Biology subjects

Link, W.

Publications and source records attributed to Link, W..

9 recordsLinked to original sources

bioRxiv2026

INPP5E interactome reveals novel connections to growth factor signaling

Primary cilia are sensory cell membrane protrusions whose malfunction causes diseases known as ciliopathies. Joubert syndrome (JBTS) is a rare recessive ciliopathy causing brain malformations and kidney cysts, among other manifestations. A key player in JBTS is INPP5E, a ciliary phosphoinositide lipid phosphatase. Although INPP5E regulates ciliary growth factor signaling, the molecular mechanisms remain poorly understood. Herein, we show that a constitutively active growth factor receptor (PDGFR-D842V) stimulates INPP5E tyrosine phosphorylation, as does the SRC tyrosine kinase. INPP5E tyrosine phosphorylation did not affect its enzyme activity but was associated with stronger binding to SH3GL1, an endocytic regulator, and SNX9, a phosphoinositide-binding protein involved, like INPP5E, in growth factor-induced ciliary ectovesicle release. Our INPP5E interactomic studies identified other growth factor signaling regulators, including among others: SIN1 (the phosphoinositide-binding subunit of the mTORC2 complex), STRAP (a TGF{beta} and PI3K/AKT signaling regulator), GRB2 (a growth factor receptor adaptor) and the JBTS-associated proteins AHI1 and NPHP1. Moreover, INPP5E strongly interacted with the phosphopeptide-binding 14-3-3 proteins, and did so only in presence of serine-85, a phosphorylated INPP5E residue. Lastly, we found that INPP5E differentially regulates two cilium-dependent growth factor signaling pathways in fibroblasts. Thus, while INPP5E downregulated PDGF-induced AKT phosphorylations, it upregulated TGF{beta}-induced SMAD2 and ERK phosphorylations. Altogether, our work provides important clues on the cilia-dependent actions of growth factors, with implications for ciliopathies like JBTS.

biochemistry↗

bioRxiv2025

TRIB2 supports a high glycolytic phenotype in melanoma cells

Metabolic adaptation plays a crucial role in driving the progression of human melanoma contributing to therapy resistance and disease relapse. The pseudo serine/threonine kinase Tribbles homolog 2 (TRIB2) is prominently expressed in melanoma tissue, promoting resistance to anti-cancer treatments and correlating with unfavorable clinical outcomes. Despite this understanding, the impact of TRIB2 expression on melanomas metabolic profile remains unexplored. Here we use UACC-62 melanoma cells which exhibit substantial endogenous expression of TRIB2 as well as engineered isogenic TRIB2 knock out (KO) cells to assess the effect of the loss of TRIB2 on metabolism. Our findings reveal that TRIB2-KO cells display reduced glycolytic activity and heightened vulnerability to pharmacological inhibition of oxidative metabolism, contrasting with the parental cell line. These metabolic and phenotypic changes are driven by TRIB2s coordinated regulation of multiple glycolytic genes, whose combined effect might produce the glycolytic phenotype observed in parental cells. Collectively, our results underscore important role of TRIB2 as a modulator of the metabolic shift implicated in therapy resistance. These insights highlight TRIB2 as a potential target for therapeutic intervention, aiming to counteract the metabolic adaptations driving melanomas resistance mechanisms. HighlightsO_LIMain problem in melanoma is the limited therapy efficacy due to resistance; C_LIO_LITRIB2 is a novel unexplored and druggable target; C_LIO_LITRIB2 expression contributes to increased glycolysis in melanoma cells; C_LIO_LITRIB2 is a driver of a metabolic switch that fuels therapy resistance. C_LI

cancer biology↗

bioRxiv2025

Combined expression of FOXO and Tribbles proteins predicts survival of glioma patients

