Target Gene Expression Analysis Research Articles

Local Competition and Enhanced Defense: How Metarhizium brunneum Inhibits Verticillium longisporum in Oilseed Rape Plants.

Metarhizium brunneum is a soil-borne fungal entomopathogen that can be associated with plant roots. Previous studies have demonstrated that root colonization by beneficial fungi can directly affect soil-borne pathogens through competition and antibiosis and can activate a systemic response in plants, resulting in a primed state for a faster and/or stronger response to stressors. However, the mechanisms by which Metarhizium inoculation ameliorates symptoms caused by plant pathogens are not well known. This study evaluated the ability of M. brunneum to protect oilseed rape (Brassica napus L.) plants against the soil-borne pathogen Verticillium longisporum and investigated whether the observed effects are a result of direct interaction and/or plant-mediated effects. In vitro and greenhouse experiments were conducted to measure fungal colonization of the rhizosphere and plant tissues, and targeted gene expression analysis was used to evaluate the plant response. The results show that M. brunneum delayed pathogen colonization of plant root tissues, resulting in decreased disease symptoms. Direct competition and antibiosis were found to be part of the mechanisms, as M. brunneum growth was stimulated by the pathogen and inhibited the in vitro growth of V. longisporum. Additionally, M. brunneum changed the plant response to the pathogen by locally activating key defense hormones in the salicylic acid (SA) and abscisic acid (ABA) pathways. Using a split-root setup, it was demonstrated that there is a plant-mediated effect, as improved plant growth and decreased disease symptoms were observed when M. brunneum was in the systemic compartment. Moreover, a stronger systemic induction of the gene PR1 suggested a priming effect, involving the SA pathway. Overall, this study sheds light on the mechanisms underlying the protective effects of M. brunneum against soil-borne pathogens in oilseed rape plants, highlighting the potential of this fungal entomopathogen as a biocontrol agent in sustainable agriculture.

Histological assessment and gene expression analysis of intra-oral soft tissue graft donor sites.

To determine the structural and gene expression features of different intra-oral soft tissue donor sites (i.e., anterior palate, posterior palate, maxillary tuberosity and retromolar pad). Standardized mucosal tissue punch biopsies were collected from at least one donor site per subject. Histological processing was performed to determine tissue morphometry and quantify collagen composition. Site-specific gene distribution was mapped using targeted gene expression analysis and validated using real time polymerase chain reaction (qPCR). A total of 50 samples from 37 subjects were harvested. Epithelial thickness did not differ between sites. However, lamina propria was thicker in the maxillary tuberosity (2.55 ± 0.92 mm) and retromolar pad (1.98 ± 0.71 mm) than in the lateral palate. Type I collagen was the predominant structural protein in the lamina propria (75.06%-80.21%). Genes involving collagen maturation and extracellular matrix regulation were highly expressed in the maxillary tuberosity and retromolar pad, while lipogenesis-associated genes were markedly expressed in the lateral palate. The retromolar pad showed the most distinct gene expression profile, and the anterior and posterior palate displayed similar transcription profiles. Tissue samples harvested from the anterior and posterior palate differed morphologically from those from the maxillary tuberosity and retromolar pad. Each intra-oral site showed a unique gene expression profile, which might impact their biological behaviour and outcomes of soft tissue augmentation procedures.

Activation of distinct inflammatory pathways in subgroups of LR-MDS

Aberrant innate immune signaling has been identified as a potential key driver of the complex pathophysiology of myelodysplastic neoplasms (MDS). This study of a large, clinically and genetically well-characterized cohort of treatment-naïve MDS patients confirms intrinsic activation of inflammatory pathways in general mediated by caspase-1, interleukin (IL)-1β and IL-18 in low-risk (LR)-MDS bone marrow and reveals a previously unrecognized heterogeneity of inflammation between genetically defined LR-MDS subgroups. Principal component analysis resolved two LR-MDS phenotypes with low (cluster 1) and high (cluster 2) levels of IL1B gene expression, respectively. Cluster 1 contained 14/17 SF3B1-mutated cases, while cluster 2 contained 8/8 del(5q) cases. Targeted gene expression analysis of sorted cell populations showed that the majority of the inflammasome-related genes, including IL1B, were primarily expressed in the monocyte compartment, consistent with a dominant role in determining the inflammatory bone marrow environment. However, the highest levels of IL18 expression were found in hematopoietic stem and progenitor cells (HSPCs). The colony forming activity of healthy donor HSPCs exposed to monocytes from LR-MDS was increased by the IL-1β-neutralizing antibody canakinumab. This work reveals distinct inflammatory profiles in LR-MDS that are of likely relevance to the personalization of emerging anti-inflammatory therapies.

Evidence of Bi-Directional Volatile-Mediated Communication between Drought-Stressed and Well-Watered Grapevines (Vitis vinifera L.)

