FungiExpresZ: an intuitive package for fungal gene expression data analysis, visualization and discovery

MTD: A cloud-based omics database and interactive platform for Myceliophthora thermophila

Nowadays, biological databases are playing an increasingly critical role in biological research. Myceliophthora thermophila is an excellent thermophilic fungal chassis for industrial enzyme production and plant biomass-based chemical synthesis. The lack of a dedicated public database has made access to and reanalysis of M. thermophila data difficult. To bridge this gap, we developed MTD (https://mtd.biodesign.ac.cn/), a cloud-based omics database and interactive platform for M. thermophila. MTD integrates comprehensive genome annotations, sequence-based predictions, transcriptome data, curated experimental descriptions, and bioinformatics analysis tools, offering a comprehensive, one-stop solution with a 'top-down' search strategy to streamline M. thermophila research. The platform supports data reproduction, rapid querying, and in-depth mining of existing transcriptome datasets. Based on analyses using data and tools in MTD, we identified shifts in metabolic allocation in a glucoamylase hyperproduction strain of M. thermophila, highlighting changes in fatty acid biosynthesis and amino acids biosynthesis pathways, which provide new insights into the underlying phenotypic alterations. As a pioneering resource, MTD marks a key advancement in M. thermophila research and sets the model for developing similar databases for other species.

Intrinsically Disordered Regions Define Unique Protein Interaction Networks in CHD Family Remodelers

Chromodomain helicase DNA-binding (CHD) enzymes play a pivotal role in genome regulation. They possess highly conserved ATPase domains flanked by poorly characterized and intrinsically disordered N- and C-termini. Using mass spectrometry, we identify dozens of novel protein-protein interactions (PPIs) within the N- and C-termini of human CHD family members. We also define a highly conserved aggregation-prone region (APR) within the C-terminus of CHD4 which is critical for its interaction with the nucleosome remodeling and deacetylase (NuRD), as well as ChAHP (CHD4, activity-dependent neuroprotective protein (ADNP), and HP1γ) complexes. Further analysis reveals a regulatory role for the CHD4 APR in gene transcription during erythrocyte formation. Our results highlight that the N- and C-termini of CHD chromatin remodelers shape protein interaction networks that drive unique transcriptional programs.

AFED, a comprehensive resource for Aspergillus flavus gene expression profiling

The Aspergillus flavus expression database (AFED) is a comprehensive resource dedicated to exploring gene expression in A. flavus, a significant fungal pathogen that threatens food security by contaminating crops with aflatoxin. Given the complex regulation of aflatoxin biosynthesis and the lack of centralized expression data resources for this important pathogen, a database integrating diverse experimental conditions is essential for understanding its biology and developing control strategies. Public RNA sequencing data were used to quantify gene expression abundance for 604 A. flavus samples from 52 experiments. Using abundance data, we created an AFED accessible through a web-based interface that allows for the expression profiles of genes to be conveniently examined across different growth conditions and life cycle stages. Expression profiles can be visualized through either an interactive bar plot for single gene queries or a heatmap for multiple gene queries. A gene co-expression network based on samples containing at least 10 million mapped reads is also available, which allows users to identify genes that are co-expressed with an individual gene or set of genes and displays the functional enrichment among the co-expressed genes. Database URL: https://a-flavus-expression-db-jyqnpeuvta-uc.a.run.app.

Synthesis of a New Purine Analogue Class with Antifungal Activity and Improved Potency against Fungal IP3-4K

New antifungals are urgently needed to treat deadly fungal infections. Targeting the fungal inositol polyphosphate kinases IP3-4K (Arg1) and IP6K (Kcs1) is a promising strategy as it has been validated genetically to be crucial for fungal virulence but never pharmacologically. We now report the synthesis of DT-23, an analogue of N2-(m-trifluorobenzylamino)-N6-(p-nitrobenzylamino)purine (TNP), and demonstrate that it more potently inhibits recombinant Arg1 from the priority pathogen Cryptococcus neoformans (Cn) (IC50 = 0.6 μM) than previous analogues (IC50 = 10-30 μM). DT-23 also inhibits recombinant Kcs1 with similar potency (IC50 = 0.68 μM) and Arg1 and Kcs1 activity in vivo. Unlike previous analogues, DT-23 inhibits fungal growth (MIC50 = 15 μg/mL) and only 1.5 μg/mL synergizes with Amphotericin B to kill Cn in vitro. DT-23/Amphotericin B is also more protective against Cn infection in an insect model compared to each drug alone. Transcription profiling shows that DT-23 impacts early stages in IP synthesis and cellular functions impacted by IPK gene deletion, consistent with its targeted effect. This study establishes the first pharmacological link between inhibiting IPK activity and antifungal activity, providing tools for studying IPK function and a foundation to potentially develop a new class of antifungal drug.

