Biol. Life Sci. Forum, 2021, ECB 2021

Antibody-drug conjugates (ADCs) are used in anticancer therapy with some limitations due to their molecular properties. An alternative to monoclonal antibodies is the affibody, composed of 58 amino acids, with lower binding affinities, small size, and rapid blood clearance and tissue distribution. We investigate the in vitro efficacy of a novel anti-HER2 ZHER2:2891 affibody conjugated to a cytotoxic drug auristatin E (MMAE) in HER2-positive human cancer cells. An adenocarcinoma cell line SK-BR-3, expressing high levels of HER2, and mammary gland adenocarcinoma MDA-MB-231, expressing basal levels of HER2, were treated with ZHER2:2891DCS-MMAE and trastuzumab (as a reference compound). ZHER2:2891DCS-MMAE induced a significant time-dependent toxic effect in SK-BR-3 cells. A 30% reduction in cell viability was found after 10 min exposure at 7 nM with an IC50 of 80.2 nM. On the contrary, MDA-MB-231 cells were not affected by the affibody complex. The HER2-specific cytotoxic effect of the ZHER2:2891DCS-MMAE has also been confirmed by measuring apoptosis by flow cytometry. In SK-BR-3 cells, the increasing concentrations of the conjugated affibody induced cell death after 10 min of treatment with the strongest effect observed after 48 h. Moreover, treatment with ZHER2:2891DCS-MMAE reduced (up to 50%) HER2 expression at both mRNA and protein levels in SK-BR-3 cells after 24 h of treatment. In conclusion, the cytotoxic conjugate based on the anti-HER2 affibody and MMAE efficiently interacts with HER2 over-expressing cancer cells, allowing the selective and specific delivery of the cytotoxic payload. The basal HER2 expressing cells are not the most affected probably due to a lower uptake of the drug conjugate. This confirms that affibodies may be used to target HER2 overexpressing cells while sparing normal cells. Full article

2-Styrylchromones (2-SC) are a group of oxygen-containing heterocyclic compounds, which are characterized by the attachment of a styryl group to the C-2 position of their chromone core. Over the years, several biological activities have been attributed to 2-SC, such as antioxidant, anti-inflammatory, antimicrobial, antiviral, and antitumor activities [1,2]. Nonetheless, there are no reports in the literature about the effect of 2-SC on human neutrophils’ oxidative burst. Therefore, the present study aims to evaluate the modulation of human neutrophils’ oxidative burst by a panel of hydroxylated 2-SC, previously obtained by chemical synthesis, and to analyze the structure–activity relationship [3]. For that purpose, freshly isolated neutrophils from human blood were stimulated with phorbol-12-myristate-13-acetate, and a chemiluminescence method was applied to evaluate the oxidative burst, using luminol as a probe [4]. Considering the OH substituents present on the B-ring of 2-SC, the tested compounds can be divided into the following three groups: group 1, with a catechol group (C-3′ and C-4′); group 2, with an OH at C-4′; group 3, without any substitution on the B-ring. The 2-SC from group 1 were the most active, with IC₅₀ values in the order of 1 µM. In conclusion, the catechol B-ring appears to play an important role in the modulation of human neutrophils’ oxidative burst by 2-SC. Full article

Personalized cancer medicine holds promise for the future of cancer treatment. One of the keys to success is the knowledge of exact molecular alterations that drive tumorigenesis in a given patient, so that a suitable targeted therapy can be selected. However, the extent of such alterations, i.e., number of various kinds of driver mutations per patient, is still not known. We have utilized the largest database of human cancer mutations—TCGA PanCanAtlas, multiple popular algorithms for cancer driver prediction and several custom scripts to estimate the number of various kinds of driver mutations in primary tumors. We have found that there are on average 12 driver mutations per patient’s tumor, of which 0.6 are hyperactivating point mutations in oncogenes, 1.5 are amplifications of oncogenes, 0.1 have both in the same oncogene, 1.2 are inactivating point mutations in tumor suppressors, 2.1 are deletions in tumor suppressors, 0.3 have both in the same tumor suppressor, 1.5 are driver chromosome losses, 1 is driver chromosome gain, 2 are driver chromosome arm losses, and 1.5 are driver chromosome arm gains. The number of driver mutations per tumor gradually increased with age, from 6.7 for < 25 y.o. to 14.9 for > 85 y.o., and cancer stage, from 10.0 to 15.2. There was no significant difference between genders (12.0 in males vs. 11.9 in females). The number of driver mutations per tumor varied strongly between cancer types, from 1.2 in thyroid carcinoma to 23.8 in bladder carcinoma. Overall, our results provide valuable insights into the extent of driver alterations in tumors and suggest that multiple possibilities to choose a suitable targeted therapy exist in each patient. Full article

