title: Evolutionary convergence of sensory circuits in the pallium of amniotes

city: Leioa

first: Fernando

last: García-Moreno

state: Bizkaia

address: Barrio Sarriena s/n Edificio Sede

institute: Achucarro BCN

summary: The amniote pallium contains sensory circuits structurally and functionally equivalent, yet their evolutionary relationshipremains unresolved. Our study employs birthdating analysis, single-cell RNA and spatial transcriptomics, and mathematical modeling to compare the development and evolution of known pallial circuits across birds (chick), lizards (gecko)and mammals (mouse). Wereveal that neurons within these circuits' stations are generated at varying developmental times and brain regions across species, and foundan early developmental divergence in the transcriptomic progression of glutamatergic neurons. Together, weshow divergent developmental and evolutionary trajectories in the pallial cell types of sauropsids and mammals. Our research highlights significant differences in circuit construction rules among species and pallial regions. Interestingly, despite these developmental distinctions, the sensory circuits in birds and mammals appear functionally similar, which suggestthe convergence ofhigh-order sensoryprocessing across amniote lineages.

sample_organism:
Gallus gallus
Mus musculus

platform_organism:
Gallus gallus
Mus musculus

overall_design: Single cell RNA sequencing of birthdated cells from chicken and mouse were obtained by Birth-seq protocol (Rueda-Alaña et al, 2023). Birthdated cells with fluorescence EdU were FAC-Sorted and then droplet captured with 10X Genomics Chronium V3 pipeline. Libraries were sequenced with Novaseq 6000 for 50000 reads.

first: Eneritz

last: Rueda-Alaña

first: Rodrigo

last: Senovilla-Ganzo

last: Grillo

first: Enrique

last: Vázquez

first: Sergio

last: Marco-Salas

first: Tatiana

last: Gallego-Flores

first: Artemis

last: Ftara

first: Laura

last: Escobar

first: Alberto

last: Benguría

first: Ana

last: Quintas

last: Dopazo

first: Miriam

last: Rábano

first: María

last: Vivanco

last: Aransay

first: Daniel

last: Garrigos

first: Ángel

last: Toval

first: José

last: Ferrán

first: Mats

last: Nilson

first: Juan

last: Encinas

first: Maurizio

last: De Pitta


title: Investigation of the RNMT/RAM RNA interactome in mouse embryonic stem cells

status: Public on Mar 11 2025

city: Dundee

first: Fiona

last: Haward

address: Life Sciences, Dow St

country: United Kingdom

institute: University of Dundee

summary: Pilot investigation to determine the endogenouse RNA-binding targets of the cap methlytransferase complex RNMT/RAM in mouse ES cells

overall_design: RNMT seCLIP (a single-end adaptation of the eCLIP method) was perfomed in undifferentiated mouse ES cells following the protocol from Van Nostrand et al (2017). After lysis, RNA was digested with an optimised concentration of RnaseI and immunprecipitation carried out using either an antibody for RNMT or an isotype control. A size-matched input control was prepared from each sample.

first: Victoria

middle: H

last: Cowling


title: Mutant CEBPA promotes tolerance to inflammatory stress through deficient AP-1 activation [HiChIP]

city: Badalona

first: LUCIA

last: LORENZI

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute

summary: The CEBPA transcription factor is frequently mutated in acute myeloid leukemia (AML). Mutations in the CEBPA gene, which are typically biallelic, result in the production of a shorter isoform known as p30. Both the canonical 42-kDa isoform (p42) and the AML-associated p30 isoform bind chromatin and activate transcription, but the specific transcriptional programs controlled by each protein and how they are linked to a selective advantage in AML is not well understood. Here, we show that cells expressing the AML-associated p30 have reduced baseline inflammatory gene expression and display altered dynamics of transcriptional induction in response to LPS, consequently impacting cytokine secretion. This confers p30-expressing cells an increased resistance to the adverse effects of prolonged exposure to inflammatory signals. Mechanistically, we show that these differences primarily result from the differential regulation of AP-1 family proteins. In addition, we find that the altered function of the AP-1 member ATF4 in p30-expressing cells alters their response to ER stress. Collectively, these findings uncover a novel link between mutant CEBPA, inflammation and the stress response, potentially revealing a new vulnerability in AML.

overall_design: HiChIP was performed with H3K27ac antibody. LPS was added for 2 hours to induce an inflammatory response.

first: Maria

last: Cadefau

first: Gerard

last: Martínez-Cebrián

first: Lucía

last: Lorenzi

first: Sergi

last: Cuartero


title: Single-cell transcriptomics of infant and adult T cells across human tissues

city: New York

first: Peter

middle: A

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

country: USA

institute: Columbia University

type: Expression profiling by high throughput sequencing

summary: We performed bulk and single-cell RNA-seq on resting and stimulated T cells from tissues and blood of infant and adult organ donors.

first: Thomas

last: Connors

last: Szabo

first: Hanna

middle: M

last: Levitin

first: Donna

middle: L

last: Farber


title: Mutant CEBPA promotes tolerance to inflammatory stress through deficient AP-1 activation [ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Chromatin immunoprecipitation (ChIP) was performed for histone marks (H3K27ac and H3K4me1), ATF4 and CEBPA transgenes by using an antibody targeting the ERT2 fusion fragment and using an antibody against CEBPA. LPS was added for 2 hours to induce an inflammatory response. Tunicamycin (Tm) was added at 2ug/mL to induce endogenous ATF4 translation

last: Cadefau-Fabregat


title: Lyl-1 links primitive macrophages and microglia development to neuropsychiatric disorders

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University Medical Center Freiburg

summary: The regulation of developmental haematopoiesis by the bHLH transcription factor Lyl-1 has been the focus of our present study. Analysing how Lyl-1 may impact mouse developmental haematopoiesis indicated that Lyl-1 marks YS-derived primitive macrophage progenitors, as well as embryonic microglia. During ontogeny, microglia which representtissue macrophages of the central nervous system emerge from haematopoietic stem cell-independent progenitors originating from the yolk sac (YS). Activation of microglia during development is often critical and my lead to neuropsychiatric diseases in the adult. Here, we show that Lyl-1 disruption alters the development of microglia with far reaching consequences. Lyl-1-deficiency leads to decreased dendritic spine density and impaired neuronal activity, as well as impaired social interactions with increased anxiety-like behaviour. We thus identify Lyl-1 as a critical regulator of primitive macrophage and microglia development, whose disruption impacts microglia development and functionality, leading to a distinct neuropsychiatric phenotype.

overall_design: Analyses of microglia from wt and Lyl1ko mice

first: Shoutang

last: Wang

last: Blank

first: Deshan

last: Ren

first: Anna-Lila

last: Kaushik

first: Katrin

last: Kierdorf

first: Marius

last: Schwabenland

first: Audrey

last: Dujardin

first: Jonas-Frederic

last: Sauer

first: Marlene

last: Bartos

first: Gabriel

last: Matherat

first: Yann

last: Lecluse

first: Dominik

middle: V

last: Elverfeldt

first: William

last: Vaichenker

first: Hana

last: Raslova

first: Isabelle

last: Plo

first: Marco

last: Prinz

last: Godin

last: Bienert


title: Bioinformatics analysis of miRNAs and mRNAs network - Xuefu Zhuyu decoction exerts neuroprotection of traumatic brain injury mice through modulation of MAPK signaling pathway

city: changsha

first: Zhaoyu

last: Yang

address: 87 of xiangya road

country: China

institute: xiangya hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: Xuefu Zhuyu decoction (XFZYD) is used to treat traumatic brain injury (TBI). XFZYD-based therapies have achieved good clinical outcomes in TBI. However, the underlying mechanisms of XFZYD in TBI remedy remains unclear. The study aimed to identify critical miRNAs and putative mechanisms associated with XFYZD through comprehensive bioinformatics analysis. We established a controlled cortical impact (CCI) mice model and treated the mice with XFZYD. The high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) confirmed the quality of XFZYD. The modified neurological severity score (mNSS) and Morris water maze (MWM) tests indicated that XFZYD improved the neurological deficit (P < 0.05) and cognitive function (P < 0.01). Histological analysis validated the establishment of the CCI model and the treatment effect of XFZYD. HE staining displayed that the pathological degree in the XFZYD-treated group was prominently reduced. The transcriptomic data was generated using microRNA sequencing (miRNA-seq) of the hippocampus. According to cluster analysis, the TBI group clustered together was distinct from the XFZYD group. Sixteen differentially expressed (5 upregulated; 11 downregulated) miRNAs were detected between TBI and XFZYD. The reliability of the sequencing data was confirmed by qRT-PCR. Three miRNAs (mmu-miR-142a-5p, mmu-miR-183-5p, mmu-miR-96-5p) were distinctively expressed in the XFZYD compared with the TBI and consisted of the sequencing results. Bioinformatics analysis suggested that the MAPK signaling pathway contributes to TBI pathophysiology and XFZYD treatment. The present research provides an adequate fundament for further knowing the pathologic and prognostic process of TBI and supplies deep insights into the therapeutic effects of XFZYD.

overall_design: Hippocampus miRNA profiles of 14-day-old TBI and XFYZD-treated mice.

first: Yang

last: Wang

first: Tao

last: Tang


title: Expression data of exosomal miRNAs extracted from plasma [Affymetrix miRNA 4.0]

status: Public on Mar 10 2025

city: Doha

first: Abdelali

last: Agouni

address: Al Tarfa

country: Qatar

institute: Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University

summary:
Exosomal miRNAs have emerged as promising disease biomarkers. We aim to investigate the potential of exosomal miRNAs to assist with AIS clinical diagnosis.
In the present research, we used the Affymetrix Genechip miRNA 4.0 Array to investgate the profiles of differentially expressed miRNAs (DEMs) in the exosomes of peripheral blood plasma. As a result, exosomal miRNA profiling yielded a total of 05 DEMs between the AIS (Acute Ischemic Stroke) patients and controls.

overall_design: Peripheral blood samples of 5 AIS patients and 5 healthy individuals were collected for the for exosomal miRNAs extraction and hybridization on Affymetrix microarrays. In AIS group samples selected were: AIS-1, AIS-2, AIS-3, AIS-4 and AIS-5. Meanwhile, 5 healthy individuals were selected as controls: Control-1, Control-2, Control-3, Control-4 and Control-5.

first: Aijaz

last: Parray

first: Ghulam

middle: J

last: Pir

first: Muhammad

last: Zahid


title: High glucose associated YTHDC1 lactaylation reduces the sensitivity of bladder cancer to enfortumab vedotin therapy

first: ruijiang

last: Zeng

address: No.139 Renmin Road Central

institute: The Second Xiangya Hospital of Central South University

summary: Hyperglycemia has been reported to be a risk factor for bladder cancer (BC). Enfortumab vedotin (EV), the first antibody-drug conjugates targeting NECTIN4, has shown promising clinical efficacy in patients with advanced BC. However, the impact of high glucose status on EV sensitivity remains unclear. In this study, we discover that EV treatment in BC patients with diabetes is less effective than those of patients with normal blood glucose. The subsequent cell and mice studies indicate that high glucose decreases the sensitivity of BC cells to EV. We previously reported that high glucose results in decreased protein levels of YTHDC1, promoting the tumorigenesis of BC cells. Our study identifies a high glucose associated lactate-AARS1-YTHDC1-JUND-NECTIN4 axis that affects EV sensitivity in BC. Targeting this axis with JUND activator or β-alanine may offer therapeutic strategies to enhance the sensitivity of BC cells to EV.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the HT1376 cells. WFI vs. Enfortumab vedotin.

