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Lopes, M.

Publications and source records attributed to Lopes, M..

At least 19 recordsLinked to original sources
bioRxiv2026

To Recover or Not to Recover: A Urinary Proteomic Perspective on Severe Acute Kidney Injury

Rationale & Objective Early prediction of renal non-recovery after acute kidney injury (AKI) could support risk-adapted follow-up and clinical decision-making. We evaluated whether a urinary fatty acid-binding protein 3 (FABP3)/apolipoprotein A-I (APOA1) ratio based on Total Protein Approach (TPA) quantification could discriminate renal recovery from non-recovery after severe AKI. Study Design Exploratory biomarker discovery study with outcome-blinded independent validation. Setting & Participants Critically ill adults with KDIGO stage 2 or 3 AKI. Urine was collected 48 hours after AKI diagnosis. The discovery cohort included 20 patients (10 recovered and 10 non-recovered), and the outcome-blinded validation cohort included 10 patients. New Predictor Urinary TPA-derived FABP3/APOA1 ratio (AKI^TPA index). Outcome Renal recovery at day 14, defined as survival with serum creatinine returning to within 0.3 mg/dL or 150% of baseline; patients not meeting these criteria were classified as having non-recovery. Analytical Approach Urinary proteins were analyzed by LC-MS/MS and quantified using TPA. Differential analysis identified FABP3 and APOA1 as oppositely associated with renal outcome. A predefined FABP3/APOA1 threshold of 1 classified patients as non-recovery-like (>1) or recovery-like (<1) and was subsequently applied to the outcome-blinded validation cohort. Results In the discovery cohort, the AKI^TPA index correctly classified 17 of 20 patients (accuracy, 85.0%; sensitivity, 80.0%; specificity, 90.0%; ROC AUC, 0.930). In the validation cohort, 9 patients were evaluable, of whom 7 were correctly classified (accuracy, 77.8%; sensitivity, 75.0%; specificity, 80.0%; ROC AUC, 0.950). Limitations The exploratory design and limited cohort size warrant further validation in larger, independent populations. Conclusions The urinary FABP3/APOA1 TPA ratio showed encouraging preliminary discrimination of renal recovery after severe AKI and warrants prospective clinical validation in larger, independent multicenter cohorts.

biochemistry↗
bioRxiv2026

High regeneration-associated stress defines a distinct HCC subgroup with therapeutically exploitable vulnerabilities

Background: To date, no precision oncology approach has been established for HCC. Despite the diverse underlying causes, HCC development exhibits a uniform pathophysiology characterised by chronic hyper-proliferation, resulting from hepatocyte apoptosis and compensatory liver regeneration. This chronic hyper-proliferative pressure, termed regeneration stress, drives genomic instability during HCC onset, yet its therapeutic potential remains poorly explored. This study aimed to identify targetable vulnerabilities tied to regeneration stress and establish clinically applicable markers for treatment stratification. Methods: Weighted gene co-expression network analysis (WGCNA) was applied on external bulk RNA-seq datasets to define a LIVer REgeneration Stress Signature (LIVRESS). The signature was functionally validated using HCC patient-derived organoids (HCC-Org), and vulnerabilities were mapped using mid-throughput drug screening, single-molecule and single-cell assays, and multi-omic integration. Results: High LIVRESS scores, characterised by enrichment in replication, mitotic and DNA damage repair pathways, identified a subset of HCC patients with aggressive disease and poorer survival across aetiologies. HCC-Org with high LIVRESS scores displayed exquisite sensitivity to multiple inhibitors of the checkpoint kinase ATR. Although HCC-Org models exhibited a baseline reduction in replication fork speed, sensitivity to ATR inhibitor (ATRi) was decoupled from replication fork dynamics and rather linked to intrinsic mitotic instability. ATR inhibition triggers mitotic failure and apoptosis in LIVRESSHigh HCC-Org. This killing effect was significantly potentiated by combining ATRi with PARPi or WEE1i. Multi-omic integration identified KPNA2 as a surrogate biomarker of ATRi sensitivity. Conclusion: Our findings demonstrate that a subset of HCC-Org, characterised by high liver regeneration-associated stress, is vulnerable to ATRi-based therapies. By focusing on a comprehensive regenerative stress model, we establish a framework to stratify HCC patients and implement biomarker-driven, ATR-based therapies for HCC patients with advanced disease. Impact and implications: Regeneration stress is a key factor that drives genomic instability in HCC, providing a basis for the LIVRESS to identify patients dependent on ATR-mediated checkpoints. These findings reveal a conceptual shift for researchers and trialists: ATRi efficacy is decoupled from replication fork dynamics and instead leverages mitotic fragility. Practically, the LIVRESS and its IHC surrogate marker (KPNA2) offer a scalable roadmap for physicians to improve patient stratification in ATRi-based precision oncology trials. While requiring prospective validation, these results pave the way toward biomarker-driven therapies for advanced HCC.

