title: SALL4 recruits BAF to activate enhancers required for cranial neural crest cell specification

city: London

first: Marco

last: Trizzino

state: UK

address: Imperial College Road

department: Life Sciences

institute: Imperial College London

summary: SALL4 is a critical transcription factor involved in early embryonic development. While its role in pluripotency remains debated, SALL4 has been implicated in various lineage specification processes. The neural crest-derived anomalies observed in individuals with SALL4 haploinsufficiency, combined with high SALL4 expression observed in mouse cranial neural crest cells (CNCCs), suggest a role for this transcription factor in CNCC specification and craniofacial development, however, this has not yet been investigated. Moreover, while SALL4 is an established interactor of the NuRD chromatin remodeling complex, recent mass-spectrometry studies from our group have suggested a novel interaction between SALL4 and the BAF complex during human CNCC specification. Here, we investigate the functional significance of this interaction and the broader role of SALL4 in CNCC development. We generated a human iPSC line with SALL4 heterozygous knock-out to model the haploinsufficient variants observed in SALL4-associated human developmental syndromes. Our findings reveal that the SALL4A isoform directly interacts with the BAF subunit DPF2 via its zinc-finger-cluster-3 and -4 domain. During early CNCC specification, SALL4A is required for BAF-mediated chromatin remodeling at enhancers essential for CNCC fate. In the absence of SALL4A, cells progress normally through the neuroectodermal stage but fail to specify into CNCCs, as CNCC lineage-specific enhancers remain repressed. Moreover, we demonstrate that the SALL4B isoform cannot compensate for SALL4A loss, as it lacks the zinc-finger-3 domain necessary for BAF interaction. These findings establish a novel role for SALL4A in CNCC specification by regulating BAF-mediated enhancer activation, shedding light on the molecular mechanisms underlying SALL4-associated craniofacial anomalies.

overall_design:
RNA-seq of SV20 WT and SV20 SALL4-het-KO iPSC lines  (2 replicates per line)
RNA-seq of SV20 WT and SV20 SALL4-het-KO at day 5 of in vitro cranial neural crest cell specification (3 replicates per line)
RNA-seq of SV20 WT and SV20 SALL4-het-KO at day 14 of in vitro cranial neural crest cell specification (2 replicates per line)
CUT&RUN of SALL4 in SV20 WT iPSC lines (1 replicate per line)
CUT&RUN of SALL4 in SV20 WT cell line at day 5 of in vitro cranial neural crest cell specification (2 replicates per line)
ChIP-seq of BRG1 in SV20 WT and SV20 SALL4-het-KO cell lines at day 5 of in vitro cranial neural crest cell specification (at least 1 replicate per line)
ATAC-seq of SV20 WT iPSC lines  (2 replicates per line)
ATAC-seq of SV20 WT and SV20 SALL4-het-KO at day 5 of in vitro cranial neural crest cell specification (2 replicates per line)

first: Martina

last: Demurtas

first: Samantha

middle: M

last: Barnada

first: Zoe

last: Mitchell

first: Laura

last: Deelen


title: Serum exosome small RNA array analysis identifies 5'tiRNA-PheGAA and tRF-1-IleAAT as potential biomarkers for rheumatoid arthritis

status: Public on Apr 08 2025

city: Changchun

first: Tingshuang

last: Xu

state: Jilin

address: No. 1 Xinmin Street

country: China

institute: First Hospital of Jilin University

summary: To screen differentially expressed tsRNA in serum exosomes of rheumatoid arthritis (RA) patients and healthy controls and conduct bioinformatics analysis for exploring the role and potential clinical application value of tsRNAs in the pathogenesis of RA.

overall_design: Serum exosomes samples were collected from 3 RA patients, and 3 healthy individuals were screened using the Agilent Human small RNA Microarray platform interrogating 5128 tsRNAs.