The volatile-mediated interplay between stressed and non-stressed plants has been described in many studies involving both biotic and abiotic stresses as a one-way channel. However, very little is known about the molecular basis and mechanisms by which volatile organic compounds (VOCs) mediate plant communication between drought-stressed ‘emitter’ plants and non-stressed ‘receiver’ neighbours for the defence against impending stress challenges. Aiming to address this in grapevine, this study investigated the effect of two-way VOC exchange between stressed and non-stressed Vitis vinifera L. cv. Shiraz during drought and recovery using four treatments: isolated well-watered (WW) vines, isolated drought-stressed (DS) vines, and co-located DS ‘emitter’ and WW ‘receiver’ vines in a growth room. The results obtained from solid-phase microextraction (SPME) gas chromatography mass spectrometry (GC-MS) analysis showed a synchronised decline in α-pinene concentration in the co-located treatment vines and higher isoprene levels in the DS emitters compared to the isolated DS vines. Targeted gene expression analysis further identified the over-expression of a key gene, allene oxide synthase (AOS), in the jasmonic acid (JA) biosynthesis pathway during peak drought in the DS emitter. Transcript expression of chorismate synthase (CHORS) and α-pinene synthase (VvPNaPin1) showed similar trends in the DS emitter. The results suggest that isoprene and α-pinene may be interplant signalling molecules used by grapevine during drought. To the best of our knowledge, this is the first report of a bi-directional interaction in grapevine between the emitters and receivers under drought stress mediated by the JA and terpenoid biosynthesis pathways.

Rapid, Point-of-Care Host-Based Gene Expression Diagnostics Using Giant Magnetoresistive Biosensors.

Host-based gene expression analysis is a promising tool for a broad range of clinical applications, including rapid infectious disease diagnostics and real-time disease monitoring. However, the complex instrumentation requirements and slow turnaround-times associated with traditional gene expression analysis methods have hampered their widespread adoption at the point-of-care (POC). To overcome these challenges, we have developed an automated and portable platform that utilizes polymerase chain reaction (PCR) and giant magnetoresistive (GMR) biosensors to perform rapid multiplexed, targeted gene expression analysis at the POC. As proof-of-concept, we utilized our platform to amplify and measure the expression of four genes (HERC5, HERC6, IFI27, and IFIH1) that were previously shown to be upregulated in hosts infected with influenza viruses. The compact instrument conducted highly automated PCR amplification and GMR detection to measure the expression of the four genes in multiplex, then utilized Bluetooth communication to relay results to users on a smartphone application. To validate the platform, we tested 20 cDNA samples from symptomatic patients that had been previously diagnosed as either influenza-positive or influenza-negative using a RT-PCR virology panel. A non-parametric Mann-Whitney test revealed that day 0 (day of symptom onset) gene expression was significantly different between the two groups (p < 0.0001, n = 20). Hence, we preliminarily demonstrated that our platform could accurately discriminate between symptomatic influenza and non-influenza populations based on host gene expression in ∼30 min. This study not only establishes the potential clinical utility of our proposed assay and device for influenza diagnostics but it also paves the way for broadscale and decentralized implementation of host-based gene expression diagnostics at the POC.

Identification and Validation of Reference Genes for Expression Analysis Using RT-qPCR in Leptocybe invasa Fisher and La Salle (Hymenoptera: Eulophidae)

Leptocybe invasa (Hymenoptera: Eulophidae) is a globally intrusive pest. Despite extensive research into the physiological responses of this pest, our understanding of the molecular mechanisms still needs to be improved. We want to accurately investigate the expression of L. invasa's target genes, so it is imperative to select fitting reference genes. In this study, eight housekeeping genes' stability (RPS30, ACTR, 18S rRNA, ACT, RPL18, GAPDH, 28S rRNA, and TUB) was tested under five different experimental conditions, including male or female adults, somites (head, thorax, and abdomen), temperatures (0 °C, 25 °C, and 40 °C), diets (starvation, clear water, 10% honey water, Eucalyptus sap), and pesticides (acetone was used as a control, imidacloprid, monosultap). Gene stability was calculated using RefFinder, which integrates four algorithms (the ∆Ct method, geNorm, NormFinder, and BestKeeper). The findings implied that ACT and ACTR were the most accurate when comparing sexes. For analyzing different somites, 28S rRNA and RPL18 were ideal; the 28S rRNA and RRS30 were perfect for analyzing at different temperatures. The combination of ACT and GAPDH helped to analyze gene expression in different diets, and GAPDH and 28S rRNA were suitable for various pesticide conditions. Overall, this research offers a complete list of reference genes from L. invasa for precise analysis of target gene expression, which can improve the trustworthiness of RT-qPCR and lay the foundation for further investigations into the gene function of this pest.

Temporal transcriptional control of neural induction in human induced pluripotent stem cells.