cancer biology↗
bioRxiv2026

Replication fork plasticity is a therapeutic vulnerability in acute myeloid leukemia

Uncontrolled proliferation of myeloid progenitor cells in acute myeloid leukemia (AML) is counteracted in most patients by toxic and often ineffective systemic treatments. Poly (ADP-ribose) polymerase inhibitors (PARPi) show subtype-restricted activity - potent in RUNX1-RUNX1T1 and PML-RAR[a] fusions, limited in KMT2A-rearranged (KMT2A-r) disease - but the lack of molecular understanding has hampered their clinical implementation. We combined single-cell and single-molecule assays on DNA replication intermediates and DNA damage signalling with therapy response readouts to investigate the role of fork plasticity factors in response to PARPi and AML standard-of-care (cytarabine, araC). In PARPi-sensitive AML models, PARP inhibition deregulates RECQ1-mediated fork restart, initially triggering fork acceleration and later fork breakage within the same S phase. Conversely, PARPi resistant KMT2A-r AML lines are protected by PrimPol-dependent DNA synthesis and its inactivation promptly induces fork breakage and PARPi sensitivity. Strikingly, PrimPol overexpression in PARPi-sensitive AML models prevents fork collapse and PARPi/araC therapy response, both in vitro and in vivo, identifying PrimPol as novel predictive biomarker and therapeutic target in AML. Our data uncover novel tissue-specific mechanisms of action for PARPi and pinpoint replication fork plasticity as key molecular determinant of AML therapy response. HighlightsO_LIFork plasticity is a key molecular determinant of treatment response in leukemia. C_LIO_LIPARP inhibition triggers fork breakage via deregulated restart of reversed forks. C_LIO_LIBypassing fork reversal, PrimPol limits therapy-induced DNA damage and cytotoxicity in AML. C_LIO_LIPrimPol drives resistance to cytarabine and PARP inhibition in vitro and in vivo. C_LI

cancer biology↗
bioRxiv2026

Integrated assessment of fatty acid metabolism and cellular energy status using HILIC-MS/MS

Acetyl-CoA and other acyl-CoA thioesters are critical intermediates in the metabolic reactions that cells rely on to produce energy and carry out biosynthesis. Therefore, the analysis of acyl-CoA provides valuable information about the metabolic activity of cells, especially when combined with stable isotope tracing. Acyl-CoA species are routinely monitored by reversed-phase liquid chromatography coupled to tandem mass spectrometry (RPLC-MS/MS). However, drastic differences in the hydrophobicity of short-chain versus long-chain acyl-CoA species have been challenging to accommodate with a single set of RPLC conditions. Here, we describe a convenient method based on hydrophilic interaction liquid chromatography (HILIC-MS/MS) for the concurrent detection of both short-chain and long-chain acyl-CoA and their corresponding acyl-carnitine species. Using this strategy, we tracked the metabolism of isotope-labeled fatty acids in multiple cell lines, which revealed differences in their propensities for fatty acid oxidation and the extent to which isotope incorporation into acyl-CoA mirrored that of acyl-carnitine. We also applied the HILIC-MS/MS workflow to the analysis of NADH and ATP, making it a useful technique for gauging cellular bioenergetics as reflected by the acetyl-CoA/CoA, NADH/NAD+, and ATP/ADP ratios. Altogether, this HILIC-MS/MS platform enables a streamlined analysis of acyl-CoA species and other key intermediates in cell metabolism.

biochemistry↗
bioRxiv2026

Non-canonical ATR signalling via NBS1 phosphorylation propagates fork slowing from stressed to unperturbed nuclear regions