first: Zhuo

last: Xing


title: The YTHDC1/GLUT3/RNF183 axis forms a positive feedback loop that modulates glucose metabolism and bladder cancer progression

summary: Aberrant glucose metabolism is a characteristic of bladder cancer. Hyperglycemia contributes to the development and progression of bladder cancer. However, the underlying mechanism by which hyperglycemia promotes the aggressiveness of cancers, especially bladder cancer, is still incompletely understood. N6-methyladenosine (m6A) modification is a kind of methylation modification occurring at the N6 position of adenosine that is important for the pathogenesis of urological tumors. Recently, it was found that the m6A reader YTHDC1 is regulated by high-glucose conditions. In our study, we revealed that YTHDC1 is not only regulated by high-glucose conditions but is also downregulated in bladder cancer tissue and associated with the prognosis of cancer. We also showed that YTHDC1 suppresses the malignant progression of and the glycolytic process in bladder cancer cells in an m6A-dependent manner and determined that this effect is partially mediated by GLUT3. Moreover, GLUT3 was found to destabilize YTHDC1 by upregulating RNF183 expression. In summary, we identified a novel YTHDC1/GLUT3/RNF183 feedback loop that regulates disease progression and glucose metabolism in bladder cancer. Collectively, this study provides new insight regarding the pathogenesis of bladder cancer under hyperglycemic conditions and might reveal ideal candidates for the development of drugs for bladder cancer.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the 5637 cells. siNC vs. siYTHDC1.


title: hnRNPA2B1 promotes osteogenesis differentiation of human adipose-derived stem cells through PHC2/GATA6/BMP axis [RIP-seq]

city: Chengdu

first: Hongyu

last: Gao

state: Sichuan

address: hengdu City, Sichuan Province, Wuhou District people's South Road, three 14

institute: Sichuan University

summary: m6A modification is prevalent on messenger RNA and plays a crucial role in various eukaryotic biological processes, including growth, development, disease, and aging. hnRNPA2B1, a member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family, has been identified as an m6A reader. In this study, hnRNPA2B1 was shown to promote osteogenesis differentiation of human adipose-derived stem cells (hASCs) in vitro. Furthermore, the overexpression of hnRNPA2B1 facilitated bone defect healing in in vivo models of bone defects. hnRNPA2B1 RIP-seq, mRNA-seq, and MERIP-seq were used to identify PHC2 as the target gene of hnRNPA2B1. hnRNPA2B1 enhances the stability of PHC2 mRNA through m6A regulation. PHC2 binds to the promoter region of GATA6 and represses GATA6 expression by increasing H3K27me3 levels. GATA6, in turn, inhibits BMP signaling pathways and the osteogenesis differentiation of hASCs. hnRNPA2B1-PHC2-GATA6-BMP axis offers a promising perspective for the development of stem cell based bone tissue engineering.

overall_design: RIP-seq was designed to identify the mRNAs directly interact with hnRNPA2B1. hnRNPA2B1 IP gourp and IgG group were set to avoid non-specific binding.

first: Yidan

last: Song

first: Yuxi

last: Gu

first: Liangyu

last: Luo

first: Jun

last: Liu


title: AGO2 slicing of a domesticated retrotransposon is necessary for normal mammalian vasculature [RNA-Seq]

city: Bethesda

first: Joana

last: Vidigal

state: MD

address: 37 Convent Dr, Room 6056

department: LBMB

institute: NIH/NCI

summary: Argonaute (AGO) mediated slicing of RNA—also known as RNAi—is a highly conserved phenomenon that is evolutionarily linked to the repression of transposons and other repeats. Although RNAi is no longer a major mechanism of repeat control in mammals, AGO2 has retained cleavage competence and is able to efficiently cut RNAs with extensive complementarity to a bound guide. The regulatory roles this activity plays in mammals however remains poorly understood. Here we show that mice carrying two catalytically inactive Ago2 alleles have extensive developmental abnormalities including systemic vascular defects that are characterized by enlarged and leaky vessels and stem from endothelial cell dysfunction. Endothelial cell defects are caused by failure to repress Rtl1, a paternally-imprinted domesticated retrotransposon, whose cleavage in wild-type animals is triggered by miRNAs of the maternally-imprinted miR-433~127 cluster. Our data pinpoint an essential mRNA cleavage target of AGO2 and suggest that the repurposing of a TE-Argonaute regulatory interaction contributes to the retention of AGO catalytic competence in mammals.

overall_design: small RNA sequencing from wild-type and Ago2 catalytic mutant placentas (3 replicates)

first: Mahendra

last: Prajapat

first: Manish

last: Kumar


title: LC/MS-Based Lipidomics and Transcriptomics Reveal Lipid Diversity and Regulatory Networks Underlying Intramuscular Fat Differences in Xingguo Grey Geese

city: Nanchang

first: mengyun

last: zou

address: No. 602, Nanlian Road, Qingyunpu District

institute: Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural

summary: Intramuscular fat (IMF) serves as a crucial economic indicator of meat quality. To investigate the heterogeneity of IMF composition and its regulatory mechanisms in Xingguo (XG) geese with varying IMF levels, lipidomics and transcriptomics were utilized. The analysis of lipid profiles revealed that the predominant lipids in the IMF of XG geese were glycerophospholipids (GPs), followed by glycerides (GLs). Interestingly, the low-IMF group exhibited an increase in GPs, specifically phosphatidylethanolamines (PEs) and phosphatidylcholines (PCs), while the high-IMF group showed elevated levels of triacylglycerols (TAGs). Transcriptomic analysis indicated that genes related to extracellular matrices (ECM)-receptor interactions, focal adhesion, mitogen-activated protein kinase (MAPK), and forkhead transcription factors O (FoxO) signaling pathways were upregulated in the low-IMF group. In contrast, genes involved in metabolic processes were more pronounced in the high-IMF group. A comprehensive analysis combining lipidomics and transcriptomics identified CD36, fatty acid-binding protein 5 (FABP5), troponin I2  (TNNI2), and coronin-6 isoform X1 (CORO6) as essential regulators influencing IMF accumulation in XG geese. This research emphasizes the significant lipids, genes, and signaling pathways that play roles in IMF accumulation, providing a theoretical basis for enhancing the meat quality of XG geese.

overall_design: RNA-seq profiling of pectoral tissues of Xingguo grey geese with low and high imf content.

first: Mengyun

last: Zou

first: Jiangnan

last: Huang

first: Weihong

last: Zhang

first: Xiaolan

last: Xiong

first: Linjie

last: Rao

first: Qipeng

last: Wei

first: Haiqin

last: Li

first: Fanfan

first: Jinfang

last: Xie

first: Zhangzhang


title: AGO2 slicing of a domesticated retrotransposon is necessary for normal mammalian vasculature [smRNA-Seq]

first: Andrea

middle: G

last: Maria


title: Gene-specific transcript buffering revealed by perturbation of coactivator complexes

city: Illkirch

first: Manuel

last: Mendoza

address: 1 rue Laurent Fries

country: France

institute: INSTITUTE OF GENETICS AND MOLECULAR AND CELLULAR BIOLOGY

summary: Transcript buffering entails reciprocal modulation of mRNA synthesis and degradation to maintain stable RNA levels under varying cellular conditions. Current models depict a global connection between mRNA synthesis and degradation, but underlying mechanisms remain unclear. Here we show that changes in RNA metabolism following depletion of TIP60/KAT5, the acetyltransferase subunit of the NuA4 transcriptional coactivator complex, reveal that transcript buffering occurs at a gene-specific level. By combining RNA sequencing of nuclear, cytoplasmic, and newly synthesised transcript fractions with biophysical modelling in mouse embryonic stem cells, we demonstrate that transcriptional changes caused by TIP60 depletion are offset by corresponding changes in RNA nuclear export and cytoplasmic stability, indicating gene-specific buffering. Disruption of the unrelated ATAC coactivator complex also causes gene-specific transcript buffering. We propose that cells dynamically adjust RNA splicing, export, and degradation in response to individual RNA synthesis alterations, thereby sustaining cellular homeostasis.

overall_design: 8 samples, 3 conditions (controls, Zzz3-AID or Yeats2-AID transgenic mESC line treated with auxin for 24h)

first: DAVID

last: MORENO


title: Transition metal-triggered immunity via an Arabidopsis NLR pair

city: Nanjing

first: cheng

last: gao

state: Jiangsu

address: Nanjing Agricultural University

institute: Nanjing Agricultural University

summary: Plants growing in soil are challenged by multiple biotic (e.g. pathogens) and abiotic (e.g. heavy metals) stressors. Stress resistance is a key determinant for plants to thrive in the environment. Resistance to pathogens requires innate immunity 1, whereas tolerance to metal ions is accomplished by mechanisms such as complexation and compartmentation2,3. Some transition metals can enhance plant’s defense against pathogens4,5, but the mechanism remains unclear. Here, we show that an Arabidopsis head-to-head gene pair of intracellular nucleotide-binding leucine-rich repeat (NLR) receptors antagonistically control transition metal-triggered immunity. One NLR, STM2 directly perceives transition metal ions, such as Cd2+, Cu2+ and Zn2+, as a ligand to activate its NAD+ hydrolytic activity and immune responses, triggering enhanced resistance to the soil-borne bacterial wilt pathogen Ralstonia solanacearum. The other NLR, STM1 suppresses STM2 to protect plants from transition metal-triggered immunity and growth inhibition in the presence of excess metals. STM1 also dampens resistance to the pathogen. Our study defines an NLR activated by transition metals and reveals a trade-off between resistance to pathogens and tolerance to transition metals that are pervasive in soil.

overall_design: To investigate the reasons for the greater sensitivity of stm1 cad1-3 compared to cad1-3 plants to cadmium (Cd). Seedlings grown for 12 days were transferred to plates  with or without Cd for 24 h. Roots and Shoots were sampled separately, and later RNA-seq data from the above tissues were used for comparative analysis of gene expression profiles.

first: Cheng

last: Gao

first: Fangjie

last: Zhao


title: Transcriptional profiling of Schistosoma mansoni male parasites after culturing with female parasites for 72 hours

city: Dallas

first: James

last: Collins

state: Texas

address: 5323 Harry Hines Blvd

department: Department of Pharmacology

institute: UT Southwestern Medical Center

summary: Retrospective analysis of RNAi hits derived from Wang et. al. has found that genes with greater transcripts-per-million (TPM) in S. mansoni are more likely to produce physical phenotypes. To create the best rate-of-return in our large-scale RNAi screen to identify essential schistosome genes that produce physical phenotypes, we quantified TPM of each gene expressed in male parasites after culturing them with female parasites for 72 hours.

overall_design: Male parasites were cultured for 72 hours with female parasites in rich media (Basch 169 media + abscorbic acid, red blood cells, and cholesterol). Male parasites were then separated from female parasites prior to RNA extraction. RNA was then subjected to mRNA-seq.

