Transcriptomic Differences Research Articles

Climate Resilience in Farm Animals: Transcriptomics-Based Alterations in Differentially Expressed Genes and Stress Pathways

The livestock sector, essential for maintaining food supply and security, encounters numerous obstacles as a result of climate change. Rising global populations exacerbate competition for natural resources, affecting feed quality and availability, heightening livestock disease risks, increasing heat stress, and contributing to biodiversity loss. Although various management and dietary interventions exist to alleviate these impacts, they often offer only short-lived solutions. We must take a more comprehensive approach to understanding how animals adapt to and endure their environments. One such approach is quantifying transcriptomes under different environments, which can uncover underlying pathways essential for livestock adaptation. This review explores the progress and techniques in studies that apply gene expression analysis to livestock production systems, focusing on their adaptation to climate change. We also attempt to identify various biomarkers and transcriptomic differences between species and pure/crossbred animals. Looking ahead, integrating emerging technologies such as spatialomics could further accelerate genetic improvements, enabling more thermoresilient and productive livestock in response to future climate fluctuations. Ultimately, insights from these studies will help optimize livestock production systems by identifying thermoresilient/desired animals for use in precise breeding programs to counter climate change.

Sensitivity of transcriptomics: Different samples and methodology alter conclusions in Gulf pipefish (Syngnathus scovelli).

Transcriptome analysis has become a central tool in evolutionary and functional genomics. However, variation among biological samples and analysis techniques can greatly influence results, potentially compromising insights into the phenomenon under study. Here, we evaluate differences in the brain transcriptome between female and male Gulf pipefish (Syngnathus scovelli). We perform comparisons between results from entire pipelines for brain transcriptome assembly, quantification, and analysis. We also offer a unique biological comparison between two sampling instances (Redfish Bay: n = 15, Port Lavaca: n = 7). Our results demonstrate crucial shortcomings with current experimental approaches. We found high variation within our results that was driven by both technical differences between pipelines and biological differences between pipefish samples. In our analysis of highly expressed genes, we found that the choice of methods influenced the degree of contamination or noise included in the identified genes. Notably, genes identified within the same pipeline were more similar than any other comparison. Our differential expression analysis revealed that both methodology and sampling location influenced the quantity and consistency of statistically significant transcripts. In the context of these results, we offer modifications to current practices that may increase the robustness of transcriptome-based conclusions. In particular, the use of a reference-guided assembly and an increase in sample sizes are likely to improve resistance to noise or error.

HPB SO33 - Transcriptomic characterisation of the diabetogenic pancreatic ductal adenocarcinoma phenotype

Abstract Background New-onset diabetes mellitus (NOD) can manifest as a consequence of pancreatic ductal adenocarcinoma (PDAC), although not all PDAC patients develop NOD. For many patients, hyperglycaemia begins 3 years prior to PDAC diagnosis, with 30% of PDAC patients experiencing NOD by the time their cancer is diagnosed. The mechanisms underlying the onset of diabetes mellitus (DM) in PDAC and its consequences for disease development, detection and treatment are not well understood. The aim of this study was to characterise the transcriptomic differences between PDAC tumours that present with NOD compared to those that do not. Method Eight tumour samples from patients undergoing surgery for PDAC (4 without DM (HbA1c <35), 4 with NOD (HbA1c >65, within 3 years of cancer diagnosis) underwent single cell-RNA sequencing (scRNAseq) after taking intra-operative biopsies using Chromium 10X Genomics technology. Unique cell clusters were identified using CellRanger and cell types annotated using scATOMIC and singleR datasets. Manual annotation was undertaken when results were not agreeable after consulting the literature. Differential expression between groups was performed using DESeq2. Significant genes were identified as having a log2 fold-change >1.5 and p<0.05. Gene set enrichment was performed using Reactome. Analysis was conducted in RStudio. Results Single cell suspensions were created with a mean cell count of 1.2 million cells and a mean viability of 90%. PDAC cells and the full complement of tumour microenvironmental cells were recovered. Significant differential expression was seen in the PDAC cells themselves, CD4+ cells, macrophages, mast cells and fibroblasts. Cancer associated fibroblasts (CAFs) seemed not to differ. PDAC cells with NOD seemed to be enriched in MYC oncogenes whereas those without DM seemed to be enriched in KRAS mutations. There was a mixture of “basal” and “classical” transcriptional subtypes between the two groups. Conclusion Differences between diabetogenic PDAC and non-diabetogenic PDAC have been observed at the transcriptional level. Diabetogenic tumours seem to be promoted by MYC oncogenes and be more inflammatory than non-diabetogenic tumours. These findings require validation which will be done on independent samples using spatial transcriptomics to allow endocrine-exocrine crosstalk to be determined. Understanding the molecular pathways in diabetogenic pancreatic tumours could enhance future strategies to detect PDAC earlier and to target diabetes-associated vulnerabilities for therapeutic purposes.