DNA replication forks frequently encounter obstacles and remodel into four-way junctions to actively slow DNA fork progression. Fork slowing can also spread to undamaged forks via an ATR-dependent mechanism that remained elusive. Here, using mild genotoxic stress, we show that fork slowing and reversal require full ATR activity, but no canonical ATR activators and signalling partners, defining a non-canonical ATR pathway distinct from origin firing control. Phospho-proteomics in S-phase cells under checkpoint-blind replication stress identified a subset of ATR-dependent phospho-sites, such as S343 on NBS1, the regulatory subunit of the MRN complex. This residue is essential to stimulate MRN exonuclease activity in vitro and required in cells for global fork slowing upon mild DNA damage. Ultimately, local UV-C micro-irradiation reveals that ATR-dependent MRN-stimulated resection dampens DNA synthesis at lesions and propagates fork slowing to undamaged chromatin, supporting MRN-mediated ssDNA exposure as a mean to coordinate replication slowdown across the nucleus.

cell biology↗
bioRxiv2026

The FANCM-RMI1/2 complex promotes genomic instability and PARP inhibitor sensitivity in BRCA2-deficicient cells.

Cancer cells lacking BRCA1 or BRCA2 must adapt to survive and proliferate despite defective DNA repair and high genomic instability. Restoration of homologous recombination (HR) through loss of DNA end protection rescues growth defects and promotes PARP inhibitor (PARPi) resistance in BRCA1-deficient cells; however, the genetic basis of adaptation to BRCA2 loss remains largely unexplored. To delineate BRCA1- and BRCA2-specific adaptation trajectories, we established a fully isogenic screening platform in mouse embryonic stem cells engineered for acute depletion of either protein. This approach uncovered hundreds of genes with shared, distinct, or even opposing effects between the two BRCA-deficiency states. We identified FANCM and its interacting partners RMI1/2, CENPS/MHF1, CENPX/MHF2, and FAAP24 as essential in BRCA1-deficient cells but toxic in BRCA2-deficient contexts. Loss of FANCM in BRCA2-deficient cells alleviated genomic instability and proliferation defects by preventing RMI1/2-dependent replication fork degradation, without rescuing HR. Moreover, we show that the FANCM-RMI1/2 complex drives PARPi sensitivity in both mouse and human BRCA2-deficient cells, in contrast to the 53BP1-SHLD-CST axis in BRCA1-deficient cells. These findings reveal distinct adaptation routes to BRCA1 and BRCA2 loss and establish FANCM as a determinant of BRCA2-specific vulnerability and therapeutic response, with direct implications for tailoring prevention and therapy according to BRCA mutation status.

cancer biology↗
bioRxiv2025

ACSS2 mediates prenatal alcohol exposure-related morphological and behavioral phenotypes

The metabolic enzyme Acetyl-CoA Synthetase 2 (ACSS2) recently emerged as an unexpected regulator of molecular and behavioral changes associated with alcohol use. Its role during prenatal exposure, however, remains unknown. Here, we use a combination of proteomic, genomic and behavioral approaches to establish ACSS2 as a key mediator of prenatal alcohol exposure-related phenotypes. We define the developmental window during which ACSS2 translocates to nuclei in the mouse brain, and show that alcohol-derived acetate is incorporated into fetal brain histone acetylation in utero. Using genetically engineered mice not expressing ACSS2, we demonstrate that loss of this enzyme attenuates chronic prenatal alcohol exposure-induced craniofacial abnormalities, motor function deficits, cognitive impairments as well as associated chromatin and gene expression changes in the dorsal hippocampus and the cerebellar vermis. Our results outline a previously unknown mechanism underlying prenatal alcohol exposure-related phenotypes regulated by ACSS2, which will inform the development of future therapeutic interventions. HIGHLIGHTSO_LIACSS2 translocates to nuclei during in utero brain development C_LIO_LIAlcohol-derived acetate is incorporated into fetal brain histone acetylation C_LIO_LIPrenatal alcohol exposure results in long-lasting and ACSS2-dependent chromatin and gene expression changes in the hippocampus and cerebellar vermis C_LIO_LILoss of ACSS2 attenuates molecular changes, craniofacial abnormalities and cognitive impairments linked to prenatal alcohol exposure C_LI

