title: Differential prognostic roles of mitochondrial and genomic tRNA-derived fragments in colorectal liver metastases: A retrospective cohort study

city: Vienna

first: Dietmar

last: Pils

address: Spitalgasse 23

department: Dept. of General Surgery

country: Austria

institute: Medical Univ. of Vienna

summary:
Background: Colorectal liver metastases (CRLM) are the leading cause of colorectal cancer (CRC)-related mortality. Transfer RNA-derived fragments (tRFs), a novel class of small non-coding RNAs (sncRNA), regulate gene expression, stress response, and immune functions in cancer. While tRFs are increasingly implicated in CRC progression, their prognostic significance in CRLM remains unknown. This study investigates the abundance and prognostic value of genomic (ge) and mitochondrial (mt) tRFs in CRLM.
Methods: This single-center retrospective cohort study included all CRLM patients who underwent curative liver resection between January 2012 and December 2015. Small RNA sequencing (sRNA-seq) quantified ge- and mt-tRF expression in tumor samples. Event-free survival (EFS) was the primary outcome, and the impact of tRFs on EFS was assessed using Cox regression, spline modeling of the effects of tRFs on EFS, and network analysis.
Results: Among 588 screened samples, 40 met eligibility criteria (18 females [45%], median age 64 [42-79]). A total of 432 tRFs were identified, with ge-tRFs (67%) being more abundant than mt-tRFs (33%). Using spline regressions, tRFs were classified into 10 ten prognostic groups. High ge-tRF abundance correlated predominantly with unfavorable EFS (FDR<0.2; 94%), whereas mt-tRFs were significantly (p<0.001; χ2 test) more often associated with favorable EFS (FDR<0.2; 26%). Network analysis of tRF abundance correlations revealed a significantly higher intra-mitochondrial network density compared to the intra-genomic tRF network. However, no significant differences in network structure were observed between prognostically significant vs. non-significant or favorable vs. unfavorable tRFs. Finally, key tRF candidates, such as tRHalve3-His-CAU (mt-tRF) or tRNAleader-Gln-UUG (mt-tRF) paired with tRFmisc-Tyr-GTA (ge-tRF), remained independent prognostic markers after adjustment for clinical covariates.
Conclusion: This study provides the first comprehensive characterization of tRF expression in CRLM, revealing distinct prognostic roles for ge- and mt-tRFs. While ge-tRFs were predominantly associated with unfavorable prognosis, a subset of mt-tRFs demonstrated a favorable impact on EFS. These findings highlight the potential of tRFs as novel prognostic biomarkers and therapeutic targets in CRLM, warranting validation in prospective studies.

overall_design: From 40 macrodissected FFPE CRLM tissue samples, small RNAs was isolated and small RNA sequencing performed.

first: Rebecca

last: Zirnbauer

first: Johannes

last: Längle


title: Characterization of ALDH2-deficient alcohol-associated liver disease (duodenum RNA seq)

status: Public on Jul 16 2025

city: Rockville

first: Yukun

last: Guan

state: MD

address: 5625 Fishers Lane, Room 2S-30

country: USA

institute: NIAAA

type: Expression profiling by high throughput sequencing

summary: Aldehyde dehydrogenase 2 (ALDH2) is a key enzyme to detoxify the ethanol first metabolite acetaldehyde. Approximately 8% world population have inactive ALDH2 and have facial flushing due to high levels of acetaldehyde after alcohol consumption. Alcohol-associated liver disease (ALD) and hepatocellular carcinoma (HCC) in those with inactive ALDH2 have not been characterized. ALD pathogeneses in these individuals are likely very different from those with normal ALDH2, different diagnosis criteria and treatment are required for these two populations. Here we studied ALD in inactive Aldh2 knockin (Aldh2KI) mice with chronic ethanol feeding.

overall_design: Male C57BL/6N and Aldh2KI mice aged 8 weeks were subjected to 1) Control diet for 8 weeks, 2) 2.5% ethanol diet for 8 weeks and gavaged with 2 g/kg ethanol twice per week (referred to as half diet), 3) 5% ethanol diet for 8 weeks and gavaged with 4 g/kg ethanol twice per week (referred to as full diet). Mice were euthanized 9 hours after the last ethanol gavage with an ethanol dose of 5 g/kg. Total RNA was extracted from duodenum using Trizol (Alkali Scientific, Fort Lauderdale, FL) and subjected to RNA seq.

last: GUAN

first: Bin

last: GAO


title: Single-cell transcriptomic profile of LAM/AML cell model exposed to hydrocortisone

city: L'Hospitalet del llobregat

first: Miquel Angel

last: Pujana

state: Barcelona

address: Gran via 199, Hospital Duran i Reynals

department: ProCURE

country: Spain

institute: Catalan Institute of Oncology IDIBELL

summary: scRNA-seq profiling of TSC2-deficient 621-101 human angiomyolipoma cells exposed to hydrocortisone or DMSO.

overall_design: scRNA-seq profiling of TSC2-deficient 621-101 cells cultured under basal conditions or treated with hydrocortisone.

first: Roderic

last: Espín


title: RNAseq of CD4 T cells treated with Insulin for 48 hours

city: Gothenburg

first: Maria

middle: I

last: Bokarewa

state: VG

address: Guldhedagatan 10A

department: Rheumatology and Inflammation Research

country: Sweden

institute: Gothenburg University

summary: RNAseq of CD4 cells from 6 healthy men. Cells were activated with anti-CD3 and treated with Insulin, 10 nM, for 48 hours.

overall_design: CD4 cells from PBMC from 6 healthy men, isolated by positive selection on Dynabeads (cat.11331D), stimulated with anti-CD3 (OKT3, Sigma-Aldrich) with addition of Insulin, 10nM or control for 48h

first: Karin

middle: M

last: Andersson

first: Malin

middle: C

last: Erlandsson

first: Eric

last: Malmhäll-Bah


title: Non-canonical ALK7 pathways promote pancreatic cancer metastasis through β-catenin/MMP-mediated basement membrane breakdown and intravasation

city: Gangneung

first: Yujin

last: Kwon

country: South Korea

institute: Korea Institute of Science and Technology

summary: Breaching the vascular barrier is a critical step in pancreatic ductal adenocarcinoma (PDAC) metastasis, yet the mechanisms enabling this process to remain incompletely understood. This study identifies two distinct but interconnected ALK7-driven non-canonical pathways that promote PDAC dissemination. The ALK7–β-catenin–EMT axis enhances intrinsic tumor cell motility, driving epithelial–mesenchymal transition (EMT) and cytoskeletal remodeling. In parallel, the ALK7–β-catenin–MMP axis facilitates metastatic invasion by upregulating MMP production, leading to ECM degradation and invadosome formation, which promote vascular barrier breakdown. An orthotopic PDAC metastasis model reveals that both pharmacological and genetic ALK7 inhibition suppresses lung metastasis, emphasizing its role in facilitating tumor invasion. A 3D microfluidic vessel-on-chip platform further demonstrates that ALK7 inhibition preserves basement membrane (BM) integrity, limiting intravasation without affecting extravasation. While MMP inhibition effectively blocks BM breakdown and intravasation, extravasation remains unaffected, highlighting distinct molecular requirements for different metastatic stages. These findings establish ALK7 as a dual-function pro-metastatic regulator that orchestrates both tumor cell plasticity and ECM remodeling, positioning ALK7 inhibition as a promising strategy to target early metastatic dissemination in PDAC.

overall_design:
To minimize the risk and determine the exact roles of ALK7 in PDAC cells, we performed short hairpin RNA (shRNA) mediated ALK7 knockdown (KD) in PDAC cells prior to inoculating them into animals.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells.
Comparative gene expression profiling analysis of RNA-seq data for PDAC cells and its KD derivative shALK7

first: Won Kyu

last: Kim

first: Esak

last: Lee

first: Anna

last: Kolarzyk


title: Effect of RIPK2 knockdown on U118 cells related behavior

city: chongqing

first: Xue

last: Zhang

address: 2 Chongwen Road, Nanan District, Chongqing

country: China

institute: Chongqing University of Posts and Telecommunications

summary: IFN-Ⅰ plays an important role in the progression of LGG. We used a set of genes from MsigDB associated with interferon alpha responses, bioinformatic screening based on public databases, and validation of internal and external data to obtain relevant biomarkers. Immunohistochemical results of clinical samples showed that the higher the grade of glioma, the higher the expression of RIPK2 gene. Subsequently, U118 knockdown RIPK2 cell line was constructed, and the knockdown group could inhibit the proliferation of tumor cells and promote apoptosis. RNA-seq sequencing results showed that, compared with the control group, GO enrichment analysis showed that the differential genes were mainly concentrated in bioregulatory and molecular function related pathways such as ion gated channel activity and cell adhesion, and KEGG enrichment analysis showed that, Genes were mainly enriched in inflammatory pathways such as NF-kappa B signaling pathway, TNF signaling pathway and IL17 signaling pathway.

overall_design: RNA-seq profiling of wildtype U118 cells and their knockdown derivatives (siRIPK2_1, siRIPK2_2, siRIPK2_3,  siRIPK2_4) at Day2 of siRNA transfection

first: Shuo

last: Song

first: Defen

last: Zhou

first: Hanwei

last: Cui

first: Jiangan

last: Xie


title: IgSF11 cooperates with RAP1 to promote cell migration and invasion of cutaneous melanoma

city: Fukushima

first: Yasuyuki

last: Kobayashi

state: Fukushima

address: Hikarigaoka 1

country: Japan

institute: Fukushima medical university

summary: IgSF11 is a member of the immunoglobulin superfamily and is homologous to the Junction Adhesion Molecule (JAM) family. IgSF11 is expressed exclusively in the testis and central nervous system in normal adult tissues. On the other hand, ectopic expression of IgSF11 at the mRNA level has been detected in several malignant tumors, including malignant melanoma. However, the lack of highly specific antibodies has prevented functional analysis of IgSF11 in cancer. In this study, we developed a specific monoclonal antibody against IgSF11 and evaluated the IgSF11 expression of malignant melanoma cases at the protein level by immunohistochemistry. As a result, more than half of the cases showed high expression of IgSF11. In this presentation, we will show the clinical significance of IgSF11 and its molecular function in malignant melanoma cell lines.

overall_design: RNA-seq analysis was performed using wild-type and IgSF11-over expression or IgSF11-knockout melanoma cell lines (A375 and 888mel).

first: Yasuyuk

last: i Kobayashi

first: Kotaro

last: Sugimoto

first: Minaka

last: Ishibashi

first: Makoto

first: Shohei

last: Igari

first: Shigeki

last: Kitamura

first: Toshiyuki

last: Yamamoto

first: Yuko

last: Hashimoto

first: Hideki

last: Chiba


title: Transcriptomic analysis of severe allergic patch test reactions to different allergens (nickel, 2-hydroxyethylmethacrylate, methylisothiazolinone and formaldehyde)

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

institute: Hospital del Mar Research Institute

summary: Background: Immune mechanisms underlying elicitation in allergic contact dermatitis (ACD) are not disclosed. Previous studies have shown a double-faceted nature of ACD with both common biomarkers between different allergens, as well as allergen-specific imprinting, with discordance in terms of relevant involved immune pathways.  Objectives: To characterize molecular signatures and their immune mechanisms between different relevant allergens (nickel, 2-hydroxyethylmethacrylate (2-HEMA), methylisothiazolinone (MI), formaldehyde) in strong and extreme patch test reactions of patients without atopic dermatitis using RNA sequencing.