Applications of single-cell RNA sequencing in rheumatoid arthritis

Single cell RNA sequencing (scRNA-seq) is a relatively new technology that provides an unprecedented, detailed view of cellular heterogeneity and function by delineating the transcriptomic difference among individual cells. This will allow for mapping of cell-type-specific signaling during physiological and pathological processes, to build highly specific models of cellular signaling networks between the many discrete clusters that are present. This technology therefore provides a powerful approach to dissecting the cellular and molecular mechanisms that contribute to autoimmune diseases, including rheumatoid arthritis (RA). scRNA-seq can offer valuable insights into RA unique cellular states and transitions, potentially enabling development of novel drug targets. However, some challenges that still limit its mainstream utilization and include higher costs, a lower sensitivity for low-abundance transcripts, and a relatively complex data analysis workflow relative to bulk or traditional RNA-seq. This minireview explores the emerging application of scRNA-seq in RA research, highlighting its role in producing important insights that can help pave the way for innovative and more effective therapeutic strategies.

ANGI-04. DISTINCT EXPRESSION OF TARGET MOLECULES BETWEEN TUMOR CELLS IN CEREBROSPINAL FLUID AND LEPTOMENINGES FOR LEPTOMENINGEAL METASTASIS

Abstract PURPOSE Metastatic brain tumor frequently present with leptomeningeal metastasis. The leptomeningeal metastasis is usually diagnosed by cerebrospinal fluid (CSF) cytology and/or contrast enhanced magnetic resonance imaging. However, it remains to be known whether tumor cells from CSF faithfully represent the tumor cells of leptomeniges. Therefore, this study aimed to clarify the transcriptome differences between tumor cells from cerebrospinal fluid, and spinal cords METHODS MDA-MB-231 cells labeled with GFP and luciferase were injected into the right ventricle of immunodeficient mice. Tumor cells from cerebrospinal fluid, and spinal cords were sorted and analyzed the transcriptome differences by RNA sequencing, RESULTS RNA sequencing analysis showed distinct transcriptome profiles between tumor cells from cerebrospinal fluid and spinal cord. Genes related to ECM receptor interaction and PI3K-Akt signaling pathway such as COL1A1, COL1A2, THBS1 were significantly highly upregulated in tumor cells from spinal cord compared to those from CSF CONCLUSIONS Tumor cells from spinal cord had different characteristics in transcriptome from those from CSF. Different therapeutic strategies might be needed to regulate tumor cells from spinal cord and those from CSF.

