Higher Transcript Expression Research Articles

BMP-2 and asporin expression regulate 5-aza-dC-mediated osteoblast/cementoblast differentiation of periodontal dental ligament mesenchymal progenitor cells

Periodontal dental ligament (PDL) is composed of heterogeneous population of mesenchymal progenitor cells. The mechanisms that regulate the differentiation of these cells towards osteoblast/cementoblast phenotype are not fully understood. Some studies have demonstrated that is possible to change the pattern of cell differentiation via epigenetic mechanisms. The proposal of this study was to investigate whether 5-aza-2'-deoxycytidine (5-aza-dC) treatment would stimulate the osteoblast/cementoblast differentiation of periodontal ligament mesenchymal progenitor cells (PDL-CD105+ enriched cells), characterized as low osteoblast potential, through bone morphogenetic protein-2 (BMP-2) modulation. PDL-CD105+ cells from a single donor were cloned and characterized in two populations as high osteoblast/cementoblast potential (HOP) and low osteoblast/cementoblast potential (LOP) by mineralization in vitro and expression of osteogenic gene markers, such as runt-related transcription factor 2 (RUNX2), alkaline phosphatase (ALP), osteocalcin (OCN), bone morphogenetic protein 2 (BMP-2) and asporin (ASPN). Next, two LOP clones (L1 and L2) were pretreated with 5-aza-dC (10 μM) for 48 h, cultured under osteogenic condition and evaluated for mineralized matrix in vitro, transcription modulation of osteogenic gene markers, methylated and hydroxymethylated DNA levels of BMP-2 and ASPN and intracellular/extracellular expression of BMP-2 protein. LOP clones showed high expression of ASPN transcripts associated with low mRNA levels of BMP-2, RUNX2, ALP, and OCN. 5-aza-dC treatment raised hydroxymethylated DNA levels of BMP-2 and increased the expression of BMP-2 transcripts in both LOP clones. However, BMP-2 protein (intracellular and secreted forms) was detected only in L1 cell clones, in which it was observed an increased expression of osteoblast/cementoblast markers (RUNX2, ALP, OCN) associated with higher mineralization in vitro. In L2 cell clones, 5-aza-dC increased gene expression of ASPN, with no great change in for osteoblast/cementoblast differentiation potential. These data show that 5-aza-dC improves osteoblast/cementoblast differentiation of PDL-CD105+ cells via BMP-2 secretion, and this effect depends on low levels of ASPN expression.

Photoprotection contributes to freezing tolerance as revealed by RNA-seq profiling of rhododendron leaves during cold acclimation and deacclimation over time.

Cold acclimation (CA) and deacclimation (DA), which are often accompanied by changes in freezing tolerance (FT), carbohydrates and hormones, are crucial for winter survival, especially under global warming. Plants with weak CA and premature DA caused by warm winters and/or unseasonal warm spells can be easily injured by adverse reactions to cold. Thus, understanding the molecular mechanisms of FT is imperative. In this study, we used high-throughput RNA-seq to profile the CA and DA of leaves of overwintering Rhododendron "Miyo-no-Sakae" over time; these leaves do not undergo dormancy but do undergo photoprotection during CA, and they do not grow during DA. Using Mfuzz and weighted gene coexpression network analysis, we identified specific transcriptional characteristics in each phase of CA and DA and proposed networks involving coexpressed genes and physiological traits. In particular, we discovered that the circadian rhythm is critical for obtaining the strongest FT, and high expression of circadian rhythm-related genes might be linked to sugar accumulation during winter. Furthermore, evergreen leaves exhibited robust photoprotection during winter, as revealed by high values of nonphotochemical quenching, high expression of transcripts annotated as "early light-induced proteins", loss of granum stacks and destacking of thylakoids, all of which were alleviated during DA. The strong requirement of photoprotection could be the reason for decreased abscisic acid (ABA) and jasmonic acid (JA) contents during CA, and decreases in ABA and JA contents may contribute to decreases in lignin content. Our data suggest that the molecular mechanisms of FT in overwintering leaves are unique, which may be due to the high requirements for photoprotection during winter.

Transcriptomics of a Greenlandic Snailfish Reveals Exceptionally High Expression of Antifreeze Protein Transcripts.

Polar fishes have evolved antifreeze proteins (AFPs) that allow them to survive in subzero temperatures. We performed deep transcriptomic sequencing on a postlarval/juvenile variegated snailfish, Liparis gibbus (Actinopterygii: Scorpaeniformes: Cottoidei: Liparidae), living in an iceberg habitat (−2°C) in Eastern Greenland and report detection of highly expressed transcripts that code for putative AFPs from 2 gene families, Type I and LS-12-like proteins (putative Type IV AFPs). The transcripts encoding both proteins have expression levels among the top <1% of expressed genes in the fish. The Type I AFP sequence is different from a reported Type I AFP from the same species, possibly expressed from a different genetic locus. While prior findings from related adult sculpins suggest that LS-12-like/Type IV AFPs may not have a role in antifreeze protection, our finding of very high relative gene expression of the LS-12-like gene suggests that highly active transcription of the gene is important to the fish in the iceberg habitat and raises the possibility that weak or combinatorial antifreeze activity could be beneficial. These findings highlight the physiological importance of antifreeze proteins to the survival of fishes living in polar habitats.

A Transcriptional Signature of IL-2 Expanded Natural Killer Cells Predicts More Favorable Prognosis in Bladder Cancer.

