imagine (Institute of molecular genetics and genetic engineering)
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Exploratory Analysis of Molecular Subtypes in Early-Stage Osteosarcoma: Identifying Resistance and Optimizing Therapy
No full textBackground: Osteosarcoma (OS) is a highly aggressive bone malignancy with limited treatment options and poor prognosis. This exploratory study aimed to identify molecular subtypes of early-stage, treatment-naive OS to guide precise therapeutic strategies. Methods: We analyzed RNA-seq data obtained from tumor tissues from 102 OS patients using a non-negative matrix factorization algorithm (NMF) to classify the tumors into three subtypes: S1, S2, and S3. Differential gene expression was evaluated using DESeq2, followed by functional enrichment analysis with clusterProfiler and CancerHallmarks. The tumor microenvironment was assessed through ESTIMATE and CIBERSORT, and drug sensitivity was predicted using OncoPredict. SAOS-2 and MG63 cells, representing the S1 subtype, were used in the viability essays to determine the effect of hesperidin, a natural phenolic compound noted for its anti-cancer potential, alone and in combination with doxorubicin and 5-fluorouracil. Results: This study revealed three OS subtypes: S1 was enriched in cell cycle regulation, vesicular transport, and RNA metabolism while S2 and S3 were enriched in pathways related to extracellular matrix organization and protein translation, respectively. S1 displayed high tumor purity, significant chemoresistance, and overexpression of KIF20 A, correlating with poor prognosis. AURKB, a hesperidin target, was implicated in S1 pathogenesis. In vitro, hesperidin significantly reduced the viability of SAOS-2 and MG63 cells and enhanced doxorubicin efficacy. Conclusions: Our findings support the molecular subclassification of OS, emphasizing subtype-specific mechanisms of tumor progression and chemoresistance, with hesperidin offering potential as a therapeutic adjunct for high-risk OS patients
Bioremediation potential of newly isolated glyphosate-degrading bacteria from agricultural and pristine soil
No full textBioeremeditation, i.e. microbial biodegradation of pollutants, presents a promising solution for the removal of
contaminants from polluted environments. This study explores the bioremediation potential of newly isolated bacteria
capable of degrading glyphosate, a widely used herbicide and the active ingredient in products like Roundup™.
Glyphosate is a synthetic amino acid analogue of glycine, bound to phosphonic acid, and its widespread use has raised
concerns about its accumulation or that of its metabolite, AMPA, in soils and food crops [1,2]. Moreover, glyphosate is
known to be toxic to aquatic organisms [1]. As such, microbial degradation of glyphosate could play a vital role in
developing effective bioremediation strategies for soils heavily treated with glyphosate-based herbicides. In this study,
we isolated microorganisms from agricultural and pristine soil samples using three different growth media. The best
candidates were identified via 16S rRNA sequencing as belonging to the genera Bacillus, Pseudomonas, Cupriavidus,
Lelliottia, and Pseudescherichia. Importantly, the last three genera have not been previously reported to degrade
glyphosate. The biotransformation of glyphosate was monitored through TLC, and HPLC analysis was used to confirm
degradation and investigate their bioremediation potential. Overall, our analysis has identified potential new species
with glyphosate-degrading activity. These isolates are currently being studied further for potential novel pathways of
glyphosate degradation.E-book: 19th International Conference on Chemistry and the Environment ICCE 2025 Belgrade 8-12 June 202
Graphene quantum dots enhanced with gold nanoparticles for advanced antibacterial applications