DDDR-05. SPATIALLY RESOLVED DRUG SENSITIVITY PROFILING IN GLIOBLASTOMA

Abstract BACKGROUND Glioblastoma is the most common malignant primary brain tumor in adults, characterized by poor overall survival and an urgent need for more effective treatment strategies. Macroscopic heterogeneity, as observed through MR imaging, divides the tumor into distinct regions: a tumor-cell dense contrast-enhancing tumor core and a non-contrast-enhancing infiltration zone that appears hyperintense on T2/FLAIR imaging. The infiltration zone contains both infiltrating tumor cells and non-malignant cells from the local brain microenvironment. Although genomic and transcriptomic differences between the tumor core and the infiltration zone have been reported, functional differences, such as differential drug sensitivities, remain largely unknown. METHODS To investigate this, we collected region-specific glioblastoma patient tissue samples from both the contrast-enhancing tumor core and the non-contrast-enhancing but 5-aminolevulinic acid (5-ALA) fluorescent infiltration zone during surgery. Using pharmacoscopy, a microscopy-based single-cell drug screening platform, we assessed drug responses across regions and patients. RESULTS To determine whether drug responses within a single tumor region were more similar compared to responses across different regions we collected multiple tissue samples from each tumor region in seven patients. We identified region-specific drug responses for temozolomide and lomustine, among other drugs, in some of the patients. However, drug sensitivities were not consistent within the same region across different patients. Thus, across patients, the region-specific drug responses were obscured by patient heterogeneity. To address intra- and inter-tumor drug response heterogeneity, we developed a complementarity score based on region-specific drug response data of 60 drugs across 23 paired samples. The complementarity score identified promising drug combinations that demonstrated strong anti-tumor activity across tumor regions and patients. CONCLUSIONS Monotherapy approaches have largely failed in glioblastoma, despite extensive molecular profiling efforts aimed at identifying tumor-specific vulnerabilities. Identifying drug combinations that synergistically target the locoregional heterogeneity of glioblastoma may open up new avenues of personalized therapy.

Genomic and Transcriptomic Comparison Between Invasive Non-Typhoidal Salmonella and Non-Invasive Isolates

Invasive non-typhoidal Salmonella (iNTS) poses a significant threat to global public health. Salmonella enterica Enteritidis and Typhimurium are the primary serovars responsible for both invasive diseases and gastroenteritis. This study aims to investigate the genomic and transcriptomic differences between isolates associated with these contrasting clinical presentations. We retrieved genomes of Salmonella Enteritidis and Salmonella Typhimurium from Enterobase, utilizing blood and stool isolates as representatives for iNTS and non-iNTS, respectively. An indistinguishable phylogenetic relationship was revealed between the blood and stool isolates for both serovars. Few genes were specifically identified in iNTS. Random forest and principal coordinates analysis permitted moderate discrimination between the two sources of isolates based on overall genome content. Notably, the blood isolates of Salmonella Typhimurium displayed an elevated level of antimicrobial resistance and genome degradation compared to stool isolates. Meanwhile, transcriptome sequencing identified few genes that were differentially expressed between blood and stool isolates. Hierarchical clustering and principal component analysis did not effectively differentiate the expression profile of iNTS from non-iNTS. In summary, few genes could serve as reliable biomarkers to distinguish iNTS and non-iNTS at either the genomic or transcriptomic level. Nevertheless, iNTS has indeed accumulated subtle genomic differences from non-iNTS, which might contribute to invasiveness.

Cytologic and Molecular Assessment of Isthmus Thyroid Nodules and Carcinomas.

Background: Isthmic thyroid nodules are more likely to be malignant and isthmic differentiated thyroid cancer demonstrates less favorable behavior compared with lobar locations. The goal of this study was to assess molecular differences of thyroid nodules and carcinomas from the isthmus relative to the lobes. Methods: The Afirma thyroid nodule database (n = 177,227) was assessed for cytologic and molecular differences between isthmus and lobar nodules in this observational cohort study. Genome-wide differential expression analysis was conducted to decipher transcriptomic differences. Histopathology reports (n = 583) of papillary thyroid cancer (PTC) (n = 389) and infiltrative follicular subtype of PTC (IF-PTC) (n = 194) from Afirma discovery cohorts and from thyroid cancer patients managed at an integrative endocrine surgery community care practice were analyzed for molecular differences between isthmic and lobar cancers. Results: In the Afirma database, 8527 (4.8%) isthmus nodules were identified. Bethesda V-VI nodules were almost twice as prevalent from the isthmus as compared with the lobes (8.2% vs. 4.3%, p < 0.0001). Isthmus nodules had twice the frequency of BRAFp.V600E (21% vs. 10.6%, p < 0.0001), an increased frequency of ALK/NTRK/RET fusions (4.6% vs. 2.5%, p < 0.0001) and SPOP variants (1.5% vs. 0.8%, p < 0.0001), and a lower frequency of NRAS mutations (7.8% vs. 13.2%, p < 0.0001), and PAX8::PPARy fusions (1.1% vs. 2.3%, p < 0.0001) than lobar nodules. Transcriptome analysis of molecular signatures and genome-wide analysis showed that isthmus nodules have higher BRAF-like scores, ERK activity, follicular mesenchymal transition scores (FMT), and lower inflammation activity scores. Pathway enrichment analysis revealed genes downregulated in isthmus tumors are enriched in immune response regulation. IF-PTC from the isthmus (n = 13) were more BRAF-like and had increased ERK and FMT scores compared with those from the lobes (n = 181) (p < 0.01 for all). Conclusions: These data suggest isthmic nodules are more likely to have malignant cytology and increased rates of higher risk molecular alterations compared with lobar nodules. IF-PTC from the isthmus is molecularly different compared with IF-PTC from the lobes. More data are needed to know if a change in surgical therapy is warranted in isthmic thyroid cancers relative to lobar cancers and if this molecular data should influence isthmic thyroid cancer management and monitoring.