neuroscience↗
bioRxiv2025

Elevations in plasma proinsulin predict the development of diabetes in NOD mice

The global incidence of type 1 diabetes (T1D) continues to rise, yet reliable biomarkers for predicting disease onset remain limited. Studies have demonstrated persistent proinsulin secretion in individuals living with T1D, suggesting a processing impairment. Proinsulin is processed into mature active insulin by the prohormone convertases PC1/3, PC2, and carboxypeptidase E. We hypothesized that elevated circulating proinsulin-to-C-peptide (PI:C) ratios precede the onset of diabetes and are associated with reduced expression of PC1/3 in pancreatic beta cells. Non-obese diabetic (NOD) mice were monitored for changes in plasma proinsulin, C-peptide, and beta cell Pc1/3 levels prior to diabetes onset. Female NOD mice that progressed to diabetes exhibited increased plasma proinsulin and PI:C ratios several weeks before the onset of diabetes compared to mice that remained normoglycemic. Plasma proinsulin levels were predictive of diabetes onset, with earlier elevations observed in mice that progressed to disease more rapidly. These increases in plasma proinsulin and PI:C ratios correlated with reduced beta cell Pc1/3 expression. These findings support the potential of plasma proinsulin and PI:C ratios as predictive biomarkers for T1D development and implicate diminished Pc1/3 expression as a possible mechanism underlying impaired proinsulin processing.

cell biology↗
bioRxiv2025

The modifiers that cause changes in gene essentiality

The phenotype of a mutation often differs across genetically distinct individuals. In the most extreme case, a gene can be essential for viability in one genetic background, but dispensable in another. Although genetic context-dependency of mutant phenotypes is frequently observed, the underlying causes often remain elusive. Here, we investigated the genetic changes responsible for differences in gene essentiality across 18 genetically diverse natural yeast strains. First, we identified 39 genes that were essential in the laboratory reference strain but not required for viability in at least one other genetic background, suggesting that the natural strain contained suppressor variants that could bypass the need for the essential gene. We then mapped and validated the causal bypass suppressor variants using bulk segregant analysis and allele replacements. Bypass suppression was generally driven by a single modifier gene that tended to differ between genetic backgrounds. The suppressors often indirectly counteracted the effect of deleting the essential gene, for instance by changing the transcriptome of a cell. Context-dependent essential genes and their bypass suppressors were frequently co-mutated across 1,011 yeast isolates and identified naturally occurring evolutionary trajectories. Overall, our results highlight the relatively high frequency of bypass suppression in natural populations, as well as the underlying variants and mechanisms. A thorough understanding of the causes of genetic background effects is crucial for the interpretation of genotype-to-phenotype relationships, including those associated with human disease.

genomics↗
bioRxiv2025

Nucleoplasmic Lamin A/C controls replication fork restart upon stress by modulating local H3K9me3 and ADP-ribosylation levels

Mild replication interference is a consolidated strategy for cancer chemotherapy. Tolerance to mild replication stress (RS) relies on active fork slowing, mediated by transient fork reversal and RECQ1-assisted restart, and modulated by PARP1 and nuclear architectural components via yet-elusive mechanisms. We combined acute protein inactivation with cell biology and single-molecule approaches to investigate the role of Lamin A/C upon mild RS. We found that Lamin A/C dynamically interacts with replication factories throughout the nucleus and, together with its nucleoplasmic partner LAP2, is required to induce active fork slowing and maintain chromosome stability upon mild genotoxic treatments. Inactivating nucleoplasmic Lamin A/C reduces poly-ADP-ribosylation (PAR) levels at nascent DNA, triggering deregulated RECQ1-mediated restart of reversed forks. Moreover, we found that the heterochromatin mark H3K9me3, previously reported at stalled forks, also accumulates in response to mild RS. H3K9me3 accumulation requires Lamin A/C, which prevents its premature removal by the histone demethylase JMJD1A/KDM3A. H3K9me3 loss per se phenocopies Lamin A/C inactivation, reducing PAR levels and deregulating RECQ1 activity at forks. Hence, nucleoplasmic Lamin A/C, H3K9me3 and PARylation levels are crucial, mechanistically-linked modulators of fork slowing, remodelling and restart upon mild RS, with important implications for chemotherapy response and Lamin A/C deregulation in human disease.