overall_design: Samples: 60 (19 controls, 9 "formaldehyde", 10 "2-hydroxyethylmethacrylate", 10 "methylisotiazolinone", 11 "nickel"). RNAseq

first: David

last: Pesqué

first: Ramon

last: Pujol

first: Ana

last: Giménez-Arnau


title: Periplocin Targets HDAC10 to Inhibit NF-κB Signaling and Induce Apoptosis in Myeloid Leukemia Cells

city: Shenzhen

first: Wenjie

last: Li

address: 3025 Shennan Middle Road

department: Department of Hematology

institute: Sun Yat-sen University

summary:
Background: Periplocin, a bioactive compound extracted from Cortex periplocae, has long been employed in traditional medicine for its diverse therapeutic effects, particularly in alleviating inflammation and inhibiting cancer progression. However, despite its potential benefits, the underlying molecular mechanisms of periplocin, especially in the context of leukemia treatment, remain poorly elucidated, warranting further investigation to uncover its precise role and therapeutic targets.
Methods: A comprehensive approach combining network pharmacology and transcriptomic analysis was utilized to identify HDAC10 as a critical downstream target of periplocin. Molecular docking and dynamic simulation studies were performed to elucidate the interaction between periplocin and HDAC10 at the molecular level. Additionally, functional assays, including apoptosis induction, cell cycle regulation, and pathway inhibition experiments, were conducted to validate the mechanistic role of HDAC10 and its relevance to periplocin's anti-leukemic effects.
Results: Periplocin was identified as an effective inhibitor of HDAC10, binding specifically to its hydrophobic active pocket and suppressing its enzymatic activity. This inhibition disrupted downstream signaling, particularly the NF-κB pathway, leading to significant apoptosis and cell cycle arrest in leukemia cells. These results therapy, offering insights into its mechanism of action through HDAC10 targeting.
Conclusion: In conclusion, periplocin, as a novel natural compound, exhibits significant anti-leukemia activity, highlighting its potential as a promising therapeutic candidate for leukemia treatment. The findings contribute to the growing interest in natural compounds as innovative solutions for addressing unmet clinical needs in hematological malignancies.

overall_design: RNA seq of  Human K562 and THP Cells in control and experiment Peri drug group


title: Integrating metabolomic and transcriptomic to reveal the dynamics of ntramuscular fat in chicken meat

city: Yinchuan

first: Wei

last: Zhao

state: Ningxia Huizu Zizhiqu

address: 489 Ningxia University, Xixia district, Yinchuan , China

institute: Ningxia university

summary: In this study, we investigated the dynamic changes of intramuscular fat (IMF) deposition in the breast muscle of Jingyuan chickens at different stages (42-, 126- and 180-day-old) using metabolomics. pH45min, a*, and L* were significantly increased in the breast muscle of 126-day-old chickens, and IMF content and b* were significantly increased in the breast muscle of 180-day-old chickens. A total of 4,643 differentially expressed metabolites (DEMs) were identified, of which 10 decreased and 29 increased with age. Key pathways associated with meat quality included oxidative phosphorylation, β-alanine metabolism, and glycerophospholipid metabolism. Combined transcriptomic and phenotypic correlation analyses revealed significant positive correlations of IMF, pH45min, a*, and L* with LysoPC 20:4, CD3E, TARP, IL7R, ENSGALG00010025331, and RASSF5. In the 42- and 180-day-old chickens, IMF, pH45min, a*, and L* were significantly and positively correlated with L-Anserine, Dihydroxyacetone phosphate, ENSGALG00010006904, and HSPB7. IMF, pH45min, a*, and L* were significantly and positively correlated with beta-Nicotinamide adenine dinucleotide in the 126- and 180-day-old. This study deepens our understanding of the differences in IMF deposition at different stages of Jingyuan chickens and its relationship with meat quality.

overall_design: A total of 300 1-day-old Jingyuan chicks were reared at the Jingyuan Chicken National Breeding Farm (Panyang County, China) using standardized temperature and humidity. All chicks were always fed and watered ad libitum under the same conditions. Group B1 was slaughtered at 42 days of age (0.422 ± 0.03 kg), Group B2 was slaughtered at 126 days (1.68 ± 0.14 kg), and Group B3 was slaughtered at 180 days (2.03 ± 0.09 kg). After rendering the hens unconscious with ether respiratory anesthetic, we severed their carotid arteries to end their lives. The remaining breast muscles were snap-frozen in liquid nitrogen and kept in a refrigerator at -80 °C after whole muscles were gathered for the purpose of determining the quality of the meat. Subsequently, 30 hens of consistent weight were chosen from each age group, and the transcriptome and non-targeted metabolome sequencing were performed on their breast muscles.


title: Translational activators align mitochondrial mRNAs at the small ribosomal subunit for translation initiation

city: Boston

first: Mary

middle: T

last: Couvillion

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: Mitochondrial gene expression is essential for oxidative phosphorylation. Mitochondrial-encoded mRNAs are translated by dedicated mitochondrial ribosomes (mitoribosomes), whose regulation remains elusive. In the baker´s yeast Saccharomyces cerevisiae, nuclear-encoded mitochondrial translational activators (TAs) facilitate transcript-specific translation by a yet unknown mechanism. Here, we investigated the function of TAs containing RNA-binding pentatricopeptide repeats (PPRs) using selective mitoribosome profiling and cryo-EM structural analysis. These analyses revealed that TAs exhibit strong selectivity for mitoribosomes initiating on their target transcripts. Moreover, TA-mitoribosome footprints indicated that TAs recruit mitoribosomes proximal to the start codon. Two cryo-EM structures of mRNA-TA complexes bound to post-initiation/pre-elongation-stalled mitoribosomes revealed the general mechanism of TA action. Specifically, the TAs bind to structural elements in the 5' UTR of the client mRNA as well as to the mRNA exit channel to align the mRNA in the small subunit during initiation. Our findings provide a structural basis for understanding how mitochondria achieve transcript-specific translation initiation without relying on general sequence elements to position ribosomes at start codons.

overall_design: Mitochondrial selective ribosome profiling of translational activators and related factors in S. cerevisiae cells

first: Joseph

last: Bridgers

first: Andreas

last: Carlstrom

first: Dawafuti

last: Sherpa

first: Jingjing

last: Gao

first: Bowen

last: Wan

first: Sichen

last: Shao

first: Martin

last: Ott

first: Stirling

last: Churchman


title: Coupling tRNAGly gene redundancy with staphylococcal cell wall integrity, antibiotic susceptibility and virulence potential

city: Patras

first: Adamantia

last: Kouvela

address: Asklipiou 1

country: Greece

institute: Department of Biochemistry, School of Medicine, University of Patras

type: Non-coding RNA profiling by high throughput sequencing

summary: Redundancy in the number of tRNA genes which occur across species is poorly understood and, in many cases, remains essentially unexplored. In Staphylococcus aureus, several tRNAGly genes encode isoacceptors that either participate in protein synthesis or cell wall formation, upon aminoacylation by the sole glycyl-tRNA synthetase (GlyRS). Transcription of GlyRS, is regulated by a glyS T-box riboswitch in the 5’UTR, which responds to all tRNAGly isoacceptors and exhibits species-specific RNA conformations. To address whether disruption of the tRNAGly expression impacts the balance between ribosomal translation and cell wall formation, we used CRISPR/Cas9 editing to ablate one proteinogenic tRNAGly gene copy which is the strongest ligand of the glyS T-box riboswitch. Interestingly, no discernible impact on the growth and general translational activity of S. aureus was observed, suggesting that the remaining tRNAs could make up for this deficiency. However, transcriptomics and proteomics analyses revealed that the edited strain had deficient cell wall integrity, and subsequent experimentation showed increased susceptibility to antibiotics targeting the cell wall and resistance to lysostaphin. Interestingly, the observed alteration in the proteome level were independent of the glycine codon usage. Moreover, the edited strain exhibited reduced biofilm formation but retained its ability to invade human cell cultures. Overall, the present study highlights the important role of tRNA gene copy redundancy in the physiology of an important pathogen like S. aureus and consolidates the regulatory role of tRNAs in metabolic homeostasis.

overall_design: Expression profiling by the Ion Torrent Genestudio S5 platform with Ion Chef (Ion torrent) and Illumina NextSeq 1000 platform.

first: Jose R

last: Jaramillo-Ponce

first: Nikoleta

last: Giarimoglou

first: Stefano

last: Marzi

first: Constantinos

last: Stathopoulos

first: Vassiliki

last: Stamatopoulou


title: Small RNA Sequencing of Exosomal miRNA from HFD and LFD Plasma Samples

first: Gerald

middle: V

last: Denis

address: 72 East Concord Street

institute: Boston University

summary: This study investigates the differential expression of small RNAs, including miRNAs, in exosomes derived from high-fat diet (HFD) and low-fat diet (LFD) plasma samples.Exosomal RNA was purified and sequenced using small RNA-seq to reveal distinct miRNA profiles influenced by metabolic conditions.

overall_design: Exosomes were isolated from plasma samples of mice fed HFD or LFD. Exosomal RNA was extracted, and small RNAs (25-200 nt) were sequenced using the Illumina platform.

first: Andrew

last: Chen

first: Pablo

last: Llevenes


title: Culture Media and Serum Conditions Alter Primary Human Macrophage Morphology and Inflammatory Function

city: OMAHA

first: Meng

last: Niu

state: NE

address: 42nd and Emile

department: Department of Neurological sciences

institute: University of Nebraska Medical Center

summary: Macrophages are central to innate immunity and defining the mechanisms by which these cells mediate inflammation is critical to understanding in situ homeostatic and pathophysiologic roles. Human monocyte derived macrophages (hMDM) are widely used to examine these processes. Stimuli that influence macrophage function could influence these studies, including differences in culture environment that have been suggested significantly impact macrophage function. We examined baseline hMDM activity and the response to the TLR4 agonist, lipopolysaccharide (LPS) in different culture media in the presence and absence of serum. We focused on the most common macrophage medias, DMEM and RPMI 1640 Medium +/- fetal bovine serum (FBS), as well as Macrophage Serum Free Media (M-SFM), a media specifically formulated for serum free culture. Cells cultured in these five distinct media were treated with vehicle (H20) or LPS and evaluated for changes in morphology, transcriptomic profile, and alterations in inflammatory response. Culture in M-SFM resulted in the greatest morphological differences (area, length-to-width, perimeter-to-area ratio) and while there were few transcriptomic differences between DMEM and RPMI with FBS, both the absence of FBS supplementation and culture in M-SFM significantly altered the baseline transcriptome. Culture in M-SFM also significantly reduced macrophage sensitivity to LPS as measured by NF-kB activation. All hMDM conditions showed a dose dependent phagocytic response and elicited cytokine and chemokine secretion in response to LPS stimulation, but the magnitude of these effects varied between conditions, with different trends depending on the cytokine. These findings suggest that culture media and the presence of serum alters baseline activation and the response to stimulus in macrophages, potentially obscuring or driving artifactual results. These studies confirm and expand on previous findings showing that in vitro microenvironment is not a benign component of experimental design and demonstrate the need to optimize experimental conditions for such plastic cells.

overall_design: Human monocyte derived macrophages from 5 human donors cultured in vitro with culture medias varying in serum supplementation were untreated or stimulated with dopamine for 3hours.