Meniscus gene expression profiling of inner and outer zone meniscus tissue compared to cartilage and passaged monolayer meniscus cells

Meniscus injuries are common and while surgical strategies have improved, there is a need for alternative therapeutics to improve long-term outcomes and prevent post-traumatic osteoarthritis. Current research efforts in regenerative therapies and tissue engineering are hindered by a lack of understanding of meniscus cell biology and a poorly defined meniscus cell phenotype. This study utilized bulk RNA-sequencing to identify unique and overlapping transcriptomic profiles in cartilage, inner and outer zone meniscus tissue, and passaged inner and outer zone meniscus cells. The greatest transcriptomic differences were identified when comparing meniscus tissue to passaged monolayer cells (> 4,600 differentially expressed genes (DEGs)) and meniscus tissue to cartilage (> 3,100 DEGs). While zonal differences exist within the meniscus tissue (205 DEGs between inner and outer zone meniscus tissue), meniscus resident cells are more similar to each other than to either cartilage or passaged monolayer meniscus cells. Additionally, we identified and validated LUM, PRRX1, and SNTB1 as potential markers for meniscus tissue and ACTA2, TAGLN, SFRP2, and FSTL1 as novel markers for meniscus cell dedifferentiation. Our data contribute significantly to the current characterization of meniscus cells and provide an important foundation for future work in meniscus cell biology, regenerative medicine, and tissue engineering.

Single-cell transcriptome unveils unique transcriptomic signatures of human organ-specific endothelial cells.

The heterogeneity of endothelial cells (ECs) across humantissues remains incompletely inventoried. We constructed an atlas of > 210,000 ECs derivedfrom 38 regions across 24 human tissues. Our analysis reveals significant differences in transcriptome, phenotype, metabolism and transcriptional regulationamong ECs from various tissues. Notably,arterial, venous, and lymphatic ECs shared more commonmarkers in multiple tissues than capillary ECs, which exhibited higher heterogeneity.This diversity in capillary ECs suggests their greater potential as targets for drug development. ECs from different tissues and vascular beds were found to be associated with specific diseases. Importantly,tissue specificity of EC senescence is moredetermined by somatic site than by tissue type (e.g. subcutaneus adipose tissue andvisceral adipose tissue). Additionally, sex-specific differences in brain EC senescencewere observed. Our EC atlas offers valuble resoursce for identifying EC subclusters in single-cell datasets from body tissues or organoids, facilitating thescreen oftissue-specific targeted therapies, and serving as a powerful tool for future discoveries.

Different transcriptomic and metabolomic analysis of Saccharomyces cerevisiae BY4742 and CEN.PK2-1C strains.

To establish efficient yeast cell factories, it is necessary to understand the transcriptional and metabolic changes among different yeasts. Saccharomyces cerevisiae BY4742 and CEN.PK2-1C strains are originated from different yeast strains and are commonly used as model organisms and chassis cells in molecular biology study and synthetic biology-based natural production. Metabolomic analysis showed that the BY4742 strain produced higher levels of phenylalanine, tyrosine than CEN.PK2-1C, while CEN.PK2-1C produced high levels of indoleacetaldehyde, indolepyruvate. Transcriptomic analysis showed that the two strains showed large differences in the glycolysis pathway and pyruvate metabolism pathway. CEN.PK2-1C had greater glycolysis flux than BY4742, whereas BY4742 has greater flux in the pathway of pyruvate metabolism to produce fumarate. These findings provide a basis knowledge of the metabolomic and transcriptomic differences between BY4742 and CEN.PK2-1C strains, and also provide preliminary information for strain selection for molecular biology study and synthetic biology-based natural product production.