Our Work focuses on the development of active molecular targeting utilizing novel conjugated specific targeting molecules that differentially target specific organ or diseased area with minimal distribution into normal organs in order to achieve optimal efficacy and safety profiles. In that regards, over the past decade, evidence from the scientific and medical communities has demonstrated that nanobiotechnology and nanomedicine have tremendous potential to affect numerous aspects of cancer and other disorders in terms of early diagnosis and targeted therapy [¹,²,³,⁴]. The utilization of nanotechnology for the development of new nanocarrier systems has the potential to offer improved targeted delivery through increased solubility and sustained retention and, more importantly, active targeting. One of the major advantages of this innovative technology is its unique multifunctional characteristics [¹,²,³,⁴]. Targeted delivery of drug-incorporated nanoparticles, through the conjugation of site-specific cell surface markers, such as tumor-specific antibodies or ligands, can enhance the efficacy of the anticancer drug and reduce the side effects [³,⁴,⁵,⁶]. Additionally, multifunctional characteristics of the nanocarrier system would allow for simultaneous imaging of tumor mass, targeted drug delivery and monitoring (theranostics). A summary of the recent progress in nanotechnology as it relates to nanoparticles and drug delivery are reviewed in the slide presentation. Nano nutraceuticals, using a combination of various natural products, provide great potential in disease prevention [⁴]. Additionally, various nanomedicine approaches for the detection and treatment of various types of organ-specific delivery, vascular targeting, and vaccines are highlighted in the slide presentation. In conclusion, this presentation highlighted the key role of nanobiotechnology in achieving effective and safe pharmaceuticals, optimizing vaccine delivery, targeting the delivery for optimal biodistribution into targeted sites as well as improving PK and PD and minimizing impact of pharmacogenomic variables. These aspects could accelerate the transition from nanomedicines into precision medicines. Full article

Polysaccharide-based carriers have become attractive materials for the delivery of therapeutics targeting the colon. Ferulated arabinoxylans (AX)—polysaccharides with gelling and antioxidant capacities that can be degraded by colonic microbiota—are ideal candidates for use as oral drug delivery systems [¹]. Recently, AX-based microspheres have demonstrated potential applications as colon-targeted drug carriers [²,³]. The non-cytotoxicity of AX-based microspheres is a required property for their use as a colon-targeted biomaterial. This study reports the antioxidant activity and cytotoxicity on human colon cells of covalently cross-linked particles based on AX (AXP). The in vitro antioxidant activity of AX before and after gelation was measured using the 2,2-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid (ABTS+), the 2,2-diphenyl-1-picrylhydrazyl (DPPH), and the ferric reducing antioxidant power (FRAP) methods. The effect of AX and AXP on the proliferation of human colon cells (CCD 841 CoN) was evaluated using the MTT assay. AXP presented a spherical shape and rough surface with a three-dimensional and porous network. Gelation decreased the antioxidant activity of AX by 61–64%. AX and AXP did not affect proliferation or show any toxic effect on the regular human colon cell line CCD 841 CoN. The results indicate that AXP are promising biocompatible materials with antioxidant activity. AXP could be suitable materials for the development of drug delivery systems targeting the colon. Full article

There are numerous computational tools which support the design of new potential ligands. They assist in the evaluation of potential compound activity as well as in the optimization of compound physicochemical and pharmacokinetic properties. Nowadays, they are an indispensable element of the drug design process; both time and money can be saved with their application. Full article