first: Breana

last: Channer

first: Marzieh

last: Daniali

first: Lexi

last: Sheldon

first: Katy

last: Emanuel

first: Yash

last: Agarwal

first: Brian

last: Murphy

first: Will

last: Dampier

first: Howard

middle: S

last: Fox

first: Peter

middle: J

last: Gaskill


title: Effects of dCas9-demethylase chimeras in vivo

city: Providence

first: Alexey

last: Fedulov

state: Rhode Island

address: 593 Eddy St.

department: RIH / Surgical Research

institute: Alpert Medical School of Brown University

summary: Gene expression profiling of transcriptional response to interferon stimulation after dCas9/gRNA -based demethylases.

overall_design: Mice were treated with dCas9 demethylases premixed with a set of gRNAs, followed by gamma-interferon exposure. Lung epithelial cells were isolated and total RNA was obtained for profiling.

first: Naohiro

last: Yano


title: Gene expression profile of colorectal carcinoma HT29 PARP13 KO cells cultivated in 2D or 3D cell culture models

city: Vilnius

first: Rimvile

last: Prokarenkaite

address: Santariskiu st 1

country: Lithuania

institute: National Cancer Institute

summary: Among the key players in the DDR networks are members of the 17 PARP (poly-ADP-ribose polymerase) protein family. Beyond their involvement in various biological processes - such as transcription control, cell death, and inflammation – some PARPs specifically contribute to attracting repair proteins to sites of DNA damage. PARP1 and PARP2, the most well-studied members, act as DNA damage sensors and signal transducers synthesizing poly-ADP-ribose chains that recruits DNA repair factors and can remodel chromatin structure around damaged DNA. In addition to the well-characterized PARPs, other members of this family hold promise for cancer therapeutic applications as they are also involved in the DNA damage response. In the present study, we investigated PARP13-dependent changes in gene expression in colorectal carcinoma HT29 cell lines. Agilent microarray technology was used to analyze gene expression levels in cells cultured under 2D and 3D culture conditions. The results of our study demonstrate the pivotal role of PARP13 in the immune response and the potential for using this target for therapeutic purposes. The profile of differentially expressed genes identified in the present study could be used for further development of diagnostic and therapeutic applications in CRC.

overall_design: The transcriptome of HT29 PARP13 KO cells was evaluated in comparison to the transcriptome of wt cells. RNA was harvested from HT29 colorectal cancer cells cultured under 2D and 3D cell culture conditions for 48 hours.

first: Vaidotas

last: Stankevicius

first: Kestutis

last: Suziedelis


title: Knockout of thyroid hormone receptor alpha a (thraa) enhances cardiac regeneration in zebrafish through metabolic and hypoxic regulation

city: Shatin

first: Man Yee

last: CHEUNG

address: Lo Kwee-Seong Integrated Biomedical Sciences  Building, Area 39

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: Thyroid hormone (TH) serves as a master regulator in our body, governing body metabolism and growth. Circulating TH level has been demonstrated to correlate with cardiac regenerative potential by modulating cell-cycle arrest and polyploidization in cardiomyocytes (CMs), while the molecular mechanism is still unknown. Here, we investigated the molecular mechanisms of TH signalling on heart regeneration through a time-course sequencing experiment. We disrupted the TH signalling in a zebrafish model by thyroid hormone receptor alpha a (thraa) knockout (KO). The thraa-KO zebrafish demonstrated an accelerated heart regenerative process, indicating that TH through thyroid hormone receptors (TRs) impaired heart regeneration. Our study discovered that diminished TH signalling in thraa-KO zebrafish alters the pro-inflammatory response and the regenerative process of cardiac tissue through myocardial metabolic switch. Moreover, TH signalling was shown to modulate the restoration of hypoxic response via hif3a. Altogether, our study highlighted that the role of TH signalling in modulating the progress of heart regeneration in zebrafish.

overall_design: We designed a time-course RNA-seq experiments to study the heart regeneration process in zebrafish. We utilized apex amputation as an approach to study heart regeneration. Apex or injured zone tissue of both WT and thraa+/- were collected in uninjured state, 8 hpi, 1 dpi , 3 dpi , 7 dpi, and 15 dpi for RNA-seq. Additionally, we sequenced the entire hearts of both WT and thraa-/- to investigate transcriptomic differences in heart development.

first: Chunmei

last: Jiang

first: ManYee

last: Cheung


title: CDK2 knockdown in prostate cancer cell lines

city: Ann Arbor

first: Karan

last: Bedi

state: MI

address: 1600 Huron Pkwy

department: Biostatistics

institute: University of Michigan

summary: CDK2 is a cyclin-dependent kinase involved in regulating cell cycle progression. In prostate cancer, CDK2 has been shown to be associated with poor survival. We sought to identify key genes and molecular pathways regulated by CDK2 in prostate cancer. We therefore knocked down CDK2 using siRNA in PC3 and ResA cell lines, and performed RNA-seq.

overall_design: PC3 and ResA cell lines were transfected with non-targeting control siRNA or siRNA targeting CDK2 in biological triplicates for 96hours.

first: Joel

middle: A

last: Yates

first: Ya-Mei

last: Hu

first: Anbarasu

last: Kumaraswamy

first: Zheng

last: Xia

first: Joshi

last: Alumkal


title: Plasma Exosomes in Insulin Resistant Obesity Exacerbate Progression of Triple Negative Breast Cancer

first: Gerald

last: Denis

summary: This dataset includes mRNA sequencing data obtained from cells treated with plasma-derived exosomes from mice fed high-fat (HFD) or low-fat (LFD) diets. RNA was extracted and sequenced to investigate differential gene expression and associated biological pathways. The aim of the study is to elucidate how metabolic dysregulation in obesity influences exosome-mediated gene expression changes, contributing to cancer aggressiveness. Data include raw and processed mRNA sequencing files from triplicates for each condition.

overall_design: Cells were treated with plasma-derived exosomes from HFD- or LFD-fed mice. Total RNA was extracted using the RNeasy Plus Mini Kit (QIAGEN, Cat. No. 74136) following the manufacturer’s instructions. Sequencing libraries were prepared and sequenced using the Illumina platform to produce paired-end reads. Data were processed using the nf-core RNA-seq pipeline, and differential expression was analyzed using DESeq2. Low-expressed genes (fewer than 3 reads per million in at least 3 samples) were filtered out, and data were normalized for library size differences. Differentially expressed genes (DEGs) were analyzed for pathway enrichment using Gene Ontology (GO) and further correlated with survival outcomes in breast cancer patients from The Cancer Genome Atlas (TCGA). Survival analysis was conducted using Cox proportional hazards models.

first: Andrew

last: Chen

first: Pablo

last: Llevenes


title: Strain-Specific Variation in the Complement Resistome of Pseudomonas aeruginosa

city: Grenoble

first: Manon

last: Janet-Maitre

address: 71 Avenue des Martyrs

country: France

institute: IBS

summary: Determination of molecular factors involved in P. aeruginosa survival to human plasma by Tn-seq performed in 3 strains of P. aeruginosa

overall_design: Tn-seq analysis of transposon insertion mutants enriched in plasma compared to heat inactivated plasma in Pseudomonas aeruginosa strains CHA, YIK and PA14, in biological duplicates

first: Ina

last: Attrée


title: Single-nuclei profiling of aged liver tissue from mice

city: New York

first: Genomics-core-facility

last: WCM

state: NY

address: 1300 York Ave.

institute: Weill Cornell Medicine

summary: The liver undergoes a slower aging process compared to other organs owing to its unique regenerative ability. Mammalian liver aging commonly manifests as impaired metabolic performance, reduced organ volume and blood/bile flow, altered cellular and organelle composition, and delayed regenerative ability after toxic insults. Although aging-induced degenerative changes in liver structure and function are not necessarily pathologic, these are associated with an increased risk and susceptibility to chronic liver diseases. However, little is known about the molecular mechanisms driving the morphological changes and functional decline of the aging liver. For an unbiased characterization of aging-driven changes in major cell types of the liver, we employed single-nucleus RNA sequencing (snRNA-seq). A total of 41,568 nuclei isolated from young and aged livers reflected the expected cell diversity of the liver. Analysis of the snRNA-seq dataset revealed that aged livers had altered percentages of hepatocytes across all zones and that aged hepatocytes were associated with zone-specific alterations in expression of genes involved in aging, senescence, and inflammation.

overall_design: Nuclei isolated from freshly frozen livers of young (2-month-old) and aged (30-month-old) mice were analyzed using single nuclei RNA sequencing

first: Saloni

last: Sinha

first: Duc-Huy

last: Nguyen

first: Robert

middle: E

last: Schwartz


title: Characterization of off-target effects of a first-in-class EGFR-directed KRAS G12V selective inhibitor, EFTX-G12V, in SKCO1 cells.

city: Chapel Hill

first: Alessandro

last: Porrello

state: NC

address: 450 West Drive

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: Despite KRAS-G12V being the second most common KRAS mutation in cancer, there are no approved direct KRAS-G12V inhibitors. Difficulties with inhibiting oncogenes using conventional approaches have prompted the use of RNAi as a therapeutic approach. RNAi has faced numerous obstacles as a cancer therapeutic, including the lack of cancer-specific tissue targeting, rapid oligonucleotide nuclease degradation and clearance from the circulation. Recently, the use of targetable ligands conjugated to chemically modified siRNAs has shown remarkable promise in circumventing these barriers. We demonstrate that EFTX-G12V is highly selective for KRAS-G12V and has improved therapeutic activity over pan-KRAS targeting, including enhanced inhibition of several cancer hallmarks. With a novel RNAi delivery platform, we demonstrate tumor silencing of KRAS-G12V and significant anti-tumor activity across several cancer models. Our findings represent a technologic advance in oncogene targeting using RNAi and reveal new biologic insights in KRAS targeting that may have broad implications with regards to safety and efficacy. This dataset collects the RNA-Seq data for the SKCO1 cell line.

overall_design: To evaluate off-target effects of a KRAS G12V-selective siRNA, EFTX-G12V, we assessed gene expression changes in SKCO1 colorectal cancer cells, which are KRAS-G12V mutant, 24 hours after transfection with siRNAs.

first: Chad

last: Pecot


title: Transcriptional effects of a first-in-class EGFR-directed KRAS G12V selective inhibitor, EFTX-G12V, on H441 cells.

summary: Despite KRAS-G12V being the second most common KRAS mutation in cancer, there are no approved direct KRAS-G12V inhibitors. Difficulties with inhibiting oncogenes using conventional approaches have prompted the use of RNAi as a therapeutic approach. RNAi has faced numerous obstacles as a cancer therapeutic, including the lack of cancer-specific tissue targeting, rapid oligonucleotide nuclease degradation and clearance from the circulation. Recently, the use of targetable ligands conjugated to chemically modified siRNAs has shown remarkable promise in circumventing these barriers. We demonstrate that EFTX-G12V is highly selective for KRAS-G12V and has improved therapeutic activity over pan-KRAS targeting, including enhanced inhibition of several cancer hallmarks. With a novel RNAi delivery platform, we demonstrate tumor silencing of KRAS-G12V and significant anti-tumor activity across several cancer models. Our findings represent a technologic advance in oncogene targeting using RNAi and reveal new biologic insights in KRAS targeting that may have broad implications with regards to safety and efficacy. This dataset collects the RNA-Seq data for the H441 cell line.

