Biology subjects

Lin, I.-H.

Publications and source records attributed to Lin, I.-H..

7 recordsLinked to original sources

bioRxiv2025

Transcriptional Circuitry in HGSOC: A Dynamic Three-State Model Informed by a Living Biobank of Purified Tumour Fractions

High-grade serous ovarian cancer (HGSOC) is a heterogeneous disease, but efforts to define transcriptional subtypes using bulk RNA sequencing have been confounded by the presence of non-malignant cells. As a result, it remains unclear whether tumour-cell-intrinsic states exist, and whether these represent stable disease subtypes or are dynamically remodelled during disease progression and treatment. Here, we address this question using a living biobank of patient-derived ovarian cancer models (OCMs) cultured as purified tumour-cell populations under uniform conditions. RNA sequencing followed by unsupervised non-negative matrix factorisation (NMF) revealed a robust, hierarchical architecture comprising three core tumour-cell-intrinsic subtypes: the Alpha cluster, marked by cell-cycle deregulation and E2F-driven replication stress; the Beta cluster, defined by tumour-cell-intrinsic immune mimicry and inflammatory signalling; and the Gamma cluster, characterised by epithelial identity, extracellular matrix engagement, and metabolic adaptation. At higher clustering resolution, a fourth cluster, Delta, emerged as a Gamma sub-lineage distinguished by a vesicle-oriented, neuronal-like secretory programme. By projecting cluster labels onto a subset of matched longitudinal OCMs using non-negative least squares, we show that while some tumours retain stable subtype identities, others display transcriptional plasticity, including transitions from epithelial-like Gamma states to more proliferative or secretory phenotypes. Together, these findings define the core architecture and dynamic potential of tumour-cell-intrinsic transcriptional states within HGSOC, thereby bridging legacy bulk classifications with emerging single-cell insights, establishing a framework for more precise patient stratification.

cancer biology↗

bioRxiv2025

Migratory dermal gamma delta T cells determine the balance between lung immunity and tissue damage during Nippostrongylus brasiliensis infection

Many helminth parasites migrate through multiple host organs during infection but how immune responses are relayed across these tissues is still poorly understood. To investigate the cellular and molecular aspects of inter-tissue communication during infection we established a percutaneous infection model with the tissue-migrating nematode Nippostrongylus brasiliensis. High-dimension profiling of the initial cutaneous immune response revealed that dermal {gamma}{delta} T cells become activated via an IL-1R-dependent mechanism, engage cell motility-associated transcriptional pathways and leave the skin after parasite invasion. Chemical and genetic inhibition of leukocyte migration prevents the accumulation of IL-17-producing {gamma}{delta} T cells in the lungs. Notably, bypassing the skin phase of infection, and therefore preventing dermal {gamma}{delta} T cell migration, dampens the increase in early IL-17 production in the lungs, and, instead, leads to enhanced IFN-{gamma} responses together with increased lung damage. Collectively, our data highlights a critical skin-lung axis regulating host-parasite interactions and safeguarding lung health.

immunology↗

bioRxiv2024

Integrin alpha1 beta1 promotes interstitial fibrosis in a mouse model of polycystic kidney disease

Fibrosis is the cause of end-stage kidney failure in patients with Autosomal Dominant Polycystic Kidney Disease (ADPKD). The molecular and cellular mechanisms involved in fibrosis are complex and anti-fibrotic therapies have so far failed to make an impact on patient welfare. Using unbiased proteomics analysis on the Pkd1nl/nl mouse, we found that expression of the integrin 1 subunit is increased in this model of ADPKD. In human ADPKD tissue and two single cell RNA kidney disease datasets, ITGA1 was also upregulated. To investigate the functional role of this integrin subunit in ADPKD, we generated a Pkd1nl/nlItga1-/- mouse. We observed a significant reduction in kidney volume and kidney dysfunction in mice lacking the integrin 1 subunit. Kidneys from Pkd1nl/nlItga1-/- mice had smaller cysts and reduced interstitial expansion and tubular atrophy. Picrosirius red staining identified a restriction in collagen staining in the interstitium and the myofibroblast marker smooth muscle actin was also downregulated. Myofibroblast cell proliferation was reduced in Pkd1nl/nlItga1-/- mice and primary fibroblast cultures demonstrated an abrogated fibrogenic phenotype in integrin 1-depleted fibroblasts. These results highlight a previously unrecognised role for the integrin 1 subunit in kidney fibrosis.

pathology↗

bioRxiv2024

Combined PARP14 Inhibition and PD-1 Blockade Promotes Cytotoxic T Cell Quiescence and Modulates Macrophage Polarisation in Relapsed Melanoma