No full textIn the era of antibiotic resistance, exploring novel nanomaterials offers a promising avenue for combating infections. This study investigates the antibacterial effects of graphene quantum dots (GQDs) combined with gold nanoparticles, synthesized in situ via gamma irradiation of GQDs with chloroauric acid and isopropyl alcohol at doses of 1, 5, 10, and 20 kGy. The composites were analyzed using several characterization methods, including photoluminescence and infrared spectroscopy, dynamic light scattering, zeta potential measurements, and scanning electron microscopy with energy-dispersive X-ray spectroscopy. Inductively coupled plasma optical emission spectrometry analysis confirmed the presence of gold in all samples, with the highest concentration of 11.14 μg/mL. Hemolytic assays confirmed excellent biocompatibility with hemolysis below 2 %, while MTT assays revealed that cell viability exceeded 80 % for most samples, confirming their non-toxic nature. The findings showed that these materials have antibacterial activity against the MRSA strain. These results demonstrate that gold nanoparticles significantly contribute to the antibacterial properties of GQDs, indicating their potential for biomedical applications
Activation of ankrd1a expression marks newly forming myofibers and regulates muscle cell differentiation in adult zebrafish skeletal muscle repair
No full textNEW & NOTEWORTHY This study identifies ankrd1a as a novel modulator of skeletal muscle repair in adult zebrafish. Revealingits dual role in newly forming and intact myofibers near injury, the work highlights ankrd1a’s function in fine-tuning myogenic dif-ferentiation during repair. We position ankrd1a as both a marker of myofibers that repopulate wounded tissue and a player incoordination of adaptive responses essential for effective muscle tissue recovery.ankrd1a; regeneration; skeletal muscle; tissue repair; zebrafishINTRODUCTIONThe mammalian skeletal muscle has an impressive capacityto regenerate and repair injuries caused by aging, diseases,myotoxic agents, trauma, and ischemia (1, 2). After an injury
Engineered 3D osteosarcoma microenvironment model: Bridging in vitro - in vivo gap in cancer research and anticancer drug screening
No full textIntroduction
Current treatments for osteosarcoma typically include
surgical excision followed by neoadjuvant and adjuvant
chemotherapy. Research attempts to streamline and
improve these treatments, but progress is slow mostly
due to limited translation of in vitro to in vivo studies.
The aim of this work was to develop and validate an
engineered three-dimensional (3D) osteosarcoma model
based on macroporous composite scaffolds, as cell
carriers, and biomimetic perfusion bioreactor for
osteosarcoma research and anticancer drug screening.
Material and method
The scaffolds (4 mm thick discs, 9 mm in diameter) were
produced by controlled gelation of hydroxyapatite (HAP)
suspension in Na-alginate solution (2 wt.% alginate and 2
wt.% HAP) followed by freeze-drying and rehydration in
the culture medium. Murine osteosarcoma K7M2-wt
cells were seeded onto the scaffolds (15x106 cells cm-3
scaffold volume) and cultivated for 7 days in "3D
Perfuse" bioreactors under continuous medium
superficial velocity of 40 μm s-1, while static cultures
served as a control. To evaluate this model for anticancer
drug screening, bioreactor cultures were treated with
doxorubicin (1 μg cm-3), on day 1 (first study) or on day
7 (second study) and lasted for 1 day, while untreated
bioreactor culture served as a control. The scaffolds were
assessed regarding the cell metabolic activity by MTT,
morphology and distribution by histological and scanning
electron microscopy analyses. Masson-trichrome and
reticulin staining were used for extracellular matrix
(ECM) analysis, while quantitative real-time PCR (qRTPCR) assessed osteosarcoma marker expression.Result and discussion
After short-term cultures, biological assessment showed
that the cells stayed viable and metabolically active,
produced ECM, expressed osteosarcoma markers and
spontaneously formed aggregates under both culture
conditions. However, cells in the bioreactor culture
exhibited higher metabolic activity, while the cell
aggregates were slightly larger (~1.2-fold), more compact
with higher amounts of reticular fibers, more numerous
and more uniformly distributed throughout the scaffold
compared to the static culture. These results could be
explained by positive effects of flow on cells due to
enhanced mass transport and adequate hydrodynamic
shear stresses. Evaluation of the model for anticancer
drug screening has shown a negligible effect of doxorubicin on individual cells as well as cell aggregates
implying that the developed model more closely mimics
in vivo drug responses than 2D cultures.
