Expression of "DNA damage response" pathway genes in diffuse large B-cell lymphoma: The potential for exploiting synthetic lethality.

Diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL) are two of the most prevalent non-Hodgkin's lymphoma subtypes. Despite advances, treatment resistance and patient relapse remain challenging issues. Our study aimed to scrutinize gene expression distinctions between DLBCL and FL, employing a cohort of 53 DLBCL and 104 FL samples that underwent rigorous screening for genetic anomalies. The NanoString nCounter assay evaluated 730 cancer-associated genes, focusing on densely tumorous areas in diagnostic samples. Employing the Lymph2Cx method, we determined the cell-of-origin (COO) for DLBCL cases. Our meticulous analysis, facilitated by Qlucore Omics Explorer software, unveiled a substantial 37% of genes with significantly differential expression patterns between DLBCL and FL, pointing to nuanced mechanistic disparities. Investigating the impact of FL disease stage and DLBCL COO on gene expression yielded minimal differences, prompting us to direct our attention to consistently divergent genes in DLBCL. Intriguingly, our Gene Set Enrichment Analysis spotlighted 21% of these divergent genes, converging on the DNA damage response (DDR) pathway, vital for cell survival and cancer evolution. Strong positive correlations among most DDR genes were noted, with key genes like BRCA1, FANCA, FEN1, PLOD1, PCNA, and RAD51 distinctly upregulated in DLBCL compared to FL and normal tissue controls. These findings were subsequently validated using RNA seq data on normal controls and DLBCL samples from public databases like The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) databases, enhancing the robustness of our results. Considering the established significance of these DDR genes in solid cancer therapies, our study underscores their potential applicability in DLBCL treatment strategies. In conclusion, our investigation highlights marked gene expression differences between DLBCL and FL, with particular emphasis on the essential DDR pathway. The identification of these DDR genes as potential therapeutic targets encourages further exploration of synthetic lethality-based approaches for managing DLBCL.

"Losing the Brakes"-Suppressed Inhibitors Triggering Uncontrolled Wnt/ß-Catenin Signaling May Provide a Potential Therapeutic Target in Elderly Acute Myeloid Leukemia.

Dysregulated Wnt/ß-catenin signal transduction is implicated in initiation, propagation, and poor prognosis in AML. Epigenetic inactivation is central to Wnt/ß-catenin hyperactivity, and Wnt/ß-catenin inhibitors are being investigated as targeted therapy. Dysregulated Wnt/ß-catenin signaling has also been linked to accelerated aging. Since AML is a disease of old age (>60 yrs), we hypothesized age-related differential activity of Wnt/ß-catenin signaling in AML patients. We probed Wnt/ß-catenin expression in a series of AML in the elderly (>60 yrs) and compared it to a cohort of pediatric AML (<18 yrs). RNA from diagnostic bone marrow biopsies (n = 101) were evaluated for key Wnt/ß-catenin molecule expression utilizing the NanoString platform. Differential expression of significance was defined as >2.5-fold difference (p < 0.01). A total of 36 pediatric AML (<18 yrs) and 36 elderly AML (>60 yrs) were identified in this cohort. Normal bone marrows (n = 10) were employed as controls. Wnt/ß-catenin target genes (MYC, MYB, and RUNX1) showed upregulation, while Wnt/ß-catenin inhibitors (CXXR, DKK1-4, SFRP1-4, SOST, and WIFI) were suppressed in elderly AML compared to pediatric AML and controls. Our data denote that suppressed inhibitor expression (through mutation or hypermethylation) is an additional contributing factor in Wnt/ß-catenin hyperactivity in elderly AML, thus supporting Wnt/ß-catenin inhibitors as potential targeted therapy.

Chickpea Peptide: A Nutraceutical Molecule Corroborating Neurodegenerative and ACE-I Inhibition.