first: Yuanyuan

last: Li

first: Meiling


title: Single cell compendium of the muscle microenvironment in peripheral artery disease reveals capillary endothelial heterogeneity and activation of resident macrophages

city: Schwerzenbach

first: Guillermo

last: Turiel

address: Schorenstrasse 16

department: D-HEST

country: Switzerland

institute: ETH Zurich

type: Expression profiling by high throughput sequencing

summary: Background Peripheral artery disease (PAD) is caused by atherosclerosis and chronic narrowing of lower limb arteries leading to decreased muscle perfusion and oxygenation. Current guidelines for treating PAD include endovascular strategies or bypass surgery but long-term outcomes have been suboptimal. This is likely due to our limited understanding of the contribution of the microvasculature as well as other cell types, in particular macrophages, to PAD skeletal muscle pathophysiology. We used single cell sequencing to investigate cellular and transcriptional heterogeneity of the skeletal muscle microenvironment in PAD. Methods Samples from the medial head of the gastrocnemius muscle of individuals undergoing either lower limb aneurysm surgery (controls) or PAD bypass surgery (PAD) were collected. Samples were either frozen for histological evaluation (control: n=4; PAD: n=6) or were immediately processed for single cell RNA sequencing of mononuclear cells (control: n=4; PAD: n= 4). Bioinformatic tools were used to annotate cell types and their subpopulations, to study transcriptional changes and to analyze cellular interactions. Results We generated a dataset comprised of 106,566 high-quality, deep-sequenced cells that compose the muscle microenvironment. Focusing on endothelial cells (ECs) and macrophages, we confirmed the presence of ATF3/4+ ECs with angiogenic and immune regulatory capacities in human muscle and found that their transcriptional profile profoundly alters during PAD. Also, capillary ECs display features of endothelial to mesenchymal transition. Furthermore, we identified LYVE1hiMHCIIlow resident macrophages as the dominant macrophage population in human muscle, even under a chronic inflammatory condition such as PAD. During PAD, LYVE1hiMHCIIlow macrophages get activated and acquire a more pro-inflammatory profile. Finally, we map strong intercellular communication in the muscle microenvironment, which is significantly altered in PAD. Conclusions The dataset we present here provides a highly valuable resource for gaining deeper insights into the critical roles that cells in the muscle microenvironment may play in PAD skeletal muscle pathology. We propose that targeting the crosstalk between ECs and macrophages could provide novel insights for developing effective treatments against this disease.

overall_design: Endothelial cells from PAD patients were isolated in vitro and incubated with vehicle (DMSO) or celastrol (125 or 250 nM) for 24h. After incubation, RNA was extracted for bulk RNA sequencing. 3 biological replicates (3 different patients) were used. For each patient, 3 different wells were incubated with vehicle or each celastrol dose. Total of 9 samples.

first: Thibaut

last: Desgeorges

first: Evi

last: Masschelein

first: Jing

last: Zhang

first: Stephan

last: Engelberger

first: Katrien

last: DeBock


title: TBX3 advances the developmental chromatin landscape towards the hepatic fate [RNA-seq II]

city: Vancouver

first: Tabea

middle: L

last: Stephan

state: BC

address: 2329 West Mall

country: Canada

institute: University of British Columbia

summary: Hepatocytes differentiate from definitive endoderm in response to external signaling cues, however it is unclear how the hepatic lineage is specified and how transcription factors shape the chromatin to allow gene expression. By mapping histone modifications using a human stem cell model of hepatic differentiation, enhancers were found to exhibit dynamic, stage specific regulation, with many primed at the definitive endoderm stage. While hepatic enhancers gained active histone modifications, non-hepatic enhancers lost H3K4me1 after hepatic specification. TBX3, and to lesser extend HNF4A, bound to the hepatic enhancers and formed an interdependent transcription factor network. TBX3 bound both hepatic enhancers and promoters with low levels of H3K4me1 and a strong TBX3 motif. However, TBX3 binding was transient and upon eviction from TBX3-bound regions, H3K4me1 increased at enhancers, while H3K4me3 was established at promoters. This suggests that TBX3 plays a role in identifying hepatic enhancers and promoters during specification, which will then be activated to drive cell idenity.