Neural induction of human induced pluripotent stem cells represents a critical switch in cell state during which pluripotency is lost and commitment to a neural lineage is initiated. Although many of the key transcription factors involved in neural induction are known, we know little of the temporal and causal relationships that are required for this state transition. Here, we have carried out a longitudinal analysis of the transcriptome of human iPSCs undergoing neural induction. Using the temporal relationships between the changing profile of key transcription factors and subsequent changes in their target gene expression profiles, we have identified distinct functional modules operative throughout neural induction. In addition to modules that govern loss of pluripotency and gain of neural ectoderm identity, we discover other modules governing cell cycle and metabolism. Strikingly, some of these functional modules are retained throughout neural induction, even though the gene membership of the module changes. Systems analysis identifies other modules associated with cell fate commitment, genome integrity, stress response and lineage specification. We then focussed on OTX2, one of the most precociously activated transcription factors during neural induction. Our temporal analysis of OTX2 target gene expression identified several OTX2 regulated gene modules representing protein remodelling, RNA splicing and RNA processing. Further CRISPRi inhibition of OTX2 prior to neural induction promotes an accelerated loss of pluripotency and a precocious and aberrant neural induction disrupting some of the previously identified modules. We infer that OTX2 has a diverse role during neural induction and regulates many of the biological processes that are required for loss of pluripotency and gain of neural identity. This dynamical analysis of transcriptional changes provides a unique perspective of the widespread remodelling of the cell machinery that occurs during neural induction of human iPSCs.

Endothelial cells derived from elephant seals blunt angiogenic transcriptional signaling during hypoxia exposure

Northern elephant seals ( Mirounga angustirostris) conduct repeated deep dives, during which arterial blood oxygen becomes depleted. Interestingly, elephant seals require little surface recovery time from these dives, and extreme hypoxemia occurs regardless of dive duration or purpose. Recent in vitro and in silica work indicates that tight regulation of the canonical hypoxia response may protect diving seals against the inflammatory injuries typically associated with repeated hypoxia exposure. In vivo assessments of these phenomena, however, remain restricted due to both technical constraints and animals' inaccessibility while diving at sea. We developed a proliferative endothelial cell culture system from expelled placental arteries to assess the real-time molecular response to hypoxia exposure in northern elephant seals. Hypoxia inducible factor 1a (HIF-1a) protein localized to the nucleus within 1 h of exposure to 1% O2 in both species[KA1]. Hypoxia increased HIF-1a protein levels to a maximum of ~70-fold over (normoxic) baseline levels in both seal and human cells (p=0.005 for both species), though the response dynamics differed between species. HIF-1a abundance in seal cells was biphasic, with an initial rapid peak occurring within 15 min of hypoxia onset. In contrast, HIF-1a levels did not peak in human cells until 1 h in hypoxia and abundance declined continuously following this peak. Interestingly, RNAseq analysis of HIF-1a target gene expression suggested that seal cells blunt angiogenic signaling and vascular remodeling during hypoxia exposure despite sustained HIF-1a protein stabilization. Seal cell expression of STC2, NHE1/SLC9A1, and PFKL lagged behind expression of these genes in human cells during hypoxia exposure, and seal cell expression of ANGPT2 and MMP14 remained stable during long term hypoxia exposure, while expression of these genes was variable or high in human cells. Cis-regulatory analyses suggested a role for altered metabolism (rather than altered oxygen delivery) in seal cells during hypoxia via FOXK1, NFKB1, JUN and ZBTB7A. In contrast, the transcriptional signature in human cells suggests altered expression of oxygen delivery pathways via homeobox A13 (HOXA13), FOS like 1 (FOSL1) and SRF, all of which regulate angiogenesis, vascular remodeling and vasodilation. Together, these data suggest that seal endothelial cells respond to hypoxia by managing metabolic factors rather than calling for increased oxygen delivery despite rapid and sustained HIF-1a stabilization. NSF GRFP and UC Berkeley startup This is the full abstract presented at the American Physiology Summit 2023 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Abstract 5788: Single-cell and spatial transcriptomic mapping of human renal cell carcinoma brain metastases uncovers actionable immune-resistance targets