first: Dylon

last: Stephens

last: Collins III


title: Valorization of seaweed hydrolysate for production of the high-value reverse antibiotic nybomycin using metabolically engineered Streptomyces explomaris

city: Bielefeld

first: Christian

last: Ruckert-Reed

address: Sequenz 1

department: Medical School OWL

institute: Bielefeld University

summary: This study develops a pipeline for high-level production  of the reverse antibiotic nybomycin from three seaweed species: Himanthalia elongata, Palmaria palmata, and Ulva lactuca. Screening Streptomyces strains identified S. explomaris, a marine species, as the best host to express the nybomycin gene cluster. The  accumulated low yields in artificial seawater with brown seaweed hydrolysate. Gene expression analysis revealed downregulation of precursor supply pathways and upregulation of repressors, limiting biosynthesis. Metabolic engineering addressed these bottlenecks, leading to a superior S. explomaris mutant achieving 57 mg/L, a five-fold increase as compared to reported yields. The strain effectively valorized commercial seaweed hydrolysates, highlighting marine feedstocks' potential for antibiotic production.

overall_design: Whole transcriptomes of a nybomycin production strain derived from four time points (early exponential phase (17 h), mid-exponential phase after glucose and mannitol depletion (33 h), stationary phase after galactose and mannose exhaustion (75 h), and late phase (175 h)) and two growth conditions (chemically defined medium using either deionized water or artificial sea water as a base) using 3 biological replicates each.

first: Wei

last: Shua

first: Julian

last: Stegmüller

last: Rückert-Reed

first: Jörn

last: Kalinowski

first: Andriy

last: Luzhetskyy

first: Christoph

last: Wittmann


title: Macrophage peroxisomes guide alveolar regeneration and limit post-acute sequelae of SARS-CoV-2 infection (PASC)

city: Charlottesville

first: Xiaoqin

last: Wei

state: Virginia

address: 2512 Fontaine Ave

institute: University of Virginia

summary: Peroxisomes are essential but often overlooked metabolic organelles. To explore how macrophage peroxisomes protect the lung, we conducted single-cell RNA sequencing (scRNA-seq) on lungs from both naïve and SARS-CoV-2-infected Pex5^flox/flox (WT) and Cd11c-cre Pex5^flox/flox (KO) mice at 7 days post-infection (d.p.i). scRNA-seq revealed an increased proportion of inflammatory monocytes, neutrophils, and monocyte-derived macrophages (MDMs) in the lungs of infected KO mice, alongside a marked reduction in alveolar type 2 (AT2) cells and alveolar macrophages (AMs) compared to infected WT mice. AMs from KO mice showed elevated expression of genes involved in inflammatory responses, innate immunity, and cellular stress signaling, while genes related to wound healing, cell differentiation, and lipid metabolism were downregulated, compared to AMs from WT mice at 7 d.p.i.

overall_design: Cd11c-cre Pex5^flox/flox or Pex5^flox/flox mice were either uninfected (day 0) or infected with 2000 PFU of SARS-CoV-2 MA30 virus. Lung cells were harvested on day 0 and day 7 post infection. For each time point, cells from three individual mice per genotype were pooled and subjected to single-cell RNA sequencing (scRNA-seq) analysis

first: Jie

last: Sun


title: Single-cell transcriptional atlas of hematopoiesis reveals genetic and hierarchy-based determinants of aberrant differentiation in AML

city: Toronto

first: Andy

last: Zeng

state: Ontario

address: 101 College Street

country: Canada

institute: Princess Margaret Cancer Centre

summary: Therapeutic targeting of acute myeloid leukemia (AML) is hampered by intra- and inter-tumoral cell state heterogeneity. To develop a more precise understanding of AML cell states, we constructed a reference atlas of human hematopoiesis from 263,159 single cell transcriptomes spanning 55 cellular states. Using this atlas, we mapped over 1.2 million cells spanning 318 leukemia samples, revealing twelve recurrent patterns of aberrant differentiation in AML. Notably, this uncovered unexpected AML cell states resembling lymphoid and erythroid progenitors that were prognostic within the clinically heterogeneous context of normal karyotype AML, independent of genomic classifications. Systematic mapping of genotype-to-phenotype associations revealed specific differentiation landscapes associated with >45 genetic drivers. Importantly, distinct cellular hierarchies can arise from samples sharing the same genetic driver, potentially reflecting distinct cellular origins for disease-sustaining leukemia stem cells. Thus, precise mapping of malignant cell states provides insights into leukemogenesis and refines disease classification in acute leukemia.

overall_design: Frozen mononuclear cells from 13 genetically diverse AML samples (12 primary AML samples, 1 xenograft sample) were obtained from the Munich Leukemia Laboratory (MLL) and were subject to scRNA-seq with 10x 5’ v1.1 technology at the St Jude Children's Research Hospital (SJCRH).

first: Zeng

last: Andy

first: Iacobucci

last: Ilaria

first: Gao

last: Qingsong


title: Modifying inhibitor specificity for homologous enzymes by machine learning

city: Be'er Sheva

first: Dor

middle: Shlomo

last: Gozlan

address: David Ben Gurion Blvd 1

country: Israel

institute: Ben Gurion University

summary: Selective inhibitors are essential for targeted therapeutics and for probing enzyme functions in various biological systems. The two main challenges in identifying such inhibitors lie in the extensive experimental effort required, including the generation of large libraries, and in tailoring the selectivity of inhibitors to enzymes with homologous structures. To address these challenges, machine learning (ML) is being used to improve protein design by training on targeted libraries and identifying key interface mutations that enhance affinity and specificity. However, such ML-based methods are limited by inaccurate energy calculations and difficulties in predicting the structural impacts of multiple mutations. Here, we present an ML-based method that leverages HTS data to streamline the design of selective inhibitors. To demonstrate its utility, we applied our new method to finding inhibitors of matrix metalloproteinases (MMPs), a family of homologous enzymes involved in both physiological and pathological processes. By training ML models on binding data for three MMPs (MMP-1, MMP-3, and MMP-9), we successfully designed a novel N-TIMP2 variant with a differential specificity profile, namely, high affinity for MMP-9, moderate affinity for MMP-3, and low affinity for MMP-1. Our experimental validation showed that this novel variant exhibited a significant specificity shift and enhanced selectivity compared to wild-type N-TIMP2. Through molecular modeling and energy minimization, we obtained structural insights into the variant’s enhanced selectivity. Our findings highlight the power of ML-based methods to reduce experimental workloads, facilitate the rational design of selective inhibitors, and advance the understanding of specific inhibitor-enzyme interactions in homologous enzyme systems.

overall_design: This study investigates the binding selectivity of human amyloid protein precursor inhibitor (APPI) variants toward the human serine proteases: kallikrein-6 (KLK6 ) and mesotrypsin. A yeast surface display (YSD) library containing 3.5 million APPI-3M variants, each with 0–2 amino acid mutations, was generated. These variants were subjected to pairwise selective screening using fluorescence-activated cell sorting (FACS) and labeled protease pairs to isolate variants with enhanced or diminished selectivity for specific proteases. The sorted variants were analyzed using next-generation sequencing (NGS) on the Illumina Miseq platform to identify mutations associated with differential binding selectivity.

first: Dor S.

first: Reut

last: Meiri

first: Gili

last: Shapira

first: Matt

last: Coban

first: Yaron

last: Orenstein

first: Evette

middle: S

last: Radisky

first: Niv

last: Papo


title: Efficient and multiplexed somatic genome editing with Cas12a mice

city: Stanford

first: Haiqing

last: Xu

state: CA

address: 327 Campus Drive

department: Biology

institute: Stanford University

summary: Somatic genome editing in mouse models has increased our understanding of the in vivo effects of genetic alterations in areas ranging from neuroscience to cancer biology and beyond. However, existing models are limited in their ability to create multiple targeted edits. Thus, our understanding of the complex genetic interactions that underlie development, homeostasis, and disease remains incomplete. Cas12a is an RNA-guided endonuclease with unique attributes that enable simple targeting of multiple genes with crRNA arrays containing tandem guides. To accelerate and expand the generation of complex genotypes in somatic cells, we generated transgenic mice with Cre-regulated and constitutive expression of enhanced Acidaminococcus sp. Cas12a (enAsCas12a). In these mice, enAsCas12a-mediated somatic genome editing robustly generated compound genotypes, as exemplified by the initiation of diverse cancer types driven by homozygous inactivation of trios of tumor suppressor genes or an oncogenic translocation. We further integrated these modular crRNA arrays with clonal barcoding to quantify the size and number of tumors with each array, as well as the efficiency of each crRNA. Efficiency and TSG combos These Cas12a alleles will enable the rapid generation of disease models and broadly facilitate the high-throughput investigation of coincident genomic alterations in somatic cells in vivo.

overall_design: We combined Cas12a-mediated gene editing with tumor barcoding and high-throughput sequencing (Tuba-seq) to generate in vivo tumor models and precisely quantify the effects of combinatorial genetic alterations in these models.

first: Jess

middle: D

last: Hebert

first: Yuning

last: Tang

first: Paloma

last: Ruiz

first: Colin

middle: R

last: Detrick

first: Jing

last: Wang

first: Nicholas

middle: W

last: Hughes

first: Oscar

last: Donosa

first: Vicky

middle: P

last: Siah

first: Laura

last: Andrejka

first: Saswati

last: Karmakar

first: Irenosen

last: Aboiralor

first: Rui

first: Rocio

last: Sotillo

first: Julien

last: Sage

first: Le

last: Cong

first: Dmitri

last: Petrov

first: Monte

last: Winslow


title: Engineering mtDNA Deletions by Reconstituting End-Joining in Human Mitochondria [Exp1_iScaI_KL_T4]

first: Yi

last: Fu

state: New York

address: 430 E 67th Street – RRL 1141

institute: MSKCC

summary: Recent breakthroughs in the genetic manipulation of mitochondrial DNA (mtDNA) have enabled the precise introduction of base substitutions and the effective removal of genomes carrying harmful mutations. However, the reconstitution of mtDNA deletions responsible for severe mitochondrial disorders and age-related diseases has not yet been achieved in human cells. Here, we developed a method to engineer specific mtDNA deletions in human cells by co-expressing end-joining (EJ) machinery and targeted endonucleases. As a proof-of-concept, we used mito-EJ and mito-ScaI to generate a panel of clonal cell lines harboring a ~3.5 kb mtDNA deletion with the full spectrum of heteroplasmy. Investigating these isogenic cells revealed a critical threshold of ~75% deleted genomes, beyond which cells exhibited depletion of OXPHOS proteins, severe metabolic disruption, and impaired growth in galactose-containing media. Single-cell multiomic analysis revealed two distinct patterns of nuclear gene deregulation in response to mtDNA deletion accumulation; one triggered at the deletion threshold and another progressively responding to increasing heteroplasmy. In summary, the co-expression of mito-EJ and programable nucleases provides a powerful tool to model disease-associated mtDNA deletions in different cell types. Establishing a panel of cell lines with a large-scale deletion at varying levels of heteroplasmy is a valuable resource for understanding the impact of mtDNA deletions on diseases and guiding the development of potential therapeutic strategies.

overall_design: ATAC-seq on ARPE-19 cells expressing mito-EJ and subjected to transfection or induction of mitochondria-localized restriction enzyme (ScaI or ApaLI) with the purpose of sequencing the generally accessible mitochondrial DNA.

first: Agnel

last: Sfeir


title: Engineering mtDNA Deletions by Reconstituting End-Joining in Human Mitochondria [Exp3_MGME1KO_KL_iApaLI]

overall_design: ATAC-seq on ARPE-19 cells expressing mito-EJ and subjected to induction of mitochondria-localized restriction enzyme ApaLI with the purpose of sequencing the generally accessible mitochondrial DNA.


title: Engineering mtDNA Deletions by Reconstituting End-Joining in Human Mitochondria [DOGMAseq]

overall_design: DOGMA-seq (with modified ATAC protocol to enrich for mtDNA) on ARPE-19 clonal cells carrying mtDNA deletions.

first: Fu

last: Yi

first: Land

last: Max

first: Sfeir

last: Agnel


title: The effect of BPDE on induced pluripotent stem cells of a Nijmegen Breakage Syndrome patient and healthy donors.

