Biology subjects

R, B.

Publications and source records attributed to R, B..

4 recordsLinked to original sources

bioRxiv2025

BC-Predict Database: A Curated Resource of Experimentally Validated Markers in Multidrug Resistance in Breast Cancer

BackgroundIn this study, we aim to develop a yearly updatable database that could predict chemotherapeutic drug resistance and overall survival probability in breast cancer patients. Existing drug sensitivity databases depend on correlation-based predictions. In our study, candidates involved in drug resistance are chosen based on cell line validation (overexpression or downregulation or inhibition of candidates) studies, curated manually. Method28,773 mRNA expression signatures from 914 breast cancer patients were extracted from cProsite. 106 of these patients had clinical information and log2 fold change information required for this study. We categorized these patients into deceased and surviving groups from TCGA. To prepare a database that can predict drug resistance and overall survival, we included mRNAs that were over-expressed in at least 80% of the breast cancer patients and mRNAs over-expressed in deceased and surviving groups. In addition, we also reported breast cancer-associated drug resistance candidates which have been reported in cell-line based studies. The database matrix preparation involved an approximate of 15000 manual searches of cell validated studies. (750 candidates x 20 drugs). The database was validated using a publicly available breast cancer patient proteomics data. ResultsOur analysis identified a list of top priority candidates associated with multidrug resistance, categorized based on their resistance to >15 drugs, 5-15 drugs, and 2-4 drugs. Analysis of patient profiles in the database revealed that the number of proteins contributing to drug resistance was high in the poor prognosis category compared to the good prognosis category. ConclusionsOur study highlights the probable gaps in breast cancer drug resistance research, as only a small subset of overexpressed mRNA candidates found in patients are studied in vitro or in vivo experiments focusing on drug resistance. We also identified candidates involved in multidrug resistance, whose role in drug resistance has not been studied in more than 15 drugs. After further validations, this will benefit the clinicians and upcoming CRISPR gene therapeutics.

cancer biology↗

bioRxiv2024

Model-based fed-batch cultivation of Viola odorata plant cells exhibiting antimalarial and anticancer activity

Viola odorata is used in the indigenous medicine to treat respiratory tract disorders and is limited in availability. Bioprocess principles can be applied to develop sustainable methods to produce high-quality V. odorata biomass. To this effect, a modified stirred tank reactor and a balloon-type bubble column reactor were used to improve biomass production. Nutrient feeding strategies were developed using first principle-based mathematical modelling to achieve higher cell density in the reactor. Experimental validation of the fed-batch model-predicted strategy resulted in a two-fold enhancement in biomass production (32.2 g DW L-1) at the bioreactor level. Also, bioreactor-cultivated biomass extracts were tested for in vitro hemolytic, cytotoxic, anti-inflammatory, and in vivo antiplasmodial activities. This is the first report on fed-batch cultivation in bioreactors and the antiplasmodial activity of V. odorata. Overall, the bioactive potential of the in vitro-generated biomass extracts is found to be similar to that in the natural plant biomass extracts. HighlightsO_LICultivation of V. odorata cell suspension culture using a modified stirred tank and balloon-type bubble column bioreactors. C_LIO_LIBatch kinetic models were developed and extrapolated into a fed-batch model. C_LIO_LIEnhanced biomass production (32.2 g DW L-1) in bioreactors using a nutrient-feeding strategy. C_LIO_LIExtracts showed anti-inflammatory effects and up to 80 % inhibition of parasite growth, with no hemolytic activity. C_LIO_LIConfirmed antiplasmodial activity in vivo, effective alongside artesunate. C_LIO_LIIn vitro-generated biomass extracts showed comparable bioactive potential to that of natural plants. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/618783v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@171c39aorg.highwire.dtl.DTLVardef@1e0eda5org.highwire.dtl.DTLVardef@121eddorg.highwire.dtl.DTLVardef@1a86215_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2024

Ceclazepide as novel Mycobacterium abscessus inhibitor

The rise of drug-resistant Mycobacterium abscessus poses a significant challenge due to its resistance to current standard treatments, highlighting the urgent need for new antibacterial solutions. In this research, ceclazepide was introduced as a promising agent with strong activity against M. abscessus. Our findings revealed that ceclazepide effectively suppressed the growth of M. abscessus wild-type strain, multiple subspecies, and clinical isolates in vitro. Notably, ceclazepide demonstrated the ability to inhibit M. abscessus growth within macrophages without causing harm. These results support the potential of ceclazepide as a candidate for further development as a clinical drug to combat M. abscessus infections effectively.

microbiology↗

bioRxiv2023

In silico approaches to identify the role of lncRNAs in Prostate cancer and Androgen receptor-targeted proteins

Long non-coding RNA (lncRNAs) are known to have a role in pathogenesis of a broad spectrum of malignancies.These are found to have a significant role as signal transduction mediators in cancer signaling pathways. Prostate Cancer (PCa) is emerging with increasing cases worldwide even as advanced approaches in clinical diagnosis and treatment of PCa are still challenging to address. To enhance patient stratification, there is an indefatigable need to understand risk that can allow new approaches of treatment based on prognosis. While PCa is known to have mediated androgen receptor (AR) stimulation, the latter plays a key role in regulating transcription of genes via nuclear translocation which in turn leads to response to androgens. LncRNAs have been implicated in developing clinical diagnostic and prognostic biomarkers in a broad spectrum of cancers. In our present study, 12 lncRNAs identified from clinical samples from our erstwhile PCa patients were docked with PCa and AR targeted 36 proteins. We identified three lncRNAs, viz. SCARNA10, NPBWR1, ANKRD20A9P are common between the targeted proteins and discern that SCARNA10 lncRNA could serve as a prognostic signature for PCa and AR biogenesis. We also sought to check the coding potential of interfacial residues associated with lncRNA docking sites.x

bioinformatics↗