Abstract Introduction: The discovery of immune checkpoint inhibitors has revolutionized metastatic renal cell carcinoma (RCC) treatment. However, in patients with RCC brain metastases, response rates are low and survival outcomes poor. To understand the tumor microenvironmental differences between primary kidney tumors, extracranial metastases, and brain metastases, we developed a detailed single-cell atlas of RCC brain metastases along with their matched extracranial and primary tumors. Methods: We performed single-nucleus RNA-seq on 27 samples (nearly 200,000 cells) from RCC patients; samples included 14 brain metastases, 8 matched primary kidney tumors, and 5 matched extracranial metastases. We performed multiplex IHC to validate selected transcriptomic findings. We used Nanostring CosMx 960-plex RNA spatial molecular imaging technique on selected samples to validate cellular interactions in a spatial context. Results: We established a multi-tissue single-cell atlas of RCC brain metastases by identifying 9 major and 37 minor malignant, immune, and stromal cell clusters. Brain metastases had higher neuronal and glial cells interacting with immune and tumor cells. Brain metastasis tumor cells were also transcriptomically reprogrammed to adapt to the brain microenvironment through enrichment of MYC targets, MTORC1 signaling, epithelial-mesenchymal transition, fatty-acid metabolism, oxidative phosphorylation, and reactive oxygen species pathways. Moreover, cell-to-cell communication and downstream target gene expression analyses showed that brain metastasis tumor cells expressed ligands and receptors that induce tumor cell proliferation in both autocrine and paracrine fashions. Among T-cell populations, we found fewer proliferating cytotoxic T lymphocytes in the brain than in other sites. Moreover, T cells in brain metastases expressed higher levels of several targetable inhibitory checkpoints than did extracranial metastases. In addition, we found that naïve/memory T cells in brain metastases were a favorable prognostic marker for overall survival after craniotomy. Our characterization of myeloid cell populations across the 3 disease sites found fewer dendritic cells and monocytes in the brain compared to other sites. Macrophages in brain metastases more highly expressed an M2 immunosuppressive gene signature than did those in primary RCC tumors. Conclusion: Our findings from the largest single-cell atlas of RCC brain metastases with matched primary and extracranial metastases suggest several unique targetable, immunosuppressive biological mechanisms in the brain microenvironment. These results provide a foundation for a deeper understanding of RCC brain metastasis biology and can serve as a resource for the scientific community to further explore therapeutically targetable tumor and immune-related mechanisms. Citation Format: Elshad Hasanov, Truong Nguyen Anh Lam, Jerome Lin, Patrick K. Reville, Merve Hasanov, Anna K. Casasent, David Shih, Sahin Hanalioglu, Mehmet Asim Bilen, Omar Alhalabi, Berrin Babaoglu, Baylar Baylarov, Adeboye O. Osunkoya, Lisa M. Norberg, Joy Gumin, Tuan M. Tran, Jianzhuo Li, Anh G. Hoang, Haidee D. Chancoco, Brittany C. Parker Kerrigan, Erika J. Thompson, Betty YS Kim, Dima Suki, Melike Mut, Figen Soylemezoglu, Giannicola Genovese, Kadir C. Akdemir, Hussain A. Tawbi, Nizar M. Tannir, Florencia McAllister, Michael A. Davies, Padmanee Sharma, Jason Huse, Frederick Lang, Nicholas Navin, Eric Jonasch. Single-cell and spatial transcriptomic mapping of human renal cell carcinoma brain metastases uncovers actionable immune-resistance targets [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5788.

Self-DNA Early Exposure in Cultivated and Weedy Setaria Triggers ROS Degradation Signaling Pathways and Root Growth Inhibition.

The accumulation of fragmented extracellular DNA reduces conspecific seed germination and plantlet growth in a concentration-dependent manner. This self-DNA inhibition was repeatedly reported, but the underlying mechanisms are not fully clarified. We investigated the species-specificity of self-DNA inhibition in cultivated vs. weed congeneric species (respectively, Setaria italica and S. pumila) and carried out a targeted real-time qPCR analysis under the hypothesis that self-DNA elicits molecular pathways that are responsive to abiotic stressors. The results of a cross-factorial experiment on root elongation of seedlings exposed to self-DNA, congeneric DNA, and heterospecific DNA from Brassica napus and Salmon salar confirmed a significantly higher inhibition by self-DNA as compared to non-self-treatments, with the latter showing a magnitude of the effect consistent with the phylogenetic distance between the DNA source and the target species. Targeted gene expression analysis highlighted an early activation of genes involved in ROS degradation and management (FSD2, ALDH22A1, CSD3, MPK17), as well as deactivation of scaffolding molecules acting as negative regulators of stress signaling pathways (WD40-155). While being the first exploration of early response to self-DNA inhibition at molecular level on C4 model plants, our study highlights the need for further investigation of the relationships between DNA exposure and stress signaling pathways by discussing potential applications for species-specific weed control in agriculture.

Abstract P5-02-08: Biomarker associated with response to CDK4/6 inhibitors in metastatic hormone receptor positive breast cancer

Abstract Background: In spite of widespread use and known mechanism of action, predictive biomarkers for the use of CDK4/6 inhibitors in conjunction with endocrine therapy have yet to emerge. Here a cohort of patients treated with standard-of-care combination regimens was utilized to explore features of disease and determinants of progression-free survival (PFS). Patients and Methods: In this cohort of 235 patients, &amp;gt;90% of patients were treated with Palbociclib in combination with either an aromatase inhibitor (AI) or fulvestrant (FUL). The PFS mirrored that observed in randomized clinical trials. A total of 151 patient tumor tissues were used for targeted gene expression analyses with the HTG-Oncology Biomarker Panel. The association of disease state and gene expression analyses were interrogated for disease evolution and association with PFS. Results: HER2 immunohistochemistry (HER20, Her21+, Her22+) was not associated with PFS in full cohort, or AI and FUL subgroup analyses. The lack of progesterone receptor (PR+, PR-), was associated with shorter PFS in the full patient cohort (p=0.012) and selectively in patients treated with AI (p=0.005), but not FUL. Gene expression-based subtyping indicated that the majority of patients, as expected, had luminal breast cancer; however, the predominant subtypes changed with treatment and disease evolution. Primary tissue from tumor resection was dominated by luminal A subtype, which diminished in the context of metastatic disease, and was rare in post-progression specimens. The luminal B, HER2, and basal subtypes exhibited shorter PFS in CDK4/6 inhibitor combinations (AI, p=0.01; FUL, p=0.03). Existing clinically developed breast cancer signatures (e.g. breast cancer index) had variable associations with PFS; however, high expression of gene signatures associated with cell cycle were broadly associated with short PFS. Concordantly, utilizing unbiased analyses, gene expression programs linked to cell cycle were associated with short PFS, while interferon response processes were associated with longer PFS. Algorithms that incorporated standard pathological and clinical variables with the gene expression data were developed that exhibited potent predictive power. Conclusions: Tumor evolution occurs on treatment with CDK4/6 inhibitors; however, analyses of pretreatment biopsies can inform the duration of PFS. These data support discrete biological processes associated with sensitivity/resistance. Predictive algorithms could be developed to inform features of treatment decision which will require prospective validation which is ongoing. Citation Format: Agnieszka Witkiewicz. Biomarker associated with response to CDK4/6 inhibitors in metastatic hormone receptor positive breast cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-02-08.