Activation of natural killer (NK) cell function is regulated by cytokines, such as IL-2, and secreted factors upregulated in the tumor microenvironment, such as platelet-derived growth factor D (PDGF-DD). In order to elucidate a clinical role for these important regulators of NK cell function in antitumor immunity, we generated transcriptional signatures representing resting, IL-2-expanded, and PDGF-DD-activated, NK cell phenotypes and established their abundance in The Cancer Genome Atlas bladder cancer (BLCA) dataset using CIBERSORT. The IL-2-expanded NK cell phenotype was the most abundant in low and high grades of BLCA tumors and was associated with improved prognosis. In contrast, PDGFD expression was associated with numerous cancer hallmark pathways in BLCA tumors compared with normal bladder tissue, and a high tumor abundance of PDGFD transcripts and the PDGF-DD-activated NK cell phenotype were associated with a poor BLCA prognosis. Finally, high tumor expression of transcripts encoding the activating NK cell receptors, KLRK1 and the CD160–TNFRSF14 receptor–ligand pair, was strongly correlated with the IL-2-expanded NK cell phenotype and improved BLCA prognosis. The transcriptional parameters we describe may be optimized to improve BLCA patient prognosis and risk stratification in the clinic and potentially provide gene targets of therapeutic significance for enhancing NK cell antitumor immunity in BLCA.

Therapeutic and Immunologic Responses Elicited By in Situ Vaccination with CpG, Ibrutinib, and Low-Dose Radiation

Introduction: In situ vaccination aims to induce an immune response locally at one tumor site that propagates systemically to all tumor sites. This approach can be effective in indolent lymphoma (Brody et al., JCO 2010, Frank et al., Cancer Discov 2018, Hammerich et al., Nat Med 2019). We designed a novel clinical strategy combining in situ vaccination with systemic ibrutinib, a kinase inhibitor that modulates B and T cells. Our preclinical work had shown that combined intratumoral CpG injection and systemic ibrutinib administration was curative of systemic disease in a mouse lymphoma model, an effect that was T cell dependent (Sagiv-Barfi, Blood, 2015). Here we report the results and correlative data from the Phase I/II clinical trial testing this combination along with local low-dose radiation in adults with recurrent low-grade B cell lymphoma (NCT02927964).Methods: Enrolled patients received intratumoral injections of CpG (SD-101, 3 mg) weekly for 5 doses and local radiation (4Gy in two fractions) to the same site. Daily oral ibrutinib (560mg) began after the second intratumoral injection. Revised Lugano criteria (Cheson et al., JCO, 2014) were used to assess overall radiographic responses to therapy. Distal responses were assessed by excluding the injected site and measuring only non-injected sites. Fine needle aspirates (FNAs) were obtained from CpG-injected and non-injected nodal tumor sites pre- and post-treatment and analyzed by flow cytometry and droplet-based single-cell RNA sequencing (scRNAseq).Results: Among the twenty patients treated on study, median age was 64, 55% were male, and all but one had a diagnosis of follicular lymphoma. All patients were previously treated with an average of 2 lines of therapy, and half had previously received chemotherapy. Adverse events (AEs) were consistent with known effects of ibrutinib (including diarrhea and rash) and of CpG (including fever and flu-like reactions). No drug-related grade 4, serious, or unexpected AEs were observed. As anticipated, all patients experienced tumor reduction at the locally treated site (median 84% reduction). Remarkably, all patients experienced some tumor reduction at non-injected non-irradiated index lesions (median 45%, range 13-100%), suggesting the generation of systemic immune responses (Figure 1A). By Cheson criteria, ten patients achieved an objective response, including one complete response (ORR 50%). Despite an overall improvement in tumor burden, three patients had new or progressing non-index lesions and scored as progressive disease. Treatment induced an expansion of naïve and effector memory T cells and reductions in T follicular helper (Tfh) and activated regulatory T cells (Tregs) at the injected site. T cells with high expression of transcripts related to oxidative phosphorylation (Toxphos) increased preferentially in patients with subsequent clinical tumor reduction (Figure 1B), implicating T cell metabolism in successful generation of immune responses. Analysis of single cell T cell receptor (TCR) sequencing data revealed>300 clones that were comprised of at least 2 cells at each timepoint and which expanded or contracted at least two-fold during treatment. Expanding clones were more likely than contracting clones to be activated or memory T cells and less likely than contracting clones to be Tfh or Tregs (Figure 1C-D). Clone dynamics were often similar at the two sampled tumor sites, reflecting systemic immune responses. Finally, in vitro assays showed treatment-induced expansion of tumor-specific T cells in the peripheral blood of all 6 evaluable patients.Conclusion: The combination of oral ibrutinib, intratumoral CpG, and local low-dose radiation is safe and can generate systemic antitumor immune responses and systemic tumor shrinkage in low-grade B cell lymphoma. [Display omitted] DisclosuresShree: Gilead: Other: Spouse's employment. Khodadoust: CRISPR Therapeutics, Nutcracker Therapeutics: Research Funding; Myeloid Therapeutics: Membership on an entity's Board of Directors or advisory committees; Alexion, AstraZeneca Rare Disease: Other: Study investigator. Frank: Kite-Gilead: Membership on an entity's Board of Directors or advisory committees; Adaptive Biotechnologies: Research Funding; Allogene Therapeutics: Research Funding. Beygi: Kite/Gilead: Current Employment. Levy: GigaGen: Membership on an entity's Board of Directors or advisory committees; Teneobio: Membership on an entity's Board of Directors or advisory committees; Nurix: Membership on an entity's Board of Directors or advisory committees; Dragonfly: Membership on an entity's Board of Directors or advisory committees; Apexigen: Membership on an entity's Board of Directors or advisory committees; Viracta: Membership on an entity's Board of Directors or advisory committees; Spotlight: Membership on an entity's Board of Directors or advisory committees; Immunocore: Membership on an entity's Board of Directors or advisory committees; Walking Fish: Membership on an entity's Board of Directors or advisory committees; Kira: Membership on an entity's Board of Directors or advisory committees; Abintus Bio: Membership on an entity's Board of Directors or advisory committees; Khloris: Membership on an entity's Board of Directors or advisory committees; Virsti: Membership on an entity's Board of Directors or advisory committees; BiolineRx: Membership on an entity's Board of Directors or advisory committees; BeiGene: Membership on an entity's Board of Directors or advisory committees; Quadriga: Membership on an entity's Board of Directors or advisory committees.