overall_design: To evaluate the transcriptional effect of mutant-selective versus pan-KRAS targeting, we used RNA-sequencing analyses of a KRAS G12V mutant cell lines, H441, 48 hours after siRNA transfection. We performed differential gene expression analysis comparing H441 cells transfected with control siRNA vs. pan-KRAS targeting siRNA and vs. G12V-specific siRNA (EFTX-G12V). We completed our assessments with gene-set based analyses using the same experimental groups (control, pan-KRAS, and EFTX-G12V).


title: Transcriptome sequencing of control and carbon tetrachloride treated mouse heart tissue

city: Hefei

first: He

last: Sun

state: Anhui province

address: No. 678, Furong Road, Shushan District

department: Department of Cardiothoracic Surgery

institute: The Second Affiliated Hospital of Anhui Medical University

summary: The heart is associated with a variety of organs, including the liver, especially under pathological conditions. In clinical practice, it has been observed that some patients with liver cirrhosis are accompanied by cardiac fibrosis and decreased cardiac function, which affects the prognosis of patients and has research significance.

overall_design: To investigate the underlying mechanism of liver cirrhosis on cardiac function, carbon tetrachloride (CCL4) was used to establish an animal model in C57BL/6J mice. Mice were divided into Control group and CCL4 group, with 6 mice in each group. At the end of modeling, the heart tissues of mice were collected for sequencing.

first: Kai

last: Song

first: Hui

last: Tao


title: Loss of pulmonary tissue protection promotes severe Aspergillus fumigatus infection during Influenza A Virus

city: Grand Forks

last: Guo

state: ND

address: 1301 N Columbia Rd Stop 9037

institute: University of North Dakota

summary: Invasive pulmonary aspergillosis (IPA) is a severe fungal disease caused by Aspergillus spp. (particularly A. fumigatus or Af) that may spread hematogenously to extrapulmonary organs. IPA is typically associated with a broad spectrum of immunocompromised conditions and immunologic disorders and constitutes a high mortality rate. While the association of influenza as a risk for secondary bacterial infections is well appreciated, emerging evidence indicates that influenza-hospitalized patients demonstrate increased susceptibility to severe aspergillosis infection. In this study, we developed a murine Influenza A Virus (IAV)-Af co-infection model and investigated the role of IAV host response in promoting severe Af infection. Our data show that in a co-infection setting, while IAV suppresses Af-induced CXCL1 and early neutrophil recruitment, no defects in neutrophil phagocytic responses were observed. On the contrary, despite similar fungal burdens and conidial germination between single Af and co-infected lungs, there was greater fungal invasiveness in the early phase of IAV-Af co-infection. These findings suggest that enhanced lung inflammation, vascular injury, and loss of tissue protection in IAV-infecetd lung likely contribute to severe secondary Af infection.

overall_design: We infected age-matched male and female C57BL/6 mice with a sublethal dose of 250 PFUs of IAV (PR8). The IAV-infected mice were co-infected seven days later with  Af resting conidia (strain NIH 5233). Co-infection with conidia resulted in approximately 70% mortality in co-infected mice, compared to nearly sublethal outcomes with single Af or IAV infections

first: Nadeem

last: Khan


title: Comparative single-cell analyses reveal evolutionary repurposing of a conserved gene program in bat wing development [RNAseq]

city: Berlin

first: Christian

middle: A.

last: Feregrino

address: Ihnestraße 63

country: Germany

institute: MPI - Molecular Genetics

summary: Bats (order Chiroptera) are the only mammals capable of self-powered flight. Unlike in humans and mice, digits II-V in the bat forelimb are not separated but connected by the chiropatagium, an elastic membrane that forms the wing. The molecular underpinnings of these morphological differences, one of the most striking adaptations in mammalian evolution, remain obscure. Here, we use a suite of omics tools and single-cell analyses to compare the development of fore- and hindlimbs, in bat and mouse. We demonstrate a clear conservation of cell states and processes between species, even at the level of apoptosis, a mechanism that removes the tissue between the digits. To trace down the cellular origin of the persistent interdigital cells in bats, we micro-dissected the embryonic chiropatagium and performed single-cell transcriptomics. We found that the chiropatagium cells develop from fibroblasts populations, and independently from the apoptosis-related retinoic acid signaling cells of the interdigital mesenchyme. These cells from the distal part of the limb repurpose a gene program otherwise only present in proximal cells. Epigenomic and gene network analyses revealed two transcription factors, MEIS2 and TBX3, among the most prominent regulators of this gene program. Transgenic ectopic expression of MEIS2 and TBX3 in interdigital cells of mice resulted in the activation of genes associated with bat wing processes. Major morphological changes in these mutants include an increase in autopod volume, extracellular matrix and the partial retention of interdigital tissue with fusion (syndactyly) of digits. Our results elucidate fundamental molecular mechanisms of wing formation in bats. More generally, we illustrate that the repurposing of existing developmental programs is an evolutionary molecular mechanism to generate morphological novelties.

sample_organism:
Mus musculus
Carollia perspicillata

platform_organism:
Mus musculus
Carollia perspicillata

overall_design: We generated RNA-seq files of distally dissected bat and mouse embryonic limbs to investigate gene expression signatures in these tissues and compare them between species. We furthermore validated our transgenic expression constructs with RNA-seq from distally dissected forelimbs of mutant embryos.

first: Magdalena

last: Schindler

first: Anna

last: Monaco


title: Comparative single-cell analyses reveal evolutionary repurposing of a conserved gene program in bat wing development [HiC]

overall_design: We generated HiC data from bat embryonic fibroblasts and bat forelimbs to determine gene regulatory domains and investigate their epigenetic profiles.

first: Bai-Wei

last: Lo


title: IGF-1 Peptide Mimetic-functionalized Hydrogels Enhance MSC Survival and Immunomodulatory Activity

city: St. Louis

first: Nathaniel

last: Huebsch

state: MO

address: 1 Brookings Drive

department: Biomedical Egnineering

institute: Washington University in St.Louis

summary: Human mesenchymal stem cells (MSCs) have demonstrated promise when delivered to damaged tissue or tissue defects for their cytokine secretion and inflammation modulation behaviors that can promote repair. Insulin-like growth factor 1 (IGF-1) has been shown to augment MSCs’ viability and survival and promote their secretion of cytokines that signal to endogenous cells, in the treatment of myocardial infarction, wound healing, and age-related diseases. Biomaterial cell carriers can be functionalized with growth factor-mimetic peptides to enhance MSC function while promoting cell retention and minimizing off-target effects seen with direct administration of soluble growth factors. Here, we functionalized alginate hydrogels with three distinct IGF-1 peptide mimetics and the integrin-binding peptide, cyclic RGD. One IGF-1 peptide mimetic (IGM-3) was found to activate Akt signaling and support survival of serum-deprived MSCs. MSCs encapsulated in alginate hydrogels that presented both IGM-3 and cRGD showed a significant reduction in pro-inflammatory cytokine secretion when challenged with interleukin-1β. Finally, MSCs cultured within the cRGD/IGM-3 hydrogels were able to blunt pro-inflammatory gene expression of human primary cells from degenerated intervertebral discs. These studies indicate the potential to leverage cell adhesive and IGF-1 growth factor peptide mimetics together to control therapeutic secretory behavior of MSCs.

overall_design: Nucleus pulposus (NP) cells from 6 human patients (66F, 61M, 62M, 53M, 56F, 44F; all passage 1) were used for this study. Cells of each patient were seeded on TCPS Transwell co-cultured with MSCs encapsulated in either alginate, cRGD-alginate, or cRGD/IGM-3-alginate in medium without serum supplemented with 1ng/mL IL-1β and allowed to culture for 4 days with 50% media changes conducted at 48-hour intervals before NP cells were harvested and lysed and RNA extracted. RNA sequencing was performed and Bulk RNAseq analysis packages from Bioconductor R studio was used to analyze the data.

first: Xiaohong

last: Tan

first: Jiufang

last: Jing

first: Sydney

last: Neal

first: Munish

last: Gupta

first: Jacob

last: Buchowski

first: Lori

last: Setton


title: Alterations in gene expression profiles of pancreatic cancer cell lines in response to benzaldehyde treatment

city: Chiyoda-ku

first: Shogo

last: Okazaki

state: Tokyo

address: 1-8-13 Kanda-Surugadai

department: School of Dentistry

institute: Nihon University

summary: Benzaldehyde (BA) is a promising candidate for cancer therapy due to its antitumor effects on a wide range of cancer cells. However, the detailed mechanism of its anti-tumor effect remains unclear. To investigate this mechanism, we examined the changes in gene expression induced by BA in three pancreatic cancer cell lines with different BA sensitivities: BxPC3 (high sensitivity), AsPC1 (medium sensitivity), and PANC1 (low sensitivity).

overall_design: BxPC3, AsPC1, and PANC1 cells were treated with DMSO or BA at concentrations of 100 μM and 500 μM. After 24 hours, total RNA was collected and gene expression was analyzed by microarray. The experiment was performed in duplicate.

first: Jun

last: Saito

first: Hideyuki

last: Saya


title: Phenotypic Screening Uncovered Anti-Myocardial Fibrosis Candidates Using a Novel 3D Myocardial Tissue Under Hypoxia

city: Beijing

first: Xiangning

last: Liu

address: Chaoyang District, N.3rd Ring Rd East

institute: Beijing University of Chinese Medicine

summary: Myocardial fibrosis (MF) is a shared hallmark among cardiovascular diseases, reflecting a common thread in their pathogenesis. However, reliable MF models simulating the pathogenesis are limited, which leads to the urgent need for more efficient drugs targeting MF. Herein, a novel contractile three-dimensional (3D) myocardial tissue model integrating cardiomyocytes (CMs), cardiac-fibroblasts (CFs), and bone-marrow-derived macrophages (BMDMs) in collagen hydrogel was developed to simulate the clinical pathological changes of terminal stage of cardiovascular disease, heart failure, and screen compounds with anti-MF activity dependably. The 3D myocardial tissue model demonstrated precise, visualizable, and quantifiable contractile characteristics under hypoxia and drug interventions. 76 compounds extracted from the resins of T.vernicifluum, a traditional Chinese medicine with clear clinical benefits for fibrotic diseases, were screened for anti-fibrotic activity. Following the in vitro assay using 3D oxygen-glucose deprivation (OGD)-treated myocardial tissue model instead of two-dimensional (2D) transforming growth factor-β (TGF-β)-treated CFs model, two candidates including LQ-40 and SQ-3 exerts impressive anti-MF activity, which was further validated in left anterior descending coronary artery (LAD)-MF mouse model. The current results demonstrate the feasibility and advantage of the novel 3D contractile multicellular types model in the discovery of potential drugs for MF, and candidates with promising potential for MF.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design:
To investigate the interactions between the three cell types, 3D-OGD-MF and three types of 2D cells at a ratio of 1:1:1 were subjected to RNA-seq.
To accurately assess the effects of LQ-40 and SQ3 on myocardial fibrosis, and investigate the potential anti-fibrotic mechanism behind structural similarity, we performed mRNA-Seq analysis on mouse myocardial tissue in sham, model, LQ-40 and SQ-3 groups in triplicate


title: Protein homeostasis impairment affects phenotypic heterogeneity of biofilms

city: Lund

first: Claes

last: von Wachenfeldt

state: State

address: Sölvegatan 35

department: Department of Biology

institute: Lund University

summary: Biofilms are well organized, cooperating communities of microorganisms encased in a self-produced extracellular matrix, providing resilience against external stress such as antimicrobial agents and host defenses. A hallmark of biofilms is their phenotypic heterogeneity, which enhances the overall growth and survival of the community. In this study, we demonstrate that removing the genes encoding the key molecular chaperones DnaK and trigger factor disrupts protein homeostasis in Bacillus subtilis and leads to the formation of extremely mucoid biofilms with aberrant architecture, compromised structural integrity, and altered phenotypic heterogeneity. These changes include a drastic reduction in the motile subpopulation and an overrepresentation of matrix producers and endospores. Overproduction of poly-γ-glutamic acid contributed crucially to the mucoid phenotype and aberrant biofilm architecture. Elevated temperatures led to protein homeostasis impairment resulting in mucoid and aberrant biofilm phenotypes. Our findings suggest that disruption of protein homeostasis, whether due to the absence of molecular chaperones or environmental factors, constrain biofilm formation.