Conclusion
This study has shown potentials of engineered 3D
osteosarcoma microenvironment model based on
macroporous composite scaffolds, and perfusion
bioreactor for relevant and reliable osteosarcoma
research and anticancer drug screening.EACR 2025 Congress Abstract
Transcriptomic Landscape of Paclitaxel-Induced Multidrug Resistance in 3D Cultures of Colon Cancer Cell Line DLD1
No full textMultidrug resistance (MDR) significantly contributes to colon cancer recurrence, making it essential to understand its molecular basis for improved therapies. This study aimed to identify genes and pathways involved in resistance to standard chemotherapeutics by comparing transcriptome profiles of sensitive and paclitaxel-induced MDR colonospheres. Cell viability and growth were assessed following treatment with 5-fluorouracil, oxaliplatin, irinotecan, bevacizumab, and cetuximab. Drug concentrations in culture media posttreatment were measured using high-performance liquid chromatography (HPLC). RNA sequencing (RNA-seq) of untreated sensitive and resistant colonospheres identified differentially expressed genes linked to baseline resistance. Our results confirmed cross-resistance in the resistant model, showing highest oxaliplatin tolerance may involve mechanisms beyond efflux. Transcriptome analysis highlighted upregulation of PIGR and activation of the ribosomal signaling pathway as potential resistance mediators. Notably, AKR1B10, a gene linked to chemotherapeutic detoxification, was overexpressed, whereas genes related to adhesion and membrane transport were downregulated. The overexpression of ribosomal protein genes suggests ribosome biogenesis plays a key role in acquired resistance. These findings suggest that targeting ribosome biogenesis and specific deregulated genes such as PIGR and AKR1B10 may offer promising strategies to overcome MDR in colon cancer
Structural characterisation of recombinant LEA protein originated from Ramonda serbica
No full textDesiccation, an extreme form of dehydration, reduces the cellular water content to below 5% and thus,
presents a significant challenge for most plants. Ramonda serbica, a resurrection plant and tertiary relict
is an excellent model for studying vegetative desiccation tolerance. Late Embryogenesis Abundant (LEA)
proteins are mostly Intrinsically Disordered Proteins (IDPs) and have an important role in this adaptive
trait. However, their precise molecular function still remains unclear. The majority of the LEA4 protein
family group exhibited a high propensity to form α-helical structure, particularly A-type of α-helix, with
differentiated charged and hydrophobic faces.
In this study, for the first time, we report the secondary structure analysis of the recombinantly produced
desiccation-induced LEA 4 protein family member from a dicotyledonous resurrection plant species.
Through immobilized metal affinity and size-exclusion chromatography, we purified this LEA protein to a
purity exceeding 95%, demonstrating a robust and scalable method for the production of other LEA
proteins. Secondary structure predictions using various algorithms suggest that more than 95% of the
amino acid sequence of this protein has a strong tendency to form α-helices. However, disorder prediction
tools reveal that approximately 85% of the sequence is intrinsically disordered, showing its structural
flexibility under varying conditions. Structural characterisation via circular dichroism (CD) spectroscopy
revealed that LEA protein is predominantly disordered. In the presence of 2,2,2-trifluoroethanol and lipid
mimetic detergent, the protein mostly folds into an α-helical structure, implying the importance of
structural plasticity. Structural disorder-to-order transitions may be a key feature enabling LEA protein
protective function in the desiccation tolerance mechanism. We suggest that this structural duality
underpins the protective function of LEA protein in chloroplasts, likely through interactions with thylakoid
membrane and desiccation-sensitive proteins associated with photosynthesis. This function may be
essential for the rapid recovery of photosynthetic components upon rehydration. Our study provides new
insights into the structure-function relationship of LEA proteins in resurrection plants. It lays the