Temporal transcriptional response of Candida glabrata during macrophage infection reveals a multifaceted transcriptional regulator CgXbp1 important for macrophage response and fluconazole resistance

Candida glabrata can thrive inside macrophages and tolerate high levels of azole antifungals. These innate abilities render infections by this human pathogen a clinical challenge. How C. glabrata reacts inside macrophages and what is the molecular basis of its drug tolerance are not well understood. Here, we mapped genome-wide RNA polymerase II (RNAPII) occupancy in C. glabrata to delineate its transcriptional responses during macrophage infection in high temporal resolution. RNAPII profiles revealed dynamic C. glabrata responses to macrophages with genes of specialized pathways activated chronologically at different times of infection. We identified an uncharacterized transcription factor (CgXbp1) important for the chronological macrophage response, survival in macrophages, and virulence. Genome-wide mapping of CgXbp1 direct targets further revealed its multi-faceted functions, regulating not only virulence-related genes but also genes associated with drug resistance. Finally, we showed that CgXbp1 indeed also affects fluconazole resistance. Overall, this work presents a powerful approach for examining host-pathogen interaction and uncovers a novel transcription factor important for C. glabrata's survival in macrophages and drug tolerance.

CAP-RNAseq: an integrated pipeline for functional annotation and prioritization of co-expression clusters

Cluster analysis is one of the most widely used exploratory methods for visualization and grouping of gene expression patterns across multiple samples or treatment groups. Although several existing online tools can annotate clusters with functional terms, there is no all-in-one webserver to effectively prioritize genes/clusters using gene essentiality as well as congruency of mRNA-protein expression. Hence, we developed CAP-RNAseq that makes possible (1) upload and clustering of bulk RNA-seq data followed by identification, annotation and network visualization of all or selected clusters; and (2) prioritization using DepMap gene essentiality and/or dependency scores as well as the degree of correlation between mRNA and protein levels of genes within an expression cluster. In addition, CAP-RNAseq has an integrated primer design tool for the prioritized genes. Herein, we showed using comparisons with the existing tools and multiple case studies that CAP-RNAseq can uniquely aid in the discovery of co-expression clusters enriched with essential genes and prioritization of novel biomarker genes that exhibit high correlations between their mRNA and protein expression levels. CAP-RNAseq is applicable to RNA-seq data from different contexts including cancer and available at http://konulabapps.bilkent.edu.tr:3838/CAPRNAseq/ and the docker image is downloadable from https://hub.docker.com/r/konulab/caprnaseq.

Classification of PTEN missense VUS through exascale simulations

Phosphatase and tensin homolog (PTEN), a tumor suppressor with dual phosphatase properties, is a key factor in PI3K/AKT signaling pathway. Pathogenic germline variation in PTEN can abrogate its ability to dephosphorylate, causing high cancer risk. Lack of functional evidence lets numerous PTEN variants be classified as variants of uncertain significance (VUS). Utilizing Molecular Dynamics (MD) simulations, we performed a thorough evaluation for 147 PTEN missense VUS, sorting them into 66 deleterious and 81 tolerated variants. Utilizing replica exchange molecular dynamic (REMD) simulations, we further assessed the variants situated in the catalytic core of PTEN's phosphatase domain and uncovered conformational alterations influencing the structural stability of the phosphatase domain. There was a high degree of agreement between our results and the variants classified by Variant Abundance by Massively Parallel Sequencing, saturation mutagenesis, multiplexed functional data and experimental assays. Our extensive analysis of PTEN missense VUS should benefit their clinical applications in PTEN-related cancer.

SIGNIFICANCE STATEMENT

Classification of PTEN variants affecting its lipid phosphatase activity is important for understanding the roles of PTEN variation in the pathogenesis of hereditary and sporadic malignancies. Of the 3000 variants identified in PTEN, 1296 (43%) were assigned as VUS. Here, we applied MD and REMD simulations to investigate the effects of PTEN missense VUS on the structural integrity of the PTEN phosphatase domain consisting the WPD, P and TI active sites. We classified a total of 147 missense VUS into 66 deleterious and 81 tolerated variants by referring to the control group comprising 54 pathogenic and 12 benign variants. The classification was largely in concordance with these classified by experimental approaches.