BackgroundGliomas, particularly high-grade variants such as glioblastoma, remain therapeutically challenging with poor survival outcomes. Current biomarkers inadequately stratify patients for therapy selection, monitoring, and early detection of progression. The FOXO transcription factors and Tribbles pseudokinases, key regulators of the PI3K/AKT pathway, have been implicated in cancer progression but their prognostic value in gliomas is unclear. The aim of this study was to determine whether transcriptional profiles of FOXO and Tribbles family members predict survival in glioma patients better than established biomarkers. MethodsUsing RNA-seq data from The Cancer Genome Atlas (TCGA, n = 705) and Chinese Glioma Genome Atlas (CGGA, n = 1018), along with microarray datasets (REMBRANDT, n = 552; Gravendeel, n = 268), we analyzed mRNA levels of FOXO1/3/4/6 and TRIB1/2/3. Survival analysis was performed via Kaplan-Meier curves, log-rank tests, and concordance indices. Gene expression differences across tumor grades and molecular subgroups were assessed using Students t-test. ResultsHigh FOXO1 and low FOXO3/4 mRNA levels, combined with elevated TRIB1/2/3 expression, formed a signature significantly associated with worse survival across all cohorts. This signature stratifies grade 4 gliomas, with a median survival difference of 4.5 months. Grade 4 tumors exhibited elevated FOXO1 and TRIB1/2/3 but reduced FOXO3/4 levels compared to lower-grade gliomas. ConclusionsThe FOXO/Tribbles transcriptional signature robustly predicts survival in glioma patients. These findings highlight its potential as a biomarker for patient stratification and a therapeutic target for high-grade gliomas. Key PointsO_LIFOXO/Tribbles mRNA signature predicts glioma survival status. Our analysis identifies a distinct transcriptional signature - characterized by high FOXO1 and TRIB1/2/3 levels along with low FOXO3 and FOXO4 - that consistently predicts poor prognosis across glioma cohorts. This FOXO/Tribbles signature demonstrates great prognostic power, particularly in grade 4 gliomas, providing an improved tool for risk stratification and clinical decision-making. C_LIO_LIHigh FOXO1 and Tribbles levels mark aggressive glioblastoma tumors. We show that elevated expression of FOXO1 and Tribbles pseudokinases is enriched in glioblastoma (GB) and grade 4 astrocytomas. These tumors, known for their aggressiveness and therapy resistance, are consistently associated with this unfavorable mRNA profile. This suggests a functional role for FOXO1 and Tribbles in glioma progression and highlights them as promising biomarkers and therapeutic targets. C_LIO_LIMulti-cohort validation (TCGA, CGGA) confirms prognostic robustness. The predictive FOXO/Tribbles expression pattern was validated across four large and independent datasets (TCGA, CGGA, REMBRANDT, and Gravendeel), demonstrating consistency despite differences in platform and population. This multi-cohort validation reinforces the robustness and generalizability of this transcriptional signature for predicting survival outcomes in glioma patients. C_LI Importance of the StudyGlioblastoma and high-grade gliomas have dismal prognoses, yet current biomarkers fail to adequately guide therapy. This study identifies a novel transcriptional signature - combining FOXO transcription factors and Tribbles pseudokinases - that robustly predicts survival in glioma patients stratifying aggressive tumors. Using multi-cohort validation (TCGA, CGGA, REMBRANDT), we demonstrate that elevated FOXO1 and Tribbles (TRIB1/2/3) levels, coupled with reduced FOXO3/4, correlate with poor outcomes in grade 4 gliomas. This signature is enriched in glioblastomas, highlighting its link to therapy resistance. Unlike prior studies focusing on individual proteins, our integrated analysis reveals their collective prognostic power, offering a pathway-specific biomarker for patient stratification. These findings provide a translational framework for targeting FOXO/Tribbles in precision oncology, addressing an urgent need for improved therapeutic strategies in neuro-oncology.

cancer biology↗

bioRxiv2024

Genome-wide association studies identify promising QTL for freezing tolerance in winter and early spring as a basis for in-depth genetic analysis and implementation in winter faba bean (Vicia faba L.) breeding