New sustainable ingredients with beneficial properties for health are a main goal for the food industry. In this regard, the cocoa shell (CS) and the coffee pulp (CP), by-products from the coffee and cocoa industry produced worldwide in large amounts, are suitable candidates. We previously stated that these by-products are sources of phytochemicals and dietary fiber with potential hypolipidemic properties. This study aimed to assess the hypolipidemic properties of CS and CP after simulated gastrointestinal digestion. The capacities of the residual fraction of each digestion phase to bind bile salts and cholesterol and inhibit the lipase activity were measured to establish the in vitro hypolipidemic properties of both by-products. Furthermore, the digested fractions’ effect on lipid accumulation was evaluated in the HepG2 cell line. From results, the CS showed a higher ability to bind cholesterol (4–24%) and bile salts (2–3%) in gastric and colonic phases. Meanwhile, during the gastrointestinal phase, CP showed a greater capacity to bind cholesterol (1–13%) and bile salts (2%). The capacity to inhibit lipase activity was more accentuated in the CS in gastrointestinal digestion (16%) whereas during gastric digestion in the CP (11%). Likewise, the digested fractions of both by-products (100 µg/mL) significantly alleviated the accumulation of fat (17–20%) in the HepG2 cell model after the stimulation of cells with palmitic acid. This comparative approach suggests that both by-products exhibit similar hypolipidemic properties after in vitro digestion. This research supports the revalorization of cocoa and coffee by-products as food ingredients and nutraceuticals with potential health benefits in preventing chronic metabolic diseases. due to their remarkable hypolipidemic properties. Full article

Chronic pain changes brain connectivity, brainwaves, and volume, often resulting in disability, anxiety, and depression. Opioid pain relievers impair function, with risk of addiction. Music analgesia research suggests that music for long-term analgesia includes slow tempo, pleasantness, and self-choice. Hypothesis: individuals listening to self-chosen music with embedded beats ½ h twice a day, could show brainwave entrainment (BWE) at healthy frequencies of healthy descending pain modulatory system. BWE may change brain activity, restoring organization in DPMS altered by chronic pain. Volunteers with chronic pain >1 year participated in a study of 4 weeks of listening to one half hour of music twice a day, and four weeks of non-listening, reporting pain and analgesic use bi-weekly using visual analog scale (VAS) and 0–10 numerical pain scores (NPS), medication types, and dosage. Volunteers selected from 27 half-hour pieces of music in several genres in a mobile app. Isochronic beats were embedded in the music with tempo, key, and isochronic theta frequencies proportional, to enhance the brain’s perception of rhythmic patterns and harmonics. Mean NPS showed a 26% reduction (p = 0.018). Significantly, mean medication dosage declined by over 60% (p = 0.008). Double-blind studies, larger populations are needed in future. Full article

Introducing an innovative drug to the market requires not only large amounts of money, but also time. Therefore, the process of repositioning, i.e., finding new indications for drugs already in use, is becoming more and more frequent. In 2020, chloroquine (CQ) and hydroxychloroquine (HCQ) were approved for the treatment of severe COVID-19 infection. However, studies have shown that the adverse effects of these drugs are too serious and the approval was revoked. The most serious and most frequently reported adverse effects were cardiotoxicity and neurotoxicity. For this reason, the study investigates the possible mechanism of cardiotoxicity and neurotoxicity of CQ and HCQ using in silico computational methods. The results of this study were found to be consistent with the literature. Full article

Photothermal therapy (PTT) is a novel therapy for cancer treatment which is based on the conversion of photon energy into heat (>43 °C), and photoacoustic imaging (PAI) is a new bioimaging method for diagnosing and monitoring cancer. To enhance the impact depth of PTT and the signal of PAI, near-infrared (NIR)-absorbing photothermal agents are usually used. The development of novel NIR-absorbing photothermal agents with excellent properties, such as a high stability under long-term irradiation, strong absorption in the NIR range, and excellent biocompatibility, is needed in modern biomedicine. Previous research has proved that gold nanostars (AuNSs) have promising potential applications in photo-based therapies owing to their strong absorption in the NIR range and strong photothermal effects. However, the reported methods to synthesize AuNSs are complicated and toxic, which can limit its practical application. In this work, we proposed a new environmental strategy to synthesize AuNSs by using chitosan and vitamin C. Chitosan plays multiple roles, acting as stabilizing, shape-directing, and size-controllable agents in this method for the first time. The obtained AuNSs show strong NIR absorption and biocompatibility toward non-cancerous and cancerous cell lines. The in vitro tests proved the high efficiency of the obtained AuNSs in both PTT and PAI. Full article