Molecular Mechanisms of Poplar Adaptation to Water–Fertilizer Coupling: Insights from Transcriptomic and Metabolomic Analyses

The aim of this paper was to investigate the transcriptomic and metabolomic differences in Populus cathayana × canadasis ‘Xinlin1’ (P. cathayana × canadasis ‘Xinlin 1’) under varying irrigation and fertilization conditions. Ten-year-old P. cathayana × canadasis ‘Xinlin 1’ was selected as the test subject in this study; different irrigation and fertilization treatments were set up, and DEGs and DAMs in response to water and fertilizer regulation were identified. Transcriptomic and metabolomic profiles were analyzed from both leaves and roots. A total of 22,870 DEGs were identified in response to water and fertilizer treatments, predominantly belonging to 48 transcription factor families, including MYB, ERF, and MYB-related ones. Additionally, 2432 DAMs were detected and categorized into 18 metabolite classes, with flavonoids being the most abundant (342 metabolites), followed by terpenoids, lipids, and others. KEGG enrichment analysis revealed that DEGs and DAMs were significantly associated with pathways such as plant hormone signal transduction and starch and sucrose metabolism pathways. The levels of ABA exhibited an initial decrease followed by an increase, with several key genes, including PYR/PYL, PP2C, SnRK2, and ABF, also differentially expressed in the plant hormone signal transduction pathway. In the starch and sucrose metabolic pathways, sucrose was more hydrolyzed into D-fructose, which gradually translocated from roots to leaves. DEGs were significantly involved in sucrose synthesis and decomposition into D-fructose and 1,3-β-glucose, as well as starch synthesis and starch decomposition into cellulose dextrin, which underwent complete hydrolysis to glucose. In the starch hydrolysis process, 29 DEGs were involved, with 12 down-regulated and 17 up-regulated.

Transcriptomic profiles of myxofibrosarcoma and undifferentiated pleomorphic sarcoma correlate with clinical and genomic features.

Myxofibrosarcoma (MFS) and undifferentiated pleomorphic sarcoma (UPS) are two common and aggressive subtypes of soft tissue sarcoma. The aim of this study was to assess potential transcriptomic differences between MFS and UPS tumours and to evaluate the extent to which differences in gene expression profiles were associated with genomic and clinical features. The study included 162 patients with tumours diagnosed as MFS (N = 62) or UPS (N = 100). The patients had been diagnosed and treated at two Swedish sarcoma centres during a 30-year period. For gene expression profiling and gene fusion detection all tumours were analysed using RNA-sequencing and could be compared with data on clinical outcome (N = 155), global copy number profiles (N = 145), and gene mutations (N = 128). Gene expression profiling revealed three transcriptomic clusters (TCs) without any clear separation of MFS and UPS. One TC was associated with longer metastasis-free survival. These tumours had lower tumour mutation burden (TMB), were enriched for a copy number signature representative of focal LOH and chromosomal instability on a diploid background, and were relatively immune-depleted. MFS and UPS showed extensive genomic overlap, with whole genome doubling occurring more frequently among the latter. The results support the idea that MFS and UPS tumours have largely overlapping genomic and transcriptomic features, with UPS tumours showing more aggressive behaviour and more complex genomes. Independently of the tumour type, clinically relevant subgroups were revealed by gene expression analysis, and the finding of multiple genomic subgroups strongly suggest the existence of subgroups of relevance to treatment stratification. © 2024 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

High RRM2 Correlates with Mitochondrial and Immune Responses in the Eosinophilic Subtype of Clear Cell Renal Cell Carcinoma.