Interest in faba bean as a locally adapted high-protein grain legume crop has increased in Europe over the past decade. Winter faba bean, which can make use of soil moisture from autumn to spring and partially escape summer droughts, exhibit greater yield potential than the spring-type. However, due to insufficient winter hardiness, winterkill is a major constraint that prevents large-scale production of current winter-type cultivars in Central and Northern Europe. Here, we extend the understanding of freezing tolerance, the main component trait of winter hardiness, during winter and against late-frost in early spring and define genomic target regions for marker-assisted selection. Comparative analysis of genome-wide association studies revealed 13 treatment-specific major QTLs with partially pleiotropic effect on four freezing tolerance related traits. In addition, we identified five treatment-unspecific pleiotropic QTLs, including two major freezing tolerance loci on chromosomes 1 and 5. Our results thus indicate both a distinct and common genetic control of tolerance to winter- and late-frost in winter faba bean. In combination with the promising prediction abilities obtained from marker score-based prediction, our work highlights the potential for marker-assisted and genomic selection toward improved freezing tolerance and winter hardiness in winter faba bean breeding programs.

genetics↗

bioRxiv2024

Resistance to Carcinogenesis in the African Spiny Mouse (Acomys) correlates with upregulation of tumor suppressor genes.

Cancer remains a leading cause of morbidity and mortality worldwide, driving extensive research into the mechanisms that contribute to its development and progression. The search for animal models capable of shedding light on mechanisms of cancer resistance has led researchers to explore various rodent species. Among these, the African Spiny Mouse (Acomys sp.) has attracted considerable attention due to its regenerative abilities. In our study, we compared the response of Mus musculus and Acomys dimidiatus mice to treatment with the carcinogen 7,12-dimethylbenz[a]anthracene (DMBA) combined with the inducer of proliferation 12-O-tetradecanoylphorbol-13-acetate (TPA). While both Acomys and Mus mice experienced carcinogenic damage to their skin cells, mounted proliferative responses and underwent immune cell infiltration, only Mus mice developed tumors, whereas Acomys remained tumor-free. To uncover the molecular mechanisms underlying this resistance, we performed RNA sequencing on tissue samples from both species at baseline and at multiple time points during the carcinogenesis protocol. The data reveal distinctly different transcriptional responses between both species. In particular, Acomys showed massive upregulation of immune related genes, including a set of tumor suppressor genes, while Mus seemed to focus its response on modifying epidermis structure and regulation of the cell cycle. These differences correlated with an increased apoptotic response in Acomys but not Mus. In summary, our study provides compelling evidence that Acomys mice exhibit remarkable resistance to tumor development under DMBA/TPA carcinogen treatment mediated through the upregulation of a range of processes related to immune surveillance.

cancer biology↗

bioRxiv2024

The inhibition of three distinct signaling pathways eliminates the oncogenic Tribbles homolog 2 from melanoma cells

Tribbles homolog 2 (TRIB2) is one of three members of the Tribbles family of pseudo serine/threonine kinases. It acts as an oncogene whose expression is correlated with tumor progression and therapy resistance in melanoma. TRIB2 has been implicated in conferring resistance to various anti-cancer therapies suggesting TRIB2 as a therapeutic target for resistant tumors. This study explores the pharmacological targeting of TRIB2, revealing several independent routes of pharmacological manipulations. TRIB2 is a short-lived protein stabilized by inhibition of the PI3K/AKT pathway. Conversely, inhibitors of BRAF, MEK and ERK significantly decrease TRIB2 expression by a mechanism that involves transcription. Additionally, Polo-Like Kinases (PLKs) inhibitors significantly reduce TRIB2 protein expression and stability. Strikingly, increasing concentrations of the kinase inhibitor PIK-75 effectively eliminate TRIB2 in melanoma cells surpassing its PI3K inhibitory activity suggesting the destabilizing effect of the inhibition of an unknown kinase. TMT-based proteomics, chemical biology and genetic manipulation revealed CDK12 as the kinase that mediates the destabilizing effect on TRIB2. Overall, we identify three distinct classes of compounds that efficiently eliminate the oncogenic TRIB2 protein from melanoma cells based on different molecular mechanisms and exhibiting 40 to 200 times greater potency than the previously reported afatinib.