overall_design: RNAseq of SV20 cells differentiated into hepatic cells. Samples were taken at Pluripotency, Mesendoerm stage, Definitive endoderm stage, posterior foregut, hepatic endoderm stage, hepatoblast stage and pancreatic progenitor stage.

first: Rebecca

last: Cullum

first: Sibyl

last: Drissler

first: Ashleigh

last: Thomas

first: Bettina

last: Fuglerud

first: Makenna

last: Clement-Ranney

first: Jeremy

last: Lotto

first: Nicole A

middle: J

last: Krentz

first: Stephen

middle: A

last: Duncan

first: Pamela

last: Hoodless


title: Transcriptomics analysis of 12 melanoma cell lines

status: Public on Apr 09 2025

city: Oxford

first: Pakavarin

last: Louphrasitthiphol

address: Old Road Campus Research Building (off Roosevelt Drive)

department: Nuffield Department of Clinical Medicine

country: United Kingdom

institute: Ludwig Institute for Cancer Research

summary: Established cancer cell lines often display a relatively homogeneous phenotype and loss of phenotypic heterogeneity compared to the tumours which they are derived from and likely reflect specific phenotypic states within the tumours that are then fixed and maintained under culture condition. Whilst this is often seen as a limitation, it also presents an oportunity to simplify the interpretation of any given experiment and allows us to better understand how distinct phenotypic states within melanoma response/behave in a given experimental setting (Louphrasitthiphol et al., 2019). To this end, we carry out transcriptomics analyses of 12 commonly used melanoma cell lines to better characterize their profiles.

overall_design: Indicated cell lines were grown in their respective culture media, 5 biological replicates were collected, of which random three were selected, total RNA extracted and sequenced using 3'-end sequencing

first: P


title: Interleukin-33 (IL-33) promotes DNA damage-resistance in lung cancer

first: Chen

last: Shao

address: 126 Xinmin ST

institute: Jilin University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Resistance to DNA damage is one of the primary mechanisms by which tumor cells evade the effects of standard chemotherapeutic agents and radiotherapy. Dynamic and complex interactions between the tumor microenvironment (TME) and tumor cells critically influence the DNA damage response. Interleukin-33 (IL-33) is a multifunctional cytokine secreted at high levels in response to cellular damage and stress. Recently, increasing evidence has suggested that IL-33 plays a key role in promoting the therapeutic resistance of tumors. However, the actual source of IL-33 during cancer therapy and how IL-33 contributes to a resistant TME remain incompletely understood. In this study, we found that both cancer-associated fibroblasts (CAFs) and tumor cells treated with DNA damage-inducing agents expressed and secreted high levels of IL-33, subsequently leading to enhanced DNA damage repair efficacy. Mechanistically, nuclear IL-33 primarily functions as a transcriptional co-activator of homologous recombination repair (HRR) genes, whereas the active form of IL-33 can drive the non-homologous end joining (NHEJ) pathway via the canonical IL-33/ST2 axis. Overall, we demonstrated that IL-33 plays a key role in mediating a DNA damage-resistant TME, which could represent a potential therapeutic vulnerability in chemoresistant cancer cells

overall_design: A549 cells stably expressing vector control, IL-33-full length and IL-33-cytokine domain were generated by lentivirus infection and puromycin selection, then cells were treated with or with out 1 μM doxorubicin for 48 h . Then total RNA was extracted to assess the differentially expressed genes after ARv7 levels changes. For CUT&Tag assay, A549 cells stably overexpressing IL-33-full length and IL-33-cytokine domain were subjected to  CUT&Tag analysis to further examine the nuclear function of IL-33.