Clear cell renal cell carcinoma (ccRCC), the predominant subtype of RCC, is distinguished by unique biological characteristics and heterogeneity, including eosinophilic and clear subtypes. Notwithstanding progress in therapy, immune checkpoint inhibitors (ICIs), and tyrosine kinase inhibitors (TKIs), the prognosis for individuals with metastatic ccRCC remains poor, presumably owing to metabolic alterations leading to mitochondrial dysfunction, which affects treatment response variability. We analyzed histological and immunohistochemical data from a cohort at Dalian Medical University's First Affiliated Hospital alongside RNA-sequencing transcriptome data from the TCGA database. Histologically, eosinophilic and clear ccRCC subtypes were evaluated using Kaplan-Meier and Cox proportional hazards models for survival analysis and prognosis. Differential gene expression (DEG) analysis and Gene Set Enrichment Analysis were performed to explore transcriptomic differences and relevant pathways. The study discovered substantial histological and molecular differences between the eosinophilic and clear cell subtypes of ccRCC. The eosinophilic subtype linked with frequent high-grade tumors (69.05% eosinophil vs 35.35% clear) and a poorer prognosis (HR=2.659, 95% CI:1.437-4.919, P=0.002). DEG analysis revealed distinct expression patterns among subtypes and identified a risk score signature that remained significant even after adjusting for clinical variables (HR=3.967, 95% CI: 1.665-9.449, P=0.002), showing less favorable survival in the high-risk group (P < 0.0001). RRM2 emerged as the most prognostic gene from this risk score, particularly in the eosinophilic subtype, alongside other clinical variables. By IHC, RRM2 shows high IHC score in eosinophilic compared to clear subtype (P=0.019). In addition, highly expressed RRM2 correlates with poor outcomes and is linked to mitochondrial genes, immunological pathways, and ICIs treatment. These findings show significant differences in prognosis between subtypes. RRM2 was the most prognostic gene from the discovered novel risk score signature associated with subtypes. Future research is essential to validate these insights and their therapeutic implications for ccRCC management.

Expression of cardiomyopathy-related genes in mononuclear blood cells predicts all-cause mortality in patients presenting with acute versus chronic coronary syndrome requiring revascularisation

Abstract Objective Despite advances in the revascularisation techniques their net clinical benefit differs substantially between patients presenting with myocardial infarction (ACS) and chronic coronary syndrome (CCS) due to obstructive coronary atherosclerosis. Considering that leukocytes represents a key pathophysiological component of myocardial ischaemia, exploration of mononuclear blood cell (PBMC) gene expression profile in CCS and ACS setting could reveal clinically relevant transcriptomic signals. The aim of the present study was to identify differences in PBMC transcriptome between ACS and CCS patients which are linked to mortality after revascularisation. Methods and Results We analysed PBMC transcriptomes from719 ACS and 486 CCS patients creating discovery cohort. The results of transcriptomic analysis were verified in replication cohort (ACS: N=682 for CCS: N=489) generated based on propensity score matching. Median time from revascularisation to blood collection (IQR) was 15.68 (-4.52, 23.23) hrs. Patients with ACS showed consistent differential expression of 8173 genes (4544 upregulated, 3629 downregulated) when compared with CCS patients. The subsequent pathway analysis also showed significant enrichment of several canonical pathways involved in major cardiovascular pathologies i.e. atherosclerosis (p = 1.22-06, enrichment = 3.39), vascular endothelial growth factor production (p = 1.16-06, enrichment = 16.73), positive regulation of vascular development (p = 2.78-06, enrichment = 5.30) and heterotopic cell adhesion including gene desmocollin 2 (DSC2, p = 3.64-04, enrichment = 6.30). In der multivariate survival analysis with differentially expressed genes, increased expression of DCS2, lamin A/C (LMNA), and UGGT2, and decreased expression of SNRNP70 predicted poor survival over the median follow-up 11.35 yrs. Consistently, controlling the false discovery rate at ≤ 5% these genes enriched pathways involved in cardiomyopathies such as arrhythmogenic right-ventricular cardiomyopathy (p = 4.19x10-4, enrichment = 58.9) and collagen disease (p = 2.29x10-3, enrichment = 23.8). Conclusion We found altered PBMC expression of multiple genes in patients requiring revascularisation for ACS versus CCS. Several differentially expressed genes included in cardiomyopathy pathways predicted long-term all-cause mortality in these patients.