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

institute: Universitätsklinikum Düsseldorf

summary: Benzo[a]pyrene diol epoxide (BPDE) is a highly carcinogenic metabolite of the environmental contaminant Benzo[a]pyrene, which is commonly found as a by-product of incomplete combustion of organic matter. BPDE reacts with the DNA to form BPDE-DNA bulky adducts which, if not removed, can lead to mutations due to DNA base-pair substitution and consequently to tumorigenesis. Due to its lipophilic nature, B[a]p can cross the placenta to reach the developing fetus and the placenta of mice, rats and humans can metabolize B[a]p into BPDE, which can lead to fetal genotoxic exposure. Besides direct embryonic exposure, BPDE-DNA adducts are detectable in the sperm and ovarian cells of cigarette smokers, and these DNA modifications can be paternally transmitted through the spermatozoa to the embryo. Human induced pluripotent stem cells (hiPSCs) can be used as a model of human embryonic stem cells (hESCs), an with that in mind, we treated hiPSCs with BPDE and performed a microarray analysis to evaluate for the first time the effects of BPDE exposure in pluripotent stem cells. Furthermore, hiPSCs derived from patients suffering from Nijmegen Breakage Syndrome, a chromosomal instability disorder characterized by microcephaly, defective DNA repair and increased risk of malignancies, were also investigated in the context of BPDE exposure and compared to their healthy counterparts. Transcriptomics analysis, coupled with protein content analysis through immunostaining and western blots, revealed that hiPSCs have a robust reaction to BPDE exposure, with an enhanced expression of several targets related to the p53 mediated DNA damage response, including DNA lesion bypass, cell cycle checkpoints and extrinsic apoptosis. Additionally, hiPSC harbouring an NBS mutation reacted differently to BPDE treatment than WT cells, showing less apoptotic response, no p53 or MDM2 protein increase, increased transcription of cancer-related targets and the repression of DNA-repair pathways transcription.

overall_design: The transcriptomes of iPSCs derived from healthy donors and Nijmegen Breakage Syndrome patients, with and without BPDE treatment, were compared by microarray analysis (PrimeView Human Gene Expression Array, Affymetrix, Thermo Fisher Scientific).

first: Wruck

last: Wasco

first: Meira

middle: d

last: Vanessa Cristina

first: Adjaye

last: James


first: Alexander

middle: James

last: Murison

address: 101 College Street, TMDT room 11-706

institute: University Health Network

summary: Library preparation for ATAC-Seq was performed on 1000-5000 cells with Nextera DNA Sample Preparation kit (Illumina), according to previously reported protocol55. 4 ATAC-seq libraries were sequenced per lane in HiSeq 2500 System (Illumina) to generate paired-end 50-bp reads. Reads were mapped to hg38 using BWA (0.7.15) using default parameters. Duplicate reads, reads mapped to mitochondria, an ENCODE blacklisted region or an unspecified contig were removed (Encode Project Consortium, 2012). MACS (2.2.5) was used to call peaks in mapped reads.

overall_design:
ATAC-Seq of Primary cord blood (CB) derived hematopoietic cells spanning B-Cell Differentiation

***************************************************************
Raw files for human/patient samples are being made available in EGA (https://www.ebi.ac.uk/ega/) for controlled access to the personally identifiable sequence data.
***************************************************************

first: Laura

last: Garcia Prat


title: Muscleblind-like proteins are novel modulators of the tumor-immune microenvironment

city: Seattle

first: Edie

middle: I

last: Crosse

state: Washington

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

summary: Exploiting the immune system to target and eradicate cancer cells is an area of intense clinical study. However, the underlying mechanisms that shape the tumor-immune microenvironment remain poorly understood. Here, we identify Muscleblind-like (MBNL) proteins as novel modulators of the tumor microenvironment across diverse cancer types. Initially, in a mouse melanoma model, we demonstrate that loss of MBNL expression drives reduced cytotoxic CD8+ T cell tumor infiltrate and increased tumor cell viability. This causes an attenuated response to inflammatory stimulation with interferon gamma and concomitantly reduced antigen presentation by MHC Class I. We then extended these studies to 29 human cancer types from extensive analysis of TCGA to find that high MBNL1 expression was consistently associated with augmented cytotoxic T cell tumor infiltration. These new insights position MBNL proteins as critical players shaping the immune landscape across diverse malignancies.

overall_design: RNA-Seq raw data from CRISPR edited C57BL/6 mouse cells with or without IFNg stimulation including the following genotypes: no-template control (NTC) or double knock out  of MBNL1 and MBNL2 (DKO). N = 3 replicates for each condition.

first: Austin

last: Gabel

first: Andrea

middle: E

last: Belleville

first: Simon

last: Hogg

first: Siegen

last: McKellar

first: Omar

last: Abdel-Wahab

first: James

last: Thomas

first: Robert

middle: K

last: Bradley


title: Macrophage peroxisomes guide alveolar regeneration and limit post-acute sequelae of SARS-CoV-2 infection (PASC).

first: Xiaoqin

last: Wei

summary: Peroxisomes are essential but often underappreciated metabolic organelles. In this study, we demonstrate that exuberant interferon signaling reshapes the macrophage peroxisome compartment following severe COVID-19. To uncover the molecular characteristics underlying the protective role of macrophage peroxisomes after viral infection, we isolated RNA from wild-type (WT) and Pex5-deficient alveolar macrophages (AMs) with or without Poly(I:C) treatment in vitro, followed by bulk RNA sequencing. Our analysis revealed enhanced expression of inflammation-associated pathways and innate immune responses in Pex5-deficient AMs. However, these cells also exhibited attenuated activation of tissue development-related pathways and impaired mitochondrial functions, regardless of Poly(I:C) treatment.

overall_design: Total RNA was extracted from in vitro cultured WT and Pex5-deficient AMs, with or without Poly(I:C) treatment for 24 hours, for bulk RNA sequencing. After quality control, only high-quality RNA (Agilent Bioanalyzer RIN > 7.0) was used to generate the RNA-seq library.

first: Jie

last: Sun


title: Peptidyl-tRNA hydrolysis rate influences the efficiency of nonsense-mediated mRNA decay

city: Aurora

first: Divya

last: Kolakada

state: CO

address: 13001 E 17th Place

department: Biochemistry and Molecular Genetics

institute: University of Colorado Anschutz

summary: Nonsense-mediated mRNA decay (NMD) is a quality control mechanism that prevents the accumulation of harmful truncated proteins by degrading transcripts with premature termination codons (PTCs). NMD activity varies across many contexts, with the variation having critical consequences during both normal development and disease. However, the factors that influence this variability remain poorly understood. Here, we investigate the relationship between the immediate sequence context of a PTC and NMD activity. We find an enrichment of glycine (Gly) codons preceding a PTC in common nonsense variants in contrast with a depletion of Gly codons preceding a normal termination codon (NTC). Furthermore, Gly-PTC enrichment is most pronounced in genes that tolerate loss-of-function variants, suggesting a biological impact for Gly-PTC contexts. Consistent with this idea, Gly-PTC contexts have higher NMD activity compared to an alanine-PTC context. We used a massively parallel reporter assay to comprehensively assess the effect of PTC sequence context on NMD activity, which revealed that peptidyl-tRNA hydrolysis rate during translation termination was the most important feature in discriminating high and low NMD activity. We show with biochemical assays in a eukaryotic system that Gly-TC contexts have the slowest termination rate compared to other codons. Based on these findings, we propose that NMD activity is modulated by the "window of opportunity" offered by peptidyl-tRNA hydrolysis rate and thus, translation termination kinetics. Gly-PTC contexts may have coevolved with NMD to ensure robust elimination of potentially toxic truncated proteins from non-essential genes.

overall_design:
To investigate the effect of PTC sequence context on EJC-independent and EJC-enhanced NMD targets, we integrated all possible combinations of the PTC Sequence context (NNNNNNTRRN, where TRR is either one of the stop codons or a TGG no NMD control) of previously validated EJC-independent and EJC-enhanced NMD reporters
We integrated these reporter libraries into HEK293T cells via Cre-Lox recombination. We treated the cells with DMSO or SMG1i (an NMD inhibitor) for 24 hours and harvested total RNA. The RNA was converted into cDNA, after which libraries were made and sent for sequencing.

first: Rui

last: Fu

first: Nikita

last: Biziaev

first: Alexey

last: Shuvalov

first: Mlana

last: Lore

first: Amy

last: Campbell

first: Michael

middle: A

last: Cortázar

first: Marcin

last: Sajek

first: Jay

last: Hesselberth

first: Neelanjan

last: Mukherjee

first: Elena

last: Alkalaeva

first: Sujatha

last: Jagannathan


title: Dysfunctional neutrophil Type 1 interferon responses in preschool children with recurrent wheezing and IL-4-mediated aeroallergen sensitization

city: Atlanta

first: Min

last: Huang

address: WMB, 101 Woodruff Circle

institute: Emory University

summary: The innate mechanisms associated with viral exacerbations in preschool children with recurrent wheezing are not understood.  We assessed differential gene expression in blood neutrophils from preschool children with recurrent wheezing, stratified by aeroallergen sensitization, at baseline and after exposure to polyinosinic-polycytidylic acid (poly(I:C)). We also examined whether poly(I:C)-stimulated blood neutrophils influenced airway epithelial gene expression. Blood neutrophils were purified and cultured overnight with poly(I:C) and underwent next-generation sequencing with Reactome pathway analysis. Primary human small airway epithelial cells were treated with poly(I:C)-treated neutrophil culture supernatants and were analyzed for Type 1 interferon gene expression with a targeted array. Symptoms and exacerbations were assessed in participants over 12 months. 436 genes were differently expressed in neutrophils from children with versus without aeroallergen sensitization at baseline, with significant downregulation of Type 1 interferons. These Type 1 interferons were significantly upregulated in sensitized children after poly(I:C) stimulation. Confirmatory experiments demonstrated similar upregulation of Type 1 interferons in IL-4 treated neutrophils stimulated with poly(I:C). Poly(I:C)-treated neutrophil supernatants from children with aeroallergen sensitization also induced a Type 1 interferon response in epithelial cells. Children with aeroallergen sensitization also had higher symptom scores during exacerbations and these symptom differences persisted for three days after prednisolone treatment.  We conclude that Type 1 interferon responses are dysregulated in preschool children with aeroallergen sensitization, which is in turn associated with exacerbation severity. Given the importance of Type 1 interferon signaling in viral resolution, additional studies of neutrophil Type 1 interferon responses are needed in this population.