overall_design: 6 samples. ΔdnaK Δtig (3 biological replicates), wild-type (3 biological replicates)

first: Judith

last: Matavacas


title: Transcriptional effects of a first-in-class EGFR-directed KRAS G12V selective inhibitor, EFTX-G12V, on H727 cells.

first: Alessandro

last: Porrello

summary: Despite KRAS-G12V being the second most common KRAS mutation in cancer, there are no approved direct KRAS-G12V inhibitors. Difficulties with inhibiting oncogenes using conventional approaches have prompted the use of RNAi as a therapeutic approach. RNAi has faced numerous obstacles as a cancer therapeutic, including the lack of cancer-specific tissue targeting, rapid oligonucleotide nuclease degradation and clearance from the circulation. Recently, the use of targetable ligands conjugated to chemically modified siRNAs has shown remarkable promise in circumventing these barriers. We demonstrate that EFTX-G12V is highly selective for KRAS-G12V and has improved therapeutic activity over pan-KRAS targeting, including enhanced inhibition of several cancer hallmarks. With a novel RNAi delivery platform, we demonstrate tumor silencing of KRAS-G12V and significant anti-tumor activity across several cancer models. Our findings represent a technologic advance in oncogene targeting using RNAi and reveal new biologic insights in KRAS targeting that may have broad implications with regards to safety and efficacy. This dataset collects the RNA-Seq data for the H727 cell line.

overall_design: To evaluate the transcriptional effect of mutant-selective versus pan-KRAS targeting, we used RNA-sequencing analyses of a KRAS G12V mutant cell lines, H727, 48 hours after siRNA transfection. We performed differential gene expression analysis comparing H727 cells transfected with control siRNA vs. pan-KRAS targeting siRNA and vs. G12V-specific siRNA (EFTX-G12V). We completed our assessments with gene-set based analyses using the same experimental groups (control, pan-KRAS, and EFTX-G12V).

first: Chad

last: Pecot


title: Transcriptome sequencing of cardiac fibroblasts from control and carbon tetrachloride-treated mice.

first: He

last: Sun

overall_design: To investigate the underlying mechanism of liver cirrhosis on cardiac function, carbon tetrachloride (CCL4) was used to establish an animal model in C57BL/6J mice. Mice were divided into Control group and CCL4 group, with 3 mice in each group. At the end of modeling, the cardiac fibroblasts(CFs) of mice were isolated for sequencing.

first: Kai

last: Song

first: Hui

last: Tao


title: A novel mutation in SMARCB1 associated with adult Coffin-Siris syndrome and meningioma

city: Zhengzhou

first: zhenglong

last: guo

state: Henan

address: NO.7, Weiwu road

institute: Henan Provincial People's Hospital

summary: SMARCB1 encodes a core subunit of the SWI/SNF chromatin remodeling complex, which plays a crucial role in the regulation of gene expression. Germline mutations in the SMARCB1 gene have been linked to early childhood Coffin-Siris syndrome type 3 (CSS3), a rare congenital malformation syndrome characterized by severe developmental delay and intellectual disability. In this study, we report two adult CSS3 patients with novel missense SMARCB1 mutation (c.1091A>C, p.Lys364Thr) identified through whole exome sequencing (WES). Both two patients exhibited selective difficulties in verbal learning and language delay. Additionally, the development of meningioma was confirmed in one of the patients. Mechanistic studies indicate that this missense mutation may abnormally activates the expression of MAPK14, a gene implicated in the pathogenesis of tumor progression and neurodevelopmental disorders. This is the first reported case of a germline mutation in SMARCB1 gene associated with both CSS3 and meningioma, thereby expanding the phenotypic spectrum of SMARCB1-related neurodevelopmental disorders.

overall_design: To investigate the impact of the missense mutation (c.1091A>C, p.Lys364Thr) on the function of the SMARCB1 protein, we established wild-type and mutant SMARCB1 overexpression IOMM-Lee cell lines via lentiviral transfection. Subsequently, we examined the effects of this mutation through transcriptome analysis, focusing on their influence on gene expression profiles.

first: Zhenglong

last: Guo

first: Bingtao

last: Hao

first: Shixiu

last: Liao


title: Comparative single-cell analyses reveal evolutionary repurposing of a conserved gene program in bat wing development [ATACseq]

first: Christian

last: Feregrino

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: We used ATAC-seq to detect open chromatin regions in bat forelimbs to identify active regulatory elements.

first: Magdalena

last: Schindler

first: Francisca

last: Real

first: Bai-Wei

last: Lo


title: Coactivator SAGA plays a crucial role in TBP recruitment for the Gcn4 transcriptome via subunits Spt3/Spt8

city: Rockville

first: SAKSHI

last: SINGH

state: Maryland

address: 6 center drive , Bldg 6

department: NICHD-DIR

institute: NIH

summary: Coactivator complexes TFIID and SAGA recruit TATA-binding protein (TBP), while SAGA also enhances transcription by histone acetylation via the HAT Gcn5. It was proposed that most yeast genes depend exclusively on TFIID, with only ~10% requiring cumulative contributions by SAGA and TFIID for efficient transcription. It was further suggested that genes induced by Gcn4, transcriptional activator of amino acid biosynthetic genes induced by amino acid starvation, depend on the HAT, but not TBP-recruitment function of SAGA. At odds with this model, ChIP-sequencing of TBP and Pol II subunit Rpb1 revealed that deleting SPT3 or SPT8, but not GCN5, reduced TBP binding at most Gcn4 target genes, whereas deleting GCN5 selectively impaired promoter histone eviction; and all three SAGA mutations reduced transcription comparably. Nuclear depletion of TFIID subunit Taf1 generally reduced TBP recruitment at these and most other SAGA-dependent genes only in cells lacking Spt3 or Spt8. We conclude that SAGA is crucial for TBP recruitment via Spt3/Spt8, beyond its role in histone acetylation, whereas TFIID plays an ancillary role for the Gcn4 transcriptome in amino acid-starved cells.

overall_design: Formaldehyde-fixed and sonicated DNA fragments were immunopurified and subjected to paired-end sequencing.

first: Sakshi

last: Singh

first: Alan

middle: G

last: Hinnebusch


title: Serotonin activates dermal papilla cells and promotes hair growth

city: Kawasaki

first: Tatsuto

last: Kageyama

state: Kanagawa

address: Life Innovation Center, 3-25-22 Tonomachi

institute: Kanagawa Institute of Industrial Science and Technology

summary: We examined effects of serotonin (5HT) or sumatriptan on the hair growth ability of dermal papilla cells.

overall_design: We annalysed gene expression of human dermal papilla cells with/without serotonin (5HT) or sumatriptan treatment.

first: Junji

last: Fukuda


title: MeRIP-seq of Alkbh5/Mettl3 knockout Bone marrow-derived macrophages

city: Guangzhou

first: Kechen

last: Chen

state: Guangdong

address: Shatai South Road

institute: Southern Medical University

summary: Alkbh5/Mettl3loxp/loxp mice were crossed with Lyz2-Cre mice to generate macrophage-specific conditional knockout mice for Alkbh5/Mettl3. Bone marrow-derived macrophages (BMDMs) were isolated from these mice, and MeRIP-seq was performed to investigate the impact of the knockout on RNA N6-Methyladenosine

overall_design: Bone marrow-derived macrophage from Mettl3loxp/loxp; Lyz2-Cre, Alkbh5loxp/loxp; Lyz2-Cre and WT

first: Tao

last: Huang

first: Shijun

first: Zhili

last: Rong


title: Overexpression of TSG101 causes cellular plasticity and development of adenosquamous mammary carcinoma

city: Detroit

first: Kay-Uwe

last: Wagner

address: 421 East Canfield, EL01TM

department: Department of Oncology

institute: Barbara Ann Karmanos Cancer Institute Wayne State University School of Medicine

summary: The mammalian Tumor Susceptibility Gene 101 (TSG101) encodes a protein with diverse functions that control the proliferation and survival of cells, but its role in malignant transformation has remained enigmatic. To study the pro-tumorigenic functions of TSG101, we developed a transgenic mouse model that expresses exogenous TSG101 along with a luciferase reporter in a ligand-controlled manner in the mammary gland epithelium. Females overexpressing TSG101 develop ductal hyperplasia, adenomyoepitheliomas, and palpable adenosquamous carcinomas at an average latency of aproximately 10 months. These metaplastic mammary tumors are comprised of transforming basal and luminal epithelial cells, and using a GFP reporter strain to monitor the transgene activation on the single-cell level, we determined that the epithelial heterogeneity within transforming ducts and carcinomas was the result of cellular plasticity wihtin the luminal epithelium. On the molecular level, TSG101-induced mammary tumors are triple-negative and exhibit gene expression signatures of Wnt and inflammatory cytokine signaling, which are key regulators of epithelial cell fate. The ligand-controlled downregulation of exogenous TSG101 in established carcinomas led to tumor regression. We demonstrated that the TSG101-mediated activation of PI3K/AKT signaling as well as upregulation of Cyclin D1 and MDM2 are dependent on the perpetual expression of the oncoprotein. The collective findings of this study provide in vivo evidence that TSG101 has pro-tumorigenic properties that extend to cancer progression and maintenance, suggesting that this protein could be a rational molecular target to prevent and treat a subset of mammary tumors.

overall_design: To classify TSG101 overexpressing mammary carcinomas, we performed comparative gene expression profiling analysis of RNA-seq data  from ten TSG101-overexpressing tumor specimens and  three normal mammary gland tissue.

first: Rayane

last: Dennaoui

first: Patrick

middle: D

last: Rädler

first: Madison

middle: N

last: Wicker

first: Kerry

last: Vistisen

first: Rosa‑Maria

last: Ferraiuolo

first: Aleata

last: Triplett

first: Hridaya

last: Shrestha

first: Tessa

last: Liner

first: Karoline

last: Manthey

first: Hallgeir

last: Rui

first: Robert

last: Cardiff

first: Teresa

last: Gunn

first: Charles

last: Perou


title: Gene expression profile of colorectal carcinoma HT29 PARP13 KO cells treated with fractionated ionizing radiation dose (5x2Gy) under 2D or 3D cell culture conditions

city: Vilnius

first: Rimvile

last: Prokarenkaite

address: Santariskiu st 1

institute: National Cancer Institute

summary: Radiotherapy is one of the most common treatments for cancer. The effects of IR are dose-dependent and different cell types have different sensitivities to IR. To reduce the damage of IR to the most sensitive cells of normal tissue, radiotherapy is administered as a fractionated dose treatment, delivering radiation in 2 Gy fractions every 24 hours, 5 times a week. However, during the course of therapy, intrinsic and acquired radioresistance of the tumor can lead to treatment failure. Therefore, there is a need for combination therapy including radiotherapy and targeted anticancer treatment. In the present study, we investigated global gene expression changes in colorectal cancer HT29 PARP13 KO cells after X-ray irradiation with a fractionated dose of 5 x 2 Gy. Agilent microarray technology was used to analyze gene expression levels in cells cultured under 2D and 3D culture conditions.