Chickpea seeds are the source of proteins in human nutrition and attribute some nutraceutical properties. Herein, we report the effects of chickpea seed bioactive peptide on albumin, insulin, lactoglobulin and lysozyme amyloid fibril formation. Employing thioflavin T (ThT) assays and circular dichroism (CD), amyloid structural binding transition was experimented to analyze the inhibition of amyloid fibril formation. The purified active peptide with a molecular mass of 934.53 Da was evaluated in vitro for its ACE-I inhibitory, antibacterial, antifungal and antidiabetic activities. Further, in vivo animal studies were carried out in wistar rats for blood pressure lowering action. In hypertensive rats, chickpea peptide decreased 131 ± 3.57 mm of Hg for systolic blood pressure and 86 ± 1.5 mm of Hg for diastolic blood pressure after 8 h intraperitoneal administration. Additionally, the peptide suppressed the fibrillation of amyloid and destabilized the preformed mature fibrils. Data emphasize efficacy of chickpea peptide vis-a-vis ACE-Inhibitory, antibacterial, antifungal, antidiabetic and anti-amyloidogenic activities, allowing us to propose this novel peptide as a suitable candidate for nutraceutical-based drugs and seems the first kind of its nature.

Phytochemical thymoquinone prevents hemoglobin glycoxidation and protofibrils formation: A biophysical aspect.

d-ribose, a reducing sugar, in diabetic hyperglycemia provokes non-enzymatic glycoxidation of hemoglobin (Hb), an abundant protein of red blood cells (RBCs). Different types of intermediates adduct formation occur during glycoxidation, such as advanced glycation end-products (AGEs) which lead to amyloid formation due to structural and conformational alterations in protein. Therefore, the study of these intermediate adducts plays a pivotal role to discern their relationship with diabetes mellitus and related disorders. Here, we investigated the interaction mechanism of d-ribose with Hb, and Hb prebound phytochemical thymoquinone (TQ). Our investigation reveals that the interaction of TQ with histidine residues of Hb interferes with the interaction of d-ribose with glycine residues at the glycation-site. Based on that, we had performed a time-based (21-days) in-vitro glycoxidation study at 37 °C to investigate the structural perturbation mechanism of Hb at different time-intervals in absence/presence of TQ. We found that prolonged glycoxidation induces amyloid formation in absence of TQ but in its presence, the process was prohibited. In summary, this study examined and characterized biophysically different intermediate-states of protein carrying glycoxidation-modification. Our findings suggested that TQ potentially affects interaction of d-ribose with Hb that prevents glycoxidation and protofibril formation, which establishes TQ as a potential therapeutic agent.

Discovery of a tetracyclic indole alkaloid that postpones fibrillation of hen egg white lysozyme protein.

Protein aggregation, such as amyloid fibril formation, is molecular hallmark of many neurodegenerative disorders including Alzheimer's, Parkinson's, and Prion disease. Indole alkaloids are well-known as the compounds having the ability to inhibit protein fibrillation. In this study, we experimentally and computationally have investigated the anti-amyloid property of a derivative of a synthesized tetracyclic indole alkaloid (TCIA), possessing capable functional groups. The fibrillation reaction of Hen White Egg Lysozyme (HEWL) was performed in absence and presence of the indole alkaloid. For quantitative analysis, we used Thioflovin T binding assay which showed ~50% reduction in fibril formation in the presence of 20 µM TCIA. Using TEM imaging, we observed a significant morphological change in our model protein in the presence of TCIA. In addition, we exploited FT-IR assay by which Amide I peak's shifting toward lower wavenumber was clearly observed. Using Molecular Docking, the interaction of the inhibitor (TCIA) with the protein's amyloidogenic region was modeled. Also, different biophysical parameters were calculated by Molecular Dynamics (MD) simulation. Various biochemical assays, conformational change, and hydrophobicity exposure of the protein during amyloid formation indicated that the compound assists HEWL to keep its native structure via destabilizing ß-sheet structure.

Gene Expression Analysis of Pediatric Acute Myeloid Leukemia Identified a Hyperactive ASXL1/BAP1 Axis Linked with Poor Prognosis and over Expressed Epigenetic Modifiers.

