Single-cell and spatial transcriptomics provide unprecedented insight into the inner workings of disease. Pharmacotranscriptomic approaches are powerful tools that leverage gene expression data for drug repurposing and treatment discovery in many diseases. Multiple databases attempt to connect human cellular transcriptional responses to small molecules for use in transcriptome-based drug discovery efforts. However, pre-clinical research often requires experiments in non-human species, which makes capitalizing on such valuable resources difficult. To facilitate the application of pharmacotranscriptomic databases to pre-clinical research models and to facilitate human orthologous conversion of non-human transcriptomes, we introduce OrthologAL. OrthologAL leverages the BioMart database to access different gene sets from Ensembl, facilitating the interaction between these servers without needing user-generated code. Researchers can input their single-cell or other high-dimensional gene expression data from any species, and OrthologAL will output a human ortholog-converted dataset for download and use. To demonstrate the utility of this application, we characterized orthologous conversion in single-cell, single-nuclei, and spatial transcriptomic data derived from common pre-clinical models, including patient-derived orthotopic xenografts of medulloblastoma, and mouse and rat models of spinal cord injury. We show that OrthologAL can convert these data types efficiently to that of corresponding orthologs while preserving the dimensional architecture of the original non-human expression data. OrthologAL will be broadly useful for applying pre-clinical, high-dimensional transcriptomics data in functional small molecule predictions using existing human-annotated databases.
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http://dx.doi.org/10.1101/2024.11.25.625000 | DOI Listing |
Mol Biol (Mosk)
December 2024
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia.
Eukaryotic translation release factor eRF1 is an important cellular protein that plays a key role in translation termination, nonsense-mediated mRNA decay (NMD), and readthrough of stop codons. The amount of eRF1 in the cell influences all these processes. The mechanism of regulation of eRF1 translation through an autoregulatory NMD-dependent expression circuit has been described for plants and fungi, but the mechanisms of regulation of human eRF1 translation have not yet been studied.
View Article and Find Full Text PDFMol Psychiatry
December 2024
Department of Psychiatry and Behavioral Neuroscience, The University of Chicago, Chicago, IL, USA.
The Bipolar-Schizophrenia Network for Intermediate Phenotypes (B-SNIP) created psychosis Biotypes based on neurobiological measurements in a multi-ancestry sample. These Biotypes cut across DSM diagnoses of schizophrenia, schizoaffective disorder, and bipolar disorder with psychosis. Two recently developed post hoc ancestry adjustment methods of Polygenic Risk Scores (PRSs) generate Ancestry-Adjusted PRSs (AAPRSs), which allow for PRS analysis of multi-ancestry samples.
View Article and Find Full Text PDFWorld J Surg Oncol
December 2024
Department of Radiation Oncology, Guangzhou Institute of Cancer Research, the Affiliated Cancer Hospital, Guangzhou, Guangdong, 510095, People's Republic of China.
Background: The combination of immunotherapy and chemotherapy has demonstrated an enhancement in progression-free survival (PFS) for individuals with advanced and metastatic triple-negative breast cancer (TNBC) when compared to the use of chemotherapy alone. Nevertheless, the extent to which different subgroups of metastatic TNBC patients experience this benefit remains uncertain.
Objectives: Our objective was to conduct subgroup analyses to more precisely identify the factors influencing these outcomes.
Biomed Eng Online
December 2024
Department of Tissue Engineering and Applied Cell Sciences, School of Medicine, Semnan University of Medical Sciences, Semnan, Iran.
Background: Despite the development of various therapeutic approaches over the past decades, the treatment of glioblastoma multiforme (GBM) remains a major challenge. The extracellular adenosine-generating enzyme, CD73, is involved in the pathogenesis and progression of GBM, and targeting CD73 may represent a novel approach to treat this cancer. In this study, three-dimensional culture systems based on three hydrogel compositions were characterized and an optimal type was selected to simulate the GBM microenvironment.
View Article and Find Full Text PDFWorld J Surg Oncol
December 2024
Department of Breast Surgery, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, No.7 Weiwu Road, Zhengzhou, Henan, 450003, China.
Background: We aim to explore the impact of excessive glutathione (GSH) intake on chemotherapy sensitivity in breast cancer.
Methods: Clinicopathological data were collected from 460 breast cancer patients who underwent adjuvant chemotherapy from January 2016 to December 2019 from Zhengzhou University People's Hospital. The clinicopathological characteristics following GSH treatment were collected and compared with those in Non-GSH group after 1:2 propensity score matching (PSM).
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