overall_design: HT29 PARP13 KO cells were irradiated with fractionated dose ionizing radiation (5x2Gy) and 4h after treatment RNA was extracted for further analysis in comparison to non-irradiated cells. Two cell culture models: 2D and 3D. Biological replicates: 3 for each cell culture model system.

first: Vaidotas

last: Stankevicius

first: Kestutis

last: Suziedelis


title: Sex Hormone Binding Globulin Controls Sex-Specific Lipolytic Activity in Human Abdominal Subcutaneous Adipocytes

city: Copenhagen

first: Søren

last: Nielsen

address: Blegdamsvej 9

department: 1The Centre for Physical Activity Research

country: Denmark

institute: Rigshospitalet

summary: Regulation of lipid metabolism is fundamental for metabolic health, and adipose tissue is a central component in this process. Adipose tissue differs considerably between women and men in terms of a higher subcutaneous capacity for storage, which is linked to metabolic health, in women. Sex hormone-binding globulin (SHBG) contributes to the regulation of circulating sex hormone bioavailability and has been shown to predict risk of metabolic dysfunction. Here, we investigate the sex-specific relationship of SHBG with metabolic status and adipocyte-dependent lipolysis. We measured serum concentrations of sex hormones, SHBG, fasting glucose, and insulin in a cohort of 63 women and 27 men from which adipose biopsies were collected and mature adipocytes isolated. In women, high serum SHBG concentrations were strongly associated with low in vivo Homeostatic Model Assessment for Insulin Resistance (HOMA-IR), and lower unstimulated ex vivo lipolysis but higher isopropanol stimulated ex vivo lipolysis. In contrast, no effect of SHBG on the above-mentioned parameters were observed in men. In vitro cultured human adipocytes also increased lipolytic activity in response to SHBG, but only in the absence of testosterone, suggesting that testosterone inhibits the catecholamine-induced lipolysis of SHBG in adipose tissue. In conclusion, we identify SHBG as a novel sex-specific regulator of adipocyte lipolysis and lipid metabolism. At the same time, our data emphasize sex-dependent effects of SHBG on adipocyte lipid metabolism, and we propose testosterone binding to SHBG as a driving factor mediating these sex differences.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from differentiated human cultured adipocytes treated with and without SHBG for the last three days of differentiation.

first: Julie

last: Abildgaard

first: Nagendra

middle: P

last: Palani

first: Søen


title: Comparative single-cell analyses reveal evolutionary repurposing of a conserved gene program in bat wing development [scRNAseq]

first: Christian

last: Feregrino

overall_design: We generated single-cell RNA-seq data from developing mouse and bat limbs at different developmental stages as well as micro-dissected chiropatagium tissue at CS18/CS19 to investigate gene expression signatures in limb developmental  clusters and compare them between species. Furthermore, we generated single cell RNAseq data from our transgenic mutants to investigate the gene expression changes in affected limb cell clusters.

first: Magdalena

last: Schindler


title: Polyamine Depletion Inhibits Ewing Sarcoma Metastasis by Inducing Ferroptosis

city: Baltimore

first: Da

last: Peng

address: 733 North Broadway, MRB 653

institute: Johns Hopkins University

summary: Polyamine metabolism and signaling play important roles in multiple cancers including neuroblastoma and breast cancer but have not previously been studied in Ewing sarcoma.  Prior work in our lab suggested that tumor microenvironment affects arginase expression -- orthotopically implanted hindlimb tumors with enhanced metastatic potential demonstrate diminished arginase expression compared to subcutaneously implanted tumors that do not metastasize.  As arginase catalyzes the conversion of arginine to ornithine, the precursor for polyamine synthesis, this suggested a potential role for polyamine synthesis in Ewing sarcoma metastasis and a target for therapeutic intervention.  Here, we show that blocking polyamine synthesis with D, L-alpha-difluoromethylornithine (DFMO) causes a G1 cell cycle arrest, dose-dependent decreases in sarcosphere formation from Ewing sarcoma cell lines growing in non-adherent conditions and a decrease in clonogenic growth in soft agar.  Further, we utilized our orthotopic implantation/amputation model of Ewing sarcoma metastasis to investigate the impact of disrupting polyamine synthesis on tumor growth and metastasis.  When mice were treated with low dose DFMO, there was no effect on primary tumor growth or metastatic potential; however, at higher concentrations, systemic DFMO slowed primary tumor growth in addition to limiting metastasis.  RNA sequencing demonstrated gene expression patterns consistent with induction of ferroptosis caused by polyamine depletion, and this was confirmed experimentally.  Collectively, these results reveal a novel mechanism by which DFMO prevents metastasis – induction of ferroptosis due to polyamine depletion, and our results suggest that DFMO may be a readily translatable and well-tolerated treatment to prevent metastatic recurrence in patients with high-risk Ewing sarcoma.

overall_design: TC-71 cells were cultured, and 100 cells were suspended in Matrigel 1:1 dilution with phosphate-buffered saline in a total volume of 0.1 ml. This suspension was injected into the subcutaneous space of the flank of NSG mice using a 25-gauge needle. When tumors reached 1.5 cm in diameter, Ewing sarcoma cells were recovered from lungs, bone marrow, and the primary tumor by flow cytometry

first: Rachel

last: Offenbacher

first: Kyle

middle: W

last: Jackson

first: Masanori

last: Hayashi

first: Jinghang

last: Zhang

first: Yuqi

last: Tan

first: Tracy

last: Stewart

first: Paul

last: Ciero

first: Jackson

last: Foley

last: Casero Jr

first: Patrick

last: Cahan

first: David

last: Loeb


title: High-throughput Sequencing Quantitative Analysis of altered genes expression in bladder cancer with anti-PD-1 treatment

first: mingrui

last: pang

address: Yanjiangxi Road

institute: Sun Yat-sen University

summary: Immune-checkpoint blockade (ICB) therapy has profoundly changed the landscape of cancer treatment strategies. Despite its success, resistance remains a significant challenge, with the majority of patients exhibiting non-response to ICB therapies. ICB reinvigorates tumor-specific T cells by interrupting inhibitory signals mediated by checkpoints like PD-1 and CTLA-4, pivotal for the reactivation of their anti-tumor functions. Within the tumor microenvironment, tumor-specific T cells enter a state of dysfunction, making it difficult to generate an effective response to ICB. This study aims to investigate the altered transcriptome in anti-PD-1 responders and non-responders of bladder cancer (BCa) and to uncover the underlying mechanisms of T cell non-responses to ICB.

overall_design: To explore T cell dysfunction contributing to ICB resistance in BCa, we developed an immunocompetent spontaneous BCa mouse model. After tumor formation, anti-PD-1 monoclonal antibody was applied to treat BCa. Total RNA from responsive and non-responsive BCa was extracted, and high-throughput sequencing was conducted to investigate the expression profile differences between non-responders and responders.

first: Mingrui

last: Pang

first: Changhao

last: Chen

first: Tianxin

last: Lin


title: FMR1 Mutant Marmosets Show Fragile X Syndrome Phenotypes

city: Tokyo

first: Maria

last: Harbers

address: 7-3-1 Hongo, Bunkyo-ku

department: Graduate School of Medicine

institute: The University of Tokyo

summary: Fragile X syndrome (FXS) is the leading monogenic cause of autism spectrum disorder and intellectual disability, caused by silencing of the FMR1 gene. To determine the effect of FMRP loss on the mRNA profile in a marmoset model of FXS, we performed RNA-sequencing of brain samples from neonatal wild-type and FMR1 mutant marmosets.

overall_design: We generated FMR1 mutant marmosets using CRISPR/Cas9 system.  We then performed gene expression profiling analysis using data obtained from RNA-seq of forebrain samples, including the cerebral cortex, striatum, and hippocampus, from wild-type and FMR1 mutant marmosets at postnatal day 5.

first: Harumi

last: Nakao

first: Zefeng

last: Wei

first: Yukiko

last: Abe

first: Motoki

last: Goto

first: Moe

last: Tamano

first: Atsu

last: Aiba


title: Transcript-specific differences in m6A modifications in endocrine-sensitive and resistant breast cancer cells II

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: Acquired resistance to endocrine therapies (ET) remains a clinical problem for breast cancer patients whose initial tumors express estrogen receptor α (ER). Epigenetic changes are among the mechanisms involved in the development of ET resistance. We tested the hypothesis that the epitranscriptomic modification N-6 methyladenosine (m6A) differentially regulates the abundance of mRNA transcripts in ET-sensitive MCF-7 versus LCC9 ET-resistant ER+ human breast cancer cells. Direct mRNA sequencing (dRNA-seq) was performed on five replicates for each cell line +/- treatment with 100 nM 4-hydroxytamoxifen (4-OHT) using Nanopore MinION long read RNA-seq. Parallel short read Illumina RNA-seq was used to quantify differential transcript abundance. Statistical analysis integrated m6Anet, a machine-learning algorithm designed to call m6A modified bases, with a generalized linear model following a binomial distribution analysis to identify significant differential m6A modification ratios (DMR). Our findings reveal distinct m6A modification patterns in ET-resistant LCC9 breast cancer cells and in response to 4-OHT treatment compared to their ET-sensitive parental MCF-7 cells, suggesting a potential role for epitranscriptomic alterations in the development of ET resistance.

overall_design: Identify transcript differences in breast cancer cells (MCF-7 versus LCC9) treated with DMSO (vehicle control) and with 4-OHT. Match Illumina transcript abundance with data from Oxford Nanopore direct RNA sequencing and determine m6A regulated transcript changes.

first: Belinda

last: Petri

first: Kellianne

last: Piell

first: Bailey

middle: L

last: Valdes

first: Laura

last: Winkler

first: Julia

middle: H

last: Chariker

first: Carolyn

last: Klinge


title: Characterisation of the regulatory landscape in Crohn’s disease reveals miRNA-associated alterations that shape anti-TNF response (CIBER-120)

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

institute: CIC bioGUNE

summary: MicroRNAs (miRNAs) play a key role in regulating gene expression in Crohn’s disease (CD). Although several studies have identified miRNAs with biomarker potential, an exhaustive characterisation of the miRNAome in CD is still lacking. We performed the largest miRNA profiling effort to date to analyse miRNA variability across intestinal tissues, disease activity status, and infliximab treatment in CD. We generated 120 transcriptomic profiles from terminal ileum and left colon biopsies of 30 individuals (10 with active CD, 10 with quiescent CD, and 10 healthy controls). Half of the samples were cultured ex vivo with infliximab, and the remaining half with basal medium. Using variance analyses and linear mixed differential expression models, we explored the determinants of miRNAome variability in CD. We also generated infliximab response signatures to identify candidates and examine interactions between miRNAs and the coding transcriptome. Tissue location was the main factor in miRNA variability in CD, although with a relevant contribution from patient-specific effects. We identified nine miRNAs with treatment-responsive behaviour particular to the terminal ileum of active CD cases. Incubation with infliximab restored the miRNA-mRNA interactome, although the changes observed in active CD cases suggest that many miRNA alterations are not offset by treatment.  Finally, we identified 13 miRNAs-mRNA pairs with potential involvement in the transcriptomic changes induced by anti-TNF treatment. A comprehensive miRNA profiling revealed significant intestinal tissue-specific variability and identified key alterations in the miRNA-mRNA interactome that might be involved in therapeutic response to anti-TNF in CD.