overall_design: Preschool children 12-59 months of age with recurrent wheezing and at least one wheezing episode treated with systemic corticosteroids in the previous 12 months were included in the study. Recurrent wheezing was defined as a lifetime history of two or more episodes of wheezing, with each episode lasting at least 24 hours and requiring repeated treatment with albuterol sulfate. Children were excluded if they had co-morbid disorders associated with wheezing (such as immune deficiency, cystic fibrosis, pulmonary aspiration, congenital airway anomalies, or premature birth before 35 weeks gestation) or if they had a significant developmental delay or failure to thrive. Preschool participants submitted blood samples for RNA-seq and determination of aeroallergen sensitization. Aeroallergen sensitization was determined by specific IgE testing with an inhalant allergen panel specific to the Atlanta region with twelve extracts: Dermatophagoides farinae, Dermatophagoides pteronyssinus, dog dander, cat dander, Blatella germanica, Alternaria tenuis, Aspergillus fumagatis, oak tree, pecan tree, Bermuda grass, Johnson grass, and common ragweed (Ambrosia artemisiifolia) (Greer® Laboratories, Lenoir, North Carolina). Tests were considered positive if specific IgE values were >0.35 kU/L.

first: Anne

middle: M

last: Fitzpatrick

first: Rishikesan

last: Kamaleswaran

first: Jocelyn

last: Grunwell


title: Hippocampal DNA methylation promote memory persistence by facilitating systems consolidation and cortical engram stabilization

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: The long-term stabilization of memory traces or engram involves the rapid formation of cortical engrams during encoding that mature functionally over time guided by the activity of the hippocampus. The molecular mechanisms that regulate this process remain largely unknown. Here, we found that hippocampal DNA methylation converts short-lasting into long-lasting memories by promoting systems consolidation and the stabilization of cortical engrams.

overall_design: Differential gene expression analysis of RNA-seq data for hippocampus tissue of mice that were trained in contextual fear conditioning and either expressed a Control or overexpressed Dnmt3a2.

first: Janina

last: Kupke

first: Stefanos

last: Loizou

first: Ana

last: Oliveira


title: Gene expression profiling of holoclones from limbus, conjunctiva and oral mucosa

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

summary: The research of a specific oral mucosa epithelial marker was performed by microarray analysis of holoclones derived from cornea, conjunctiva and oral mucosa tissues. The results identified SOX2 and PAX6 as positive and negative markers to assess the presence (or absence) of oral epithelium onto the ocular surface.

overall_design: Holoclones were isolated from the culture of biopsy from 2 donors of conjunctiva, 2 donors of limbus and  2 donors of oral mucosa and total cellular RNA was extracted. GEP was performed using Affymetrix platform and data were processed by means of Partek Genomics Suite Software.

first: Eustachio

last: Attico

first: Giulia

last: Galaverni

first: Elisa

last: Bianchi

first: Lorena

last: Losi

first: Alessandro

last: Lambiase

first: Paolo

last: Rama

first: Graziella

last: Pellegrini


title: Sex-specific transcriptome of Artemia franciscana in embryogenesis

status: Public on Mar 09 2025

city: Mainz

first: Frank

last: Rühle

address: Ackermannweg 4

department: Bioinformatics Core Facility

institute: Institute of Molecular Biology (IMB)

summary: Differences in lifespan are influenced by chromosome organization and histone dynamics. Unequal sex chromosome copy numbers impact chromatin modification levels between males and females, especially the ones involved in dosage compensation (DC). Those differences could shape sex-specific traits such as lifespan, but the mechanisms and evolutionary prevalence of this phenomenon remain incompletely understood. However, the onset and stability of DC across life stages are currently unknown. Notably, all well-understood DC mechanisms share a common feature: their establishment early in embryogenesis. In Artemia, embryonic development lasts approximately five days, ending with the hatching of free-swimming nauplii. This is followed by a juvenile stage during which the sexes are immature and visually indistinguishable. Sexually mature adults with visible male-female differences emerge at 20–25 days post-fertilization (dpf). To investigate the onset of DC, we performed low-input RNA-seq on single embryos at 1-2 dpf and 4 dpf. Those stages correspond to Blastula (1-2 dpf) and post-Gastrulation (4 dpf) stages, respectively.

overall_design: Each group (1-2 dpf and 4 dpf) contains six biological replicates. Sex of the embryos was determined by expressed SNPs on the sex chromosomal areas.

first: Frederic

last: Zimmer

first: Claudia

last: Keller Valsecchi


title: Human mood disorders risk gene synaptotagmin14 affects mania-like behaviors in mice

city: Kunming

first: Ming

last: Li

state: Yunnan

address: NO 32 Jiao-Chang Donglu

institute: Kunming Institute of Zoology, Chinese Academy of Sciences

summary: Major depressive disorder (MDD) and bipolar disorder (BD) are the most prevalent mood disorders and cause considerable burden worldwide. Compelling evidence suggests a pronounced overlap between these two diseases in clinical symptoms, treatment strategies, and genetic etiology. Here we use a BD GWAS (1822 cases and 4650 controls) and a MDD GWAS (5303 cases and 5337 controls) of Han Chinese origin to investigate their shared genetic basis, followed by exploration of the underlying mechanisms. The lead SNP in the Han Chinese meta-analysis, rs126277 at the 1q32.2 locus, also exhibited nominal associations with mood disorders as well as several sub-clinical phenotypes (e.g., mania) related to mood disorders (UK biobank samples) in European populations. Bulk tissue and single-cell eQTL studies suggest that the risk G-allele of rs126277 predicted lower SYT14 mRNA expression in human brain tissues and cells, indicating possible involvement of this gene in mood disorders. We generated mice lacking Syt14 (Syt14–/–) and mice with insufficient expression of Syt14 in the hippocampus (Syt14-KD). We found that depletion of Syt14 resulted in mania-like behaviors including hyperactivity and anti-depressive behaviors, resembling aspects of mood disorders. We also confirmed that deficiency of this gene in the hippocampus was sufficient to induce hyperactivity in the mice. RNA-sequencing analyses of the hippocampus of Syt14–/– mice revealed significant upregulation of Per1 as well as downregulation of Slc7a11 and Ptprb. Ultrastructural analyses showed significant alteration of the number of vesicles within 50 nm to the active zone and the width of synaptic cleft in the ventral hippocampus of Syt14–/– mice compared with control mice. And Syt14–/– mice exhibit aberrant glutamate signaling patterns in the hippocampus. Overall, we have identified a novel mood disorder risk gene SYT14, and confirmed its impact on mania-like behaviors and essential roles in synaptic function. While the current study provides clues for the pathological mechanisms of mood disorders, further investigations elucidating the detailed mechanisms by which SYT14 regulates mood disorders-related traits are needed.

overall_design: To investigate the function of Syt14 in mood disorder and motor coordination, we procured the hippocampus and cerebellum tissues from three Syt14 knockout (Syt14-/-) mice and three wild-type (Syt14+/+) mice. Subsequently, we conducted a comprehensive gene expression profiling analysis, leveraging the data derived from RNA sequencing (RNA-seq) of these tissues. Comparative gene expression profiling analysis of RNA-seq data for Syt14-/- mice and Syt14 +/+ mice.

first: Yue

last: Zhang

first: Chuyi

first: Xiao

last: Xiao


title: A mechanistic basis for genetic assimilation in natural fly populations

city: Barcelona

first: Gonzalo

last: Sabarís

address: Passeig del Migdia s/n

institute: IBB-CSIC

summary: RNA-sequencing polyA library preparation in wing discs (WD) and pupal wings (PW) from inbred (D907) and outbred (Mix) fly populations from lines selected for the ectopic veins trait under genetic assimilation (assimilated) or direct artificial selection under normal conditions (non-assimilated) and unselected (control) flies.

overall_design: RNA-seq libraries were prepared from third instar larval wing imaginal discs and pupal wings (24-27h APF) of female individuals of the D907 and Mix lines.

first: Bernd

last: Schuettengruber

first: Giorgio

middle: L

last: Papadopoulos

first: Marta

last: Coronado-Zamora

first: Maximilian

middle: H

last: Fitz-James

first: Josefa

last: González

first: Giacomo

last: Cavalli


summary: Hi-C experiments on wing discs (WD) from D907 inbred fly populations from lines selected for the ectopic veins trait by genetic assimilation (assimilated) or direct artificial selection under normal conditions (non-assimilated) and unselected (control) flies.

overall_design: Hi-C experiments in third instar larval wing imaginal discs of the D907 fly lines.


title: Neutrophil KLF2 regulates inflammasome-dependent neonatal mortality from endotoxemia

city: Cleveland

first: Ernest

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

summary: Preterm neonates die at a significantly higher rate from sepsis than full-term neonates, attributable to their dysregulated immune response. In addition to tissue destruction caused directly by bacterial invasion, an overwhelming cytokine response by the immune cells to bacterial antigens also results in collateral damage. Sepsis leads to decreased gene expression of a critical transcription factor, Kruppel-like factor-2 (KLF2), a tonic repressor of myeloid cell activation. KLF2 gene expression is also lower in murine pups at an earlier postnatal age. Using a murine model of myeloid-KLF2 deletion, we show that loss of KLF2 leads to decreased survival after endotoxemia in a developmentally dependent manner, with increased mortality at postnatal day 4 (P4) compared to P12 pups. This survival is significantly increased by neutrophil depletion before endotoxemia. P4 knockout pups have increased pro-inflammatory cytokine levels after endotoxemia compared to P4 controls or P12 pups, with significantly increased levels of IL-1b, an end product of the activation of the NLRP3 inflammasome complex. Both loss of myeloid KLF2 and a younger postnatal age lead to increased NLRP3 protein expression and release of IL-1b in bone marrow neutrophils. Inhibition of NLRP3 inflammasome activation by MCC950 significantly increased survival after endotoxemia in P4 pups. Transcriptomic analysis of bone marrow neutrophils showed that loss of myeloid-KLF2 is associated with gene enrichment of pro-inflammatory pathways in a developmentally dependent manner. These data suggest that targeting KLF2 could be a novel strategy to decrease the pro-inflammatory cytokine storm in neonatal sepsis and improve survival in neonates with sepsis.

overall_design: Bone marrow neutrophil total RNA from postnatal day 4 andn 12 pups from two genotypes, Klf2fl/fl Lyz2Cre and Lyz2Cre. Bone marrows were isolated from bilateral femurs and tibias, crushed in RPMI-1640 media, and neutrophils were isolated using immunomagnetic negative selection (StemCell Mouse Neutrophil Enrichment Kit, Vancouver, BC, Canada). Total RNA was extracted using Qiagen RNeasy Micro Kit.

first: Devashis

last: Mukherjee

first: George

last: Dubyak

first: Lalitha

last: Nayak


summary: Whole-genome sequencing in inbred (D907) and outbred (Mix) fly populations from lines selected for the ectopic veins trait under genetic assimilation (assimilated) or direct artificial selection under normal conditions (non-assimilated), unselected (control) and ancestral (P0) fly populations.