Genetic aberrations in the epigenome are rare in pediatric AML, hence expression data in epigenetic regulation and its downstream effect is lacking in childhood AML. Our pilot study screened epigenetic modifiers and its related oncogenic signal transduction pathways concerning clinical outcomes in a small cohort of pediatric AML in KSA. RNA from diagnostic BM biopsies (n = 35) was subjected to expression analysis employing the nCounter Pan-Cancer pathway panel. The patients were dichotomized into low ASXL1 (17/35; 49%) and high ASXL1 (18/35; 51%) groups based on ROC curve analysis. Age, gender, hematological data or molecular risk factors (FLT3 mutation/molecular fusion) exposed no significant differences across these two distinct ASXL1 expression groups (P > 0.05). High ASXL1 expression showed linkage with high expression of other epigenetic modifiers (TET2/EZH2/IDH1&2). Our data showed that high ASXL1 mRNA is interrelated with increased BRCA1 associated protein-1 (BAP1) and its target gene E2F Transcription Factor 1 (E2F1) expression. High ASXL1 expression was associated with high mortality {10/18 (56%) vs. 1/17; (6%) P < 0 .002}. Low ASXL1 expressers showed better OS {740 days vs. 579 days; log-rank P= < 0.023; HR 7.54 (0.98-54.1)}. The association between high ASXL1 expression and epigenetic modifiers is interesting but unexplained and require further investigation. High ASXL1 expression is associated with BAP1 and its target genes. Patients with high ASXL1 expression showed poor OS without any association with a conventional molecular prognostic marker.

Enzyme immobilization onto the nanomaterials: Application in enzyme stability and prodrug-activated cancer therapy.

Nanoparticles (NPs) have been widely used for immobilization of wide ranges of enzymes. However, the stabilization of enzymes on NPs is a major challenge, crucial for regulating enzymatic activity and their medical applications. To overcome these challenges, it is necessary to explore how enzymes attach to nanomaterials and their properties are affected by such interactions. In this review we present an overview on the different strategies of the enzyme immobilization into the NPs and their corresponding stability against temperature and pH. The effects of surface charge, particle size, morphology, and aggregation of NPs on the stability of immobilized enzymes were summarized. The activity of immobilized enzyme into the NPs was reviewed to disclose more detail regarding the interaction of biomolecules with NPs. The combination of enzyme immobilization with prodrugs was also reviewed as a promising approach for biomedical application of enzyme in cancer therapy. Finally, the current challenges and future applications of NPs in enzyme immobilization and the utilization of immobilized enzyme toward prodrug activation in cytoplasm of cancer cells were presented. In conclusion, this review may pave the way for providing a perspective on development to the industrial and clinical translation of immobilized enzymes.

Spectroscopic studies on the gemini surfactant mediated refolding of human serum albumin.

Refolding of guanidinium hydrochloride (GdCl) denatured human serum albumin (HSA) using a combination of cationic gemini surfactants; pentanediyl-α,ω-bis(cetyldimethylammonium bromide) (C16H33(CH3)2N+-(CH2)5-N+(CH3)2C16H33)2Br- designated as G5 and methyl- ß-cyclodextrin, is attempted in the present study. The studies were carried out in an aqueous medium (pH 7.4) using dynamic light scattering (DLS), circular dichroism (CD) and fluorescence spectroscopy. A careful study of the DLS data indicates that against the hydrodynamic radius (Rh) of 3.5nm in native human serum albumin (HSA), hydrodynamic radius after attempting refolding by simple dilution increases to 33.8nm. The large Rh values of the diluted protein sample is associated with the formation of aggregates as dilution is an aggregation prone pathway. Hydrodynamic radii equal to 5.4nm, that is very near to the native protein (3.5nm), is obtained on the sequential addition of G5 and methyl- ß-cyclodextrin to the denatured protein. The results obtained from the multi-technique approach are associated with the presence of two charged head-groups and two hydrocarbon tails in the gemini surfactants resulting in very strong electrostatic and hydrophobic interactions.The present study suggests that gemini surfactants may be utilised in the protein refolding studies and may prove to be inexpensive and efficient folding agents.

Refolding of bovine serum albumin via artificial chaperone protocol using gemini surfactants.

