Biology subjects

Goncalves, T.

Publications and source records attributed to Goncalves, T..

8 recordsLinked to original sources

bioRxiv2026

Weak supervision of H&E slides reveals systems-level biology and functional states that govern therapeutic resistance

Precision oncology lacks scalable methods to identify the mechanisms that mediate therapeutic resistance for individual patients. Resistance often arises from focal cellular niches that are obscured by bulk profiling and costly to resolve with multi-omics. Here, we show that deep learning (DL), applied to routine histology, can localize focal tissue regions enriched for therapeutically relevant biology. Using 3111 breast cancer H&E slides with matched bulk transcriptomics, we trained weakly-supervised DL models to infer activities of immune, metabolic, and tumor-intrinsic phenotypes implicated in therapeutic resistance (AUROC>0.80; PCC>0.64). Accurate inference of these phenotypes should identify tissue regions enriched for the corresponding biological signal. Therefore, we validated phenotype inference and spatial localization with complementary analyses. Tissue-matched multiplexed immunofluorescence showed concordance between inferred immune states and corresponding cell fractions (p=0.006-0.106). Across multi-institutional cohorts, model-derived phenotypes recovered expected relationships with therapeutic outcomes (p<0.045). Finally, in a blinded evaluation, pathologists confirmed that model-derived high-attention regions were enriched for phenotype-specific morphology (p<2.408*10-5). Because evaluated phenotypes represent diverse mechanisms of resistance across therapeutic modalities, these findings provide a foundation for resistance-directed localization using therapeutic outcomes as supervision. By directing deep profiling toward model-prioritized regions, this framework could enable scalable nomination of candidate mediators of resistance for subsequent functional validation across real-world patient populations. One sentence summaryWeakly supervised deep learning localizes focal tissue regions enriched for therapeutically relevant biology in routine histology, thus offering a scalable strategy to study therapeutic resistance across large patient populations.

biophysics↗

bioRxiv2025

ESPWA: a deep learning-enabled tool for precision-based use of endocrine therapy in resource-limited settings

Immunohistochemistry for estrogen receptor (ER) expression is often unavailable in low-and-middle-income countries (LMICs), leading to empiric use of endocrine therapy (ET) and unnecessary toxicity in ER-negative patients. To address this unmet need, we developed ESPWA, a deep-learning model trained on 3448 H&E slides and tissue-matched ER status from breast cancer patients treated at Zanmi Lasante (ZL), Haiti. A model trained on The Cancer Genome Atlas (TCGA) exhibited substantial domain shift when applied to the ZL cohort, with AUROCs dropping from 0.846 on TCGA cross-validation to 0.671 on the ZL cohort. In contrast, ESPWA demonstrated improved performance on ZL cross-validation (AUROC=0.790; p=0.005). In an independent test set of 134 Haitian patients with parallel slides prepared and scanned in Mirebalais Hospital (Haiti) and Brigham and Womens Hospital, ESPWA was robust to variations in slide preparation, quality, and scanners, achieving AUROCs of 0.794 on BWH-prepared WSIs and 0.805 on Mirebalais-prepared WSIs. Prospective studies using ESPWA are underway in sub-Saharan Africa to evaluate its utility in informing precision-based use of ET.

cancer biology↗

bioRxiv2024

Th17 cells require the DNA repair sensor XPC to control oxidative DNA damage

Th17 cells are critical for mucosal immunity, producing IL-17A, IL-17F, and IL-22, but dysregulated Th17 responses are implicated in autoimmune diseases. Despite their susceptibility to oxidative stress in certain conditions, Th17 cells exhibit reduced oxidative DNA damage and cell death compared to other T helper subsets. However, the mechanisms that protect Th17 cells from oxidative stress are poorly understood. Here, we identify Xeroderma Pigmentosum Complementation Group C (XPC) as a key regulator of DNA repair and genomic stability in Th17 cells. In XPC-deficient mice, we demonstrate that the absence of XPC impairs Th17 differentiation, as evidenced by reduced expression of key differentiation markers, including Rorc and Il17a, along with decreased IL-17A production. This deficiency leads to increased oxidative stress, DNA damage, and a metabolic shift from glycolysis to oxidative phosphorylation. Moreover, the transcription factor BATF directly regulates XPC expression, linking the BATF-XPC axis to the maintenance of Th17 cell function. Importantly, we find that restoring antioxidant capacity with N-Acetylcysteine (NAC) rescues IL-17A production and reduces DNA damage in XPC-deficient Th17 cells. Mechanistically, we find that XPC interacts with OGG1, a DNA glycosylase involved in the repair of oxidative DNA damage, highlighting XPCs role in maintaining genomic integrity during Th17 cell differentiation. Our findings reveal a previously unrecognized role for XPC in protecting Th17 cells from oxidative stress, ensuring their proper differentiation and function, with potential implications for targeting DNA repair pathways in autoimmune and inflammatory diseases.

immunology↗

bioRxiv2024

Brain-wide neuronal circuit connectome of human glioblastoma

Glioblastoma (GBM), a universally fatal brain cancer, infiltrates the brain and can be synaptically innervated by neurons, which drives tumor progression1-6. Synaptic inputs onto GBM cells identified so far are largely short-range and glutamatergic7-9. The extent of integration of GBM cells into brain-wide neuronal circuitry is not well understood. Here we applied a rabies virus-mediated retrograde monosynaptic tracing approach10-12 to systematically investigate circuit integration of human GBM organoids transplanted into adult mice. We found that GBM cells from multiple patients rapidly integrated into brain-wide neuronal circuits and exhibited diverse local and long-range connectivity. Beyond glutamatergic inputs, we identified a variety of neuromodulatory inputs across the brain, including cholinergic inputs from the basal forebrain. Acute acetylcholine stimulation induced sustained calcium oscillations and long-lasting transcriptional reprogramming of GBM cells into a more invasive state via the metabotropic CHRM3 receptor. CHRM3 downregulation suppressed GBM cell invasion, proliferation, and survival in vitro and in vivo. Together, these results reveal the capacity of human GBM cells to rapidly and robustly integrate into anatomically and molecularly diverse neuronal circuitry in the adult brain and support a model wherein rapid synapse formation onto GBM cells and transient activation of upstream neurons may lead to a long-lasting increase in fitness to promote tumor infiltration and progression.