Equine Endometrosis Pathological Features: Are They Dependent on NF-κB Signaling Pathway?

Endometrosis is an important mares’ disease which considerably decreases their fertility. As classic endometrial classification methods might be insufficient for tissue pathological evaluation, further categorization into active/inactive and destructive/non-destructive types was developed by Hoffmann and others. This study aimed to compare NF-κB pathway genes transcription among histopathological types of endometrosis, following Hoffmann and co-authors’ classification. Endometrial samples, collected postmortem from cyclic mares (n = 100) in estrus or diestrus, were classified histologically and used for gene transcription assessment. Gene transcription of NF-κB subunits (RelA, NF-κB1, NF-κB2), pro-inflammatory molecules (MCP-1, IL-6), and hyaluronan synthases (HAS 1, HAS 2, HAS 3) was compared among endometrosis types (active, non-active, destructive, non-destructive). Most individual mRNA samples showed high expression of RelA, NF-κB1, and MCP-1 gene transcripts and the destructive type of endometrosis, simultaneously. The expression of RelA and NF-κB1 genes was higher in active destructive group than in the other groups only in the follicular phase, as well as being higher in the inactive destructive group than in the others, only in the mid-luteal phase. The increase in gene transcription of the NF-κB canonical activation pathway in destructive endometrosis may suggest the highest changes in extracellular matrix deposition. Moreover, the estrous cycle phase might influence fibrosis pathogenesis.

302 Characterization of TIGIT and PVR expression in colorectal liver metastases

BackgroundMetastatic colorectal cancer (CRC) is common and lethal and generally not responsive to current immunotherapies. We hypothesize that efficacious T cell-based immunotherapy can be developed for this malignancy, provided that immune checkpoints relevant to liver metastasis, the first site of disease progression, are targeted. Here, we characterized CRC liver metastases by RNAseq, FACS and in vitro functional assays to identify candidate immune checkpoints.MethodsWe performed deep RNAseq clustering and differential gene expression analysis on bulk RNA extracted from 52 mismatch repair gene proficient CRC liver metastases. By multiparameter FACS, we analyzed the expression of candidate immune checkpoints in cell suspensions derived from 18 liver metastases, matched non-tumoral livers, and pre-operative PBMCs. We evaluated IFN-γ (ELISA) secretion and tumor lysis (Incucyte) of tumor-infiltrating T lymphocytes (TILs) expanded from liver metastases stimulated by autologous cancer cells with or without monoclonal antibodies blocking candidate immune checkpoints.ResultsOut of 52 metastases, 21 (40.3%) clustered as immune reactive (IR) defined by concurrent high expression of transcripts related to antigen processing, immune cell lineage, immune checkpoints, interferon-gamma response, cytokines, and chemokines, whereas 25 (48.1%) were classified as non-IR. Of all inhibitory ligands assessed, PVR and PVRL2 had the highest expression, both in IR and non-IR metastases, and higher than PD-L1 and PD-L2 expression. The expression of corresponding receptors TIGIT and CD226 was significantly higher in IR compared to non-IR metastases, at absolute levels higher than PD-1. By FACS analysis, PVR and PVRL2 expression by tumor-infiltrating myeloid and tumor cells was higher than PD-L1 and PD-L2 expression. High PVR expression was also found in hepatocytes, liver macrophages and circulating monocytes in the same patients. In TILs, TIGIT was significantly overexpressed in activated CD4+CD25+ (74.8 ±3.0%) and CD8+CD25+ (68.7 ± 8.4%) compared to resting CD25neg T cells, an expression pattern that was not seen for PD-1 or in T cells infiltrating the liver or circulating in the blood. The majority of cancer cell lines derived from liver metastases expressed PVR, but low levels of PD-L1. TIL clones expanded from liver metastases expressed TIGIT at various levels inducible by TCR stimulation. Upon co-culture with autologous cancer cell lines, TIL clones were more lytic and secreted more IFN-γ in presence of anti-TIGIT blocking antibody.ConclusionsBy expression and functional data, the TIGIT/PVR immune suppressive axis appears as a biologically promising target for the development of immunotherapy in patients with CRC metastatic to the liver.AcknowledgementsThis work is supported by Bristol Myers Squibb and by the Quebec Cancer Consortium. A.B. holds a postdoctoral scholarship award from the Institut du cancer de Montréal. S.T. holds a Junior 2 clinical-scientist salary award from the Fond de recherche Santé-Québec. The University of Montreal Roger des Groseillers Research Chair in hepatopancreatobiliary surgical oncology supports the biobanking and clinicopathological database associated with this project.Ethics ApprovalInstitutional review board approvals were obtain to conduct this project (16.262) and all patients provided informed consent to contribute to this project with biospecimens and clinicopathological data (09.237).