overall_design: We collected gut biopsies from three groups of patients: 10 individuals with active CD (aCD), 10 with quiescent CD (qCD), and 10 who were healthy controls (HC). For each patient, we collected four samples: two ascertained from the terminal ileum and two from the left colon, for a total of 120 specimens in the overall study.  We generated 120 transcriptomic profiles from terminal ileum and left colon biopsies of 30 individuals (10 with active CD, 10 with quiescent CD, and 10 healthy controls). Half of the samples were cultured ex vivo with infliximab, and the remaining half with basal medium.

first: Luis

last: Cervera-Seco

first: Montse

last: Baldán-Martín

first: Samuel

last: Fernández-Tomé

first: Lorena

last: Ortega

first: Juan

last: Lozano

middle: M

first: María

last: Chaparro

first: Javier

last: Gisbert

first: Urko

last: Marigorta


title: GADD45G operates as a pathological sensor orchestrating reactive gliosis and neurodegeneration

city: Dallas

first: tianjin

last: shen

state: Texas

address: 5323 Harry Hines Boulevard, Dallas, TX 75390

department: Molecular Biology

institute: UT Southwestern Medical Center

summary: Emerging evidence indicates that AD progression is associated with astrocytes transitioning from a homeostatic state to a disease-associated state. This transition is characterized by changes in their morphology, gene expression, and function. We here report GADD45G as a key regulator of the pathogenesis of AD.

overall_design:
To determine the role of GADD45G in astrocytes, we conducted unbiased RNA-seq analysis on astrocytes transduced with a virus expressing GADD45G or the control GFP.
In addition, we also conducted RNA-seq analysis on astrocytes following shRNA-mediated knockdown of endogenous Gadd45g (shGadd45g).

first: Tianjin

last: Shen

first: Chun-li

last: Zhang


title: Immediate and delayed hypothalamic response to monochromatic green illumination during the avian embryonic period are mediated thorough epigenetic modulations

city: Rehovot

first: Joanna

last: Bartman

address: Hertzl 229

country: Israel

institute: The Hebrew University of Jerusalem

summary: In this study, we investigated the effects of light-induced fetal responses in avian species, specifically focusing on green monochromatic illumination (GMI). Broiler eggs were exposed to GMI either throughout the entire incubation period (Green) or specifically during the final three days before hatching (G3D), with control groups incubated in dark or white light conditions. Unbiased genome-wide analyses at day of hatch (DOH) revealed significant transcriptional changes in the hypothalamus of the G3D group, highlighting over 500 differentially expressed genes. In parallel with these transcriptional changes, our epigenetic analysis revealed that GMI exposure in the G3D group resulted in increased binding of phosphorylated CREB1 (pCREB1) and elevated levels of Histone H3 Lysine 27 acetylation (H3K27ac) at gene promoters linked to growth, appetite, and metabolism. Mechanistically, we found that pre-exposure to blue light, which disrupts green photoreceptor activity, reduced retinal green opsin levels and nullified the epigenetic modifications typically induced by GMI in the G3D group. Phenotypically, the G3D group exhibited increased post-hatch body weight at several stages, suggesting enhanced growth plasticity and metabolic efficiency, though these effects diminished with age. This study underscores the significant role of specific wavelengths and timing of light exposure in shaping developmental trajectories, and highlight the crucial role of epigenetics in shaping organismal responses to their environment.

overall_design: broiler hypothalami from day of hatch incubated in 4 diffrenet illumination regimes: dark incubation (control), white illumination (white), green illumination throught the entire incubation (green) and green illumination only at the last three days of incubation (g3d)

first: Tali

last: Rosenberg

first: Hadar

last: Parnas

first: Natalie

last: Avital-Cohen

first: Israel

last: Rozenboim

first: Asaf

last: Marco


title: Characterisation of the regulatory landscape in Crohn’s disease reveals miRNA-associated alterations that shape anti-TNF response

first: Ana

last: Aransay

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Expression data from Rhabdomyosarcoma human cells treated with Ipatasertib or Miransertib.

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

institute: Hospital del Mar Research Institute

summary:
The AKT inhibitors Ipatasertib and Miransertib show differential anti-tumor activity against RMS.
We use microarrays to compare the transcriptomic effects of each AKT inhibitor in RMS and to identify the diffential gene signature of each drug in RMS.

overall_design: Rhabdomyosarcoma fusion positive cell line (RH4) was treated with vehicle (DMSO), Ipatasertib or Miransertib for 24h. The analysis of differential expressed genes was based on the comparison of RH4 cells treated (Ipatasertib or Miransertib)  versus vehicle (control) cells.

first: Estela

last: Prada

first: Jaume

last: Mora

first: Inmaculada

last: Muñoz


title: Characterisation of the regulatory landscape in Crohn’s disease reveals miRNA-associated alterations that shape anti-TNF response (CIBER-121)

first: Luis

last: Cervera-Seco

first: Montse

last: Baldán-Martín

first: Samuel

last: Fernández-Tomé

first: Lorena

last: Ortega

first: Juan

last: Lozano

first: María

last: Chaparro


title: Transcript-specific differences in m6A modifications in endocrine-sensitive and resistant breast cancer cells

first: Eric

last: Rouchka

first: Belinda

last: Petri

first: Kellianne

last: Piell

first: Bailey

last: Valdes

first: Laura

last: Winkler

first: Julia

last: Chariker

middle: C

first: Carolyn

last: Klinge


title: The key regulation of LncRNA MALAT1/miR-124-3p/PI3K axis during reprogramming of primary mouse hepatocytes into insulin-producing cells

city: Nanchang

first: yunfei

last: Luo

address: No. 1 Min De Road

institute: nanchang university

summary: In this study, a considerable augmentation in the expression of the endogenous long noncoding RNA MALAT1 (lncRNA MALAT1) and PI3K was discerned, in contrast to a significant diminution in miR-124-3p expression, during the progression of in vitro induced differentiation of primary mouse hepatocytes. Bioinformatics scrutiny and the luciferase reporter assay unveiled the binding of miR-124-3p to specific loci in lncRNA MALAT1 and PI3K, suppressing their expression. Elevated expression of lncRNA MALAT1 potently diminished the expression levels of PI3K and attenuated the efficacy of primary mouse hepatocytes differentiation into insulin-producing cells. Furthermore, the in vitro responsiveness of primary mouse hepatocytes-derived β islet-like cells to high glucose stimuli and insulin release by these cells were significantly diminished in the overexpression of lncRNA MALAT1 transfection group, while the outcomes were converse in the si-lncRNA MALAT1 group. The experimental findings suggest that lncRNA MALAT1 effectively sustains PI3K gene expression through competitive binding to miR-124-3p, accomplishing regulation of primary mouse hepatocytes directed β islet-like cell differentiation efficiency.

overall_design: To differentiate the primary mouse hepatocytes into IPCs using our step-wise protocol,We further extracted the RNA from various stages cells, and performed a high throughput RNA-seq analysis, upon dissecting differentially expressed mRNA and lncRNA,

first: Yunfei

first: Shuang

last: Liu

first: Haixia

last: Zeng

first: Jianping


title: Comparative single-cell analyses reveal evolutionary repurposing of a conserved gene program in bat wing development [ChIPseq]

city: Berlin

first: Christian

last: Feregrino

address: Ihnestraße 63

institute: MPI - Molecular Genetics

summary: Bats (order Chiroptera) are the only mammals capable of self-powered flight. Unlike in humans and mice, digits II-V in the bat forelimb are not separated but connected by the chiropatagium, an elastic membrane that forms the wing. The molecular underpinnings of these morphological differences, one of the most striking adaptations in mammalian evolution, remain obscure. Here, we use a suite of omics tools and single-cell analyses to compare the development of fore- and hindlimbs, in bat and mouse. We demonstrate a clear conservation of cell states and processes between species, even at the level of apoptosis, a mechanism that removes the tissue between the digits. To trace down the cellular origin of the persistent interdigital cells in bats, we micro-dissected the embryonic chiropatagium and performed single-cell transcriptomics. We found that the chiropatagium cells develop from fibroblasts populations, and independently from the apoptosis-related retinoic acid signaling cells of the interdigital mesenchyme. These cells from the distal part of the limb repurpose a gene program otherwise only present in proximal cells. Epigenomic and gene network analyses revealed two transcription factors, MEIS2 and TBX3, among the most prominent regulators of this gene program. Transgenic ectopic expression of MEIS2 and TBX3 in interdigital cells of mice resulted in the activation of genes associated with bat wing processes. Major morphological changes in these mutants include an increase in autopod volume, extracellular matrix and the partial retention of interdigital tissue with fusion (syndactyly) of digits. Our results elucidate fundamental molecular mechanisms of wing formation in bats. More generally, we illustrate that the repurposing of existing developmental programs is an evolutionary molecular mechanism to generate morphological novelties.

overall_design:
We used ChIP-seq against H3K27ac histone modification to identify active regulatory elements in developing limbs. We used ChIP-seq against Meis2 to detect bound downstream targets of this transcription factor.

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.

Processed data file(s): Meis2_mm39_forelimb_E105.narrowPeak
***************************************************************

first: Magdalena

last: Schindler

first: Bai-Wei

last: Lo


title: Assembly and annotation of Solanum dulcamara and Solanum nigrum plant genomes, two nightshades with contrasting susceptibilities to Ralstonia solanacearum

city: Heslington, York

first: Sara

last: Franco Ortega

address: Wentworth Way

country: United Kingdom

institute: Centre for Novel Agricultural Products, University of York

type: Methylation profiling by high throughput sequencing

summary: Ralstonia solanacearum causes disease in more than 200 plant species including bacterial wilt of tomatoes and brown rot of potatoes. This bacterium is a soilborne and waterborne pathogen, with a worldwide distribution and belongs to the EPPO A2 list of quarantine pathogens. ln the UK, the bacterium is present in the rivers, but its prevalence depends on the season; it is highly abundant in the summer and undetectable during winter. To survive the cold winter temperatures, R. solanacearum overwinters inside plants growing alongside the rivers such as Solanum dulcamara. Solanum nigrum is a closely related species to Solanum dulcamara, and to another susceptible hosts of this pathogen. We assemble the genome of this species to identify differences and similarities between hosts.

overall_design: Solanum nigrum (Royal Botanic Gardens, Kew ID=170516) leaves were collected from 3-month old adult plant. DNA was extacted following the High molecular weight gDNA extraction from plant leaves protocol, Oxford Nanopore Technologies [ONT]), which utilised Carlson buffer and further purification using QIAGEN genomic-tip, see preprint Vaillancourt and Buell (2019) for details.The libraries were run in a PromethION R10.4.1 . Base calling was obtained onboard with Guppy. F5C v1.2  was used to identify the methylated regions as well as the frequency of methylation  in the whole genome (accession number JAZKKB000000000).