Colorectal cancer (CRC) is among the most commonly occurring cancers. The management of CRC includes laparoscopic surgery, radiotherapy, chemotherapies and neoadjuvant treatment. However, conventional chemotherapies have poor impact on combating CRC and are associated with severe toxic effects and high rates of relapse. Therefore, searching for a new combination regimen is a favorable consideration. The aim of this study was to elucidate the synergistic effect of 5-fluorouracil (5-FU) and diosmetin in an in vitro model on colorectal cancer cells. An MTT assay was conducted on HCT-116 cancer cells and they were treated with a concentration gradient of 5-FU and diosmetin individually and in combination. The combination index (CI) and dose reduction index (DRI) were calculated using CompuSyn software. Isobologram analysis and synergism determination were performed using the Combenefit software tool and the synergy score was calculated using the SynergyFinder 2.0 software tool. The apoptotic features of the cells were determined via an AO/PI double staining assay and an annexin V assay using a fluorescent microscope and the flow cytometry technique, respectively. The findings showed that the DRI of 5-FU was three-fold lower in the combination with a CI value of less than one, which indicates that there was a synergistic effect. The AO/PI microscopic results revealed signs of apoptosis and dead cells after 72 h of treatment. Flow cytometry analysis confirmed that the apoptotic effect of the combination was more prominent compared to 5-FU alone. The findings of this study offer a potential strategy for reducing the cytotoxicity and enhancing the efficacy of 5-FU on colorectal cancer cells through a synergistic study model. Full article

Some studies demonstrate that gallic acid (GA) and myricetin (MYR) isolated from Rhus trilobata provide the therapeutic activity of this plant against cancer. However, few reports demonstrate that both compounds could also have therapeutic potential in ovarian cancer. Therefore, evaluating the cytotoxic activity of GA and MYR against ovarian cancer cells and determining the possible action mechanism present are important. For this purpose, SKOV-3 cells (ovarian adenocarcinoma; HTB-77™, ATCC^®) were cultivated according to the supplier’s instructions (37 °C and 5% CO₂) to determine the biological activity of GA and MYR by confocal/transmission electron microscopy, PI-flow cytometry, H₂DCF-DA, MTT, and Annexin-V assays. Possible molecular targets of the compounds were determined by the Similarity Ensemble approach. Results showed that GA and MYR treatments decreased the viability of SKOV-3 cells at 50 and 166 μg/mL, respectively (p ≤ 0.05, ANOVA vs. vehicle group). They also induced morphological changes (cytoplasmic reduction, nuclear chromatin condensation, cytoplasmic vesicles increment, polymerized actin, and stabilized tubulin), cell cycle arrest (GA: 8.3% G₂/M and MYR: 78% G₁), and apoptosis induction (GA: 18.9% and MYR: 8.1%), due to ROS generation (34 to 42%) for 24 h (p ≤ 0.05, ANOVA vs. vehicle group). In silico studies demonstrated that GA and MYR interact with carbonic anhydrase-IX and PI3K, respectively. In conclusion, GA and MYR show cytotoxic activity against SKOV-3 cells through ROS production, which modifies the cytoskeleton and induces apoptosis. Therefore, GA and MYR could be considered as base compounds for the development of new treatments in chemotherapy for ovarian cancer. Full article

Wound infection is a serious issue because of multi-drug resistance bacteria, thus developing an advanced therapy is a needed demand. Photothermal therapy (PTT) is a novel noninvasive strategy that utilizes PTT agents to convert near-infrared (NIR) light energy into heat to kill living cells. In this work, we developed the PTT agent containing membrane to treat the wound infection for the first time. Palladium nanoparticles (PdNPs) were chosen as PTT agents owing to their high stability, good biocompatibility, excellent photothermal property, and simple-green preparation. Chitosan (CS) has been widely studied in tissue engineering due to its good properties such as biocompatible, biodegradable, antibacterial, and wound-healing abilities. However, the poor workability and high brittleness of CS limit the applications of CS in tissue engineering. Thus, we combined polyvinyl alcohol (PVA) and CS to have the membrane with high flexibility, wettability, highly porosity. The test on cells showed that the membrane has high biocompatibility. The combination of PdNPs loading CS/PVA membrane and laser irradiation killed most of the bacteria in vitro. Full article

According to the World Health Organization, neuropsychiatric disorders pose an increasingly greater burden on health, society, and economy of countries. Currently, there are strategies to prevent some of these disorders, and there are treatments or means to alleviate their symptoms. In the case of depression, the medication consists of antidepressant drugs. Such drugs can also be used in other conditions like anxiety, pain, or insomnia. A shortcoming of the currently used antidepressants is the occurrence of side effects that sometimes are unbearable for the patient. In this respect, a promising direction is the usage of medicinal plants. Plant parts are rich in phytochemicals that could be beneficial in mental disorders by acting on various targets. Here, we investigated the antidepressant effect of ten natural compounds from sage, mint, and citrus. The biological activity of these compounds was investigated by calculating pKi values and affinities for dopamine receptor D2, serotonin transporter (SERT), and 5-hydroxytryptamine receptor 1A (5-HT1A) using quantitative structure-activity relationship (QSAR) models. Our results showed that linalyl acetate, 1,8-cineole, and neryl acetate could be efficient antidepressants and neuroleptics. Full article