Predictive capacity of IL-8 expression in head and neck squamous carcinoma patients treated with radiotherapy or chemoradiotherapy

ObjectiveTo analyse the relationship between the transcriptional expression of interleukin-8 (IL-8) and response to treatment with radiotherapy or chemo-radiotherapy in patients with squamous cell carcinoma of the head and neck (SCCHN). Material and methodsRetrospective study from tumour biopsies obtained before a treatment with radiotherapy or chemo-radiotherapy in 87 patients with SCCHN. We had a sample of healthy mucosa in 35 cases. We determined the transcriptional expression of IL-8 with RT-PCR. The transcriptional expression of IL-8 was categorized according to the local control of the disease with a recursive partitioning analysis. ResultsThe transcriptional expression of IL-8 in tumour tissue was about 50 times higher than that in the samples of healthy mucosa. Patients with a high transcriptional expression of IL-8 (n = 56) had a 5-year local recurrence-free survival of 65.6%, and for patients with low expression (n = 31) it was 90.2% (P = 0.017). According to the results of a multivariate analysis, patients with high expression of IL-8 had a 4.1 higher risk of local recurrence of the tumour. ConclusionsSCCHN have a significant increase in transcriptional expression of IL-8 in relation to non-tumour tissue. Tumours with high IL-8 expression have an increased risk of local recurrence after treatment with radiotherapy or chemo-radiotherapy.

A Transcriptional Signature of PDGF-DD Activated Natural Killer Cells Predicts More Favorable Prognosis in Low-Grade Glioma.

The binding of platelet-derived growth factor D (PDGF-DD) to the NKp44 receptor activates a distinct transcriptional program in primary IL-2 expanded human natural killer (NK) cells. We were interested in knowing if the PDGF-DD-NKp44 pathway of NK cell activation might play a clinically relevant role in anti-tumor immunity. In order to address this question, we determined transcriptional signatures unique to resting, IL-2 expanded, and PDGF-DD activated, NK cells, in addition to different T cell subsets, and established the abundance of these immune cell phenotypes in The Cancer Genome Atlas (TCGA) low-grade glioma (LGG) dataset using CIBERSORT. Our results show that LGG patient tumors enriched for either the PDGF-DD activated NK cell or memory CD8+ T cell phenotypes are associated with a more favorable prognosis. Combined cell phenotype analyses revealed that patients with LGG tumors enriched for the PDGF-DD activated NK cell phenotype and the CD4+ T helper cell phenotype had a more favorable prognosis. High expression of transcripts encoding members of the killer cell lectin-like receptor (KLR) family, such as KLRK1 and KLRC2, KLRC3 and KLRC4 in LGG tumors were associated with more favorable prognosis, suggesting that these NK cell family receptors may play a prominent role in LGG anti-tumor immunity. Finally, many of the TCGA findings were reciprocated in LGG patients from the Chinese Glioma Genome Atlas (CGGA) dataset. Our results provide transcriptomic evidence that PDGF-DD activated NK cells and KLR family receptors may play an important clinical role in immune surveillance of LGG.

Abstract 131: Gata4 Ablation In Smooth Muscle Cells Reduces Aortic Root Dilation In A Murine Model Of Loeys-Dietz Syndrome

Loeys-Dietz syndrome (LDS) is a connective tissue disorder characterized by predisposition to aneurysm. Although dilation can develop in all segments of the arterial tree, the aortic root is especially prone to disease. This aortic region is primarily composed of vascular smooth muscle cells (VSMCs) derived from secondary heart field (SHF) progenitors, while VSMCs derived from the cardiac neural crest (CNC) predominate in the more distal ascending aorta. Although intrinsic differences have been found between these two types of VSMCs, it remains unclear how these may contribute to localized risk. To identify transcripts associated with the vulnerability of the aortic root in LDS, we performed single cell transcriptomic analysis on proximal aortas from 16-week-old control and Tgfbr1 M318R/+ LDS mice, which carry a kinase-inactivating mutation in TGF-β Receptor 1. We identified four major VSMC clusters regardless of genotype, with two clusters being defined by CNC-enriched transcripts and two clusters by SHF-enriched transcripts. The latter were defined by expression of Gata4 , which codes for a transcription factor required for development of SHF-derived vascular structures, as well as by higher expression of transcripts previously involved in aneurysm pathogenesis such as Thbs1 , Tgfb1, and Tgfb3. In situ RNA hybridization confirmed that Gata4 -expressing VSMCs were enriched in the aortic root and proximal ascending aorta, with almost no expression in the more distal ascending aorta, suggesting that this transcript defined the aortic region most susceptible to the effects of the Tgfbr1 M318R/+ mutation. GATA4 protein levels were also upregulated in the aortic root of LDS mice. To test if excessive GATA4 expression or activity in VSMCs contributed to aortic root dilation in LDS, we generated LDS mice in which Gata4 was specifically deleted in VSMCs by tamoxifen administration at 6 weeks of age. We found that this intervention significantly reduced aortic root growth from 8 to 20 weeks of age. Although the mechanisms remain under investigation, these data suggest that expression of Gata4 might sensitize specific subsets of aortic VSMCs to the effects of an LDS mutation, rendering the aortic root more susceptible to disease.

