imagine (Institute of molecular genetics and genetic engineering)
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Perfusion-based 3D in vitro cell culture model for osteosarcoma cells: Biological and chemical engineering perspectives
No full textOsteosarcoma is a primary malignant bone tumor affecting 3-4 per million people worldwide
each year. The scarcity of novel therapies for osteosarcoma patients indicates persistent
weaknesses in anticancer drug research, primarily due to heavy reliance on inadequate
conventional models - cell monolayers and animals. 3D in vitro cell culture models, as
physiologically more relevant have the potential to address this issue. Therefore, we aimed to
develop a 3D in vitro osteosarcoma cell culture model based on bone-mimicking scaffolds and
a perfusion bioreactor to achieve a closer imitation of the osteosarcoma cell microenvironment.
Macroporous alginate hydrogel scaffolds with embedded hydroxyapatite particles (2 wt%
alginate, 2 wt% hydroxyapatite) were seeded with murine osteosarcoma cells (K7M2-wt) at the
density 15x106 cells/cm3 of scaffold volume. Cells were then cultivated in a perfusion
biomimetic bioreactor („3D Perfuse“, Innovation Center of the Faculty of Technology and
Metallurgy, Belgrade, Serbia) for 7 days under continuous medium flow with a superficial
velocity of 40 μm/s while static cell cultures served as control. In both perfusion and static
cultures cells self-aggregated into spheroid-like structures, with those under perfusion
conditions being more compact and larger. In addition, cells under perfusion exhibited higher
metabolic activity, secreted more extracellular matrix, and possessed higher quantities of
intracellular protein tubulin. Finally, a chemical engineering approach was employed to
correlate cell biological characteristics with parameters in their microenvironment such as mass
transport rates of oxygen and nutrients, and the presence of shear stresses in perfusion
cultures. Mass transport of oxygen was modeled in both static and perfusion cultures and
values of shear stresses in perfusion cultures were calculated as up to 2 mPa acting on the
average spheroid. Overall, more favorable conditions were observed to be achieved in perfusion
cultures, as further clarified by the chemical engineering approach.Twenty-fifth Jubilee Annual Conference YUCOMAT 2024 & Thirteenth World Round Table Conference on Sintering XIII WRTCS 2024, Herceg Novi, Montenegro, September 2 to 6, 202
Različite uloge SOX gena u promovisanju malignog fenotipa ćelija glioblastoma
No full textThe presence of 20 SOX genes in human genome was identified and they are divided into eight
distinct groups designated from A to H. SOX genes encode proteins that display properties of both
architectural components of chromatin and classical transcription factors. SOX transcription
factors have crucial roles during development, including blastocyst formation, gastrulation, germ
layer formation, maintaining the pluripotency of stem cells, cell proliferation, sex determination,
neurogenesis, gliogenesis, and pituitary development. In adult tissues, they are involved in
regulation of cell survival, regeneration and homeostasis. On the other hand, numerous SOX genes
are expressed in brain tumors and play crucial roles in their development and maintenance.
Glioblastoma (GBM), grade IV glioma tumor, is the most common, most aggressive, and deadliest
brain tumor, with a median survival time of 15 months regardless of surgical resections, radio- and
chemotherapy. Its initiation, progression, relapse and resistance to treatments are associated with
glioma stem cells. GBMs contain different subsets of glioma stem cells characterized by high
proliferation rate, self-renewal capacity and ability to differentiate into different cell types and a
quiescent state of these cells protect them against chemotherapy and radiotherapy. Almost all SOX
genes are expressed in GBM and play roles in induction, progression and maintenance of
malignant phenotype of GBM, acting as oncogenes, tumor suppressors, or both, depending on the
cellular context. They influence stemness, self-renewal, proliferation, viability, migration,
invasion and sphere-forming capacity of glioma stem cells. Furthermore, SOX transcription factors
contribute to the malignant phenotype of GBM by affecting proliferation, differentiation, viability,
migration, invasion and apoptosis of GBM cells. SOX genes which function as oncogenes are
usually associated with a poor prognosis and shorter survival. Also, roles of the SOX2 and SOX9
genes in the chemo- and radioresistance of this type of tumor are revealed.