first: Haoge

last: Luo

first: Dong

last: Li


title: Effect of Rnf111 S254A mutant on chromatin accessibility

city: Beijing

first: Zhiqiang

last: Peng

address: 38 Life Science Park Road

institute: State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics

summary: ATAC analysis of DNAs extracted from cells of wild type or Rnf111 S254A

overall_design: ATAC-seq profiling of WT or Rnf111 S254A cells

first: Lingqiang

last: Zhang

first: Cuihua

last: Liu


title: Tissue Resident CD8+T cells as mediators of protective immunity in breastmilk transmission of HCMV

city: Birmingham

first: Steffanie

last: Sabbaj

state: AL

address: 845 19th Street South

department: Medicine

country: USA

institute: University of Alabama at Birmingham

summary: Breast milk T cells are an understudied cell population.  We used single cell RNA sequencing (scRNA-seq) to analyze these cells in breast milk of HCMV seropositive women who did or did not transmit HCMV to their babies via breast feeding.

overall_design: Breast milk was collected, and mononuclear cells were isolated by centrifugation.  Isolation of leukocytes followed using a CD45 positive selection kit per manufacturer’s instructions (EasySep HumanCD45 Positive Selection Kit, STEMCELL Technologies, Cambridge, MA).  Cells where analyzed using scRNAseq

first: David

last: Crossman


title: The ZBTB24-CDCA7-HELLS axis suppresses the totipotent 2C-like reprogramming by maintaining Dux methylation and repression

city: 昆明市

first: youqi

last: liu

state: 云南省

address: wujiaying

institute: Kunming University Of Science And Technology

summary: Two-cell-like cells (2CLCs), a rare population (~0.5%) in murine embryonic stem cell (mESC) cultures, are in a transient totipotent-like state resembling that of 2C-stage embryos, and their discovery and characterization have greatly facilitated the study of early developmental events, such as zygotic genome activation. However, the molecular determinants governing 2C-like reprogramming remains to be elucidated. Here, we show that ZBTB24, CDCA7 and HELLS, components of a molecular pathway that is involved in the pathogenesis of immunodeficiency, centromeric instability and facial anomalies (ICF) syndrome, function as negative regulators of 2C-like reprogramming by maintaining DNA methylation of the Dux cluster, a master inducer of the 2C-like state. Disruption of the ZBTB24-CDCA7-HELLS axis results in Dux hypomethylation and derepression, leading to dramatic upregulation of 2C-specific genes, which can be reversed by site-specific re-methylation in the Dux promoter. We also provide evidence that CDCA7 is enriched at the Dux cluster and recruits the CDCA7-HELLS chromatin remodeling complex to constitutive heterochromatin. Our study uncovers a key role for the ZBTB24-CDCA7-HELLS axis in safeguarding the mESC state by suppressing the 2C-like reprogramming.

overall_design: To assess the impact of the deficiency of Zbtb24, Cdca7 or Hells on H3K9me3 occupancy at Dux cluster and 2C-specific genes, we conducted CUT&Tag sequencing (CUT&Tag-Seq) with H3K9me3 antibody (ab8898, abcam) in WT, two to three independent Zbtb24-, Cdca7-, or Hells-KO mESC lines.To assess the impact of the deficiency of Zbtb24, Cdca7 or Hells on H3K9me3 occupancy at Dux cluster and 2C-specific genes, we conducted CUT&Tag sequencing (CUT&Tag-Seq) with H3K9me3 antibody (ab8898, abcam) in WT, two to three independent Zbtb24-, Cdca7-, or Hells-KO mESC lines.