Molecular characterization of fshb and lhb subunits and their expression profiles in captive white-edged rockfish, Sebastes taczanowskii

Fundamental knowledge on the regulation of reproduction by gonadotropins (Gths) is quite limited in viviparous fishes. In the present study, we performed molecular cloning and characterization of cDNAs encoding two Gth subunits (fshb and lhb) from the pituitaries of viviparous white-edged rockfish, Sebastes taczanowskii; expression profiles of both gene transcripts were elucidated in the pituitaries of reproductive males and females which were kept in a captive environment. The cloned fshb and lhb fragments exhibited high sequence identities with corresponding β-subunit sequences from black rockfish, S. schlegelii. Notably, the fshb of white-edged rockfish appeared to lack a putative N-glycosylation site, whereas lhb conserved it. Expression of fshb and lhb transcripts in the rockfish pituitaries largely changed in synchrony but for minor exceptions. In males, levels of both transcripts increased with progression of spermatogenesis, although the peak for fshb (October) appeared slightly earlier than that for lhb (November). In females, both gene transcripts exhibited synchronous bimodal changes. High expression of fshb and lhb transcripts in the female pituitary during the gestation period, followed by the drastic decrease at parturition, suggest their possible involvement in regulation of gestation of this species. The knowledge gained for Sebastes in this study superimposes fundamental information necessary for further physiological understanding of viviparity in teleost fish.

Screening and evaluation of the strong endogenous promoters in Pichia pastoris

BackgroundDue to its ability to perform fast and high-density fermentation, Pichia pastoris is not only used as an excellent host for heterologous protein expression but also exhibits good potential for efficient biosynthesis of small-molecule compounds. However, basic research on P. pastoris lags far behind Saccharomyces cerevisiae, resulting in a lack of available biological elements. Especially, fewer strong endogenous promoter elements available for foreign protein expression or construction of biosynthetic pathways were carefully evaluated in P. pastoris. Thus, it will be necessary to identify more available endogenous promoters from P. pastoris.ResultsBased on RNA-seq and LacZ reporter system, eight strong endogenous promoters contributing to higher transcriptional expression levels and β-galactosidase activities in three frequently-used media were screened out. Among them, the transcriptional expression level contributed by P0019, P0107, P0230, P0392, or P0785 was basically unchanged during the logarithmic phase and stationary phase of growth. And the transcriptional level contributed by P0208 or P0627 exhibited a growth-dependent characteristic (a lower expression level during the logarithmic phase and a higher expression level during the stationary phase). After 60 h growth, the β-galactosidase activity contributed by P0208, P0627, P0019, P0407, P0392, P0230, P0785, or P0107 was relatively lower than PGAP but higher than PACT1. To evaluate the availability of these promoters, several of them were randomly applied to a heterogenous β-carotene biosynthetic pathway in P. pastoris, and the highest yield of β-carotene from these mutants was up to 1.07 mg/g. In addition, simultaneously using the same promoter multiple times could result in a notable competitive effect, which might significantly lower the transcriptional expression level of the target gene.ConclusionsThe novel strong endogenous promoter identified in this study adds to the number of promoter elements available in P. pastoris. And the competitive effect observed here suggests that a careful pre-evaluation is needed when simultaneously and multiply using the same promoter in one yeast strain. This work also provides an effective strategy to identify more novel biological elements for engineering applications in P. pastoris.

Abstract 2408: Targeted bioinformatics analysis identifies high ABAT transcript expression as a multi-cancer marker of favorable patient prognosis

Abstract Unsupervised analysis of γ-aminobutyric acid (GABA) system genes has identified some genes as correlated with indicators of severity in several cancers. Central to GABA system function is the GABA shunt, a series of reactions bypassing two steps of the tricarboxylic acid (TCA) cycle, which encompasses the synthesis and metabolism of the non-proteinaceous amino acid GABA. Here, we have undertaken a targeted bioinformatics study utilizing publicly available databases - including cBioPortal, UALCAN, the Human Protein Atlas, and the Human Cancer Metastasis Database - to evaluate the expression of transcripts encoding GABA shunt enzymes, and their correlation with clinical outcomes, across nearly three dozen cancers from The Cancer Genome Atlas (TCGA) Pan-Cancer Atlas initiative dataset. Of the three genes encoding enzymes of the GABA shunt, we have focused on ABAT, which encodes the GABA-catabolizing enzyme γ-aminobutyrate aminotransferase (ABAT; aka GABA-transaminase or GABA-T). ABAT is widely expressed across all 32 TCGA studies, ranging from moderate to high expression in skin cutaneous melanoma and low-grade glioma (average ± SEM = 6.5 ± 0.08; 13.3 ± 0.03 log2 RSEM), respectively. For the majority of these tissues, the expression of ABAT in tumor is lower than its expression in adjacent normal tissue. Importantly, ABAT expression is prognostic in 11 cancers: upregulation is favorably prognostic for ACC, BLCA, BRCA, and PAAD, while downregulation is unfavorably prognostic for KIRC, KIRP, LGG, LIHC, LUAD, MESO, and SKCM (Kaplan-Meier survival estimates, z-score = 0.5, p &amp;lt; 0.05). A subset of these cancers, as well as 4 other TCGA cancers, show a decrease in ABAT transcript expression with increasing tumor stage (p &amp;lt; 0.05). Furthermore, 7 cancers express lower levels of ABAT transcripts in the primary tumors of patients with metastases vs the primary tumors of patients without metastases. Additionally, metastases of 4 cancers express elevated levels of ABAT transcripts vs their respective primary tumors. These results imply a dynamic regulation of ABAT expression throughout cancer progression. As very few studies have directly addressed the role of ABAT in cancer progression, the identification of ABAT transcript expression as a broadly applicable multi-cancer prognostic marker may ultimately benefit a wide variety of patients. We would like to thank the Feist-Weiller Cancer Center and LSU Health, Shreveport for supporting this work. Citation Format: Erika L. Knott, Nancy J. Leidenheimer. Targeted bioinformatics analysis identifies high ABAT transcript expression as a multi-cancer marker of favorable patient prognosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2408.