Improvement of treatment outcomes in patients with locally advanced or metastatic urothelial carcinoma represents an important unmet need, since survival remains poor in patients who progress beyond first-line treatment. The purpose of this study was to investigate the effects of ramucirumab, a human monoclonal antibody that binds to VEGFR-2, in the treatment of locally advanced or metastatic urothelial carcinoma. A literature search of PubMed and CENTRAL was conducted. Outcomes of interest were overall survival (OS), progression-free survival (PFS) and the rate of adverse events. Time-to-event outcomes were combined using the generic inverse-variance method and presented as hazard ratio (HR) with 95% confidence intervals (95% CI), while dichotomous events were combined using the Mantel–Haenszel method and presented as odds ratio (OR) with 95% CI. All of the analyses were performed in RevMan 5.3. The literature search identified two randomized controlled trials. The addition of ramucirumab to docetaxel resulted in a statistically significant improvement in PFS (HR = 0.55, 95% CI 0.31–0.96, p = 0.030), while the difference was not significant for OS (HR = 0.86, 95%CI 0.71–1.04, p = 0.12). Subgroup analysis by sex, age (<65 and ≥65 years), baseline hemoglobin (<10 g/dL and ≥10 g/dL), presence of visceral metastases and presence of liver metastases did not identify a subgroup in which improvement in OS was present. The difference in treatment-related grade ≥ 3 adverse events was not significant (OR = 1.47, 95%CI 0.95–2.27, p = 0.08). Ramucirumab in addition to docetaxel significantly improved PFS in patients with locally advanced or metastatic urothelial carcinoma. Future studies are necessary to identify a subset of patients who might experience a significant improvement in OS. Full article

The metabolic syndrome is a cluster of conditions that occur together, increasing the risk of chronic diseases such as obesity, type II diabetes, or cardiovascular disease. Nutritional interventions improving inflammation, bioenergetics, and oxidative stress are proposed as effective tools in preventing metabolic syndrome. The cocoa shell is a by-product generated in large amounts during cocoa production. This by-product contains alkaloids and phenolic compounds as main compounds and has been investigated as an anti-obesity and anti-diabetic agent. Here, we used network pharmacology to explore the potential mechanism of the phytochemicals from the cocoa shell. We searched the cocoa shell’s phytochemical composition; then, oral bioavailability and drug-likeness were screened. We predicted the targets for the phytochemicals found in this by-product and used different databases to search for compound–protein and compound–gene interactions, and then protein–protein interaction networks were constructed. Moreover, pathway enrichment analysis was performed, and biological processes and signaling pathways were identified and illustrated through bioinformatics analyses. Theobromine, caffeine, procyanidin B2, (−)-epicatechin, (+)-catechin, and protocatechuic acid were identified in the cocoa shell as main components. Those phytochemicals were associated with inflammation (TNF-α, NF-κB, JNK)-, oxidative stress (CAT, SOD)-, obesity (adiponectin, leptin, FASN, PPAR-α)-, and diabetes (insulin, AKT)-related pathways. Results demonstrated that cocoa shell phytochemicals could modulate multiple biological processes and signaling pathways in a multimechanistic manner. Hence, cocoa shell consumption could support the nutritional prevention of metabolic syndrome. Future in vivo and clinical investigations will be needed to validate this potential nutraceutical and healthy ingredient’s effects and mechanisms. Full article

Objective. To study the effect of biopsychological age indicators on the likelihood and severity of COVID-19 disease in adults in 2020. We have examined 447 people aged 35–70 years using methods for assessing biological and psychological age in terms of health indicators and subjective psychological age. Results. The number of cases at the end of 2020 in the group of working adults was 31%, in the risk group 0%; representatives of the risk group complied with the quarantine requirements 1.75 times stricter. Indicators of biopsychological age affected the development of the disease in working adults. The relative biological age of an individual had a direct impact on the risk of infection (p < 0.05), and on the probability of the patient’s death (p < 0.001). The relative psychological age had an inverse effect on the risk of infection at the tendency level (p = 0.06) and the death risk of those infected, (p < 0.001). Calendar age increases the risk of infection and the risk of death at the trend level. Conclusions. Indicators of relative biological and psychological aging of an individual affect the frequency and severity of the disease, while the combination of high indicators of biological age and underestimated psychological age dangerously increases the likelihood of developing severe forms of the disease. Full article

