Biology subjects

Hussein, S. M. I.

Publications and source records attributed to Hussein, S. M. I..

9 recordsLinked to original sources

bioRxiv2026

LncRNA-mediated organization of oncogenic chromatin state is a targetable vulnerability in leukemia

Long non-coding RNAs (lncRNAs) are increasingly recognized as critical regulators of gene expression underlying various cellular functions, however, the functional and mechanistic contributions of most lncRNAs to tumorigenesis remain poorly defined, and targeting of lncRNAs is challenging with conventional therapeutic approaches. Here, we uncover human PAN3-AS1 and its murine ortholog Lnc35682, previously uncharacterized lncRNAs embedded within a conserved syntenic genomic locus, as highly expressed in acute myeloid leukemia (AML). Using genetic mouse models, human cell lines and primary patient samples, we show that PAN3-AS1 is essential for leukemia maintenance but dispensable for normal hematopoiesis. Mechanistically, we find that elevated PAN3-AS1 influences chromatin accessibility, thus promoting leukemia gene expression programs. This is mediated, at least in part, by PAN3-AS1s association with the nuclear lamina through a defined functional region that is required for its leukemogenic function. We further characterize a feed-forward regulatory circuit between PAN3-AS1 and its neighboring gene FLT3 that directly links the aberrant lncRNA functions to the FLT3-mutant AML subtype. To therapeutically exploit the regulatory node, we engineer a myeloid leukemia-preferentially targeted lipid nanoparticle (LNP) formulation and demonstrate effective delivery of siRNAs against endogenous targets into leukemia cells in experimental animals. LNP-siPAN3-AS1 alone or in combination with a clinically used FLT3 inhibitor, Gilteritinib, reduces leukemia burden and significantly delay leukemogenesis in vivo. Overall, our study uncovers a therapeutic vulnerable lncRNA-centric circuitry and provides compelling preclinical evidence for the development and application of a novel RNA targeting-LNP based therapy for treatment of myeloid leukemia. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/744058v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@10c9d42org.highwire.dtl.DTLVardef@12864e7org.highwire.dtl.DTLVardef@f87f6aorg.highwire.dtl.DTLVardef@750cbf_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2026

Matrix Stiffness-driven FAK Splicing Tunes Cell Mechanosensing

The extracellular matrix (ECM) stiffness influences many physiological and pathological processes. Cells can sense mechanical changes within the ECM through mechanosensors, most notably through the focal adhesion kinase (FAK). Using human-derived data and 2D/3D engineered models, we identified a ubiquitous and uncharacterized FAK isoform lacking exon 4 (FAK{Delta}e4). We demonstrated that FAK{Delta}e4 splicing is regulated by substrate stiffness in a biphasic manner, in which an optimal stiffness is required for a maximal FAK{Delta}e4 expression. We further showed that FAK{Delta}e4 dictates at which stiffness optimal migration speed and invasion occur, impairs focal adhesion dynamics and maturation, and shifts its autophosphorylation and downstream YAP nuclear translocation toward lower stiffness compared to the canonical FAK isoform. Moreover, the FAK{Delta}e4 expression levels to canonical FAK determine at which stiffness cells will converge during durotaxis. Our results reveal how FAK{Delta}e4 acts as a fine-tuning mechanosensing switch and reframe our understanding of mechanotransduction.

cell biology↗

bioRxiv2026

Snhg26 long non-coding RNA regulates pluripotent cell states through a SINEB2-derived sequence

Abstract/SummaryLong-non coding RNAs (lncRNAs) are now well established players in gene expression regulation, but their detailed molecular mechanisms of action and underlying regulating sequences remain poorly understood. An emerging concept supports the idea that repeated sequences, more notably sequences derived from transposable elements (TEs), contribute to functional domains of lncRNAs. Here, we undertake the characterization of the function, interactors and functional domains of Snhg26, a lncRNA involved in reprogramming towards induced pluripotent stem cells (iPSCs) and maintenance of the pluripotent state of embryonic stem cells (ESCs). First, we show that modulation of Snhg26 expression levels affects expression and splicing of genes involved in pluripotency and chromatin remodeling during the early steps of reprogramming and in ESCs. We also find that down-regulation of Snhg26 increases the expression of SINEB2 transposable elements. Moreover, we identify hundreds of transcripts directly interacting with Snhg26 with a significant enrichment of RNAs containing SINEB2 elements. Strikingly, loss of a SINEB2 sequence embedded within Snhg26 abolishes its function in regulating pluripotent states. Our results thus support the idea that TEs constitute a source of functional units for lncRNAs and encourages further efforts to explore this concept.

cell biology↗

bioRxiv2025

Concomitant acetylation and loading of H2A.Z by NuA4/TIP60 regulate target gene transcription

