Biology subjects

Sippl, W.

Publications and source records attributed to Sippl, W..

6 recordsLinked to original sources

bioRxiv2026

Lineage-restricted dependency on an oncofetal SNHG29-IGF2BP1 RNA axis in acute megakaryoblastic leukemia

Acute megakaryoblastic leukemia (AMKL) is a rare, aggressive subtype of acute myeloid leukemia with developmental origins in early childhood. To uncover long noncoding RNAs (lncRNAs) sustaining this high-risk malignancy, we conducted CRISPR interference screens targeting lncRNAs overexpressed in primary AMKL samples. This analysis identified SNHG29 as a previously unrecognized lineage-specific dependency, whose silencing profoundly impaired leukemic proliferation and clonogenic growth in vitro and reduced leukemic burden in vivo. RNA pulldown coupled with proteomic analysis revealed that SNHG29 interacts with the oncofetal RNA-binding protein IGF2BP1, which is aberrantly expressed in AMKL. SNHG29 was required to maintain expression of IGF2BP1 target transcripts, including MYC- and E2F-driven proliferative programs, thereby reinforcing fetal transcriptional programs essential for leukemic maintenance. Pharmacologic inhibition of IGF2BP1-RNA interactions with the small-molecule BTYNB induced potent and selective cytotoxicity in patient-derived AMKL models. Together, these findings uncover a developmental co-dependency between SNHG29 and IGF2BP1 that defines a lineage-restricted oncogenic circuit and an actionable therapeutic vulnerability in AMKL.

cancer biology↗

bioRxiv2024

Dona Flor and her two husbands: Discovery of novel HDAC6/AKT2 inhibitors for myeloid cancer treatment

Hematological cancer treatment with hybrid kinase/HDAC inhibitors is a novel strategy to overcome the challenge of acquired resistance to drugs. We collected IC50 datasets from the ChEMBL database for 13 cancer cell lines (72 h cytotoxicity, measured by MTT), known inhibitors for 38 kinases, and 10 HDACs isoforms, that we identified by target fishing and literature review. The data was subjected to rigorous biological and chemical curation leaving the final datasets ranging from 76 to 8173 compounds depending on the target. We generated Random Forest classification models, whereby 14 showed greater than 80% predictability after 5-fold external cross-validation. We screened 30 hybrid kinase/HDAC inhibitor analogs through each of these models. Fragment-contribution maps were constructed to aid the understanding of SARs and the optimization of these compounds as selective kinase/HDAC inhibitors for cancer treatment. Among the predicted compounds, 9 representative hybrids were synthesized and subjected to biological evaluation to validate the models. We observed high hit rates after biological testing for the following models: K562 (62.5%), MV4-11 (75.0%), MM1S (100%), NB-4 (62.5%), U937 (75.0), and HDAC6 (86.0%). This aided the identification of 6b and 6k as potent anticancer inhibitors with IC50 of 0.2-0.8 {micro}M in three cancer cell lines, linked to HDAC6 inhibition below 2 nM, and blockade of AKT2 phosphorylation at 2 M, validating the ability of our models to predict novel drug candidates. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=47 SRC="FIGDIR/small/626092v1_ufig1.gif" ALT="Figure 1"> View larger version (13K): org.highwire.dtl.DTLVardef@76705dorg.highwire.dtl.DTLVardef@1cb1d32org.highwire.dtl.DTLVardef@1e9cbdforg.highwire.dtl.DTLVardef@47b819_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LINovel kinase/HDAC inhibitors for cancer treatment were found using machine learning C_LIO_LI61 QSAR models for hematological cancers and its targets were built and validated C_LIO_LIK562, MV4-11, MM1S, NB-4, U937, and HDAC6 models had hit rates above 62.5% in tests C_LIO_LI6b and 6k presented potent IC50 of 0.2-0.8 {micro}M in three cancer cell lines C_LIO_LI6b and 6k inhibited HDAC6 below 2 nM, and blockade of AKT2 phosphorylation at 2 M C_LI

cancer biology↗

bioRxiv2023

More than just an Eagle Killer: The freshwater cyanobacterium Aetokthonos hydrillicola produces highly toxic dolastatin derivatives