middle: F

first: Ville-Petri

last: Friman

first: Andrea

last: Harper


title: Classically activated macrophages undergo functionally significant nucleotide metabolism remodelling driven by nitric oxide

city: Madison

first: Jing

last: Fan

state: WI

address: 330 N Orchard St., Fan Lab

department: Metabolism

institute: Morgridge Institute for Research

summary: During an immune response, macrophages specifically reprogramme their metabolism to support functional changes. Here, we revealed that nucleotide metabolism is one of the most significantly reprogrammed pathways upon classical activation. Specifically, de novo synthesis of pyrimidines is maintained up to uridine monophosphate, but blocked at cytidine triphosphate and deoxythymidine monophosphate synthesis; de novo synthesis of purines is shut off at the last step (catalysed by AICAR transformylase/IMP cyclohydrolase), and cells switch to increased purine salvage. Nucleotide degradation to nitrogenous bases is upregulated but complete oxidation of purine bases (catalysed by xanthine oxidoreductase) is inhibited, diverting flux into salvage. Mechanistically, nitric oxide was identified as a major regulator of nucleotide metabolism, simultaneously driving multiple key changes, including the transcriptional downregulation of Tyms and profound inhibition of AICAR transformylase/IMP cyclohydrolase and XOR. Inhibiting purine salvage using HGPRT knockout or inhibition alters the expression of many stimulation-induced genes, suppresses macrophage migration and phagocytosis, and increases the proliferation of the intracellular parasite Toxoplasma gondii. Together, these results thoroughly uncover the dynamic reprogramming of macrophage nucleotide metabolism upon classical activation and elucidate the regulatory mechanisms and functional significance of such reprogramming.

overall_design: To investigate how gene expression changes in Hprt Knockout macrophages, RNA was collected from both wild-type and Hprt Knockout macrophages that were either unstimulated or stimulated with LPS+IFNy for 48h.

first: Steven

middle: V

last: John

first: Gretchen

last: Seim

first: Billy

last: Erazo-Flores

first: James

last: Votava

first: Uzziah

middle: S

last: Urquiza

first: Nicholas

last: Arp

first: John

last: Steill

first: Jack

last: Freeman

first: Lauren

last: Carnevale

first: Isaiah

last: Roberts

first: Xin

last: Qing

first: Stuart

last: Lipton

first: Ron

last: Stewart

last: Knoll


title: Lipoprotein(a) integrates monocyte-mediated thrombosis and inflammation in atherosclerotic cardiovascular disease

city: Ann Arbor

first: Sascha

last: Goonewardena

state: Michigan

address: 1500 E Medical Center Dr

department: Department of Internal Medicine

institute: University of Michigan

summary: Although therapies for atherosclerotic cardiovascular disease (ASCVD) have advanced, substantial residual risk of cardiovascular (CV) events remains.  Lipoprotein (a) [Lp(a)] is a low-density lipoprotein (LDL) particle that is causally linked to both ASCVD and CV events.  Lp(a) is thought to drive ASCVD through multiple mechanisms including its effects on cholesterol accumulation, inflammation, and thrombosis.  Although the associations between Lp(a) and ASCVD drivers are clear, the mechanisms that integrate Lp(a)-mediated cholesterol accumulation, inflammation, and thrombosis remain largely unknown.  In this study, we employed systems biology approaches consisting of proteomics, transcriptomics, and mass cytometry to define the immune cellular and molecular phenotypes in ASCVD subjects with high and low Lp(a) levels and the mechanisms through which Lp(a) mediates monocyte activation. In a cohort of stable ASCVD subjects (n=64 [41 with high Lp(a) and 23 with low Lp(a]), we found that circulating markers of inflammation (CCL28, IL-17D) and vascular dysfunction (BNP), tissue factor [TF]) was elevated in subjects with high Lp(a) levels compared with those with low Lp(a) levels.  Additionally, although total monocytes levels and hs-CRP levels were similar between the groups, CD14+ monocytes from ASCVD subjects with an elevated Lp(a) were primed and expressed more TF at baseline and in response to stress.  Mechanistically, we found that Lp(a) itself can activate monocytes through Toll-like receptors (TLR) and nuclear factor kappa B (NFκB) signaling, driving both the induction of TF and TF activity.  Overall, these studies are the first to link Lp(a) to monocyte-mediated inflammation and thrombosis, demonstrating a novel mechanism through TLR2, NFκB, and monocyte TF which Lp(a) amplifies immunothrombotic risk.

overall_design: Double-blind, placebo-controlled trial randomized 41 ASCVD subjects with high Lp(a) and 23 with low Lp(a]), we found that circulating markers of inflammation (CCL28, IL-17D) and vascular dysfunction (BNP), tissue factor [TF]) was elevated in subjects with high Lp(a) levels compared with those with low Lp(a) levels. The primary outcomes were the change in lipoproteins, blood viscosity, and circulating immune cell transcriptional response at 2 weeks and 12 weeks with evolocumab compared with matching placebo. Safety was assessed in all subjects who received at least one dose of assigned treatment and analyses were conducted in the intention-to-treat population.

first: Robert

last: Rosenson

first: Ashley

last: Tate

first: Qinzhong

last: Chen

first: Olga

last: Grushko

first: Dilna

last: Damodaran

first: Hannah

last: Pacheco

first: Priscilla

last: Mejia

first: Michael

last: Boffa

first: Marlys

last: Koschinsky

first: Jagat

last: Narula


title: Transcriptome comparsion of HB-orgs/P-heporgs cultured under static (HB-S/hep-S) or dynamic (HB-D/hep-D) conditions

first: Wu

last: Haibin

address: Waihuan east road

institute: South china university of technology

summary: Differentiated HB-orgs and P-heporgs from hESCs were cultured under static and dynamic conditions, RNAseq was performed to compare the differences.

overall_design: HB-orgs and P-heporgs were cultured under  static and dynamic conditions.

first: Yuyou

last: Duan

first: Haibin

last: Wu


title: Transcriptomic analysis in 6 primary RMS tumors and their corresponding PDX.

first: Júlia

last: Perera-Bel

summary:
Gene expression analysis of Rhabdomyosarcoma patient biopsies and their Patient derived xenograft tissues. Transcriptimic and Functional analysis correlated with in vivo Ipatasertib efficacy.
PRKG1 mRNA levels in Rhabdomyosarcoma biopsies and PDX.

overall_design: Patient biopsy of pediatric rhabdomyosarcoma tumors and their corresponding subcutaneous patient derived xenograft were studied at trasncriptomic level using Human Genome U219 Array Plate (Thermo Fisher Scientific).

first: Estela

last: Prada

first: Jaume

last: Mora

first: Inmaculada

last: Muñoz


title: Gene Expression in Human Rhabdomyosarcoma


title: Set1 is a critical transcriptional regulator in response to external signals

city: Chuncheon-si, Gangwon-do

first: Jueun

last: Kim

address: 1 Kangwondaehak-gil

institute: Kangwon National University

summary: Set1-mediated methylation of histone H3 at lysine 4 (H3K4) is a well-established marker of active transcription in eukaryotes. However, absence of Set1 did not significantly alter the overall gene expression; interestingly, some genes exhibited enhanced expression in Candida albicans. The present study aimed to elucidate the role of Set1 in transcription of genes that exhibited increased expression levels in its absence. Ideally, these genes should be repressed and activated in response to specific signals. The hypha-specific genes of C. albicans were expressed in the absence of Set1, even without any external activating signals. These inducible genes displayed atypical H3K4 modification patterns. During the initial induction stages, H3K4 methylation was not involved in the rapid and explosive expression of these genes; instead, acetylation of the same residue was involved. H3K4 acetylation significantly increased in the absence of H3K4 methylation, allowing genes that did not receive external transcriptional signals to initiate mRNA expression, leading to morphological changes. With continued exposure to induction signals, the heightened H3K4 acetylation decreased while H3K4 methylation increased in these genes. Thus, inducible genes receive a positive feedback for stable and sustainable expression. In conclusion, Set1 is a key regulator of transcription in response to external environment changes.

overall_design: Chromatin immunoprecipitation (ChIP) sequencing for histone H3K4me3, and H3K4 acetylation in murine macrophage RAW264.7 cells, generated by deep sequencing, in duplicate, by NovaSeq 6000 system

first: Jiyeon

last: Park

first: Eun-Jin

last: Lee

first: Yong-Joon

last: Cho

first: Jung-Shin


title: Set1 is a critical transcriptional regulator in response to external signals [RNA-Seq]

overall_design: mRNA profiles of wild-type and Δset1 under normal yeast and hypha-inducing conditions were generated by deep sequencing, in duplicate (yeast conditions) or triplicate (hyphal conditions), by Illumina HiSeq 2500


first: Jing

last: Fan

overall_design: To investigate how gene expression changes in macrophages over a timecourse of stimulation, wild-type bone-marrow derived macrophages were treated with an acute (2h) LPS+IFNy stimulation. Then the stimulants were washed off and RNA was collected from macrophages at various time points after initial stimulation.

first: Steven

last: John

first: Gretchen

last: Seim

first: Billy

middle: J

last: Erazo-Flores

first: James

middle: A

last: Votava

first: Uzziah

last: Urquiza

first: Nicholas

last: Arp

first: John

last: Steill

first: Jack

last: Freeman

first: Lauren

last: Carnevale

first: Isaiah

last: Roberts

first: Xin

last: Qing

first: Stuart

last: Lipton

first: Ron

last: Stewart

first: Laura

last: Knoll


title: PRKG1 is a master regulator of the myogenic and malignant transcriptome of RMS cells.

first: Júlia

last: Perera-Bel

summary: Silencing PRKG1 in RMS cell lines resulted in decreased tumor-forming capacity and enrichment of genes associated with muscle differentiation.

overall_design: The role of PRKG1 was investigated in PRKG1-depleted RMS cells using a transcriptomic approach.

first: Estela

last: Prada

first: Jaume

last: Mora

first: Inmaculada

last: Muñoz


title: Genome-wide DNA methylation profiles in post-mortem autistic brains

city: Setagaya

first: Kazuhiko

last: Nakabayashi

institute: NCCHD

summary: Previous studies indicate that autism has a strong genetic component; however, the underlying genetic mechanisms remain unclear. Recently, it was reported that genetic heritability is lower than previously estimated, and that environmental factors have a greater influence on the development of autism spectrum disorder (ASD). Epigenetic processes such as DNA methylation are considered to be at the interface of genetic and environmental factors. Additionally, two well-characterized epigenetic processes, parental imprinting and X chromosome inactivation, are involved in several conditions that mimic autism spectrum disorders, such as Rett and Fragile-X syndromes, suggesting that epigenetic processes may play an important role in the pathophysiology of autism. We investigated genome-wide DNA methylation profiles in post-mortem brain tissue from individuals with autism using the Infinium HumanMethylation450 BeadChip (Illumina), which includes CpG sites of intragenic and intergenic regions.

overall_design: We investigated genome-wide DNA methylation profiles in the dorsal raphe (DR) region of the post-mortem brain from male individuals with autism as well as normal controls. The Autism Tissue Program (Princeton, New Jersey; http://www.autismtissueprogram.org), National Institute of Child Health and Development Brain and Tissue Bank for Developmental Disorders (Baltimore, Maryland; http://medschool.umaryland.edu/btbank/) and the Harvard Brain Tissue Resource Center (Belmont, Maryland; http://www.brainbank.mclean.org/) provided us with frozen post-mortem brain tissues from the DR regions (5 with autism and 7 control subjects).

first: Keiko

last: Iwata

first: Hideo

last: Matsuzaki