cancer biology↗

bioRxiv2023

Pollen production, pollen viability and autofertility in faba bean (Vicia faba L.) and their relationship with realized paternal success

In animal-pollinated plants, pollen dispersal depends on several plant and animal characteristics which may influence a plants paternal success. Different paternal success influences the genetic contribution of a genotype to the next generation. In breeding of partially allogamous faba bean (Vicia faba L.), synthetic populations are developed where equal contributions of genotypes to the next generation are desired to reduce inbreeding. Since direct assessments of paternity are elaborate and costly, we studied whether components of plant fitness such as pollen production and pollen viability can be used as estimates for paternity. In a field experiment and a caged outdoor pot experiment, a total of 18 genotypes (14 inbred lines, 4 F1 hybrids) of faba bean were evaluated for pollen production, pollen viability and autofertility. Pollen production was higher at the lower than at the upper inflorescences and we found mid-parent heterosis for this trait. The relative pollen viability was high (93 % - 97 % in pots, 88 % - 95 % in field) indicating that fertilization success is rather not limited by a low pollen quality. Only in the field, pollen of F1 hybrids was more viable than pollen of inbred lines. Autofertility ranged from 0 % - 98 %, with very marked average mid-parent heterosis for this trait. Autofertility did not seem to be related to either pollen production, pollen viability or paternal success. However, pollen production and pollen viability were highly correlated with paternal success. Hence, data on pollen production and viability might be useful in breeding of synthetic populations to choose parents with small differences in paternal successes, to reduce inbreeding and better exploit heterosis.

plant biology↗

bioRxiv2022

Genetic analysis of global faba bean germplasm maps agronomic traits and identifies strong selection signatures for geographical origin

Faba bean (Vicia faba L.) is a high-protein grain legume crop with great potential for further cultivation. However, little is known about the genetics underlying trait diversity. In this study, we use 21,345 high-quality SNP markers to genetically characterise 2,678 faba bean genotypes. We perform genome-wide association studies of key agronomic traits using a Seven-parent-MAGIC population and detect 238 significant marker-trait associations linked to 12 traits of agronomic importance, with 65 of these being stable across multiple environments. Using a non-redundant diversity panel of 685 accessions from 52 countries, we identify 3 subpopulations differentiated by geographical origin and 33 genomic regions subject to strong diversifying selection between subpopulations. We find that SNP markers associated with the differentiation of northern and southern accessions were able to explain a significant proportion of agronomic trait variance in the Seven-parent-MAGIC population, suggesting that some of these traits have played an important role in breeding. Altogether, our findings point to genomic regions associated with important agronomic traits and selection in faba bean, which can be used for breeding purposes. Key MessageWe identified marker-trait associations for key faba bean agronomic traits and genomic signatures of selection within a global germplasm collection.

genetics↗

bioRxiv2021

Zooming into the genomic vicinity of the major locus for vicine and convicine in faba bean (Vicia faba L.)

The versatility of faba bean (Vicia faba L.) seed as valuable protein feed is hampered by its relatively high level of the compounds vicine and convicine (VC), which are antinutritive factors in poultry and further non-ruminant feed. The objective here was to develop the first-ever genetically low-VC winter faba bean. Hence, the low VC allele vc-, that should be the basis of a known, major locus for VC, need verification and molecular identification and be based on appropriately developed DNA-markers; the low VC feature awaited its transfer into the high-performing winter faba bean germplams. Based on bi-parental F2-families and isogenic lines, we thus developed highly useful SNP markers exploiting transcriptomic data. Furthermore, we fine-mapped and, based on synteny to Medicago truncatula and Cicer arietinum, we identified a candidate gene for the VC locus. A novel, genetically low VC winter faba bean population was bred. The path is now well-prepared for further marker-based breeding progress.

genetics↗