Abstract 590: Multiplex liquid biopsy for AR pathway activity in metastatic androgen receptor-positive triple negative breast cancer

Abstract Introduction: The androgen receptor (AR) is expressed in up to 50% of patients with triple negative breast cancer (TNBC), and a luminal androgen receptor (LAR) subtype has been identified that is dependent on androgen receptor signaling, but AR protein expression by immunohistochemistry (IHC) has been a suboptimal biomarker for response to anti-androgen therapies in AR-TNBC and there remains an unmet need for biomarkers to identify patients likely to benefit from anti-androgens. We have developed a multiplex liquid biopsy encompassing AR protein expression and downstream gene expression analysis in circulating tumor cells (CTCs). We report here the longitudinal evaluation of this liquid biopsy as part of a phase I trial (NCT03090165) of the anti-androgen bicalutamide with selective CDK4/6 inhibitor ribociclib in metastatic AR-TNBC. Methods: Peripheral blood was collected (n=11) prior to treatment, after two cycles of treatment, and at progression and processed using the VERSA (Versatile Exclusion-based Rare Sample Analysis) microfluidic chip that integrates CTC capture and downstream analysis. For protein expression, fixed CTCs were captured immunomagnetically and stained on chip for AR followed by quantitative fluorescent microscopy. For gene expression analysis, live CTCs were captured immunomagnetically followed by RNA isolation on chip, reverse transcription, and RT-qPCR for a panel of 40 luminal AR genes. Results: AR protein and transcript were detected in CTCs from 10/11 patients, and AR target gene expression in 8/11 patients. The pathologic ligand independent AR splice variant AR-V7 was detected in 2/11 patients. Pretreatment CTC number was higher in patients with anti-androgen resistant (range 3-753) than anti-androgen sensitive (range 0-30) disease. Among patients with low AR IHC (&amp;lt;10%) on biopsy, high AR protein and transcript expression in pre-treatment CTCs was associated with anti-androgen sensitivity. Among patients with high AR IHC (&amp;gt;50%) on biopsy, AR-V7 was detected in CTCs of 2/3 of patients with resistant disease and 0/2 of patients with sensitive disease. Conclusions: This study demonstrates the feasibility of a longitudinal multiplex liquid biopsy as a pharmacodynamic biomarker of AR pathway activity in AR-TNBC, and suggests that AR pathway activity in CTCs may provide additional information to solid tumor biopsy AR expression in predicting sensitivity to anti-androgens. This work also demonstrates for the first time the detection of AR-V7 in CTCs in anti-androgen resistant AR-TNBC, suggesting that AR-V7 expression may be a mechanism of anti-androgen resistance in AR-TNBC as it is in advanced prostate cancer. Citation Format: Marina N. Sharifi, Serena K. Wolfe, Jamie M. Sperger, Jennifer L. Schehr, Saswati Bhattacharya, Kari B. Wisinski, Joshua M. Lang, Ruth M. O'Regan. Multiplex liquid biopsy for AR pathway activity in metastatic androgen receptor-positive triple negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 590.

Mode of action evaluation for reduced reproduction in Daphnia pulex exposed to the insensitive munition, 1-methyl-3-nitro-1-nitroguanidine (MeNQ)

The US Department of Defense (DOD) is developing insensitive munitions (IMs) that are resistant to unintended detonation to protect warfighters. To enable material life-cycle analysis for the IM, 1-methyl-3-nitro-1-nitroguanidine (MeNQ), ecotoxicological impacts assessment was required. A previous investigation of MeNQ exposures in Daphnia pulex revealed concentration-responsive decreases in reproduction relative to controls (0 mg/L) across a 174, 346, 709, 1385, and 2286 mg/L exposure range. The present study used those exposures to conduct global transcriptomic expression analyses to establish hypothetical mode(s) of action underlying inhibited reproduction. The number of significantly affected transcripts and the magnitude of fold-change differences relative to controls tended to increase with increasing MeNQ concentration where hierarchical clustering analysis identified separation among the “low” (174 and 346 mg/L) and “high” (709, 1385, and 2286 mg/L) exposures. Vitellogenin is critical to Daphnia reproductive processes and MeNQ exposures significantly decreased transcriptional expression for vitellogenin-1 precursor at the lowest exposure level (174 mg/L) with benchmark dose (BMD) levels closely tracking concentrations that caused inhibited reproduction. Additionally, juvenile hormone-inducible protein, chorion peroxidase, and high choriolytic enzyme transcriptional expression were impacted by MeNQ exposure having potential implications for egg production / maturation and overall fecundity. In concert with these effects on specific genes involved in Daphnia reproductive physiology, MeNQ exposures caused significant enrichment of several canonical-pathways responsible for metabolism of cellular energy substrates where BMD levels for transcriptional expression were observed at ≤100 mg/L. These observations imply possible effects on whole-organism energy budgets that may also incur indirect costs on reproduction.