overall_design:
Evolve and resequence assays by performing whole-genome sequencing (WGS) of pools of individuals (Pool-seq) from D907 and Mix fly lines.
Pool-seq assay by performing whole-genome sequencing (WGS) of pools of individuals from D208 inbred fly line.


title: Development of a new model of Parkinson´s disease

city: Pamplona

first: Ana

last: Garcia Osta

state: Navarra

address: Juslarrocha 10, 3H

department: neuroscience

institute: Cima

summary: To get insight the molecular mechanism underlying neuronal loss in Parkinson´s disease.  We  performed gene expression profiling analysis using data obtained from RNA-seq of midbrain of mice injected with an AAV control or an AAV expressing human tyrosinase that induces neuromelanin accumulation and subsequent neuronal loss.

overall_design: Comparative gene expression profiling analysis of RNA-seq data  of midbrain of mice injected with an AAV control or an AAV expressing human tyrosinase.

last: García-Osta

last: Garcia-Gomara

first: Mar

last: Cuadrado-Tejedor

first: Naroa

last: Legarra


title: Engineering mtDNA Deletions by Reconstituting End-Joining in Human Mitochondria [Exp2_POLGD274A_MGME1KO_ScaI]

city: New York

first: Yi

last: Fu

overall_design: ATAC-seq on ARPE-19 cells expressing mito-EJ and subjected to transfection of mitochondria-localized restriction enzyme ScaI with the purpose of sequencing the generally accessible mitochondrial DNA.

first: Agnel

last: Sfeir


last: Sabarís

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

overall_design: Refer to individual Series


title: Wound Induces Multi-Layered Barrier Formation in Mature Leaves via Phytohormone Signaling and ATML1-Mediated Epidermal Specification

city: Seoul

first: Yuree

last: Lee

address: 1 Gwanak-ro, Gwanak-gu

department: Biological Sciences

country: South Korea

institute: Seoul National University

summary: The epidermis of plants forms a protective barrier against biotic and abiotic stress. Little is known about how breaches in the epidermis are repaired, especially those of mature leaves. Here, we investigated wound healing in the mature leaves of Arabidopsis. We discover a novel wound protection mechanism comprising a multi-layered ligno-suberized barrier covered with cuticular wax. This barrier is formed by mesophyll cells that adopt an epidermal fate. This cell fate transition is regulated in two steps by ATML1, a key transcription factor in epidermal specification. First, mesophyll cells of protective layer 1 (P1), just beneath the wound, transition into epidermal cells, sealing the wound by depositing cuticle, a mechanism that involves signaling through ethylene and reactive oxygen species produced by RBOHE. This signaling also promotes P1 cell death, ensuring wax accumulation on the surface. Second, the underlying protective layer 2 (P2) undergoes ligno-suberization, driven by jasmonic acid and RBOHD, forming a cork-like layer on the leaf surface. ATML1 regulates this process in P2 as well. Thus, wound healing in mature leaves involves integration of ethylene and jasmonic acid signaling with ATML1-mediated epidermal cell specification to coordinate cell layer-specific functions, including cuticular wax formation and ligno-suberization. This novel protective mechanism also occurs in the leaves of tobacco and Capsella, suggesting it is widespread.

overall_design: RNA-sequencing of 4-week-old 8th Arabidopsis leaf given mechanical wound

first: Jung-Min

first: Woo-Taek

last: Jeon

first: Hoon

last: Jung


title: Similar metabolic pathways are affected in both Congenital Myasthenic Syndrome-22 and Prader-Willi Syndrome

city: Leuven

first: Alvaro

last: Cortés Calabuig

address: Herestraat 49 PO box 602

country: Belgium

institute: Genomics Core Leuven

summary: Loss of prolyl endopeptidase-like (PREPL) encoding a serine hydrolase with (thio)esterase activity leads to the recessive metabolic disorder Congenital Myasthenic Syndrome-22 (CMS22). It is characterized by severe neonatal hypotonia, feeding problems, growth retardation, and hyperphagia leading to rapid weight gain later in childhood. The phenotypic similarities with Prader-Willi syndrome (PWS) are striking, suggesting that similar pathways are affected. The aim of this study was to identify changes in the hypothalamic-pituitary axis in mouse models for both disorders and to examine mitochondrial function in skin fibroblasts of patients and knockout cell lines. We have demonstrated thatPreplis downregulated in the brains of neonatal PWS-IC deleted (PWS-ICdel)mice. In addition, the hypothalamic-pituitary axis is similarly affected in bothPrepl knockoutand PWS-ICdelmice resulting in defective orexigenic signaling and growth retardation. Furthermore, we demonstrated that mitochondrial function is altered inPREPLknockout HEK293T cells and can be rescued with the supplementation of coenzyme Q10. Finally, PREPL-deficient and PWS patient skin fibroblasts display defective mitochondrial bioenergetics. The mitochondrial dysfunction in PWS fibroblasts can be rescued by overexpression of PREPL. In conclusion, we provide the first molecular links between CMS22 and PWS, raising the possibility that PREPL substrates might become therapeutic targets for treating both disorders.

overall_design:
To investigate molecular similarities betweenCongenital Myasthenic Syndrome-22 and Prader-Willi Syndrome, we used the brain tissues from two mouse models, Prepl knockout and PWS-IC deleted mice. 4 WT samples were compared with 4 knockout or deleted samples for each Prepl knockout and PWS-IC deletedmice.
We then performed comparative gene expression profiling analysis using the data from RNA-seq of Prepl knockout and PWS-IC deleted mice with their respective controls

first: Kritika

last: Bhalla

first: Karen

last: Rosier

first: Yenthe

last: Monnens

first: Sandra

last: Meulemans

first: Ellen

last: Vervoot

first: Lieven

last: Thorrez

first: Patrizia

last: Agostinis

first: Daniel

middle: T

last: Meier

first: Anne

last: Rochtus

first: James

last: Resnick

first: John

last: Creemers


title: NCBR-123: ILC1s and T cells in the Oral Mucosa

city: Bethesda

first: Heather

last: Hickman

address: Building 10 Rm 11N244A

department: LCIM

institute: NIAID

summary: This project was bulk RNAseq on naïve oral mucosa biospys in three different mouse lines (B6, Tac111, Tac146), attempting to idenitfy differences between each cell line. Samples were prepared using illumia truseq protocols and sequenced on a NovoSeq SP.

overall_design: bulk RNA sequencing comparison of 3 mouse strains to identify differences between strains.

first: Tom

last: Hill

first: Sophie

last: Vrba


first: Gonzalo

last: Sabarís

summary: CUT&RUN assays in inbred (D907) and outbred (Mix) fly populations from lines selected for the ectopic veins trait under genetic assimilation (assimilated) or direct artificial selection under normal conditions (non-assimilated) and unselected (control) flies.

overall_design: CUT&RUN assays in third instar larval wing imaginal discs using H3K9me3, H3K27ac and IgG (control) antibodies in D907 and Mix fly lines.

first: Bernd

last: Schuettengruber

first: Giorgio

last: Papadopoulos

first: Marta

last: Coronado-Zamora

first: Maximilian

last: Fitz-James

first: Josefa

last: González

first: Giacomo

last: Cavalli


title: Transcriptomic effects of progesterone and mifepristone in the cycling endometrium

city: Rancagua

first: Nicolas

last: Santander

address: Libertador Bernardo O'Higgins 611

country: Chile

institute: Universidad de O´Higgins

summary: Mifepristone is an antagonist of the progesterone receptor in clinical use. Here, we explored the effects of mifepristone alone, and the effect of progesterone after the dose of mifepristone, on the transcriptomic signature in endometria from cycling women.

overall_design: We obtained total RNA from endometrial biopsies taken 7 days after the LH maximum in consecutive cycles. In each cycle, women were treated with mifepristone alone, progesterone alone, a combination of both, or placebo.

first: Alejandro

last: Tapia

first: Pilar

last: Vigil


title: PP1γ regulates Pol II occupancy and elongation rate

city: Shanghai

first: Aiwei

last: Wu

state: Shanghai

address: 800 Dongchuan Road

department: School of Life Sciences and Biotechnology

institute: Shanghai Jiao Tong University

summary: Protein phosphatase 1 complex (PP1C), consisting of one of the phosphatases, PP1α, β and γ, and three regulatory subunits PNUTS, TOX4 and WDR82, plays critical roles in gene regulation and is mutated in over 20% uterine corpus endometrial carcinoma cases. Here we show that knockdown of PP1γ reduced chromatin occupancy of RNA polymerase II (Pol II), but increased the cellular level and chromatin occupancy of Ser-2 phosphorylated Pol II and Ser-5 phosphorylated Pol II. 4sUDRB-seq data showed that the Pol II elongation rate decreased upon PP1γ loss. These results advanced our understanding of the roles of PP1γ in transcriptional regulation.

overall_design: Study the roles of PP1γ in transcriptional regulation.

first: Ming

last: Yu

first: Ziling

last: Liu

first: Talang

last: Wang


title: Exosomal miRNAs from Ewing sarcoma cells and mesenchymal stem cells

city: Beijing

first: Hua

address: 38 Xueyuan Road

department: Department of Pathology

institute: Peking University Health Science Center

summary:
Sarcoma-derived exosomes play an important role in its development and metastasis. Besides the increased secretion of exosomes, the selective packaging of miRNA may contribute to the pathogenesis of sarcoma.
Exosomes derived from Ewing sarcoma cells and human mesenchymal stem cells were isolated. Exosomal miRNAs were analyzed by microarray.

overall_design: Three group including exosomes derived from Ewing sarcoma cells (A673 and SK-N-MC) and human mesenchymal stem cells were set up and each group had three biological replicates.

first: Weiwen

last: Zhang


title: Integrative spatially-resolved multi-omics analysis reveals metabolic evolution of the transition to invasive breast cancer

status: Public on Mar 08 2025

city: Xiamen

first: Lin

last: Shuhai

state: Fujian

address: Room B205, Huang Zhaoyang Building, School of Life Sciences, Xiamen University

institute: Xiamen University

summary: Tumor metastasis is one of the primary causes of death among cancer patients, including those with breast cancer. We conducted a spatial transcriptomics study to analyze the progression of breast cancer from carcinoma in situ to invasive carcinoma, aiming to identify changes in genes, metabolic pathways, and cellular composition during this evolution. Our analysis revealed alterations in genes, metabolic pathways, and cellular composition during the transition from carcinoma in situ to invasive carcinoma, providing theoretical support for blocking breast cancer metastasis.

overall_design: We performed spatial transcriptomic sequencing on frozen tissue sections from six breast cancer patients. Following dimensionality reduction and clustering, the clustering results were pathologically distinguished by a pathologist. Subsequently, analyses were conducted on the regions of carcinoma in situ and invasive carcinoma.

first: Shuhai

last: Lin

first: Jia

last: Song

first: Yadong

first: Lvening

last: Gui

first: Meichen

last: Jiang

first: Longfeng

last: Yang

first: Bo

last: Yao

first: Yiting


title: Longitudinal analysis of antigen-specific T cells after Shingrix vaccination