The pharmacologic properties of gold compounds have been known since the end of the 19th century. In the last decade gold complexes have received increased attention due to the variety of their applications. Rhodopsin-like receptors are a family of proteins that belong to the largest group of G-protein-coupled receptors (GPCRs). In this paper the molecular interactions between the active binding sites of rhodopsin-like receptors (RLRs) and synthesized gold(III) complexes ([Au(DPP)Cl₂]⁺, where DPP = 4,7-diphenyl-1,10-phenanthroline) were investigated through molecular docking simulations. The crystal structure of investigated RLRs (PDB ID: 4A4M) was extracted from the RCSB Protein Data Bank in a PDB format. The native bound ligand (11-cis-retinal) was extracted from receptors and a binding pocket analysis was performed. Redocking was performed with gold(III) complexes to generate the same docking pose as found in the cocrystallized form of receptors. The binding energy of gold(III) complexes to RLRs was found to be −35.35 kJ/mol, as opposed to 11-cis-retinal, where it was about −40.5 kJ/mol. The obtained results revealed that gold(III) complexes bind at the same binding pockets to RLRs, as well as native bound ligands, via weak noncovalent interactions. The most prominent interactions are hydrogen bonds, alkyl–π and π–π interactions. The preliminary results suggest that gold(III) complexes showed good binding affinity against RLRs as well as the native bound ligand 11-cis-retinal, as evident from the free binding energy (ΔG_bind in kJ/mol). Full article

G-protein-coupled receptors (GPCR) belong to a large family of molecules eliciting different responses to a variety of signaling molecules. These receptors participate in various physiological functions such as metabolism, growth, immune responses, inflammation, vision, taste, olfaction, and neurotransmission as well as in pathologic responses including chronic inflammatory and vascular diseases. Receptors contributing to the biological responses of the renin–angiotensin system (RAS) are members of the GPCR family. COVID-19-induced inflammatory cascade has been attributed to acute ACE2 downregulation and imbalance of proinflammatory ACE/AngII/AT1R and anti-inflammatory ACE2/angiotensin (1–7)/Mas axes in favor of the former. Some of the receptors contributing to activities of proteins in RAS, including AT1R, AT2R, Mas receptors, and Mas-related GPCR-member D receptor are members of the GPCR family. It is notable that these receptors induce their effects both through G-protein and β-arrestin pathways; the former exerts temporary and the latter more sustained effects. In addition to the imbalance of GPCR responses contributing to RAS activities, it has been suggested that SARS-CoV2 pathogenesis might be attributed to the activation of GPCRs or modulating G proteins involved in the adenosine–CFTR regulation system and epithelial Na-channel function. This article includes a minireview of the physiological functions of GPCRs and their contribution to COVID-19. Full article

Cutaneous melanoma (CM) is a public health issue and a significant challenge for scientists. At the dawn of the “omics era”, we witnessed groundbreaking advances in CM molecular stratification and therapeutic management assisted by genomic profiling and sequencing technologies. However, melanomagenesis is a complex and multifactorial process that cannot be restricted to genomic aspects, requiring investigation from a multi-omics perspective. Recently, droplet digital polymerase chain reaction (ddPCR) emerged as a powerful omics technology that can be used for absolute allele quantification, copy number variation (CNV) analysis, rare mutation and DNA methylation detection, genetic rearrangements, and transcriptomic evaluations in different types of biological samples, revolutionizing CM biomedical research and clinical care. This paper presents how ddPCR can complement existing approaches in the field to detect multiple types of alterations in both body fluids as well as formalin-fixed paraffin-embedded (FFPE) tissues harvested from CM patients and highlights how these findings may broaden our vision on CM diagnosis, prognosis and therapy in the context of precision medicine. Full article