Amyloid beta accumulations and enhanced neuronal differentiation in cerebral organoids of Dutch-type cerebral amyloid angiopathy patients.

ADutch-type cerebral amyloid angiopathy (D-CAA) is a hereditary brain disorder caused by a point mutation in the amyloid precursor protein (APP) gene. The mutation is located within the amyloid beta (Aβ) domain of APP and leads to Aβ peptide accumulation in and around the cerebral vasculature. There lack of disease models to study the cellular and molecular pathological mechanisms of D-CAA together with the absence of a disease phenotype in vitro in overexpression cell models, as well as the limited availability of D-CAA animal models indicates the need for a D-CAA patient-derived model. We generated cerebral organoids from four D-CAA patients and four controls, cultured them up to 110 days and performed immunofluorescent and targeted gene expression analyses at two time points (D52 and D110). D-CAA cerebral organoids exhibited Aβ accumulations, showed enhanced neuronal and astrocytic gene expression and TGFβ pathway de-regulation. These results illustrate the potential of cerebral organoids as in vitro disease model of D-CAA that can be used to understand disease mechanisms of D-CAA and can serve as therapeutic intervention platform for various Aβ-related disorders.

Insights into microRNA regulation of flower coloration in a lily cultivar Vivian petal

MicroRNAs are a class of non-coding small RNAs involved in the negative regulation of gene expression, which plays critical roles in developmental and metabolic pathways. However, it is not well understood how miRNA regulation the anthocyanin biosynthesis pathway in lily flowers. Using miRNA sequencing and target gene expression analysis, we explored the regulatory networks of miRNAs and their target-related flower coloration in lily petals. A total of 326 miRNAs were obtained by miRNA sequencing, including 285 known miRNAs and 41 new miRNAs. According to the psRNATarget prediction, there were a total of 75 differentially expressed miRNAs (DEMs) that target 898 potential genes. We also screened the target genes including <italic>LvSPL, LvMYB5, LvWD, Lv3GT, LvGRF, LvARF, LvNAC, and LvMADS,</italic> which were targeted by LvmiR156, LvmiR828, LvmiR166, LvmiR396, LvmiR160, LvmiR167, LvmiR164, and LvmiR5179. These genes may be involved in regulating other secondary metabolic pathways, and formeing a complex regulatory network of anthocyanin biosynthesis. We therefore proposed a putative miRNA-target module associated with anthocyanin biosynthesis. In addition, we predicted the binding site of <italic>LvMYB5</italic>, the target gene of miR828, and speculated that miR828 targets regulate <italic>LvMYB5</italic> transcriptional translation through a cleavage site, which then inhibits anthocyanin synthesis. Our findings contribute to an understanding of the functional characterization of miRNAs and their targets in controlling anthocyanin production in plants and may lead to future identification and characterization of miRNAs in lilies.

Effect of Ecklonia cava polyphenol on adiposity reduction is associated with gut microbiota composition in subjects with abdominal obesity: A secondary analysis

• Ecklonia cava polyphenol (EP) reduced adiposity in abdominal obese adults. • EP changed gut Firmicutes -to- Bacteroidetes ratio and microbiota composition. • EP-induced microbiota alterations were associated with improved adiposity. • Predicted KEGG pathway revealed metabolic functional alterations by EP. A previous randomized controlled trial showed that Ecklonia cava polyphenol (EP) has the potential to reduce fat accumulation based on clinical outcomes and target gene expression analysis. Here, we investigated whether EP affects gut microbiota composition and impacts clinical outcomes. To this end, we analyzed 16S rRNA sequencing on fecal samples from subgroup subjects with abdominal obesity ( n = 20/group). Compared with the placebo treatment, EP supplementation attenuated the increase of the Firmicutes -to- Bacteroidetes ratio and changed 18 genera composition, including genera related to obesity and fermentation of unabsorbed compounds. Furthermore, Spearman's correlation and Tax4Fun analysis demonstrated that alterations in genera are tightly associated with reducing adiposity via regulating oxidative stress. Together, these findings suggest that the gut microbiota-regulating effect might be a possible mechanism of EP-induced adiposity reduction in subjects with abdominal obesity.