Overall, understanding the molecular mechanisms underlying the GBM is crucial for the discovery
of more efficient therapeutic approaches for this type of tumor and many SOX genes have been
recognized as promising candidates in the examination of new therapeutic targets
Development and Emergence of Ganoderma-Based Industry: A Global Perspective
No full textMedicinal mushrooms have been used for centuries as a remedy for treating various diseases and/or as an elixir for prolonging life. Among them, species belonging to the genus Ganoderma were especially valued due to the belief that they can improve health and strengthen energy and spirit. Once regarded as a traditional medicine common to Asian countries, in the past few decades, their popularity has escalated across the globe due to remarkable nutritive and medical potential. In general, over the past 2,000 years, Ganoderma species have crossed the path from prized ancient “herbal” medicine to the establishment of a multi-billion dollar industry. Nowadays, thousands of Ganoderma products, developed from different parts of fruiting bodies, mycelia or spore powder, are available in the market mainly in the form of foods, beverages, dietary supplements, cosmeceuticals and nutricosmetics. The objective of this chapter is to present development, potential and trends of various industries and products based on the Ganoderma genus
From physical to biological information and the genetic code
No full textAccording to the modern scientific developments, the information is getting to be a fundamental
notion like space, time and matter. These four fundamental concepts are substantially
interconnected and represent the basic ingredients of the universe. Being fundamental, there
is no complete definition of the information. According to our intuition, we distinguish between
what is and what is not information. In the present contribution, I consider information as a
very special state of the matter with a definite meaning which affects the evolution of the
universe as a whole or its parts. Depending on complexity of the system one can speak about
physical, biological and other information.
By physical information, first of all, I mean definite values of fundamental physical constants
(c –the speed of light in vacuum, h – the Planck constant, and G – the universal gravitational
constant). These constants are valid in every space, at every time and for every kind of matter.
Physical informtion also includes basic properties of elementary particles (mass, electric
charge, spin, ...). Physical informaton should mean everything that was given at the beginning
of the universe and does not change over time.
Biological information (bioinformation) is a very special state of the biological system, which
was given at the beginning of life or became during evolution. A basic example of a biological
information system is DNA, which is a special long sequence of pairs of nucleotides. A part
of DNA codes proteins, while the other one should be related to the regulation functions.
The DNA contains special sequences of codons to which certain sequences of amino acids
correspond. The special connection between 64 codons (elements of mRNA) and 20 amino
acids (building blocks of proteins) with the stop signal is known as the genetic code.
In this talk, I will speak about physical and biological information as well as about some
modeling of the genetic code.Book of abstracts: 5th Belgrade Bioinformatics Conference, Serbia, Belgrade,17-20 june 2024
ZEB2 as a driver of human-specific traits: Insights from comparative ChIP-Seq and RNA-Seq
No full textDespite near-identical protein sequences, humans exhibit striking phenotypic differences
from other primates. These differences likely stem from subtle changes in gene
regulation, not just gene sequences. The transcription factor ZEB2, known for its diverse
roles in development and cancer, has emerged as a key player in brain development
and neuronal differentiation. We investigated its functional divergence in primates by
performing ChIP-Seq with a ZEB2 antibody and RNA-Seq following ZEB2 knockdown
in human, chimpanzee, and orangutan B-lymphoblastoid cell lines. Our results showed
that ZEB2 binding extends beyond its canonical motif, revealing diverse, potentially
species-specific, regulatory preferences. Numerous binding sites within promoter regions
exhibited significantly higher affinity in humans, suggesting accelerated evolution of
these regulatory elements. While a conserved core of immune-related ZEB2 targets was
identified across species, we uncovered 437 potential human-specific targets enriched
for chromatin organization and DNA replication functions. Notably, an exceptionally high
number of non-coding RNA genes was seen among human-specific targets. Furthermore,
ZEB2 knockdown induced a unique pattern of differential gene expression in humans,
affecting genes involved in neural development and synaptic organization. This highlights
a human-specific functional shift in ZEB2 regulation towards brain-related processes. Our
findings not only illuminate ZEB2’s potential role in the evolution of uniquely human traits
but also provide valuable gene candidates for further functional studies into the genetic
basis of our species’ distinctive features.Book of abstracts: 5th Belgrade Bioinformatics Conference, Serbia, Belgrade,17-20 june 2024
Detecting somatic copy number variations in 245,388 participants from All of Us biobank
No full textattention due to advancement in methodology and late data biobanks. As part of that
clonal hekotapaisis (CHIP) and its implications in age-related diseases, has attracted
considerable attention. CHIP, a prevalent phenomenon in aging individuals, is linked
with all-cause mortality, blood cancer, and cardiovascular disease risks, but also exhibits
protective effects against conditions like Alzheimer’s disease.
We have developed a new methodology implemented in CNVpytor, that detects mosaic
copy number variation (mCNV) from WGS by leveraging two independent signals from
sequencing data: (1) depth of mapped reads; (2) B-allele frequency of SNPs and small
indels. This technique allows for the detection of somatic mCNVs, down to 1% cell
frequency. To improve quality of our detection we considered evidence from discordant
read pairs and SNP genotyping array data.