Surfactants prevent the irreversible aggregation of partially refolded proteins, and they are also known to assist in protein refolding. A novel approach to protein refolding that utilizes a pair of low molecular weight folding assistants, a detergent and cyclodextrin, was proposed by Rozema and Gellman (D. Rozema, S.H. Gellman, J. Am. Chem. Soc. 117 (1995) 2373). We report the refolding of bovine serum albumin (BSA) assisted by these artificial chaperones, utilizing gemini surfactants for the first time. A combination of cationic gemini surfactants, bis(cetyldimethylammonium)pentane dibromide (C(16)H(33)(CH(3))(2)N(+)-(CH(2))(5)-N(+)(CH(3))(2)C(16)H(33)·2Br(-) designated as G5 and bis(cetyldimethylammonium)hexane dibromide (C(16)H(33)(CH(3))(2)N(+)-(CH(2))(6)-N(+)(CH(3))(2)C(16)H(33)·2Br(-) designated as G6 and cyclodextrins, was used to refold guanidinium chloride (GdCl) denatured BSA in the artificial chaperone assisted two step method. The single chain cationic surfactant cetyltrimethylammonium bromide (CTAB) was used for comparative studies. The studies were carried out in an aqueous medium at pH 7.0 using circular dichroism, dynamic light scattering and ANS binding studies. The denatured BSA was found to get refolded by very small concentrations of gemini surfactant at which the single chain counterpart was found to be ineffective. Different from the single chain surfactant, the gemini surfactants exhibit much stronger electrostatic and hydrophobic interactions with the protein and are thus effective at much lower concentrations. Based on the present study it is expected that gemini surfactants may prove useful in the protein refolding operations and may thus be effectively employed to circumvent the problem of misfolding and aggregation.

Tertiary butanol induced amyloidogenesis of hen egg white lysozyme (HEWL) is facilitated by aggregation-prone alkali-induced molten globule like conformational state.

Proteins may form undesirable aggregates during the process of folding. Increasing evidence suggests that amyloid fibrils may arise from partially folded precursor molecules. We have previously demonstrated that hen egg white lysozyme [HEWL] exists as molten globule at pH 12.7. Here, we report that lysozyme at pH 7.0 and 11.0 are nearly stable to the addition of up to 45% t-butanol, but treatment of the alkali-induced molten globule form of HEWL [AMGL] with 20% t-butanol caused the formation of amyloid-like fibrils as evidenced by enhanced Thioflavin T binding and DLS measurements.

Influence of urea additives on micellar morphology/protein conformation.

The present study highlights the fact that the effect of additives (urea, monomethylurea, thiourea) on the supramolecular assemblies and proteins is strikingly similar. To investigate the effect, a viscometeric study on sphere-to-rod transition (s-->r) was undertaken in a system (3.5% tetradecyltrimethylammonium bromide+0.05 M NaBr + 1-pentanol [P.M. Lindemuth, G.L. Bertand, J. Phys. Chem. 97 (1993) 7769]) in the presence and absence of the said additives. [1-pentanol] needed for s-->r (i.e. [1-pentanol]s-->r) was determined from the relative viscosity versus [1-pentanol] profiles. It was observed that the additives preponed as well as postponed s-->r depending upon their nature and concentrations. These effects are explained in terms of increased polarity of the medium and the adsorption ability of urea/monomethylurea on the charged surfactant monomers of the micelle. In case of thiourea, postponement of s-->r was observed throughout which is attributed to its structure. To derive an analogy between micelles and proteins the additive-induced conformational changes of the protein, bovine serum albumin (BSA) was taken to monitor secondary structural changes and tryptophanyl fluorescence. A marked increase in secondary structure (far-UVCD) and increased tryptophanyl fluorescence with a marked blue shift in lambdamax was observed in presence of low concentrations of urea or alkylurea. This indicates that a more compact environment is created in presence of these additives, if added judiciously. Addition of thiourea to BSA caused a marked quenching without any significant change in lambdamax. The large decrease in tryptophanyl emission in presence of low thiourea concentrations seems to be specific and related to thiourea structure as no corresponding changes were observed in urea/alkylurea. All these effects pertaining to protein behavior fall in line with that of morphological observations on the present as well as surfactant systems studied earlier [S. Kumar, N. Parveen, Kabir-ud-Din, J. Phys. Chem. B 108 (2004) 9588].