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: SHINGRIX vaccination was used to investigate the fate of antigen specific memory CD4+ T cell at both cellular and transcriptional level upon immunization in a one-year longitudinal study. SHINGRIX is a subunit vaccine with glycoprotein E (gE) of varicella zoster virus (VZV) as the immunogen and requires two doses at least 60 days apart for protection against Herpes Zoster in adults over 50 years old. Flow cytometry and single-cell RNA sequencing were used to evaluate cellular and transcriptomic changes of VZV gE epitope-specific CD4+ T cells in a TCR clonotypic fashion pre and post vaccination. Antigen-specific T cells remained at a higher frequency compared to baseline and retained markers of cell activation such as ICOS and PD1 even one year post-vaccination. Persistent TCR clonotypes amongst epitope-specific T-cells were common across different time points within each individual. Antigen-specific memory T cells with a dominant TCR clonotype at baseline remained at a relatively high frequency one year later after two doses of vaccine. In contrast, T cells with TCR clonotypes from naïve antigen specific cells at baseline could not be detected post-vaccination. Differential gene expression analyses of cells with identical TCR clonotypes show that cells post vaccination, including those at one year post vaccination, were distinct from cells at baseline, with upregulation of genes related to T cell differentiation, negative T cell regulation and T cell activation. Thus, in addition to an increase in frequency, committed memory T cells gain additional transcriptional changes upon vaccination that could alter the immune response against cognate immunogens compared to pre-vaccinated quiescent memory T cells.

overall_design: Varicella-Zoster virus  glycoprotein E-specific CD4 T Cells were sorted from blood from 7 patients treated with the Shingrix vaccine in two doses at days 0, 60, 74, and 365. Flow cytometry and single-cell RNA-Seq measured surface protein markers and RNA expression of these cells. TCR sequences were assembled from the RNA-Seq data.

first: Xiaomin

last: Wen

first: Alex

last: Hu

first: Scott

last: Presnell

first: David

last: Koelle

first: William

last: Kwok


title: SIX2-Mediated Microglial M2 Polarization and Exosomal miR-3470b Delivery Protect Dopaminergic Neurons in Parkinson's Disease [EV treatment]

city: XuZhou

first: xinxing

last: huang

state: JiangSu

address: 209 Tongshan Road

institute: university

summary: Parkinson's disease (PD) is characterized by the progressive loss of dopaminergic neurons, with neuroinflammation playing a critical role in disease progression. The transcription factor SIX2 has been identified as an anti-inflammatory factor in microglial cells; however, the underlying mechanisms remain poorly understood. In this study, we demonstrated that SIX2 overexpression protects dopaminergic cells by promoting the polarization of microglial cells from the pro-inflammatory M1 phenotype to the anti-inflammatory M2 phenotype. Mechanistically, SIX2 upregulates DDIT4 expression by binding to its promoter region. DDIT4, in turn, facilitates microglial M2 polarization by inhibiting mTOR, thereby activating autophagy. Furthermore, SIX2-induced M2-polarized microglial cells secrete exosomes carrying miR-3470b. These exosomes are taken up by dopaminergic neurons, where miR-3470b inhibits GREM1 expression and enhances TGF-β signaling activity. Consequently, SIX2-mediated mechanisms prevent and restore damaged dopaminergic neurons in PD mice. Our findings reveal a novel regulatory mechanism of microglial M2 polarization and provide new insights into PD immunotherapy. Additionally, the discovery of exosome-mediated miR-3470b communication between microglia and dopaminergic neurons offers a theoretical foundation for developing exosome-based miRNA therapies.

overall_design: In this study, SIX2 was overexpressed in microglia, and the mechanism of SIX2-mediated microglial M2 polarization was studied, and the overexpressing SIX2 microglia exosomes were purified and co-cultured with Mes23.5 cells to study the mechanism of exosome protection of Mes23.5 cells

first: Jia-shuo

last: Kan

first: Xia-yi

last: Cao

first: Yu-xin

last: Ye

first: Xin-xing

last: Huang

first: Guo-jing

last: Sun

first: Can-tang

first: Jin

last: Gao


title: IQGAP3 bridges matrix stiffness with cancer stem cell maintenance and radioresistance by stabilizing SOX2

city: Pittsburgh

first: Po

last: Zhang

state: Pennsylvania

address: 5115 Centre Ave

institute: University of Pittsburgh,

summary: Drivers of therapeutic resistance in cancer include evolution of tumor cell heterogeneity and the tumor microenvironment (TME). Here, we found that increased matrix stiffness promotes radioresistance in glioblastoma (GBM) and maintains the tumor cell hierarchy. Differential gene expression revealed that stiff matrices induced expression of IQGAP3 (IQ Motif Containing GTPase Activating Protein 3) specifically in GBM stem cells (GSCs). IQGAP3 promoted GSC self-renewal and survival upon radiation treatment through binding and stabilization of the core stem cell transcription factor, SOX2. Targeting IQGAP3 reduced SOX2 protein levels in vitro and in vivo, increasing GSC radiosensitivity and inhibiting tumor growth. Structure-function drug screening of FDA-approved agents blocking IQGAP3 binding to SOX2 identified Trimetrexate as a brain penetrant pharmacologic disruptor of IQGAP3 function in radioresistance, sensitizing GSCs to radiotherapy. Our results identify molecular underpinnings for biomechanical promotion of cancer stem cell maintenance and therapeutic resistance, informing a therapeutic strategy to augment efficacy of radiotherapy.

overall_design: SOX2 ChIP-seq in GSCs (MES20 and 3028) cultured on stiff matrix gel, with or without IQGAP3 knockdown.

first: Donghai

last: Wang

first: Jeremy

last: Rich


title: Ginsenoside compound K plays an anti-inflammatory effect without inducing glucose metabolism disorder in adjuvant-induced arthritis rats [human]

first: Li

last: Cheng

address: 500 Quxi Road, Shanghai 200011

department: Department of Rehabilitation Medicine

institute: The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine

summary: We investigated mRNA expression levels in fibroblast-like synoviocytes (FLS) from rheumatoid arthritis (RA) patients, after no treatment, or after ginsenoside CK or dexamethasone treatment. The aim of the study was to determine the differences in the effects of ginsenoside CK and dexamethasone on mRNA levels in RA-FLS. Both ginsenoside CK and dexamethasone regulate some of the same inflammatory genes.

first: Jingyu

last: Chen


title: Effect of Abscissic acid on Brassica napus guard cells

city: Farmington

first: Yasir

last: Suhail

state: Connecticut

address: 263 Farmington Avenue

department: BME

institute: UCHC

summary: Plants acclimate to drought and water stress through diverse physiological responses, primarily mediated by the hormone abscisic acid (ABA). The closure of stomatal pores on aerial surfaces of plants is one of the rapid responses mediated by ABA to reduce transpirational water loss because plants lose the majority of their water through stomatal pores. Stomatal guard cells have been an important cellular system for studying ABA signaling. The dynamic changes in the transcriptome of stomatal guard cells in response to ABA have been investigated in the model plant Arabidopsis thaliana. In this study, we analyzed the dynamics of ABA-regulated transcriptomes in stomatal guard cells of Brassica napus.

overall_design:
Guard cells were exposed to abscisic acid for 0 (control), 15, and 60 minutes for 3 replicates each.

Grant Title: Cell-type Specific Networks in Brassica Guard Cell Responses to Drought
Grant Award number: 1025837
Grantee: June Kwak
Funding Agency: NSF

first: June

last: Kwak

first: Florent

last: Villiers

first: Joel

last: Bader


title: Analyses of ZNF143 reveal single-nucleotide architectural principles of the Pcdh HS5-1 enhancer

first: Mo

institute: Shanghai Jiaotong University

summary: DNA looping and TAD formations are critical for multiple basic physiological activities of cells. The ZNF143 protein contains 7 zinc fingers, and is involved in 3D genome construction. Here, we show that ZNF143 regulates the chromosome folding through two kinds of mechanisms. First, ZNF143 interacts with CTCF at CTCF binding sites (CBS) and stabilizes the interaction between CTCF and cohesin. The CTCF or cohesin depletion disrupts the binding of ZNF143 on CBS, and ZNF143 knockout narrows the space between CTCF and cohesin, and decreases the chromosome interaction. Second, ZNF143 could directly bind DNA, which is enriched at the boundaries of TADs. Removing them slightly decreases the interactions of TADs and loops, but significantly causes A/B compartment transformation, perhaps due to the changes of the gene expressions after removing ZNF143.  In summary, ZNF143 is recruited by CTCF to regulate loops and TADs, while ZNF143 itself also influences TAD formations and higher-order compartment segregation.

first: Qiang

last: Wu


title: Effect of devH deprivation on gene expression in the cyanobacterium Nostoc/Anabaena sp. PCC 7120 [RNA-seq]

status: Public on Mar 07 2025

city: Wuhan

first: Xiaoli

last: Zeng

state: Hubei

address: No. 7 Donghu South Road, Wuchang District

institute: Institute of Hydrobiology, Chinese Academy of Sciences

summary: How new functions emerge as genes diversify during evolution is an important question in biology. cyclic adenosine monophosphate receptor protein (CRP) -type transcription factors are widespread in bacteria, often with several members coexisting in the same organism. How do they achieve functional specificity with highly conserved structures? In the filamentous cyanobacterium Nostoc/Anabaena sp. PCC 7120, both NtcA and DevH belong to the CRP family, yet DevH is essential while NtcA is not. Together with previously published data, we demonstrate here that ntcA and devH mutually and positively regulate each other for enhanced expression. Furthermore, NtcA and DevH share a common consensus DNA binding site, and both of them exert global regulation functions for metabolism, photosynthesis and cell development. We show that compared to NtcA, DevH achieved functional specificity and essentiality by structural innovations and increased cellular concentrations, leading to a stronger and broader regulatory function independent of allosteric control. Based on our data, we propose a model on how these two conserved transcription factors provide both overlapping and distinct regulatory functions, to better coordinate transcriptional activities under different conditions. This study constitutes an example illustrating how functional divergence can be achieved following gene diversification of transcription factors, leading to increased complexity in gene regulation networks.

overall_design: RNA-seq profiling of cells from PcoaT-devH, an Anabaena conditional mutant strain, in which the devH gene is controlled by the stringent Co2+/Zn2+-inducible promoter (PcoaT) during a time course after cobalt removal, which is to deplete devH. Samples were collected in triplicate from cultures at 48, 72, and 96 hours without cobalt, and cells cultured with cobalt at the corresponding time points served as controls.

first: Xiaomei

last: Xu

first: Ling

last: Meng

first: Emmanuel

last: Talla

first: Min

first: Cheng

middle: C


title: Nelfb promotes dWAT formation through RNA Polymerase II-mediated adipogenic gene regulation

city: San Diego

first: Samiksha

last: Mahapatra

address: 9452 Medical Center Dr

institute: University of California San Diego

summary: Deletion of Nelfb in preadipocyte lineages in mice cause failure in dWAT and other fat depot formation, perinatal lethality, and reduced expression of adipogenic genes

overall_design: RNA seq on Day 14 CTL and Nelfb depleted cells

first: George

last: Sen


title: Emergence of essential functions of a transcription factor in the cyanobacterium Nostoc/Anabaena sp. PCC 7120 [ChIP-seq]

overall_design: ChIP-seq of FLAG in the Anabaena devH-flag strain, in which the native devH was replaced by an allele encoding a DevH variant tagged with 3×FLAG at the C-terminus, and in the wild type strain as a control.