Syk Activation in Circulating and Tissue Innate Immune Cells in Antineutrophil Cytoplasmic Antibody-Associated Vasculitis.

Syk is a cytoplasmic protein tyrosine kinase that plays a role in signaling via B cell and Fc receptors (FcR). FcR engagement and signaling via Syk is thought to be important in antineutrophil cytoplasm antibody (ANCA) IgG-mediated neutrophil activation. This study was undertaken to investigate the role of Syk in ANCA-induced myeloid cell activation and vasculitis pathogenesis. Phosphorylation of Syk in myeloid cells from healthy controls and ANCA-associated vasculitis (AAV) patients was analyzed using flow cytometry. The effect of Syk inhibition on myeloperoxidase (MPO)-ANCA IgG activation of cells was investigated using functional assays (interleukin-8 and reactive oxygen species production) and targeted gene analysis with NanoString. Total and phosphorylated Syk at sites of tissue inflammation in patients with AAV was assessed using immunohistochemistry and RNAscope in situ hybridization. We identified increased phosphorylated Syk at critical activatory tyrosine residues in blood neutrophils and monocytes from patients with active AAV compared to patients with disease in remission or healthy controls. Syk was phosphorylated in vitro following MPO-ANCA IgG stimulation, and Syk inhibition was able to prevent ANCA-mediated cellular responses. Using targeted gene expression analysis, we identified up-regulation of FcR- and Syk-dependent signaling pathways following MPO-ANCA IgG stimulation. Finally, we showed that Syk is expressed and phosphorylated in tissue leukocytes at sites of organ inflammation in AAV. These findings indicate that Syk plays a critical role in MPO-ANCA IgG-induced myeloid cell responses and that Syk is activated in circulating immune cells and tissue immune cells in AAV; therefore, Syk inhibition may be a potential therapeutic option.

Activation of Distinct Inflammatory Pathways in LR-MDS Is Determined By Genetics

Background Dysregulated innate immune signaling has been identified as a driver of the complex pathophysiology of myelodysplastic syndromes (MDS), predominantly in low risk (LR)-MDS (Basiorka et al., Blood 2016). The pharmacological targeting of inflammation may therefore help to retard disease development. However, since MDS is a heterogeneous disease, a personalized approach is likely to be necessary, requiring a more detailed knowledge of distinct inflammatory patterns and their variation between genetically defined subgroups of LR-MDS patients (Winter et al., J Clin Oncol 2020). Aims The aim of this work was to describe inflammation states in the bone marrow of LR-MDS patients (IPSS-R ≤ 3.5) compared to controls with and without clonal hematopoiesis of indeterminate potential (CHIP) and to high-risk (HR)-MDS patients (IPSS-R ≥ 4). Methods Cryopreserved bone marrow mononuclear cells (BM-MNCs) and corresponding bone marrow plasma samples from non-CHIP controls (n = 15), CHIP individuals (n = 12) and patients with LR-MDS (n = 47) or HR-MDS (n = 14) were obtained from the MDS registry and the BoHemE study (NCT02867085) at the University Hospitals in Dresden and Leipzig. Targeted expression analysis of 11 inflammasome-related genes (S100A9, NLRP3, PYCARD, CASP1, IL1B, IL18, NLRP1, NLRC4, AIM2, CASP3, CASP4) and multiplex cytokine measurements were performed. To investigate heterogeneity in the LR-MDS cohort, a principle component analysis (PCA) was performed and a cumulative gene expression score was calculated as summed log2 fold changes (mean non-CHIP = 0) of all 11 mRNA expression values for each sample. Furthermore, BM-MNCs of selected non-CHIP (n = 3) and CHIP (n = 3) individuals as well as LR-MDS (n = 14) and HR-MDS (n = 5) patients were FACS-sorted for hematopoietic stem and progenitor cells (HSPCs), monocytes, monocytic and polymorphonuclear myeloid-derived suppressor cells (MDSCs) and lymphocytes. The expression of IL1B, IL18, S100A9, NLRP3, PYCARD, CASP1 and NLRC4 was assessed in each population by qRT-PCR. Finally, colony forming assays were used to assess the effect of the IL-1β-neutralizing antibody canakinumab (100 µg/ml) on the hematopoietic potential of healthy CD34+ HSPCs pre-cultured with CD14+ monocytes from patients with SF3B1-mutated (n = 3) or del(5q) (n = 3) LR-MDS. Results The expression of inflammasome-related genes in the bone marrow increased from non-CHIP through CHIP to LR-MDS individuals, with overall levels of inflammasome-related gene expression being 40% higher in LR-MDS than in non-CHIP controls (p = 0.002). The precise signature of inflammation gene expression varied widely within LR-MDS patients. A PCA identified two separable inflammation states with low (cluster 1, n = 24) and high (cluster 2, n = 23) inflammation patterns (Figure 1), with CASP1, PYCARD and NLRC4 contributing most to the PCA dimensions. The clusters were associated with distinct clinical features and disease genotypes: more than 80% of the SF3B1 mutations were found in cluster 1, while all del(5q) cases were in cluster 2 (Figure 1). Compared to del(5q) samples, those with SF3B1-mutation showed lower expression of IL-1β at both mRNA (3.9-fold decrease, p = 0.0005) and protein level (8.3-fold decrease, p = 0.03). Targeted gene expression analysis of sorted cell populations revealed distinct contributions to the differential patterns of inflammation. IL1B, NLRP3, NLRC4 and S100A9 were expressed in all disease states predominantly by monocytes and monocytic MDSCs, consistent with a dominant role for monocytic cells in determining the inflammatory bone marrow environment. However, IL18 mRNA levels were highest in HSPCs. Compared to untreated controls, canakinumab augmented the colony forming activity of healthy HSPCs pre-cultured with monocytes from SF3B1-mutated MDS (+70%, p = 0.002). The effect in co-cultures with del(5q) MDS-derived monocytes was weaker (+56%, p = 0.188), showing that canakinumab efficacy in this assay does not depend on IL-1β expression level alone. Conclusion We conclude that inflammation patterns in LR-MDS are heterogeneous, highlighting the need for personalization of targeted anti-inflammatory therapies currently entering clinical trials. Our analysis suggests that high resolution studies of gene expression in specific populations or single cells will further resolve a spectrum of inflammation states relevant to prognosis and personalized therapy. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