The NIPBL-gene mutation of a Cornelia de Lange Syndrome patient causes deficits in the hepatocyte differentiation of induced Pluripotent Stem Cells via altered chromatin-accessibility

The Cornelia de Lange syndrome (CdLS) is a rare genetic disease, which is characterized by a cohesinopathy. Mutations of the NIPBL gene are observed in 65% of CdLS patients. A novel iPSC (induced Pluripotent Stem Cell) line was reprogrammed from the leukocytes of a CdLS patient carrying a missense mutation of the NIPBL gene. A mutation-corrected isogenic iPSC-line and two iPSC-lines generated from the healthy parents were used as controls. The iPSC lines were differentiated along the hepatocyte-lineage. Comparative immunofluorescence, RNA-seq and ATAC-seq analyses were performed on undifferentiated and differentiated iPSCs. In addition, chromatin organization was studied by ChIP-Seq analysis on the patient derived iPSCs as well as the respective controls. Relative to the mutation-corrected and the healthy-parents iPSCs, the patient-derived counterparts are defective in terms of differentiation along the hepatocyte-lineage. One-third of the genes selectively up-regulated in CdLS-derived iPSCs and hepatic cells are non-protein-coding genes. By converse, most of the selectively down-regulated genes code for transcription factors and proteins regulating neural differentiation. Some of the transcriptionally silenced loci, such as the DPP6 gene on chromosome 7q36.2 and the ZNF gene cluster on chromosome 19p12, are located in closed-chromatin regions. Relative to the corresponding controls, the global transcriptomic differences observed in CdLS undifferentiated iPSCs are associated with altered chromatin accessibility, which was confirmed by ChIP-Seq analysis. Thus, the deficits in the differentiation along the hepatocyte lineage observed in our CdLS patient is likely to be due to a transcriptional dysregulation resulting from a cohesin-dependent alteration of chromatin accessibility.

Transcriptome analysis identifies potential molecular mechanisms for growth of fast muscle in Chinese perch juvenile

Chinese perch (Siniperca chuatsi) is an important commercial fish species in China. Understanding the molecular mechanisms of growth and development of skeletal muscle is helpful for selection breeding and improving the growth rate of Chinese perch. We analyzed histological and transcriptomic differences in fast muscle of Chinese perch between 30 days post hatching (dph) and 60 dph using histological sections and high-throughput RNA-Seq. The results showed that the diameter of muscle fibers in 30 dph Chinese perch was mainly distributed in range of 30 − 40 μm, and that of 60 dph was primarily in the range of 40 − 50 μm. 34 differentially expressed genes (DEGs) were identified in the fast muscle of Chinese perch between 30 and 60 dph, of which 9 were up-regulated and 25 were down-regulated (60 dph vs 30 dph). The DEGs, including MYH4, ENO3, Bag3, krt13 and krt18, are associated with muscle cell differentiation and fusion in Chinese perch. The analysis of the protein–protein interaction network of DEGs revealed that FOS, junb and EGR1 may involve in the development of fast muscle. KEGG enrichment results showed that the up-regulated genes in the 60 dph were associated with several pathways related to metabolism and protein synthesis, such as glycosphingolipid biosynthesis and aminoacyl-tRNA biosynthesis. The results suggest that the development of fast muscle in Chinese perch from 30 to 60 dph is accompanied by an increase in muscle fiber diameter and changes in gene expression related to muscle cell differentiation and protein synthesis.Abbreviations: DEGs, differentially expressed genes; dph, days post hatching; FC, fold change; FDR, False Discovery Rate; GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; MyHCs, Myosin heavy chains; qRT-PCR, quantitative real-time PCR.

PINK1-Mediated Mitochondrial Activity Confers Olaparib Resistance in Prostate Cancer Cells.