groundwork for the development of future bioengineering strategies aimed at enhancing drought
tolerance in crops.Book of abstract: 3rd ML4NGP MEETING on Machine Learning and Non-globular proteins
May 20-23, 2025. Vilnius, Lithuani
Combining two biocompatible singlet oxygen generators into a potent photoactive agent: graphene quantum dots-curcuma hybrid
No full textAs a cutting-edge treatment strategy, photodynamic therapy (PDT) utilizes light-sensitive compounds to selectively destroy target cells, offering extensive possibilities for managing numerous medical conditions, including bacterial infections and tumors. Graphene quantum dots (GQDs), zero-dimensional nanomaterials, possess unique properties that make them ideal for biomedical applications, including high dispersibility, biocompatibility, and luminescent emission. In this study, we synthesized GQDs and modified them by incorporating curcumin, a natural compound known for its antimicrobial properties. Both UV-Vis and infrared spectroscopies confirmed the formation of the hybrid material. AFM and DLS analyses revealed an increase in particle size and changes in zeta potential, indicating successful incorporation of curcumin. Notably, the modified GQDs exhibited enhanced singlet oxygen production under blue light irradiation, as proven with EPR spectroscopy and ABDA degradation, demonstrating their potential as a photosensitizer of a new generation for PDT
Genetic Determinants of Response to Neoadjuvant Chemoradiotherapy in Rectal Cancer Identified by Whole Exome Sequencing
No full textBackground Neoadjuvant chemoradiotherapy (nCRT) is essential for treating locally advanced rectal cancer (LARC), however response to nCRT varies, and reliable predictors are lacking. Methods This study used whole exome sequencing analysis to investigate genetic differences between tumors highly responsive and non-responsive to nCRT. Five patients with good response and two patients without response to nCRT were used as a discovery set. Results The analysis identified 15 InDels and 202 non-synonymous SNVs exclusively present in tumors of non-responders, mainly in genes regulating the cell cycle, adhesion, and migration. In contrast, 9 InDels and 122 non-synonymous SNVs were exclusively present in tumors of good responders, primarily in extracellular matrix remodeling and immunity-related genes. Six variants in transmembrane transporter genes were selected as candidate biomarkers and validated in 33 LARC patients. Conclusion The results suggest that SLC16A6 rs7222013 and SLC25A2 rs3749780 may serve as potential predictors of poor nCRT response in LARC patients
ST1-YtnP lactonase from extreme environment: A promising antivirulence agent against multidrug-resistant Pseudomonas aeruginosa
No full textThe emergence of multidrug-resistant (MDR) pathogens, particularly Pseudomonas aeruginosa, requires innovative therapeutic strategies. This study investigates the potential of ST1-YtnP lactonase, an enzyme isolated from the thermophilic bacterium Bacillus licheniformis, which is found in the extreme environment of the Vranjska Banja hot springs. The extreme conditions in this habitat offer untapped potential for the discovery of biotechnologically valuable, resilient enzymes. ST1-YtnP lactonase was shown to effectively degrade acyl-homoserine lactones (AHLs), thereby disrupting the quorum sensing (QS) system of P. aeruginosa and reducing its virulence. ST1-YtnP significantly reduced biofilm formation without inhibiting bacterial growth Furthermore, in vitro analysis revealed that ST1-YtnP lactonase exhibited a synergistic effect with gentamicin and an additive effect with meropenem, enhancing the efficacy of these antibiotics against P. aeruginosa MMA83. In vivo, the combination of meropenem and ST1-YtnP lactonase completely rescued Caenorhabditis elegans from infection, surpassing the protective effect of meropenem alone. ST1-YtnP lactonase showed no adverse effects on the survival of uninfected nematodes, while it significantly enhanced the survival of P. aeruginosa-infected nematodes treated with the enzyme. These findings emphasize the potential of ST1-YtnP lactonase as a novel antivirulence agent with promising biotechnological applications to combat antibiotic-resistant infections