A Transcriptional Classifier Identifies Pediatric T-Cell Acute Lymphoblastic Leukemias at High Risk for End of Induction Minimal Residual Disease

Upfront risk stratification with incorporation of risk-adapted therapy continues to be a pressing need for pediatric T-ALL. However, robust molecular or cytogenetic biomarkers are currently lacking. Instead, initial response to therapy, measured as end of induction minimal residual disease (MRD), is the only prognostic factor used in most cooperative groups. This inability to stratify patients at diagnosis limits the early introduction of rationally-designed therapies that may better achieve long-term remissions. To address this, we asked whether gene expression profiling performed at diagnosis may identify patients at high risk for future MRD+, enabling earlier therapeutic intervention. To test this, we used a training dataset of RNA-seq data from diagnostic samples from patients enrolled on the Children's Oncology Group (COG) AALL0434 trial. Using leave-one-out cross-validation, we defined a risk score (RS) for MRD+ based on the expression of 119 genes. This RS indicates the probability of being MRD+ for a given gene expression pattern. Gene ontology analysis of the genes in our model demonstrated enrichment for genes involved in signal transduction, lymphocyte differentiation and activation, and cell death. Using this model, we found that early T-cell precursor (ETP) samples (n=19), of which 79% were MRD+, had uniformly high RS, with an average of 78 (SD=17). In contrast, non-ETP samples (n=146), of which 26% were MRD+, had an average RS of 26 (SD=21), with MRD+ patients having a significantly higher RS relative to MRD- patients (p<0.0001). When we analyzed the expression pattern of the 119 genes, we found that ETP samples had a relatively uniform pattern, consistent with their high rate of MRD+. Non-ETP samples with RS<50 had a pattern that was inverted relative to the ETP samples, while those with RS>50 closely mirrored the ETP samples. Using a RS cutoff of 50 to identify patients at high risk for MRD+ gives a 97% specificity in this training cohort. Given the similar gene expression pattern between ETPs and RS>50 non-ETPs, we hypothesized that this RS classification may relate to differences in developmental stage. We found that ETP and RS>50 non-ETP samples were significantly enriched for the LMO2/LYL1, HOXA, and TLX3 subgroups of T-ALL, with the subgroup distribution in the RS>50 non-ETP samples differing significantly from the RS<50 non-ETP samples (p=0.001). Furthermore, we found that the RS>50 non-ETP samples, relative to the RS<50 samples, were enriched for lacking a TCRb rearrangement (p<0.0001), indicative of an earlier developmental stage. To determine the generalizability of our gene expression classifier, we applied our fixed model to an independent validation cohort of 826 non-ETP samples from the same COG AALL0434 trial. Here, we again found that RS>50 non-ETP samples (n=130) were significantly enriched for MRD+ relative to RS<50 samples (n=696; p<0.0001). Next, we applied our classifier model to a pilot cohort of samples from patients enrolled on COG AALL1231, which used dexamethasone rather than prednisone as the induction steroid. In this group of 31 diagnostic non-ETP samples, RS>50 samples were similarly enriched for MRD+ (p=0.05), suggesting that this classifier may retain its prognostic value across multiple induction steroids. Finally, to facilitate clinical implementation of this prognostic tool, we transitioned to the NanoString nCounter platform, a more rapid and cost-effective means of performing targeted gene expression analysis. Using 364 samples from COG AALL0434 for which we had corresponding RNA-seq data, we assessed the performance of our custom NanoString assay and found a strong correlation between the RS calculated using each of the two platforms (concordance correlation coefficient = 0.98), suggesting that the prognostic value of the classifier is retained on the NanoString assay. In conclusion, while ETP samples are commonly MRD+ and are readily identifiable by their unique cell surface immunophenotype, non-ETP samples lack a surface immunophenotype that correlates with MRD+. Here, we present a targeted gene expression classifier, validated on a clinically-tractable platform, that identifies at diagnosis a subset of non-ETP T-ALLs with a gene expression pattern that resembles that of ETP T-ALLs and that are at high risk for future MRD+.

