Biology subjects

Tekin, M.

Publications and source records attributed to Tekin, M..

5 recordsLinked to original sources

bioRxiv2026

Divergent regulation of STING-mediated innate immune responses by CBP and p300

Dysregulation of cGAS-STING pathway contributes to various disorders, including autoimmunity, infectious diseases and cancer. Transcription factors, particularly IRF3 which presumably recruits CBP/p300 as transcription coactivators, drive innate immune responses to STING activation. Here we show that CBP/p300 inhibitors (p300i) boost, not repress as expected, the cGAMP-induced transcription of innate immune genes. Mechanistically, p300i and a CBP/p300 degrader markedly enhance the cGAMP-induced IRF3 phosphorylation and slightly increase NF-{kappa}B activation. Furthermore, cGAMP stimulation increases the presence of p300, not CBP, in the cytoplasm to interrupt interactions between TBK1 and IRF3. Conversely, p300i enhances TBK1-IRF3 interactions, resulting in higher IRF3 phosphorylation. After STING activation, CBP, not p300, is recruited to chromatin along with IRF3 and is coupled with H3K27ac upregulation. At later stages of STING activation, nearly all CBP and p300 are detached from chromatin, which is associated with global histone deacetylation, IRF3 chromatin eviction, and the termination of IRF3-driven transcription programs. p300i robustly enhances IRF3 chromatin engagement which consequently amplifies type 1 interferon responses to STING activation. Together, these findings suggest that CBP, not p300, acts as a transcription coactivator in the nucleus. In contrast, p300, not CBP, is a suppressor of STING signaling in the cytoplasm.

immunology↗

bioRxiv2025

Dysregulation of cell migration by matrix metalloproteinases in geleophysic dysplasia

Geleophysic dysplasia (GD) is characterized by short stature, brachydactyly, joint limitations, a distinctive facial appearance, as well as cardiac and respiratory dysfunction that can be life-threatening. GD is caused by pathogenic variants in the ADAMTSL2, FBN1, or LTBP3 genes. While dermal fibroblasts derived from affected individuals have shown poor organization of the extracellular matrix (ECM), it remains elusive how the disorganized ECM contributes to GD pathogenesis. To understand the molecular mechanisms in GD, we isolated and characterized primary human dermal fibroblasts from affected individuals with ADAMTSL2 and FBN1 variants. We found that the secretion of ECM proteins including ADAMTSL2, FBN1, and Fibronectin were impaired in GD fibroblasts. Increased cell migration was observed in GD fibroblasts carrying ADAMTSL2 or FBN1 variants, which was associated with up-regulation of MMP-1 and MMP-14, two proteases related to cell mobility. The enhanced cell migration and up-regulation of MMP-1 and MMP-14 were corroborated in mouse primary dermal fibroblasts carrying pathogenic variants in Adamtsl2 and in lung and heart tissues from Adamtsl2-knockout mice. A pan MMP inhibitor, GM6001, inhibited the migration of GD fibroblasts. Overall, our results suggest that MMP-1/-14 up-regulation play a role in the development of GD and may be utilized as a treatment target.

cell biology↗

bioRxiv2023

RExPRT: a machine learning tool to predict pathogenicity of tandem repeat loci

Tandem repeats (TRs) are polymorphic sequences of DNA that are composed of repeating units of motifs, whose lengths can vary depending on the type of TR. Expansions of TRs are responsible for approximately 50 monogenic diseases, compared to over 4,300 disease causing genes disrupted by single nucleotide variants and small indels. It appears thus reasonable to expect the discovery of additional pathogenic repeat expansions, which has the potential of significantly narrowing the current diagnostic gap in many diseases. Recently, short and long-read whole genome sequencing with the use of advanced bioinformatics tools, have identified a growing number of TR expansions in the human population. The majority of these loci are expanded in <1% of genomes. Categorizing and prioritizing such TR loci is a growing challenge to human genomic studies. We present a first-in-class machine learning tool, RExPRT (Repeat EXpansion Pathogenicity pRediction Tool), which is designed to distinguish pathogenic from benign TR expansions. Leave-one-out cross validation results demonstrated that an ensemble approach comprised of support vector machines (SVM) and extreme gradient boosted decision tree (XGB) classify TRs with a precision of 92% and a recall of 90%. Further validation of RExPRT on unseen test data demonstrate a similar precision of 86%, and a recall of 60%. RExPRTs high precision in particular, will be of significant value to large-scale discovery studies, which require the prioritization of promising candidate loci for time-consuming and costly functional follow-up studies. Application of RExPRT to ~800,000 TRs in the reference genome identified ~30,000 TRs that would be likely pathogenic upon expansion. Thus, RExPRT establishes a foundation for the application of machine learning approaches to categorize the pathogenicity of tandem repeat loci.

bioinformatics↗

bioRxiv2020

Radixin modulates stereocilia function and contributes to cochlear amplification

The stereocilia of the sensory cells in the inner ear contain high levels of the actin-binding protein radixin, encoded by the RDX gene. Radixin which is associated with mechanotransduction process such as PIP2 is known to be important for hearing but its functional role remains obscure. To determine how radixin influences hearing sensitivity, we used a custom rapid imaging technique to directly visualize stereocilia motion while measuring the amplitude of the electrical potentials produced by sensory cells during acoustic stimulation. Experiments were performed in guinea pigs, where upon blocking radixin, a large decrease in sound-evoked electrical potentials occurred. Despite this decrease other important functional measures, such as electrically induced sensory cell motility and the sound-evoked deflections of stereocilia, showed a minor amplitude increase. This unique set of functional properties alterations demonstrate that radixin is necessary to ensure that the inner ear converts sound into electrical signals at acoustic rates. Radixin is therefore a necessary and important component of the cochlear amplifier, the energy-consuming process that boosts hearing sensitivity by up to 60 dB.

neuroscience↗

bioRxiv2019

ClinGen Expert Clinical Validity Curation of 164 Hearing Loss Gene-Disease Pairs

PurposeProper interpretation of genomic variants is critical to successful medical decision making based on genetic testing results. A fundamental prerequisite to accurate variant interpretation is the clear understanding of the clinical validity of gene-disease relationships. The Clinical Genome Resource (ClinGen) has developed a semi-quantitative framework to assign clinical validity to gene-disease relationships. MethodsThe ClinGen Hearing Loss Gene Curation Expert Panel (HL GCEP) uses this framework to perform evidence-based curations of genes present on testing panels from 17 clinical laboratories in the Genetic Testing Registry. The HL GCEP curated and reviewed 142 genes and 164 gene-disease pairs, including 105 nonsyndromic and 59 syndromic forms of hearing loss. ResultsThe final outcome included 82 Definitive (50%), 12 Strong (7%), 25 Moderate (15%), 32 Limited (20%), 10 Disputed (6%), and 3 Refuted (2%) classifications. The summary of each curation is date stamped with the HL GCEP approval, is live, and will be kept up-to-date on the ClinGen website (https://search.clinicalgenome.org/kb/gene-validity). ConclusionThis gene curation approach serves to optimize the clinical sensitivity of genetic testing while reducing the rate of uncertain or ambiguous test results caused by the interrogation of genes with insufficient evidence of a disease link.

genomics↗