Olaparib, a PARP inhibitor, is a targeted therapy used in treating various cancers including castration-resistant prostate cancer (CRPC). Despite its efficacy, resistance to Olaparib remains a significant challenge. Understanding the molecular mechanisms underpinning this resistance is crucial for developing more effective treatment strategies. This study focuses on elucidating the role of mitochondrial alterations and the PINK1 gene in conferring Olaparib resistance in CRPC cells. We investigated the transcriptomic and functional differences in mitochondrial activity between Olaparib-resistant (2B-OlapR, LN-OlapR) and treatment naïve prostate cancer (PCa) cells (C4-2B, LNCaP) in both castration sentitive and resistant settings. Through RNA sequencing and Gene Set Enrichment Analysis (GSEA), we identified significant enrichment of mitochondrial and oxidative phosphorylation-related gene sets in Olaparib Resistant derived cell lines. Resistant lines exhibited enhanced mitochondrial functionality including increased basal and maximal respiration rates, as well as elevated ATP production and spare respiratory capacity compared to parental cells. Subsequent investigations revealed a substantial increase in mitochondrial mass and electron transport chain complex I activity in Olaparib-resistant cells. Furthermore, overexpression of the PINK1 gene was observed in resistant cells, which was correlated with resistance to Olaparib and poor clinical outcomes in prostate cancer patients. Inhibition of PINK1 expression significantly reduced mitochondrial function and mass, impaired cell growth, and decreased resistance to Olaparib. These findings suggest that PINK1 plays a crucial role in modulating mitochondrial dynamics that confer therapeutic resistance, highlighting its potential as a therapeutic target for overcoming Olaparib resistance in PCa.

No two clones are alike: characterization of heterologous subpopulations in a transgenic cell line of the model diatom Phaeodactylum tricornutum

BackgroundConjugation-based episome delivery is a highly efficient method used to transfer DNA into the diatom Phaeodactylum tricornutum, facilitating the production of recombinant proteins and high-value metabolites. However, previous reports have indicated phenotypic heterogeneity among individual cells from clonally propagated exconjugant cell lines, potentially affecting the stability of recombinant protein production in the diatom.ResultsHere, we characterized the differences between subpopulations with distinct fluorescence intensity phenotypes derived from a single exconjugant colony of P. tricornutum expressing the enhanced green fluorescent protein (eGFP). We analyzed the expression cassette sequence integrity, plasmid copy number, and global gene expression. Our findings reveal that lower copy numbers and the deletion of the expression cassette in part of the population contributed to low transgene expression. Gene co-expression analysis identified a set of genes with similar expression pattern to eGFP including a gene encoding a putative Flp recombinase, which may be related to variations in fluorescence intensity. These genes thus present themselves as potential candidates for increasing recombinant proteins production in P. tricornutum episomal expression system.ConclusionsOverall, our study elucidates genetic and transcriptomic differences between distinct subpopulations in a clonally propagated culture, contributes to a better understanding of heterogeneity in diatom expression systems for synthetic biology applications.

Exogenous 5-aminolevulinic acid enhanced saline-alkali tolerance in pepper seedlings by regulating photosynthesis, oxidative damage, and glutathione metabolism.

A plant growth regulator, 5-aminolevulinic acid, enhanced the saline-alkali tolerance via photosynthetic, oxidative-reduction, and glutathione metabolism pathways in pepper seedlings. Saline-alkali stress is a prominent environmental problem, hindering growth and development of pepper. 5-Aminolevulinic acid (ALA) application effectively improves plant growth status under various abiotic stresses. Here, we evaluated morphological, physiological, and transcriptomic differences in saline-alkali-stressed pepper seedlings after ALA application to explore the impact of ALA on saline-alkali stress. The results indicated that saline-alkali stress inhibited plant growth, decreased biomass and photosynthesis, altered the osmolyte content and antioxidant system, and increased reactive oxygen species (ROS) accumulation and proline content in pepper seedlings. Conversely, the application of exogenous ALA alleviated this damage by increasing the photosynthetic rate, osmolyte content, antioxidant enzyme activity, and antioxidants, including superoxide dismutase, catalase, glutathione reductase, and glutathione peroxidase, and reducing glutathione to reduce ROS accumulation and malonaldehyde content. Moreover, the transcriptomic analysis revealed the differentially expressed genes were mainly associated with photosynthesis, oxidation-reduction process, and glutathione metabolism in saline-alkali stress + ALA treatment compared to saline-alkali treatment. Among them, the change in expression level in CaGST, CaGR, and CaGPX was close to the variation of corresponding enzyme activity. Collectively, our findings revealed the alleviating effect of ALA on saline-alkali stress in pepper seedlings, broadening the application of ALA and providing a feasible strategy for utilize saline-alkali soil.