The human NuA4/TIP60 complex is a multi-subunit, dual enzymatic epigenetic factor and gene regulator. It bears histone acetyltransferase (HAT) activity towards the canonical histones H2A and H4 and the histone variant H2A.Z, a function that has been linked to gene activation. It also acts as a chromatin remodeling enzyme through ATP-dependent exchange of nucleosomal H2A-H2B dimers with H2A.Z-H2B, leading to incorporation of H2A.Z into chromatin at gene regulatory elements. NuA4/TIP60 is unique in merging two enzymatic activities targeting H2A.Z. Both NuA4/TIP60-dependent H2A.Z acetylation and remodeling have been linked to several physiological functions and pathologies, but studies have only focused on either one or the other enzymatic activity, and insights on functional coordination between them are lacking. Here, we leverage our EP400 rapid depletion system to explore and untangle the intricate links between H2A.Z acetylation by Tip60 (the HAT subunit) and loading on chromatin by EP400 (the remodeling subunit) through functional genomic and biochemical analyses. Our data support a mechanism in which H2A.Z is first pre-acetylated to allow for H2A.Zac-H2B dimer association with the complex before incorporation into chromatin, particularly at gene promoters to positively regulate transcription. As both H2A.Z-targeted enzymatic functions of NuA4/TIP60 have been linked to disease, albeit separately, our findings hold important implications for therapeutic intervention, where combinatorial targeting is a promising avenue.

molecular biology↗

bioRxiv2025

Establishment of human glioblastoma cell culture collection

Glioblastoma (GBM) is a highly aggressive primary brain cancer with poor prognosis (<15 months), highlighting the urgent need for more effective therapies. As current treatments are not effective, the need for a deeper understanding of the biology of GBM cells, including how they reprogram their metabolism to support their aberrant and uncontrolled growth, is critical. To this end, we established a collection of 41 human glioma cell lines derived from freshly resected tumour tissues from 99 patients. We characterized 12 of these cell lines by combining histologic, genetic, stem cell derivation and self-renewal, and metabolomic analyses. Histological and genetic profiles included IDH mutation status, Ki-67 proliferation index, ATRX status, mutant TP53 expression, chromosome 10q loss, EGFR amplification, and MGMT promoter methylation. Of these, only p53 mutation expression status showed weak segregation of the cell lines into 2 separate metabolic groups based on amino acid levels, but none showed an effect on stem cell derivation or self-renewal. Further characterization of these 12 cell lines revealed significant metabolic and phenotypic differences when comparing mesenchymal versus proneural gene expression subtyping. We show significant increases in TCA cycle metabolites in mesenchymal-like GBM cells and higher overall metabolic activity compared to proneural-like cells. These findings highlight the complexity of GBM and the need for personalized treatments that consider the metabolome of each subtype as a potential therapeutic avenue.

cancer biology↗

bioRxiv2021

MRG proteins are shared by multiple protein complexes with distinct functions

MRG15/MORF4L1 is a highly conserved protein in eukaryotes that contains a chromodomain recognizing H3K36me3 in chromatin. Intriguingly, it has been reported in the literature to interact with several different factors involved in chromatin modifications, gene regulation, alternative mRNA splicing and DNA repair by homologous recombination. In order to get a complete and reliable picture of associations in physiological conditions, we used genome editing and tandem affinity purification to analyze the stable native interactome of human MRG15, its paralog MRGX/MORF4L2 that lacks the chromodomain, and MRGBP (MRG-binding protein) in isogenic K562 cells. We found stable interchangeable association of MRG15 and MRGX with the NuA4/TIP60 histone acetyltransferase/chromatin remodeler, Sin3B histone deacetylase/demethylase, ASH1L histone methyltransferase and PALB2/BRCA2 DNA repair protein complexes. These associations were further confirmed and analyzed by CRISPR-tagging of endogenous proteins and comparison of expressed isoforms. Importantly, based on structural information, point mutations could be introduced that can specifically disrupt MRG15 association with some complexes but not others. Most interestingly, we also identified a new abundant native complex formed by MRG15/X-MRGBP-BRD8-EP400NL that is functionally similar to the yeast TINTIN (Trimer Independent of NuA4 for Transcription Interactions with Nucleosomes) complex. Our results show that EP400NL, being homologous to the N-terminal region of NuA4/TIP60 subunit EP400, creates TINTIN by competing for BRD8 association. Functional genomics indicate that human TINTIN plays a role in transcription of specific genes. This is most likely linked to the H4ac-binding bromodomain of BRD8 along the H3K36me3-binding chromodomain of MRG15 on the coding region of transcribed genes. Taken together, our data provide a complete detailed picture of human MRG proteins-associated protein complexes which is essential to understand and correlate their diverse biological functions in chromatin-based nuclear processes. HighlightsO_LIMRG15 and MRGX are stably associated with several different protein complexes important for genome expression and stability. C_LIO_LISeveral MRG-containing complexes are chromatin modifiers. C_LIO_LISpecific point mutations in the MRG domain differentially affect associated complexes. C_LIO_LIA major human complex homologous to the yeast TINTIN complex is identified. C_LIO_LIThe protein EP400NL competes with EP400 to functionally separate TINTIN from the NuA4/TIP60 complex. C_LIO_LITINTIN contains a bromodomain and a chromodomain to regulate transcription. C_LI

molecular biology↗

bioRxiv2021

Signal requirement for cortical potential of transplantable human neuroepithelial stem cells