CLLU1 Expression Is Not Confined to Chronic Lymphocytic Leukemia Cells; Putative Role of Gene-Body Hypomethylation in Regulating Splice Variant-Specific Transcriptional Dynamics

Background: Alternative splicing of the CLLU1 gene generates 6 transcript variants (accession numbers from the National Center for Biotechnology Information: AJ845162-AJ845167), two of which comprise a putative coding DNA sequence (AJ845165 and AJ845166, CDS transcripts). Previous studies showed that CLLU1 overexpression is highly confined to chronic lymphocytic leukemia (CLL) cells and that only the AJ845162 is expressed in both high- and low-risk CLL patients, while expression of the CDS-transcripts is confined to the high-risk subgroup.Pair-wise linear regression analysis revealed a powerful linear relation between the expression levels of all the splice variants, thereby it was deduced that CLLU1 transcription is orchestrated by a common promoter, which is located upstream of CLLU1 exon 1 (Buhl et al., Leukemia 2009). We recently documented (Papamichos et al., Haematologica 2016; s1) that this promoter was evolutionarily derived by an endogenous retrovirus sequence.Herein we argue that CLLU1 expression is not restricted to CLL cells while also we highlight that transcription of CDS transcripts is regulated by an alternative intronic promoter.Methods:CLLU1 high-throughput sequencing of polyadenylated RNA (RNA-Seq) data across 51 human tissues and 2 human cell lines, generated by the Genotype-Tissue Expression (GTEx) project of the US National Institutes of Health Common Fund (GTEx Analysis Release V6p), were analyzed via GTEx Portal. CLLU1 GeneChip expression data (AJ845164 transcript-specific probe set 1558185_at from Affymetrix GeneChip® Human Genome U133 Plus 2.0 Array), generated by Genevestigator project, were downloaded from Genevisible portal.CLLU1 chromatin immunoprecipitation coupled with high throughput sequencing (ChIP-Seq) on histone H3 protein subunit modified at lysine position 4 with trimethylation (H3K4me3) as well as transcription factor (TF) ChIP-Seq data were downloaded from the Encyclopedia of DNA Elements (ENCODE) Regulation supertrack, which is available in UCSC Genome Browser Database. Data on CLLU1 gene-body methylation status in 63 cell lines from ENCODE were downloaded from the HAIB Methyl450 ENCODE track.Results:CLLU1 GeneChip expression data show that the AJ845164 transcript (corresponding to the RP11-693J15.4 long non-coding RNA) is promiscuously expressed in various normal B-cell subpopulations andin mature B-cell neoplasms other than CLL, especially in mantle cell lymphoma.RNA-Seq data analysis reveals that AJ845162 transcript is expressed in normal somatic tissues such as skeletal muscle, salivary gland, and esophageal mucosa. Vice versa, expression of CLLU1 CDS transcripts is confined to transformed lymphocytes.Structure interrogation of CDS transcripts indicates that these variants initiate from an alternative transcriptional start site which is located 2429 nucleotides downstream from the canonical one. H3K4me3 ChIP-Seq data signify the presence of an alternative intronic promoter in this genomic segment. TF Chip-Seq data reveal that the alternative promoter region comprises high affinity binding sites for signal transducer and activator of transcription 3 (STAT3) and Activator protein 1 (AP-1). Analysis of CLLU1 -body methylation status in five lymphoblastoid cell lines reveals that the alternative promoter remains heavily methylated in these cell types. This finding is in accordance with previous studies reporting that CLLU1 gene body is hypermethylated in B-cells from healthy individuals and in IgVH-mutated (IgVH-M) CLL cases while appears hypomethylated in IgVH-unmutated (IgVH-UM) CLL cells.Conclusion: Not all CLLU1 transcripts are equal in discriminating CLL from other mature B-cell malignancies.Whilst of retroviral origin, CLLU1 upstream promoter is not subjected to stringent epigenetic repression but remains active in somatic cells, a tantalizing finding that warrants further investigation.The level of intragenic DNA methylation represents a decisive regulator of alternative promoter usage (Neri et al., Nature 2017). It would be tantalizing to speculate that CLLU1 -body hypomethylation, occuring exclusively in IgVH-unmutated CLL, is mechanistically linked to the epigenetic derepression of the alternative intronic CLLU1 promoter and the subsequent high expression of CLLU1 CDS transcripts in high-risk CLL. DisclosuresNo relevant conflicts of interest to declare.

Identification and characterization of the SIFamide receptor in the hemimetabolous Chagas disease vector, Rhodnius prolixus Stål, 1859, (Hemiptera, Reduviidae, Triatominae)

Within arthropods, the SIFamide family of neuropeptides appears to be involved in the modulation of a range of physiological and behavioral events. In Rhodnius prolixus, we have previously shown the presence of SIFamidergic-like processes in neurohemal release sites and provided evidence for a role for Rhopr-SIFa in modulating heartbeat frequency and feeding behaviors. Here, the R. prolixus SIFamide receptor (RhoprSIFR) has been identified, cloned, and sequenced. Sequence analyses show high similarity and identity between the RhoprSIFR and other cloned SIFamide receptors. Quantitative PCR shows that the RhoprSIFR transcript is found in a variety of tissues, including those involved in feeding and reproduction. In unfed insects, high transcript expression is observed in the central nervous system and midgut, suggesting a role of Rhopr-SIFa in various processes related to feeding and digestion. Expression of the RhoprSIFR transcript changes between unfed, 24 h post-fed, and 7 d post-fed conditions. Expression of the RhoprSIFR transcript significantly increases in the anterior midgut and posterior midgut 7 d post-feeding and knockdown of the RhoprSIFR transcript significantly reduces the size of blood meal consumed. This data suggests a possible role for Rhopr-SIFa in regulating long-term post-feeding osmotic balance and digestion of the blood meal. Lastly, transcript expression of Rhopr-SIFa and RhoprSIFR also varies temporally in relation to the reproductive stage, suggesting an involvement of this signaling pathway in reproductive activities. Identification of the RhoprSIFR and its expression profile now provide tools for a more detailed understanding into the precise coordination of feeding and other physiological processes in R. prolixus.