Cyanobacteria are infamous producers of toxins. While the toxic potential of planktic cyanobacterial blooms is well documented, the ecosystem level effects of toxigenic benthic and epiphytic cyanobacteria are an understudied threat. The freshwater epiphytic cyanobacterium Aetokthonos hydrillicola has recently been shown to produce the "eagle killer" neurotoxin aetokthonotoxin causing the fatal neurological disease Vacuolar Myelinopathy. The disease affects a wide array of wildlife in the southeastern United States, most notably waterfowl and birds of prey, including the bald eagle. In an assay for cytotoxicity, we found the crude extract of the cyanobacterium to be much more potent than pure aetokthonotoxin, prompting further investigation. Here, we describe the isolation and structure elucidation of the aetokthonostatins, linear peptides belonging to the dolastatin compound family, featuring a unique modification of the C-terminal phenylalanine derived moiety. Using immunofluorescence microscopy and molecular modeling, we confirmed that aetokthonostatin acts as a potent tubulin binder. We also show that aetokthonostatin inhibits reproduction of the nematode C. elegans, resulting in increased population lethality of the combined action of the two toxins produced by A. hydrillicola. Bioinformatic analysis revealed the aetokthonostatin biosynthetic gene cluster encoding a non-ribosomal peptide synthe-tase/polyketide synthase accompanied by a unique tailoring machinery. The biosynthetic activity of a specific N-terminal methyltransferase was confirmed by in vitro biochemical studies, establishing a mechanistic link between the gene cluster and its product. Significance StatementCyanotoxins have adverse effects on ecosystems. Our understanding of their potential risk has recently been expanded by the discovery of aetokthonotoxin, produced by the cyanobacterium Aetokthonos hydrillicola growing on invasive plants. Via trophic transfer, it acts as a neurotoxin causing mortality in animals including top predators like Bald Eagles. Closer examination of A. hydrillicola revealed that it also produces highly toxic dolastatin derivatives. A. hydrillicola is the first cultured cyanobacterium producing dolastatin derivatives, allowing us to uncover biosynthetic gene clusters of this compound family. In contrast to all other known dolastatin-producers, which are marine cyanobacteria, A. hydrillicola thrives in freshwater reservoirs, making it a potential threat also for human health. Monitoring of the cyanobacterium and its toxins is strongly recommended.

microbiology↗

bioRxiv2023

IGF2BP1 induces high-risk neuroblastoma and forms a druggable feedforward loop with MYCN promoting 17q oncogene expression

BackgroundNeuroblastoma is the most common solid tumor in infants accounting for approximately 15% of all cancer-related deaths. Over 50% of high-risk neuroblastoma relapse, emphasizing the need of novel drug targets and therapeutic strategies. In neuroblastoma, chromosomal gains at chromosome 17q, including IGF2BP1, and MYCN amplification at chromosome 2p are associated with adverse outcome. Recent, pre-clinical evidence indicates the feasibility of direct and indirect targeting of IGF2BP1 and MYCN in cancer treatment. MethodsCandidate oncogenes on 17q were identified by profiling the transcriptomic/genomic landscape of 100 human neuroblastoma samples and public gene essentiality data. Molecular mechanisms and gene expression profiles underlying the oncogenic and therapeutic target potential of the 17q oncogene IGF2BP1 and its cross-talk with MYCN were characterized and validated in human neuroblastoma cells, xenografts and PDX as well as novel IGF2BP1/MYCN transgene mouse models. ResultsWe reveal a novel, druggable feedforward loop of IGF2BP1 (17q) and MYCN (2p) in high-risk neuroblastoma. This promotes 2p/17q chromosomal gains and unleashes an oncogene storm resulting in fostered expression of 17q oncogenes like BIRC5 (survivin). Conditional, sympatho- adrenal transgene expression of IGF2BP1 induces neuroblastoma at a 100% incidence. IGF2BP1- driven malignancies are reminiscent to human high-risk neuroblastoma, including 2p/17q-syntenic chromosomal gains and upregulation of Mycn, Birc5, as well as key neuroblastoma circuit factors like Phox2b. Co-expression of IGF2BP1/MYCN reduces disease latency and survival probability by fostering oncogene expression. Combined inhibition of IGF2BP1 by BTYNB, MYCN by BRD inhibitors or BIRC5 by YM-155 is beneficial in vitro and, for BTYNB, also in vivo. ConclusionWe reveal a novel, druggable neuroblastoma oncogene circuit settling on strong, transcriptional/post-transcriptional synergy of MYCN and IGF2BP1. MYCN/IGF2BP1 feed-forward regulation promotes an oncogene storm harboring high therapeutic potential for combined, targeted inhibition of IGF2BP1, MYCN expression and MYCN/IGF2BP1-effectors like BIRC5.

cancer biology↗

bioRxiv2023

Novel hydroxamic acid derivative induces apoptosis and constrains autophagy in leukemic cells