Our initial analysis of data from 245,388 individuals in the All of Us (AoU) cohort led to
the identification of 2,607 large (>10Mbp) confident somatic mCNVs. We observed an
expected trend where older individuals exhibited a higher number of somatic CNAs,
consistent with the understanding that detectable clonal hematopoiesis increases with
age. Our investigation into chromosome Y loss (LOY) among male samples revealed
that over 20% exhibit LOY, indicating a higher prevalence than other somatic mCNVs.
Additionally, we found hundreds of thousands smaller mCNVs. The discovery of a small
mCNVs in a young individuals, presumed to have originated during development, indicates
that analysis of all AoU samples can be useful for understanding of the differences in the
occurrence and nature of CNAs during development compared to those in aging.
This comprehensive analysis is expected to result in a shared computational resource,
offering mCNV calls for the wider research community. By providing these resources, we
aim to not only augment the value of AoU data but also establish a foundation for future
research methodologies as the AoU’s sample collection expands.Book of abstracts: 5th Belgrade Bioinformatics Conference, Serbia, Belgrade,17-20 june 2024
Epigenome-wide analysis identifies a methylome profile linked to Obsessive-Compulsive Disorder, disease severity, and treatment response
No full textObsessive-compulsive disorder (OCD) is a prevalent mental disorder affecting ~2–3%
of the population. This disorder involves genetic and, possibly, epigenetic risk factors.
The dynamic nature of epigenetics also presents a promising avenue for identifying
biomarkers associated with symptom severity, clinical progression, and treatment
response in OCD. We, therefore, conducted a comprehensive case-control investigation
using Illumina MethylationEPIC BeadChip, encompassing 185 OCD patients and 199
controls recruited from two distinct sites in Germany. Rigorous clinical assessments
were performed by trained raters employing the Structured Clinical Interview for DSM-IV
(SCID-I). We performed a robust two-step epigenome-wide association study that led to
the identification of 305 differentially methylated CpG positions. Next, we validated these
findings by pinpointing the optimal set of CpGs that could effectively classify individuals
into their respective groups. This approach identified a subset comprising 12 CpGs that
overlapped with the 305 CpGs identified in our EWAS. These 12 CpGs are close to or in
genes associated with the sweet-compulsive brain hypothesis which proposes that aberrant
dopaminergic transmission in the striatum may impair insulin signaling sensitivity among
OCD patients. We replicated three of the 12 CpGs signals from a recent independent study
conducted on the Han Chinese population, underscoring also the cross-cultural relevance
of our findings. In conclusion, our study further supports the involvement of epigenetic
mechanisms in the pathogenesis of OCD. By elucidating the underlying molecular
alterations associated with OCD, our study contributes to advancing our understanding
of this complex disorder and may ultimately improve clinical outcomes for affected
individuals.Book of abstracts: 5th Belgrade Bioinformatics Conference, Serbia, Belgrade,17-20 june 2024
Navigating ELSI for FAIR multiomics data management within STEPUPIORS international rectal cancer project
No full textThe STEPUPIORS project entails a multi-omics approach to studying neoadjuvant
chemoradiotherapy (nCRT) response in locally-advanced rectal cancer (LARC) patients through
retrospective and prospective longitudinal sample and data collection. Through a multinational
collaboration including four partnering institutions (IORS - Serbia, NKI - Netherlands, BRFAA -
Greece, FRCB-IDIBAPS - Spain) different layers of omics data are being generated and integrated
to derive biomarkers and models for prediction of patient’s response to nCRT. Consideration
of Ethical, legal and societal issues (ELSI) is mandatory for projects dealing with personal and
sensitive data, and collection of biological material from patients. The international nature of
the project necessitates compliance with both national (Serbian) and EU laws and regulatory
provisions governing data privacy and patient protection.
Ethics approvals were sought with the IORS’ local Committee for retrospective use of
samples and health records, and for prospective collection and biobanking of samples and
associated metadata, supplying patient information sheet and 2-tiered informed consent
form. Prospectively collected samples and data will be managed by a Laboratory Information
Management System (LIMS) acquired within the newly established IORS Biobank.
International collaboration was facilitated through signing of Consortium and Joint controller
agreements specifying terms for transfer of material including data, non-disclosure of
information and data processing activities.
A Data Management Plan (DMP) was made considering a wide range of data types including
structured information from patients’ medical records, radiology images, genomics,
transcriptomics and proteomics data. DMP contained detailed descriptions of type of
processing, source of data, data format and quantity. Means of maintaining confidentiality
were described, which include access control, pseudonymization, separate processing of
data collected for different purposes. Free access to data was achieved through deposition
of raw data in appropriate repositories (Zenodo, EGA, cBioPortal) and as Supplementary data in open access publications in accordance with EU’s Open Science policy and in line with
Findable, Accessible, Interoperable Research data (FAIR) principles.
