Biology subjects

Farahi, N.

Publications and source records attributed to Farahi, N..

5 recordsLinked to original sources

bioRxiv2026

Binding of long non-coding RNAs within the androgen receptor N-terminal tail modulates interdomain communication and liquid-liquid phase separation

The androgen receptor (AR) is a transcription factor whose overactivation is a primary driver of prostate cancer. Although AR interactions with several long non-coding RNAs (lncRNAs) have been implicated in castration-resistant prostate cancer, their underlying molecular mechanisms and functional consequences remain poorly understood. Here, we identify the N-terminal 37 residues of the intrinsically disordered AR N-terminal domain as the primary RNA-binding region that mediates selective interactions with the lncRNAs HOTAIR and SLNCR1. Residue-level mapping and mutational analysis define Y11, R13, and Q24 as key determinants of RNA recognition. This RNA-binding region partially overlaps with the F23QNLF27 motif, previously shown to mediate N/C interdomain communication with the ligand-binding domain through folding upon binding. We observe a partner-dependent binding mode in which this motif remains dynamically disordered upon RNA binding. LncRNA binding promotes phase separation of the N-terminal domain, indicating that lncRNAs upregulated in late-stage prostate cancer may lower the threshold for AR condensate formation and contribute to ligand-independent AR signaling. LncRNAs modulate communication between the N-terminal and ligand-binding domains within condensates, suggesting that lncRNA binding may tune hormone-dependent full-length AR signaling. These findings provide a mechanistic framework for AR-lncRNA regulation, laying the groundwork for future therapeutic strategies against advanced prostate cancer. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=83 SRC="FIGDIR/small/728402v1_ufig1.gif" ALT="Figure 1000"> View larger version (22K): org.highwire.dtl.DTLVardef@bee76dorg.highwire.dtl.DTLVardef@14bb6edorg.highwire.dtl.DTLVardef@1d693b5org.highwire.dtl.DTLVardef@7b70d1_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2026

Circulating pre-osteoclasts are primed for osteoclast fate and synovial tissue homing in psoriatic arthritis.

Psoriatic arthritis (PsA) is a complex immune-mediated inflammatory disease with heterogenous clinical features. Osteoclasts have a unique ability to destroy bone, playing key roles in both healthy bone turnover and pathological erosions in arthritis. They are believed to arise from monocytic precursors migrating to inflamed synovial tissue, though the identity of this precursor in humans has remained elusive. Here, we sought to determine whether monocytes home to psoriatic joints and their phenotype. We find that monocytes are recruited to inflamed joints in PsA but not uninvolved or healthy joints, and identify a pre-osteoclast (preOC) cell state derived from classical monocytes. PreOC are transcriptionally distinct from classical monocytes, are enriched for NFACT1, the master regulator of osteoclastogenesis, and form multinucleated osteoclasts in vitro without exogenous RANKL. They are expanded in the circulation of donors with active treatment naive PsA, compared to both healthy controls and those with cutaneous psoriasis only. Finally, using a customised spatial transcriptomics workflow, we identified these cells within human synovial tissue, and radiolabelling confirmed their recruitment from the circulation. These findings highlight the role of systemic immune priming in macrophage pathophysiology.

immunology↗

bioRxiv2023

Phase-separating fusion proteins drive cancer by dysregulating transcription through ectopic condensates

Numerous cellular processes rely on biomolecular condensates formed through liquid-liquid phase separation (LLPS), thus, perturbations of LLPS underlie various diseases. We found that proteins initiating LLPS are frequently implicated in somatic cancers, even surpassing their involvement in neurodegeneration. Cancer-associated LLPS scaffolds are connected to all cancer hallmarks and tend to be oncogenes with dominant genetic effects lacking therapeutic options. Since most of them act as oncogenic fusion proteins (OFPs), we undertook a systematic analysis of cancer driver OFPs by assessing their module-level molecular functions. We identified both known and novel combinations of molecular functions that are specific to OFPs and thus have a high potential for driving tumorigenesis. Protein regions driving condensate formation show an increased association with DNA- or chromatin-binding domains of transcription regulators within OFPs, indicating a common molecular mechanism underlying several soft tissue sarcomas and hematologic malignancies where phase-separation-prone OFPs form abnormal, ectopic condensates along the DNA, and thereby dysregulate gene expression programs.

cancer biology↗

bioRxiv2021

Concentration and dosage sensitivity of proteins driving liquid-liquid phase separation

Liquid-liquid phase separation (LLPS) is a molecular process that leads to the formation of membraneless organelles (MLOs), i.e. functionally specialized liquid-like cellular condensates formed by proteins and nucleic acids. Integration of data on LLPS-associated proteins from dedicated databases revealed only modest overlap between them and resulted in a confident set of 89 human LLPS driver proteins. Since LLPS is highly concentration-sensitive, the underlying experiments are often criticized for applying higher-than-physiological protein concentrations. To clarify this issue, we performed a naive comparison of in vitro applied and quantitative proteomics-derived protein concentrations and discuss a number of considerations that rationalize the choice of apparently high in vitro concentrations in most LLPS studies. The validity of in vitro LLPS experiments is further supported by in vivo phase-separation experiments and by the observation that the corresponding genes show a strong propensity for dosage sensitivity. This observation implies that the availability of the respective proteins is tightly regulated in cells to avoid erroneous condensate formation. In all, we propose that although local protein concentrations are practically impossible to determine in cells, proteomics-derived cellular concentrations should rather be considered as lower limits of protein concentrations, than strict upper bounds, to be respected by in vitro experiments.

molecular biology↗

bioRxiv2019

Cell type specific novel lincRNAs and circRNAs in the BLUEPRINT haematopoietic transcriptomes atlas.

Transcriptional profiling of hematopoietic cell subpopulations has helped characterize the developmental stages of the hematopoietic system and the molecular basis of malignant and non-malignant blood diseases for the past three decades. The introduction of high-throughput RNA sequencing has increased knowledge of the full repertoire of RNA molecules in hematopoietic cells of different types, without relying on prior gene annotation. Here, we introduce the analysis of the BLUEPRINT consortium gene expression data for mature hematopoietic cells, comprising 90 total RNA and 32 small RNA sequencing experiments, from 27 different cell types. We used these data to describe the transcriptional profile of each we used guided transcriptome assembly to extend the annotation of the transcribed genome, which led to the identification of hundreds of novel non-coding RNA genes, which display a high degree of cell type specificity. We also characterized the expression of circular RNAs and found that these are also highly cell type specific. This resource refines the active transcriptional landscape of mature hematopoietic cells, highlights abundant genes and transcriptional isoforms for each cell type, and provides valuable data and visualisation tools for the scientific community working on hematological development and diseases.

genomics↗