IntroductionPosttranslational modification of proteins by reversible acetylation regulates key biological processes. Histone deacetylases (HDACs) catalyze protein deacetylation and are frequently dysregulated in tumors. This has spurred the development of HDAC inhibitors (HDACi). Such epigenetic drugs modulate protein acetylation, eliminate tumor cells, and are approved for the treatment of blood cancers. ObjectivesWe aimed to identify novel, nanomolar HDACi with increased potency over existing agents and selectivity for the cancer-relevant class I HDACs (HDAC1/-2/-3/-8). Moreover, we wanted to define how such drugs control the apoptosis-autophagy interplay. As test systems, we used human leukemic cells and embryonic kidney-derived cells. MethodsWe synthesized novel pyrimidine-hydroxamic acid HDACi (KH9/KH16/KH29) and performed in vitro activity assays and molecular modeling of their direct binding to HDACs. We analyzed how these HDACi affect leukemic cell fate, acetylation, and protein expression with flow cytometry and immunoblot. The publicly available DepMap database of CRISPR-Cas9 screenings was used to determine sensitivity factors across human leukemic cells. ResultsNovel HDACi show nanomolar activity against class I HDACs. These agents are superior to the clinically used hydroxamic acid HDACi vorinostat. Within the KH-series of compounds, KH16 (yanostat) is the most effective inhibitor of HDAC3 (IC50 = 6 nM) and the most potent inducer of apoptosis (IC50 = 110 nM; p<0.0001) in leukemic cells. KH16 though spares embryonic kidney-derived cells. Global data analyses of knockout screenings verify that HDAC3 is a dependency factor in human blood cancer cells of different lineages, independent of mutations in the tumor suppressor p53. KH16 alters pro- and anti-apoptotic protein expression, stalls cell cycle progression, and induces a caspase-dependent processing of the autophagy proteins ULK1 and p62. ConclusionThese data reveal that HDACs are required to stabilize autophagy proteins through a suppression of apoptosis in leukemic cells. HDAC3 appears as a valid anti-cancer target for pharmacological intervention. HighlightsO_LINovel HDACi with nanomolar activity against leukemic cells were synthesized. C_LIO_LIHDACi of the KH-series are superior to a clinical grade HDACi. C_LIO_LIHDACi of the KH-series modulate acetylation and phosphorylation of proteins. C_LIO_LIThe new HDACi KH16 regulates cell cycle arrest, apoptosis, and autophagy. C_LIO_LIApoptosis acts upstream of autophagy in KH16-treated cells. C_LI

pharmacology and toxicology↗

bioRxiv2019

Pharmacological inhibition of lysine-specific demethylase 1 (LSD1) induces global transcriptional deregulation and ultrastructural alterations that impair viability in Schistosoma mansoni

Treatment and control of schistosomiasis still rely on only one effective drug, praziquantel (PZQ), and due to mass treatment, the increasing risk of selecting for schistosome strains that are resistant to PZQ has alerted investigators to the urgent need to develop novel therapeutic strategies. The histone-modifying enzymes (HMEs) represent promising targets for the development of epigenetic drugs against Schistosoma mansoni. In the present study, we targeted the S. mansoni lysine-specific demethylase 1 (SmLSD1), a transcriptional corepressor, using a novel and selective synthetic inhibitor, MC3935. We synthesized a novel and potent LSD1 inhibitor, MC3935, which was used to treat schistosomula or adult worms in vitro. By using cell viability assays and optical and electron microscopy, we showed that treatment with MC3935 affected parasite motility, egg-laying, tegument, and cellular organelle structures, culminating in the death of schistosomula and adult worms. In silico molecular modeling and docking analysis suggested that MC3935 binds to the catalytic pocket of SmLSD1. Western blot analysis revealed that MC3935 inhibited SmLSD1 demethylation activity of H3K4me1/2. Knockdown of SmLSD1 by RNAi recapitulated MC3935 phenotypes in adult worms. RNA-seq analysis of MC3935-treated parasites revealed significant differences in gene expression related to critical biological processes. Collectively, our findings show that SmLSD1 is a promising drug target for the treatment of schistosomiasis and strongly support the further development and in vivo testing of selective schistosome LSD1 inhibitors. Author SummarySchistosomiasis mansoni is a chronic and debilitating tropical disease caused by the helminth Schistosoma mansoni. The control and treatment of the disease rely almost exclusively on praziquantel (PZQ). Thus, there is an urgent need to search for promising protein targets to develop new drugs. Drugs that inhibit enzymes that modify the chromatin structure have been developed for a number of diseases. We and others have shown that S. mansoni epigenetic enzymes are also potential therapeutic targets. Here we evaluated the potential of the S. mansoni histone demethylase LSD1 (SmLSD1) as a drug target. We reported the synthesis of a novel and potent LSD1 inhibitor, MC3935, and show that it selectively inhibited the enzymatic activity of SmLSD1. Treatment of juvenile or adult worms with MC3935 caused severe damage to the tegument of the parasites and compromised egg production. Importantly, MC3935 proved to be highly toxic to S. mansoni, culminating in the death of juvenile or adult worms within 96 h. Transcriptomic analysis of MC3935-treated parasites revealed changes in the gene expression of hundreds of genes involved in key biological processes. Importantly, SmLSD1 contains unique sequences within its polypeptide chain that could be explored to develop a S. mansoni selective drug.

molecular biology↗