last: Huang


title: SIX2-Mediated Microglial M2 Polarization and Exosomal miR-3470b Delivery Protect Dopaminergic Neurons in Parkinson's Disease

first: xinxing

last: huang

overall_design: RNA-seq profiling of wildtype BV-2 cells and their knockdown derivatives (shSIX2).

first: Jia-shuo

last: Kan

first: Xia-yi

last: Cao

first: Yu-xin

last: Ye

first: Xin-xing

first: Guo-jing

last: Sun

first: Can-tang

last: Zhang

first: Jin

last: Gao


title: The role of structural vs cellular remodeling in arrhythmogenesis: personalized computer models of atrial fibrillation

city: Chicago

first: Igor

last: Efimov

state: Illinois

address: 303 E Superior St

institute: Northwestern University

summary: Atrial fibrillation (AF) is a progressive disease involving both structural and functional remodeling. To investigate the contribution of cell-scale functional remodeling to AF pathogenesis, we combined personalized 3D anatomical models with pathology-specific ionic models. The latter were developed using recordings in myocytes isolated from patients in sinus rhythm, paroxysmal, postoperative, and persistent AF. To quantify AF dynamics, we developed a novel algorithm for locating RDs by backtracking the conduction velocity field from the wavebreak regions. We demonstrate that our novel algorithm is at least 700 times faster than the traditional phase singularity analysis. The inducibility of simulated AF was not pathology-dependent, but pathological models demonstrate a more extensive arrhythmogenic substrate compared to the sinus rhythm. AF driver locations depend on electrophysiological remodeling; differences between pathology-specific models are explained by differences in wavebreak patterns. Specifically, RDs tend to dwell in the regions with the highest wavebreak probability.

overall_design: Right atrial appendages from human patients were collected and sequenced with RNA-Seq. Samples were grouped based on diagnosis: Sinus Rhythm (SR), postoperstive AF (poAF), paroxysmal AF (pAF), and persistent AF (persAF). Each diagnosis group had at least five patient samples.

first: Pikunov

middle: V

last: Andrey

first: Syunyaev

last: Roman

first: Ali

last: Rheeda

first: Prakosa

last: Adityo

first: Boyle

last: Patrick

first: Steckmeister

last: Vanessa

first: Kutschka

last: Ingo

first: Gams

last: Anna

first: Rytkin

last: Eric

first: Voigt

last: Niels

first: Trayanova

last: Natalia

first: Efimov

last: Igor


title: Predictable Engineering of Signal-Dependent Cis-Regulatory Elements

city: London

first: Jake

last: Cornwall-Scoones

address: 1 Midland Rd

institute: The Francis Crick Institute

summary: Cis-regulatory elements (CREs) control how genes respond to external signals, but the principles governing their structure and function remain poorly understood. While differential transcription factor binding is known to regulate gene expression, how CREs integrate the amount and combination of inputs to secure precise spatiotemporal profiles of gene expression remains unclear. Here, we developed a high-throughput combinatorial screening strategy, that we term NeMECiS , to investigate signal-dependent synthetic CREs (synCREs) in differentiating mammalian stem cells. By concatenating fragments of functional CREs from genes that respond to Sonic Hedgehog in the developing vertebrate neural tube, we found that CRE activity follows hierarchical design rules. While individual 200-base-pair fragments showed minimal activity, their combinations generated thousands of functional signal-responsive synCREs, many exceeding the activity of natural sequences. Statistical modelling revealed CRE function can be decomposed into specific quantitative contributions in which sequence fragments combine through a multiplicative rule, tuned by their relative positioning and spacing. These findings provide a predictive framework for CRE redesign, which we used to engineer synthetic CREs that alter  the pattern of motor neuron differentiation   in neural tissue. These findings establish quantitative principles for engineering synthetic regulatory elements with programmable signal responses to rewire genetic circuits and control  stem cell differentiation, providing a basis for understanding developmental gene regulation and designing therapeutic gene expression systems.

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: The NeMECiS plasmid library (PLASMID) was constructed by sequential, nested Golden Gate, assembling exhaustive three-way concatemers of 25x 200bp CRE fragments (synCREs), generating a theoretical library of 15,625. CRE fragment composition and order are defined by a set of deterministic barcodes, which are flanked by Nextera partial adaptors.  The sequencing libraries for both the raw plasmid library and the flow-sorted neural progenitor library were prepared in an equivalent manner. DNA was extracted, and barcode concatemers were amplified through Nextera-primed PCR.  Reads have a generic form: [NexteraRd1]AGCA[8bpBarcode]GATT[8bpBarcode]AGCA[8bpBarcode]GATT[Terminator][NexteraRd2] Where:  [NexteraRd1] = TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG  [Terminator] = GATTAATAAAGGAAATTTATTTCATTGCAATAGTGTGTTGGAATTTGTGTCTCTCA  [NexteraRd2] = CTGTCTCTTATACACATCTCCGAGCCCACGAGAC  For neural progenitor experiments:  To measure SAG-dependent activity of synCREs, the following was performed. In duplicate, 10^7 mESCs were infected with the NeMECiS lentivirus library in ESGRO at MOI<1, maintained in CellBIND T175 flasks, selected with Puromycin Dihydrochloride. Cells were then expanded for one passage. mESCs were then differentiated to neural progenitors under 0nM or 500nM SAG, plating per replicate 6x10^7 cells onto 1% vitronectin coated plates. Briefly, cells were maintained in bFGF for 48 hours, bFGF + CHIR99021 for 20 hours, then each replicate was replated onto 1% GelTrex coated plates at a 1:1 ratio in 100nM RA, supplementing one of the halves with 500nM SAG. At day 6 of the protocol, 30% of each sample (two replicates x two SAG conditions) was pelleted and frozen. The remaining 70% were flow sorted into four fluorescence bins corresponding to four evenly spaced 15% percentile intervals (13.3% spacing between bins). Unsorted and sorted samples were run on a flow analyser to measure fluorescence of each pool. Sorted samples were then pelleted. Both the sorted and unsorted pellets were processed with the Zymo Research Quick-DNA Miniprep Plus Kit to extract genomic DNA, then barcode concatemers were amplified with Nextera-primed PCRs. All sequencing libraries were checked for quality before sequencing using a Bioanalyzer and KAPA Library Quanitification Complete Kit Universal.  Sequencing files for sorted and unsorted neural progenitors have the following naming structure:  SAMPLEINFO_ID_LANE_READ_001.fastq.gz  SAMPLEINFO contains information about the replicate, the SAG concentration, and the sort-status. For example: “102” represents replicate 1, 0nM SAG and sort bin 2; “10A” represents replicate 1, 0nM SAG and unsorted (‘all’); “251” represents replicate 2, 500nM SAG and sort bin 1.  Data was processed using a custom pipeline (see below for details). By-experiment processed data files (Rep1/2; SAG=0nM/500nM) are provided.

first: M Joaquina

last: Delas

first: James

last: Briscoe


title: RNA-sequencing of PC3M prostate cancer cells depleted of the RNA binding protein HNRNPA2B1

first: Prabhakar

last: Rajan

address: Charterhouse Sq

department: BCI

institute: QMUL

summary: RNA binding proteins (RBPs) play important roles in cellular stress responses. Here we investigated the association between HNRNPA2B1, an RBP upregulated in prostate cancer, and expression of genes in stress response pathways. HNRNPA2B1 depletion in vitro using siRNA resulted in altered expression of multiple genes in the unfolded protein response (UPR) pathway in PC3M prostate cancer cells.

overall_design: 6 total samples, 3 replicates per condition

first: J

middle: G

last: Foster

first: E

last: Gea

first: C

last: Bessant

first: P


title: Activation of the ERRα Transcriptional Pathway Alleviates Anthracycline-induced Cardiotoxicity by Improving Mitochondrial Metabolism

first: Xiaoping

last: Wang

state: Beijing

address: No. 5, Dongdan Santiao, Dongcheng District, Beijing

institute: Peking Union Medical College

summary: Anthracycline-induced metabolic remodeling and mitochondrial damage are critical early events that contribute to cardiac dysfunction. However, the gene regulatory pathways governing the derangements in myocardial bioenergetics have not yet been fully delineated. Estrogen-related receptor alpha (ERRα) is a key regulator of energy metabolism, especially in tissues with high energy demands. Here, we demonstrate that ERRα acts as a beneficial modulator of mitochondrial metabolism in anthracycline-induced cardiotoxicity (AIC). ERRα gain-of-function enhances cardiomyocyte metabolism and mitochondrial function, thereby alleviating AIC. Conversely, cardiomyocyte-specific knockdown of ERRα exacerbates mitochondrial bioenergetic collapse and worsens heart failure phenotypes in AIC mice. Additionally, our research identifies a top-ranking isoflavone phytoestrogen as a novel ERRα agonist with favorable pharmacological properties. This compound promotes the transcriptional activity of metabolic genes, representing a significant step toward developing natural ERRα agonists for AIC therapy.

overall_design: RNA-seq profiling of cardiac tissue of miniature pigs from control group and Dox group.

first: Guanjing

first: Yan

last: Wei

first: Weili

last: Li

first: Ziyi

last: Yin

first: Yun

last: Chen

first: Qi

last: Qiu

first: Wei

first: Yong


title: Single-cell gene expression profile of the postnatal mouse arcuate nucleus in the hypothalamus

city: Philadelphia

first: Yachen

last: Shen

address: 3400 Civic Center Blvd, Philadelphia, PA 19104

institute: University of Pennsylvania

summary: m6A, the most prevalent internal modification on mRNAs, plays important roles in the nervous system. Whether neurogenesis in the hypothalamus, a region critical for controlling appetite, is regulated by m6A signaling, especially in humans, remains unclear. Here we showed that deletion of m6A writer Mettl14 in the mouse embryonic hypothalamus led to adult obesity, with impaired glucose-insulin homoeostasis and increased energy intake. Mechanistically, deletion of Mettl14 leads to hypothalamic arcuate nucleus neurogenesis deficits with reduced generation of feeding-related neurons and dysregulation of neurogenesis-related m6A-tagged transcripts. Deletion of m6A writer Mettl3, or m6A reader Ythdc1, shared similar phenotypes. METTL14 or YTHDC1 knockdown also led to reduced generation of feeding-related neurons in human brain subregion-specific arcuate nucleus organoids. Our studies reveal a conserved role of m6A signaling in arcuate nucleus neurogenesis in mice and human organoids and shed light on the developmental basis of epitranscriptomic regulation of food intake and energy homeostasis.

overall_design: The arcuate nucleus of the hypothalamus was micro-dissected from both control and NM14KO mice, followed by analysis using single-cell RNA sequencing (scRNA-seq).

first: Hongjun

last: Song


title: Impact of Mettl14 depletion on gene expression in hypothalamic neural progenitor cells [bulk RNA-seq]

overall_design: We knocked out Mettl14 in neural progenitor cells (NPCs) derived from the embryonic hypothalamus of Mettl14 flox/flox mice using lentivirus-mediated Cre expression and performed RNA-seq on these samples.


title: The m6A profile of human Arcuate nucleus-specific organoids (ARCOs)

overall_design: m6A sequencing of day 12 induced human arcuate nucleus-specific organoids (ARCOs) from iPSCs