Differential gene expression analysis of common target genes for the detection of SARS-CoV-2 using real time-PCR

COVID-19 currently is the main cause of the severe acute respiratory disease and fatal outcomes in human beings worldwide. Several genes are used as targets for the detection of SARS-CoV-2, including the RDRP, N, and E genes. The present study aimed to determine the RDRP, N, and E genes expressions of SARS-CoV- 2 in clinical samples. For this purpose, 100 SARS-CoV-2 positive samples were collected from diagnostic laboratories of Mazandaran province, Iran. After RNA extraction, the real-time reverse transcription PCR (real-time RT-PCR) assay was performed for differential gene expressions’ analysis of N, E, and RDRP. The threshold cycle (Ct) values for N, RDRP, and E targets of 100 clinical samples for identifying SARS-CoV-2 were then evaluated using quantitative real-time PCR (qRT-PCR). This result suggests N gene as a potential target for the detection of the SARS-CoV‐2, since it was observed to be highly expressed in the nasopharyngeal or oropharynges of COVID-19 patients (P < 0.0001). Herein, we showed that SARS-CoV- 2 genes were differentially expressed in the host cells. Therefore, to reduce obtaining false negative results and to increase the sensitivity of the available diagnostic tests, the target genes should be carefully selected based on the most expressed genes in the cells.

Perinatal Morphine Exposure Leads to Sex-Dependent Executive Function Deficits and Microglial Changes in Mice.

Children exposed prenatally to opioids are at an increased risk for behavioral problems and executive function deficits. The prefrontal cortex (PFC) and amygdala (AMG) regulate executive function and social behavior and are sensitive to opioids prenatally. Opioids can bind to toll-like receptor 4 (TLR4) to activate microglia, which may be developmentally important for synaptic pruning. Therefore, we tested the effects of perinatal morphine exposure on executive function and social behavior in male and female mouse offspring, along with microglial-related and synaptic-related outcomes. Dams were injected once daily subcutaneously with saline (n = 8) or morphine (MO; 10 mg/kg; n = 12) throughout pregestation, gestation, and lactation until offspring were weaned on postnatal day 21 (P21). Male MO offspring had impairments in attention and accuracy in the five-choice serial reaction time task, while female MO offspring were less affected. Targeted gene expression analysis at P21 in the PFC identified alterations in microglial-related and TLR4-related genes, while immunohistochemical analysis in adult brains indicated decreased microglial Iba1 and phagocytic CD68 proteins in the PFC and AMG in males, but females had an increase. Further, both male and female MO offspring had increased social preference. Overall, these data demonstrate male vulnerability to executive function deficits in response to perinatal opioid exposure and evidence for disruptions in neuron–microglial signaling.

Persistent γ-H2AX Formation and Expression of Stem Cell Markers in N-Butyl-N-(4-Hydroxybutyl)Nitrosamine-Induced Bladder Carcinogenesis in Rats.

We investigated γ-H2AX formation, a biomarker of DNA damage, and expression of stem cell markers (SCMs), including cytokeratin 14, aldehyde dehydrogenase 1A1 (ALDH1A1), and CD44, in the development of rat bladder tumors induced by short-term administration of N-butyl-N-(4-hydroxybutyl)nitrosamine (BBN). Histopathological examination showed that diffuse simple hyperplasia of the bladder urothelium induced by BBN recovered to the normal-appearing urothelium after withdrawal, whereas focal proliferative lesions were newly developed and subsequently progressed to benign papilloma and carcinoma. Immunohistochemical analysis revealed that BBN-induced γ-H2AX formation and ALDH1A1 and CD44 expression persisted at higher levels in the normal-appearing urothelium than those in the control group for long periods after withdrawal. Since persistent chronic inflammation was observed even after withdrawal, targeted gene expression analysis of inflammation-related factors revealed 101 genes, including Stat3 and Myc, that showed persistent high expression. Pathway analysis suggested that Stat3 and/or Myc activation may be associated with SCM expression. We focused on hepatocyte growth factor (Hgf), one of the genes predicted in relation to Stat3/Myc, and confirmed that HGF-positive cells increased by BBN persisted in the normal-appearing urothelium after withdrawal and colocalized with γ-H2AX and SCMs. These results suggested that the long-term persistence of γ-H2AX formation and SCM expression, which occurred during the early stages of bladder tumorigenesis, is not a transient response to exposure and might contribute to bladder tumorigenesis. Although further studies are needed, BBN-induced rat bladder tumors may originate from focal hyperplasia arising from SCM-positive cells via activation of the STAT3/MYC pathway after DNA damage involving γ-H2AX formation.