Predictive value of transcriptional expression of Krüppel-like factor-6 (KLF6) in head and neck carcinoma patients treated with radiotherapy.

To analyse the relationship between the transcriptional expression of Krüppel-like factor-6 (KLF6) and local response to treatment with radiotherapy in patients with head and neck squamous cell carcinoma (HNSCC). We determined the transcriptional expression of KLF6 in tumour biopsies obtained before treatment with radiotherapy in 83 HNSCC patients. The KLF6 expression was categorized according to the local control of the disease with a recursive partitioning analysis. During the follow-up period, 27 patients (32.5%) had a local recurrence of the tumour. Patients with local recurrence had significantly higher levels of KLF6 expression than patients in which radiotherapy achieved local control of the disease (P = 0.029). Five-year local recurrence-free survival for patients with a high transcriptional expression of KLF6 (n = 46) was 51.1% (95% CI 36.4-66.2%), and for patients with low expression it was 85.6% (95% CI 73.9-97.3%) (P = 0.0001). The results of a multivariate analysis showed that patients with a high KLF6 expression had a 3.8 times higher risk of local recurrence after treatment with radiotherapy (95% CI 1.4-10.5, P = 0.008). Transcriptional expression of KLF6 was significantly related to local control in HNSCC patients treated with radiotherapy. Patients with high levels of KLF6 expression had a significantly higher risk of local recurrence after treatment.

Single‐cell transcriptomic profiling of satellite glial cells in stellate ganglia reveals developmental and functional axial dynamics

Stellate ganglion neurons, important mediators of cardiopulmonary neurotransmission, are surrounded by satellite glial cells (SGCs), which are essential for the function, maintenance, and development of neurons. However, it remains unknown whether SGCs in adult sympathetic ganglia exhibit any functional diversity, and what role this plays in modulating neurotransmission. We performed single-cell RNA sequencing of mouse stellate ganglia (n = 8 animals), focusing on SGCs (n = 11,595 cells). SGCs were identified by high expression of glial-specific transcripts, S100b and Fabp7. Microglia and Schwann cells were identified by expression of C1qa/C1qb/C1qc and Ncmap/Drp2, respectively, and excluded from further analysis. Dimensionality reduction and clustering of SGCs revealed six distinct transcriptomic subtypes, one of which was characterized the expression of pro-inflammatory markers and excluded from further analyses. The transcriptomic profiles and corresponding biochemical pathways of the remaining subtypes were analyzed and compared with published astrocytic transcriptomes. This revealed gradual shifts of developmental and functional pathways across the subtypes, originating from an immature and pluripotent subpopulation into two mature populations of SGCs, characterized by upregulated functional pathways such as cholesterol metabolism. As SGCs aged, these functional pathways were downregulated while genes and pathways associated with cellular stress responses were upregulated. These findings were confirmed and furthered by an unbiased pseudo-time analysis, which revealed two distinct trajectories involving the five subtypes that were studied. These findings demonstrate that SGCs in mouse stellate ganglia exhibit transcriptomic heterogeneity along maturation or differentiation axes. These subpopulations and their unique biochemical properties suggest dynamic physiological adaptations that modulate neuronal function.

Role of PRDM1 in Tumor Immunity and Drug Response: A Pan-Cancer Analysis.

Background: PR domain zinc finger protein 1 (PRDM1) is a regulator of both B cell and T cell differentiation and plays a critical role in immunosuppression. Its role in tumor immunity and correlation with drug response remain unknown. Methods: This work comprehensively analyzed the transcriptional expression pattern of the PRDM1 among 33 types of malignancies from The Cancer Genome Atlas and the Genotype-Tissue Expression projects. Besides, correlation of the PRDM1 with cancer prognosis, immune infiltrates, checkpoint markers, cancer stemness and drug response were explored. Results: High expression level of PRDM1 were observed in ACC, COAD, LAML, LGG, LUAD, OV, PAAD, STAD, TGCT. Cox regression model showed high expression of PRDM1 in tumor samples correlates with poor prognosis in LGG, PAAD, UVM while favorable prognosis in KIRC, SKCM and THCA. PRDM1 expression positively correlates with the expression of LAG3, CTLA4, PDCD1 (PD-1), CD274 (PD-L1), PDCD1LG2 (PD-L2), TIGIT in the majority of 33 cancer types. PRDM1 positively correlated with TNFRSF14 in LGG and UVM among cancers with unfavorable prognosis; this correlation were weak or even negative in cancers with favorable prognosis. The top negatively enriched KEGG terms in high PRDM1 subgroup were B cell receptor signaling, T cell receptor signaling, and the top negatively enriched HALLMARK terms included IL-2-STAT5 signaling and allograft rejection. The expression of PRDM1 was found positively correlated with cancer stemness in CHOL, KIRP, TGCT, THYM and UVM. A series of targeted drugs and small-molecule drugs with promising efficacy predicted by PRDM1 level were identified. Conclusion: The clinical significance and biological impact of high transcriptional expression of PRDM1 differs across different cancers. Inhibiting the PRDM1-dependent signaling could be a novel and promising strategy of immunotherapy in cancers including LGG, PAAD and UVM.