Here we provide the roadmap and examples for navigating the complex ELSI landscape
required for FAIR biomedical and multi-omics data management in accordance with the
applicable regulatory provisions relating to the protection of the personal data and to medical
confidentiality.Book of abstracts: 5th Belgrade Bioinformatics Conference, Serbia, Belgrade,17-20 june 2024
Enhancing Cancer Genomics: A Pipeline for Spatial Transcriptomics Analysis on the CGC
No full textSpatial transcriptomics field has grown significantly in recent years. This hybrid method,
inspired by in situ hybridization and next-generation sequencing, particularly single-cell RNA
sequencing (scRNA-seq), enables whole transcriptome profiling while maintaining spatial
context at high resolutions, offering new insights in cancer research.
We present a highly configurable sequencing-based technology solution for comprehensive
spatial analysis. Available on the NCI-funded Cancer Genomics Cloud (CGC) platform by
Seven Bridges, this pipeline provides a collaborative cloud infrastructure. The CGC platform
integrates computation, over 1000 bioinformatics workflows, and 4+ PB of data, making
Cancer Research Data Commons (CRDC) datasets accessible from any environment.
Developed with widely adopted packages, this pipeline processes datasets from leading
technologies, 10x and Slide-seq. It includes steps such as quality control, data preprocessing,
dimensionality reduction, cluster identification, detection of spatially variable features, and
integration with scRNA-seq references. The pipeline is highly configurable, allowing various
settings to be optimized for better results, and some specific components can be selectively
executed. Key steps are visually represented for detailed insights.
Here, we demonstrate spatial transcriptomics analysis flow on publicly available datasets
using this pipeline, showing the impact of different settings on analysis outcomes. We identify
spatially variable genes with distinct tissue localization and integrate data to predict cell type
composition within spatial domains.
Spatial transcriptomics analysis significantly enhances cancer research by characterizing
tumor microenvironments, discovering novel biomarkers, and clarifying drug resistance
mechanisms. This CGC-hosted workflow is expected to contribute to significant advancements
in understanding complex spatial relationships within tissues.Book of abstracts: 5th Belgrade Bioinformatics Conference, Serbia, Belgrade,17-20 june 2024
Cultivation of Streptomyces sp. BV365 wild type and mutant in 5 L fermenter
No full textAbstract: The data and files contained in this dataset are related to research on cultivation and actinomycin production by Streptomyces sp. BV365 wild type and mutant. Streptomyces are aerobic Gram-positive bacteria with complex lifecycles that usually live in the soil, but inhabit a wide range of other ecological niches. They are known as producers of different secondary metabolites with important functions, including variety of antibiotics, but also pigments, and anticancer drugs. In our previous study, Streptomyces sp. BV365 wild type strain was shown to produce high amounts of orange extracellular pigments on mannitol-soy flour (MSF) agar, identified as actinomycin D, C2 and C3 that showed antibacterial activity [https://doi.org/10.3389/fbioe.2024.1466757]. Our aim was to establish conditions for scaled-up cultivation of Streptomyces sp. BV365 in 5 L fermenter, in MSF and waste bread-based (Bread Crumbs –BC) medium. The growth of Streptomyces sp. BV365 mutant (Streptomyces sp. BV365-m, obtained by chemical mutagenesis with N-methyl-N′-nitro-N-nitrosoguanidine) was also followed. We analyzed oxygen consumption, one of the fundamental physiological characteristics of culture growth, within 68 hours of fermentation. The Streptomyces sp. BV365 cultures were grown in 5 L stirred tank bioreactor, in 2.5 L of previously described media, following these conditions: 30.0 ±2.0 °C, pH 7.0±1.0, with a maximum agitation rate of 400 rpm and an air flow of 1654 mL min-1, to secure adequate aeration level during the fermentation process. It has been shown that the growth and actinomycins production in this strain could be successfully scaled-up and optimized. All details about the data structure, methods and research conditions are given in the metadata file readme.txt which is accessible and machine-readable.readme.txt (5.435Kb)
***Dataset contents*** Ferm_BV365.xlsx (234.8Kb)
Ferm_BV365m r1.csv (5.681Kb)
Ferm_BV365wt r1.csv (6.163Kb)
Ferm_BV365wt r2.csv (5.918Kb)
Ferm_BV365wt r3.csv (7.495Kb)
Ferm_BV365wt r4.csv (9.760Kb)
Figure 1.png (135.6Kb)
Figure 2.png (186.9Kb)
Figure 3.png (123.4Kb)
Figure 4.png (111.0Kb)Pevious study: [https://doi.org/10.3389/fbioe.2024.1466757]File readme.txt (5.435Kb) is under licence public domain CC