molecular biology↗
bioRxiv2024

An optimized and robust workflow for quantifying the canonical histone ubiquitination marks H2AK119ub and H2BK120ub by LC-MS/MS

The eukaryotic genome is packaged around histone proteins, which are subject to a myriad of post-translational modifications. By controlling DNA accessibility and the recruitment of protein complexes that mediate chromatin-related processes, these modifications constitute a key mechanism of epigenetic regulation. Since mass spectrometry can easily distinguish between these different modifications, it has become an essential technique in deciphering the histone code. Although robust LC-MS/MS methods are available to analyze modifications on the histone N-terminal tails, routine methods for characterizing ubiquitin marks on histone C-terminal regions, especially H2AK119ub, are less robust. Here we report the development of a simple workflow for the detection and improved quantification of the canonical histone ubiquitination marks H2AK119ub and H2BK120ub. The method entails a fully tryptic digestion of acid-extracted histones followed by derivatization with heavy or light propionic anhydride. A pooled sample is then spiked into oppositely labeled single samples as a reference channel for relative quantification, and data is acquired using PRM-based nanoLC-MS/MS. We validated our approach with synthetic peptides as well as treatments known to modulate the levels of H2AK119ub and H2BK120ub. This new method complements existing histone workflows, largely focused on the lysine-rich N-terminal regions, by extending modification analysis to other sequence contexts.

biochemistry↗
bioRxiv2024

Fusion of blood vessel organoids with human pancreatic islets improves insulin response over time.

Pancreatic islet transplantation is a promising treatment strategy for type 1 diabetes, however there are still major challenges to overcome, including vascularization. Novel strategies for the generation of prevascularized islets with native microvessels have reported improved islet functionality, vascularization and engraftment emphasizing integral role of microvascular bed. Recently a new model of self-organizing three-dimensional human blood vessel organoids (BVOs) has been developed from human pluripotent stem cells (hPSCs), composed of both endothelial and mural cells. BVO recapitulate key features of human microvasculature such as formation of vascular network, vascular lumen and basement membrane, and have been shown to be perfusable. Here, we report a new strategy to construct prevascularized islets by fusion with hPSC-derived BVOs. We demonstrate that islets and BVOs in co-culture leads to fusion and improved insulin secretion over time, on two independent human islet donors, suggesting a new therapeutic approach for pancreatic islet transplantation and type 1 diabetes modeling.

bioengineering↗
bioRxiv2023

H2AX promotes replication fork degradation and chemosensitivity in BRCA-deficient tumours

Histone H2AX plays a key role in DNA damage signalling in the surrounding regions of DNA double-strand breaks (DSBs)1,2. In response to DNA damage, H2AX becomes phosphorylated on serine residue 139 (known as {gamma}H2AX), resulting in the recruitment of the DNA repair effectors 53BP1 and BRCA13-6. Here, by studying resistance to poly(ADP-ribose) polymerase (PARP) inhibitors in BRCA1/2-deficient mammary tumours7,8, we identify a novel function for {gamma}H2AX in orchestrating drug-induced replication fork degradation. Mechanistically, {gamma}H2AX-dependent replication fork degradation is elicited by the inhibition of CtIP-mediated fork protection. As a result, H2AX loss restores replication fork stability and increases chemoresistance in BRCA1/2-deficient tumour cells without restoring homology-directed DNA repair, as highlighted by the lack of DNA damage-induced RAD51 foci. Furthermore, in the attempt to discover acquired genetic vulnerabilities, we find that ATM inhibition overcomes PARP inhibitor (PARPi) resistance in H2AX-deficient tumours by interfering with CtIP-mediated fork protection of stalled forks. In summary, our results demonstrate a novel role for H2AX in replication fork biology in BRCA-deficient tumours and establish a function of H2AX separable from its classical role in DNA damage signalling and DSB repair.

cancer biology↗
bioRxiv2023

TGFβ controls alveolar type 1 epithelial cell plasticity and alveolar matrisome gene transcription

