects. Two studies in Orthoptera and Coleoptera species have shown that suppressing intestinal enzymes degrading external dsRNA can improve insect mortality rates. Ceratitis capitata (Tephritidae), the Mediterranean fruit fly (Medfly), is a major dipteran pest significantly impacting fruit and vegetable farming. Currently, its control heavily relies mainly on chemical insecticides, which pose health risks and have effects on beneficial pollinators. Previous attempts to induce mortality by adult dsRNA-feeding in this and other Tephritidae species, such as Bactrocera tryoni and B. dorsalis, showed some effectiveness, but were often limited. We improved this method by simultaneously silencing two intestinal nucleases and a vital gene. We have found a mix of three dsRNAs able to induce much higher mortality (79%) within one week, following only three days of adult feeding.

genetics↗

bioRxiv2020

PBAP chromatin remodeler mediates enhancer-driven transcription inDrosophila

Chromatin remodeler SWI/SNF is an important participant of gene activation acting predominantly by opening chromatin structure on promoters and enhancers. Here we describe its novel mode of action by mediating targeted action of enhancer. We studied functions of two signature subunits of PBAP subfamily, BAP170 and SAYP, in Drosophila. These subunits were stably tethered onto transgene reporter carrying hsp70 core promoter. Tethered subunits mediate transcription of reporter in a pattern prescribed by nearby enhancer in multiple loci throughout the genome, where the reporter construct was located. Both tethered SAYP and BAP170 recruit the whole PBAP complex onto reporter promoter. Studying difference between these subunits, we found that BAP170-dependent transcription is more resistant to depletion of other PBAP subunits, what may imply the principal role of BAP170 in establishing enhancer-dependent transcription. Author SummaryChromatin remodelers are key molecular machines that are responsible for local changes in chromatin structure in the nucleus. However, their functions in gene expression regulation seem to be broader. We describe the involvement of the SWI/SNF family of remodelers in establishing enhancer-promoter communication, which is apparently independent of its local remodeling activity. Using an artificial tethering of a remodeler on a promoter, we demonstrated that promoters of a certain type become responsive to activation by a nearby enhancer only in the presence of the remodeler, while a remodeler tethering itself is insufficient for gene activation. Thus, our approach helps to uncover novel aspects of molecular interplay on regulatory elements during the gene activation process.

genetics↗

bioRxiv2019

Maleness-on-the-Y (MoY) orchestrates male sex determination in major agricultural fruit fly pests

In insects, rapidly evolving primary sex-determining signals are transduced by a conserved regulatory module producing sex-specific proteins that direct sex determination and sexual differentiation1-4. In the agricultural pest Ceratitis capitata (medfly), a Y-linked maleness factor (M) is thought to repress the autoregulatory splicing of transformer (Cctra), which is required in XX individuals to establish and maintain female sex determination5,6. Despite previous attempts of isolating Y-linked genes using the medfly whole genome, the M factor has remained elusive7. Here, we report the identification of a Y-linked gene, Maleness-on the-Y (MoY), and show that it encodes a small novel protein which is both necessary and sufficient for medfly male sex determination. Transient silencing of MoY in XY individuals leads to the development of fertile females while transient expression of MoY in XX individuals results in fertile males. Notably, a cross between these sex reverted individuals gives rise to both fertile males and females indicating that a functional MoY can be maternally transmitted. In contrast to the diversity of M factors found in dipteran species8-11, we discovered MoY orthologues in seven other Tephritid species spanning [~]111 millions of years of evolution (Mya). We confirmed their male determining function in the olive fly (Bactrocera oleae) and the oriental fruit fly (Bactrocera dorsalis). This unexpected conservation of the primary MoY signal in a large number of important agricultural pests12 will facilitate the development of transferable genetic control strategies in these species, for example sterile male releases or sex-ratio-distorting gene drives.

genetics↗