The cerebral cortex develops from dorsal forebrain neuroepithelial progenitor cells. Initial expansion of the progenitor cell pool is followed by the generation of neurons of all the cortical layers and later, astrocytes and oligodendrocytes. However, the regulatory pathways that control the expansion and maintenance of the neuroepithelial progenitor cell pool are currently unknown. Here we define six basic pathway components that regulate proliferation of cortically specified human neuroepithelial stem cells (cNESCs) in vitro without the loss of developmental potential. We show that activation of FGF and inhibition of BMP and ACTIVIN A signalling are required for long-term cNESC proliferation. We also demonstrate that cNESCs preserve dorsal telencephalon-specific potential when GSK3, AKT and nuclear CATENIN-{beta}1 activity are low. Remarkably, regulation of these six pathway components supports the clonal expansion of cNESCs. Moreover, cNESCs differentiate to lower and upper layer cortical neurons both in vitro and in vivo. Identifying the mechanisms that drive the self-renewal and fate of cNESCs decision of neuroepithelial stem cells is key to developing new stem cell-based therapeutic approaches to treat neurological conditions.

developmental biology↗

bioRxiv2021

Oncogenic ZMYND11-MBTD1 fusion protein anchors the NuA4/TIP60 histone acetyltransferase complex to the coding region of active genes

A chromosomal translocation found in cannibalistic acute myeloid leukemia (AML) leads to an in-frame fusion of the transcription elongation repressor ZMYND11 to MBTD1, a subunit of the NuA4/TIP60 histone acetyltransferase (HAT) complex. In contrast to the NuA4/TIP60 complex, ZMYND11 is linked to repression of actively transcribed genes through recognition of H3.3K36me3. To understand the abnormal molecular events that expression of this ZMYND11-MBTD1 fusion protein can create, we performed its biochemical and functional characterization in comparison to each individual fusion partner. ZMYND11-MBTD1 is stably incorporated into the endogenous NuA4/TIP60 complex but does not bring any additional interactors as the fusion lacks the MYND domain of ZMYND11. Nevertheless, this truncated ZMYND11 moiety in the fusion leads to mislocalization of the NuA4/TIP60 complex on the body of genes normally bound by ZMYND11 in the genome, in a PWWP-H3.3K36me3 interaction-dependent manner. This can be correlated to increased chromatin acetylation and altered gene transcription, most notably on the MYC oncogene, and alternative splicing. Importantly, expression of ZMYND11-MBTD1, but not the individual fusion partners, during embryonic stem cell differentiation, leads to decreased expression of specific differentiation markers, while favoring Myc-driven pluripotency. It also favors self-renewal of hematopoietic stem/progenitor cells. Altogether, these results indicate that the ZMYND11-MBTD1 fusion protein functions primarily by mistargeting the NuA4/TIP60 complex to the body of genes, altering normal transcription of specific genes, likely driving oncogenesis in part through the Myc regulatory network. Highlights-A recurrent chromosomal translocation detected in cannibalistic acute myeloid leukemia leads to the production of a ZMYND11-MBTD1 fusion protein. -The ZMYND11-MBTD1 fusion protein is stably incorporated into the endogenous NuA4/TIP60 complex. -ZMYND11-MBTD1 leads to mistargeting of NuA4/TIP60 activity to the coding region of ZMYND11-target genes, altering gene expression and splicing. -ZMYND11-MBTD1 binds the MYC gene leading to its upregulation, favoring growth and pluripotency while inhibiting differentiation markers.

molecular biology↗

bioRxiv2021

Misregulation of translation drives prostate cancer drug resistance

Emerging evidence associates translation factors and regulators to tumorigenesis. Recent advances in our ability to perform global translatome analyses indicate that our understanding of translational changes in cancer resistance is still limited. Here, we generated an enzalutamide-resistant prostate cancer (PCa) model, which recapitulated key features of clinical enzalutamide-resistant PCa. Using this model and polysome profiling, we investigated global translation changes that occur during the acquisition of PCa resistance. We found that enzalutamide-resistant cells exhibit a discordance in biological pathways affected in their translatome relative to their transcriptome, a deregulation of proteins involved in translation, and an overall decrease in translational efficiency. We also show that genomic alterations in proteins with high translational efficiency in enzalutamide-resistant cells are good predictors of poor patient prognosis. Additionally, long non-coding RNAs in enzalutamide-resistant cells show increased association with ribosomes, higher translation efficiency, and an even stronger correlation with poor patient prognosis. Taken together, this suggests that aberrant translation of coding and non-coding genes are strong indicators of PCa enzalutamide-resistance. Our findings thus point towards novel therapeutic avenues that may target enzalutamide resistant PCa.

cancer biology↗