Premature birth disrupts normal lung development and places infants at risk for bronchopulmonary dysplasia (BPD), a disease increasing in incidence which disrupts lung health throughout the lifespan. The TGF{beta} superfamily has been implicated in BPD pathogenesis, however, what cell lineage it impacts remains unclear. We show that Tgfbr2 is critical for AT1 cell fate maintenance and function. Loss of Tgfbr2 in AT1 cells during late lung development leads to AT1-AT2 cell reprogramming and altered pulmonary architecture, which persists into adulthood. Restriction of fetal lung stretch and associated AT1 cell spreading through a model of oligohydramnios enhances AT1-AT2 reprogramming. Transcriptomic and proteomic analysis reveal the necessity of Tgfbr2 expression in AT1 cells for extracellular matrix production. Moreover, TGF{beta} signaling regulates integrin transcription to alter AT1 cell morphology, which further impacts ECM expression through changes in mechanotransduction. These data reveal the cell intrinsic necessity of TGF{beta} signaling in maintaining AT1 cell fate and reveal this cell lineage as a major orchestrator of the alveolar matrisome.

cell biology↗
bioRxiv2023

Replication fork plasticity upon replication stress requires rapid nuclear actin polymerization

Cells rapidly respond to replication stress actively slowing fork progression and inducing fork reversal. How replication fork plasticity is achieved in the context of nuclear organization is currently unknown. Using nuclear actin probes in living and fixed cells, we visualized nuclear actin filaments in unperturbed S phase, rapidly extending in number and thickness upon genotoxic treatments, and taking frequent contact with replication factories. Chemically or genetically impairing nuclear actin polymerization shortly before these treatments prevents active fork slowing and abolishes fork reversal. Defective fork plasticity is linked to reduced recruitment of RAD51 and SMARCAL1 to nascent DNA. Conversely, PRIMPOL gains access to replicating chromatin, promoting unrestrained and discontinuous DNA synthesis, which is associated with increased chromosomal instability and decreased cellular resistance to replication stress. Hence, nuclear F-actin orchestrates replication fork plasticity and is a key molecular determinant in the rapid cellular response to genotoxic treatments.

cancer biology↗
bioRxiv2023

Single molecule MATAC-seq reveals key determinants of DNA replication origin efficiency

SummaryStochastic origin activation gives rise to significant cell-to-cell variability in the pattern of genome replication. The molecular basis for heterogeneity in efficiency and timing of individual origins is a long-standing question. Here, we developed Methylation Accessibility of TArgeted Chromatin domain Sequencing (MATAC-Seq) to determine single-molecule chromatin accessibility of specific genomic loci after targeted purification in their native chromatin context. Applying MATAC-Seq to selected early-efficient (EE) and late-inefficient (LI) budding yeast replication origins revealed large heterogeneity of chromatin states. Disruption of INO80 or ISW2 chromatin remodeling complexes leads to changes at individual nucleosomal positions that correlate with changes in their replication efficiency. We found a chromatin state with an optimal 100-115bp nucleosome-free region in combination with surrounding well-positioned nucleosomes and open +2 linker region is a strong predictor for efficient origin activation. Thus, MATAC-Seq identifies the large spectrum of alternative chromatin states that co-exist on a given locus previously masked in population-based experiments and provides a mechanistic basis for origin activation heterogeneity during DNA replication of eukaryotic cells. Consequently, our single-molecule assay for chromatin accessibility will be ideal to define single-molecule heterogeneity across many fundamental biological processes such as transcription, replication, or DNA repair in vitro and ex vivo.

biochemistry↗
bioRxiv2022

MDC1 counteracts restrained replication fork restart and its loss causes chemoresistance in BRCA1/2-deficient mammary tumors

MDC1 is a key protein in DNA damage signaling. When DNA double-strand breaks (DSBs) occur, MDC1 localizes to sites of damage to promote the recruitment of other factors, including the 53BP1-mediated DSB repair pathway. By studying mechanisms of poly(ADP-ribose) polymerase inhibitor (PARPi) resistance in BRCA2;p53-deficient mouse mammary tumors, we identified a thus far unknown role of MDC1 in replication fork biology. MDC1 localizes at active replication forks during normal fork replication and its loss reduces fork speed. We show that MDC1 contributes to the restart of replication forks and thereby promotes sensitivity to PARPi and cisplatin. Loss of MDC1 causes MRE11-mediated resection, resulting in delayed fork restart. This improves DNA damage tolerance and causes chemoresistance in BRCA1/2-deficient cells. Hence, our results show a role for MDC1 in replication fork progression that mediates PARPi- and cisplatin-induced DNA damage, in addition to its role in DSB repair.

molecular biology↗