Programmed Cell Death 1 (PD-1) signaling blockade effectively restores immune surveillance to treat melanoma. However, chronic interferon-gamma (IFN{gamma}) -driven immune homeostatic mechanisms in melanoma cells contribute to immune evasion and acquired resistance. We previously demonstrated that poly ADP ribosyl polymerase 14 (PARP14), an IFN{gamma}-responsive gene product, in part mediates IFN{gamma}-driven resistance, as its inhibition prolonged PD-1 blockade responses in preclinical models. Nevertheless, PARP14 inhibition alone could not achieve full tumor clearance, indicating additional resistance mechanisms. Herein, we identify a robust PARP14 catalytic inhibitor (PARP14i) gene signature associated with improved patient survival. We elucidate immune and tumor cell adaptations to PARP14 inhibition combined with PD-1 blockade using preclinical models. This combination therapy suppressed tumor-associated macrophages while increasing pro-inflammatory memory macrophages. Notably, it preserved cytotoxic T cell function by inducing a quiescent state, mitigating terminal exhaustion. Despite enhancing immune responses, adaptive resistance mechanisms emerged in tumor cells, engaging alternative immune evasion pathways. These findings indicate that this combination therapy primes immune cells for further therapeutic intervention, providing a promising strategy to overcome resistance and optimize treatment outcomes. SummaryWhile immune checkpoint inhibitors, such as -PD-1 therapy, provide significant clinical benefits, many tumors develop resistance and relapse. Re-treatment with -PD-1 often fails because T cells lose their function (a process called exhaustion), and immune-suppressing cells like tumor-associated macrophages (TAMs) increase in the tumor environment, enabling tumors to evade immune attack. Recent studies have shown that a small molecule inhibitor of PARP14 can restore sensitivity to -PD-1 therapy by remodeling the tumor environment. This includes increasing immune cell infiltration and improving antigen presentation, which helps the immune system recognize tumor cells. Using single-cell RNA sequencing, we discovered that this therapy induces a new state of T cell dormancy, where cytotoxic T cells temporarily stop attacking but retain the potential to be reactivated by additional treatments. This finding opens new opportunities to sustain immune responses and improve outcomes for patients who relapse after immunotherapy. Graphical Summary O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/615178v2_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1e6dcf4org.highwire.dtl.DTLVardef@1b44548org.highwire.dtl.DTLVardef@309cb1org.highwire.dtl.DTLVardef@17f6202_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

The level of HAND1 controls the specification of multipotent cardiac and extraembryonic progenitors

Diverse sets of progenitors contribute to the development of the embryonic heart, but the mechanisms of their specification have remained elusive. Here, using a human pluripotent stem cell (hPSC) model, we deciphered cardiac and non-cardiac lineage trajectories in differentiation and identified transcription factors underpinning cell specification, identity and function. We discovered a concentration-dependent, fate determining function in mesodermal progenitors for the basic helix-loop-helix transcription factor HAND1 and uncovered its gene regulatory network. At low level, HAND1 directs differentiation towards multipotent juxta-cardiac field progenitors able to make cardiomyocytes and epicardial cells, whereas at high level it promotes the development of extraembryonic mesoderm. Importantly, HAND1-low progenitors can be propagated in their multipotent state. This detailed mechanistic insight into human development will accelerate the delivery of effective disease modelling, including for congenital heart disease, and cell therapy-based regenerative medicine.

developmental biology↗

bioRxiv2020

Reduced PABPN1 levels causes cytoskeleton disorganization and aberrant differentiation

The polyadenylation binding protein nucleus 1 (PABPN1), a multifactorial regulator of mRNA processing, regulates muscle wasting and atrophy. Previously, we elucidated the PABPN1-dependent proteome and found that levels of structural proteins, sarcomeric and cytoskeletal, were highly altered. We identified MURC, a plasma membrane-associated protein, to be affected by the cytoskeletal stability and suggest that MURC is a novel marker for impaired regeneration in muscles. We also studied the spatial organization of muscle structural proteins in 2D and 3D cell models with reduced PABPN1 levels (named here as shPAB). We show that dysregulation of cytoskeletal proteins in the shPab proteome is associated with a cytoskeleton lacking a polarized organization in muscle cells. We show that consequently, the cell mechanical features as well as myogenic differentiation are significantly reduced. We then show that restoring cytoskeletal stability, by actin overexpression in shPAB was beneficial for cell fusion and for the expression of sarcomeric proteins in shPAB models. We suggest that poor cytoskeleton mechanical features are caused by altered expression levels and contribute to aging-associated muscle wasting and atrophy.

cell biology↗

bioRxiv2019

Neuroprotective effects of exogenous erythropoietin in Wistar rats by downregulating apoptotic factors to attenuate N-methyl-D-aspartate-mediated retinal ganglion cells death

The aim of this study was to investigate whether exogenous erythropoietin (EPO) administration attenuates N-methyl-D-aspartate (NMDA)-mediated excitotoxic retinal damage in Wistar rats. The survival rate of retinal ganglion cells (RGCs) were investigated by flat mount analysis and flow cytometry. A group of male Wistar rats were randomly assigned to five groups: negative control, NMDA80 (i.e., 80 nmoles NDMA intravitreally injected), NMDA80 + 10ng EPO, NMDA80 + 50ng EPO, and NMDA80 + 250ng EPO. The NMDA80 + 50ng EPO treatment group was used to evaluate various administrated points (pre-/co-/post-administration of NMDA80). Meanwhile, the transferase dUTP Nick-End Labeling (TUNEL) assay of RGCs, the inner plexiform layer (IPL) thickness and the apoptotic signal transduction pathways of -calpain, Bax, and caspase 9 were assessed simultaneously using an immunohistochemical method (IHC). When EPO was co-administered with NMDA, attenuated cell death occurred through the downregulation of the apoptotic indicators: -calpain was activated first (peak at [~]18hrs), followed by Bax and caspase 9 (peak at [~]40hrs). Furthermore, the morphology of RGCs has clearly demonstrated the visual recovery of IPL thickness at 40 hours after injection. Exogenous EPO successfully protected RGCs by downregulating apoptotic factors to attenuate NMDA-mediated excitotoxic retinal damage.

pharmacology and toxicology↗