Aberrant crypt foci (ACF) are early lesions in the neoplastic induction found in the rat colon of a carcinogenic model. ACF are one of the first changes in the colon that lead to colorectal cancer (CRC). Probiotics and fermented foods are well known for their beneficial role in gut health and previous studies showed their therapeutic effects on gastrointestinal diseases. The aim of this study was to investigate the preventive role of Propionibacterium freudenreichii and Faecalibacterium prausnitzii probiotics against CRC in rats induced with azoxymethane (AOM). Microscopical examination of the rat’s colon stained with methylene blue showed that the total number and multiplicity of ACF were significantly lower in the probiotic treated rats (p < 0.05) than in the AOM control group. Histological examination of the colon revealed severe hyperplasia and dysplasia of the ACF in the colon of the AOM control group compared to the treatment groups. Probiotics administration also reduced the levels of malondialdehyde (MDA) in the colon of treated rats compared to the rats in the AOM control group. These results suggest that probiotics play a preventive role in CRC initiation and development by slowing down ACF formation, reducing the severity of ACF lesions and reducing lipid peroxidation levels in the colon. Full article

Medium-chain triglycerides (MCT) have demonstrated a wide range of neuroprotective effects, although the mechanisms still remain poorly understood. Animal models are indispensable for such research. Metabolic effects of regular diet supplementation with fats must be considered. Male Wistar rats aged 2.5 months received (o/g) 3 g/kg/day of MCT oil, lard, or water (control) as a supplement to standard chow for 28 days. On the 17th day, the animals were tested in Y-maze. On the 28th day, blood was collected for biochemical testing (glucose, triglycerides (TG), total cholesterol (TC), HDL cholesterol). In a separate experiment, animals received 3 g/kg MCT, lard, or water, and were then sacrificed 30 or 120 min after. Blood was collected for biochemical testing (glucose, lactate, pyruvate, acetoacetate, β-hydroxybutyrate (BHB), TC, TG, aspartate transaminase (AST), alanine transaminase (ALT)). In the Y-maze test, the MCT-fed rats demonstrated an increased frequency of spontaneous alterations compared to both the control and lard groups, indicating improved working memory. Chronic administration of neither fat affected the blood glucose, TG, TC, and HDL cholesterol. Acutely, MCT supplementation elevated blood BHB, while lard did not. Lard increased blood TG, TC, and ALT, while MCT did not. Daily supplementation of standard feed with MCT led to mild intermittent ketosis and improved working memory in rats. Neither chronic nor acute MCT administration had any adverse effect on metabolic health markers. This animal model may be used to study the mechanisms of the cognitive-enhancing effects of MCT. Full article

(1) Background: Various Machine Learning (ML) methods are applied for the prediction of individual efficiency of cancer treatment regimens. As features for ML, different multi-omics data may be used. We proposed a next-generation ML approach termed FloWPS (FLOating-Window Projective Separator) that filters features before building the ML models to preclude extrapolation in the feature space. (2) Methods: Using Gene Expression Omnibus (GEO), The Cancer Genome Archive (TCGA), and Tumor Alterations Relevant for GEnomics-driven Therapy (TARGET) project databases, as well as our own data, we selected 32 gene expression datasets for cancer patients, annotated with a clinical response status. The biggest dataset included 235 patient cases, and the smallest one had only 41. (3) Results and Discussion: We demonstrated essential improvement of ML quality metrics for FloWPS-based clinical response classifiers for all global ML methods applied, including support vector machines (SVM), random forest (RF), binomial naïve Bayes (BNB), adaptive boosting (ADA), and multi-level perceptron (MLP). Namely, AUC for these classifiers increased from the 0.61–0.88 range to 0.70–0.98. (4) Conclusion: In our ML trial with 32 cancer gene expression datasets, the BNB method with FloWPS showed the best performance, with minimal, median, and maximal AUC values equal to 0.77, 0.86, and 0.98, respectively. Full article

During the search for new active compounds, at first, the focus is put mainly on the provision of compound activity towards considered targets. However, at the same time, or in the subsequent stages, the compound needs to be adequately profiled in terms of its physicochemistry and ADMET properties. Here, we present a tool for optimization of physicochemical and pharmacokinetic properties based on the application of machine learning tools. It considers several compound properties: solubility, metabolic stability, biological membrane permeability, hERG channel blocking, and mutagenicity. Separate models are constructed for each property and the predictive power of the models is verified on the ligands of serotonin receptor 5-HT₇. The models use various fingerprints for compound representation (including interaction fingerprints in the cases, where docking to the target protein can be performed). The results obtained within the study will be used for the design of new serotonin receptor ligands with optimized physicochemical and ADMET profiles. Full article