cancer biology↗

bioRxiv2023

Loss of FAM111B protease mutated in hereditary fibrosing poikiloderma syndrome negatively regulates telomere length

Hereditary fibrosing poikiloderma (HFP) is a rare human dominant negative disorder caused by mutations in the FAM111B gene that encodes a nuclear trypsin-like serine protease. HFP patients present with symptoms including skin abnormalities, tendon contractures, myopathy and lung fibrosis. We characterised the cellular roles of human FAM111B using U2OS and MCF7 cell lines and report here that the protease interacts with components of the nuclear pore complex. Loss of FAM111B expression resulted in abnormal nuclear shape and reduced telomeric DNA content suggesting that FAM111B protease is required for normal telomere length; we show that this function is independent of telomerase or recombination driven telomere extension. Even though FAM111B-deficient cells were proficient in DNA repair, they showed hallmarks of genomic instability such as increased levels of micronuclei and ultra-fine DNA bridges. Interestingly, FAM111B variants, including mutations that cause HFP, showed more frequent localisation to the nuclear lamina suggesting that accumulation of mutant FAM111B at the nuclear periphery may drive the disease pathology.

cell biology↗

bioRxiv2021

Transcriptional regulation of neural stem cell expansion in adult hippocampus

Experience governs neurogenesis from radial-glial neural stem cells (RGLs) in the adult hippocampus to support memory. Transcription factors in RGLs integrate physiological signals to dictate self-renewal division mode. Whereas asymmetric RGL divisions drive neurogenesis during favorable conditions, symmetric divisions prevent premature neurogenesis while amplifying RGLs to anticipate future neurogenic demands. The identities of transcription factors regulating RGL symmetric self-renewal, unlike those that regulate RGL asymmetric self-renewal, are not known. Here, we show that the transcription factor Kruppel-like factor 9 (Klf9) is elevated in quiescent RGLs and inducible, deletion of Klf9 promotes RGL activation state. Clonal analysis and longitudinal intravital 2-photon imaging directly demonstrate that Klf9 functions as a brake on RGL symmetric self-renewal. In vivo translational profiling of RGLs lacking Klf9 generated a blueprint of RGL symmetric self-renewal for stem cell community. Together, these observations identify Klf9 as a transcriptional regulator of neural stem cell expansion in the adult hippocampus.

neuroscience↗

bioRxiv2021

Activity-dependent LTP in the dentate gyrus promotes epileptic seizures

Epilepsy is a devastating brain disorder whose cellular mechanisms remain poorly understood. Excitatory mossy cells (MCs) in the dentate gyrus of the hippocampus are implicated in temporal lobe epilepsy, the most common form of focal epilepsy in adults. However, the role of MCs during initial seizures, before MC loss occurs, is unclear. Here, we show that initial seizures induced with kainic acid (KA) intraperitoneal injection in adult mice, a well-established model of experimental epilepsy, not only increased MC and granule cell (GC) activity in vivo, but also triggered a BDNF-dependent long-term potentiation at MC-GC synapses (MC-GC LTP). In vivo induction of MC-GC LTP worsened KA-induced seizures, whereas selective MC silencing and Bdnf genetic removal from GCs, which abolishes LTP, were both anti-epileptic. Thus, initial seizures strengthen MC-GC synaptic transmission, thereby promoting epileptic activity. Our findings reveal a potential mechanism of epileptogenesis that may help develop therapeutic strategies for early intervention.

neuroscience↗

bioRxiv2020

Selective Elimination of Osteosarcoma Cell Lines with Short Telomeres by ATR Inhibitors

To avoid replicative senescence or telomere-induced apoptosis, cancers employ telomere maintenance mechanisms (TMMs) involving either the upregulation of telomerase or the acquisition of recombination-based alternative telomere lengthening (ALT). The choice of TMM may differentially influence cancer evolution and be exploitable in targeted therapies. Here, we examine TMMs in a panel of seventeen osteosarcoma-derived cell lines defining three separate groups according to TMM. Eight were ALT-positive, including the previously uncharacterised lines, KPD and LM7. ALT-negative cell lines were further classified into two groups according to their telomere length. HOS-MNNG, OHSN, SJSA-1, HAL, 143b and HOS displayed sub-normally short telomere length, while MG-63, MHM and HuO-3N1 displayed long telomeres. Importantly, sub-normally short telomeres were significantly associated with hypersensitivity to three different therapeutics targeting the ataxia telangiectasia and Rad3-related (ATR) kinase - AZD-6738/Ceralasertib, VE-822/Berzoserib and BAY-1895344 - compared to long telomeres, maintained via ALT or telomerase. Within 24 hours of ATR inhibition, cells with short but not long telomeres displayed chromosome bridges and underwent cell death, indicating a selective dependency on ATR for chromosome stability. Collectively, our work provides a resource to identify links between TMMs and drug sensitivity in osteosarcoma and indicates that telomere length predicts ATR-inhibitor sensitivity in cancer.

cancer biology↗