first: Jiameng

last: Dan

first: Dan

last: Guo

first: Zeling

last: Du

first: Youqi


title: Tubular-specific ablation of Tiki2 exacerbates inflammation in ischemia/reperfusion-induced acute kidney injury by derepressing Wnt5a/Ror signaling

city: Wuhan

first: Cui

last: Yang

state: hubei

address: Luoyu Road 1037

department: College of Life Science and Technology

institute: Huazhong University of Science and Technology

summary: Ischemia/reperfusion-induced acute kidney injury (AKI) occurs in several clinical conditions accompanied by inflammation, but the underlying mechanisms remain elusive. The Wnt inhibitor Tiki2 is highly expressed in the kidney with unknown function. Here, we demonstrated that Tiki2 is highly expressed in proximal tubular epithelial cells (PTECs) and is dynamically regulated in AKI. Tubular epithelial cell-specific ablation of Tiki2 aggravated immune cell infiltration and tubular injury in IR-induced AKI. Mechanistically, Tiki2 ablation increased the activity of Wnt5a/Ror signaling, which is activated in PTECs in IR-induced AKI, leading to increased active JNK/ERK signaling and the secretion of chemokines and cytokines to promote the infiltration of immune cells. Furthermore, the increased severity of injury and inflammation caused by Tiki2 ablation could be relieved by knocking down Ror2 in PTECs. Our study reveals the critical roles of Wnt5a/Ror signaling and its negative regulator Tiki2 in IR-induced AKI, which are potential therapeutic targets for treating AKI

overall_design: RNA-seq profiling of Tiki2 tubular specific knockout mice and littermate control mice kidney suffering ischemical reperfusion injury on day 7.

first: Xinjun


title: RUNX1 promotes colorectal tumor growth and metastasis by regulating CDK8

city: Nanjing

first: Li

middle: ming

last: yue

address: 163 Xianlin Dadao

institute: Nanjing university

summary: Unresectable hepatic metastasis of colorectal cancer (CRC) responds poorly to existing therapies and is the leading cause of CRC mortality. Runt-related transcription factors (RUNXs) have recently come to prominence because of their important, at times paradoxical, roles in tumor development. However, the expression status, biological function and underlying mechanism of RUNX1 in human CRC remain unknown.

overall_design: ChIP-seq analysis for RUNX1 to identify the genes that are directly regulated by RUNX1 at the transcriptional level

first: Mingyue

last: Wang

first: Shuaidong

last: Zhu

first: Yuqian


title: Transcriptomics profiling of gonadal white adipose tissue (gWAT) of wild-type (WT) and macrophage-specific Bnip3 knockout (MKO) mice fed a normal chow diet (NCD) or high-fat diet (HFD)

city: Seoul, Republic of Korea

first: Sangseob

last: Kim

address: 1, Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

summary: Obesity induces phenotypic changes and pro-inflammatory polarization of adipose tissue macrophages, contributing to chronic inflammation and insulin resistance. This study investigates the influence of Bnip3 on adipose tissue inflammation and the metabolic dysfunction prompted by a high-fat diet. Our objective involves examining the impact of a 12-week HFD feeding on both WT and Bnip3 MKO mice, comparing the differentially regulated genes based on dietary intake.

overall_design: Deep sequencing generated the gWAT mRNA profiles of WT and Bnip3 MKO mice fed a NCD or HFD. Three biological replicates were analyzed for each condition.

first: Yun-Hee

last: Lee


title: Coactosin-like F-actin Binding Protein (Cotl1) Plays a Key Role in Adipocyte Differentiation and Obesity

city: Suwon

first: Seon-Yong

last: Jeong

address: 206, World cup-ro, Yeongtong-gu

department: Department of Medical Genetics

institute: Ajou University School of Medicine

summary: Actin dynamics, mediated by various actin-binding proteins, plays an important role in adipocyte differentiation. We investigated the role of coactosin-like F-actin binding protein (Cotl1) in adipocyte differentiation in vitro and in vivo. Cotl1 expression level was increased during adipocyte differentiation in mouse 3T3-L1 cells and primary cultured adipose-derived stem cells (ADSCs) and during weight gain in adipose tissues. However, Cotl1 deficient in 3T3-L1 and ADSCs inhibited adipocyte differentiation, and Cotl1-/- mice displayed resistance to high-fat diet (HFD)-induced weight gain, hepatic steatosis and adipocyte enlargement compared to HFD-fed wild type (WT) mice. Ingenuity Pathway Analysis of RNA-sequencing in adipose tissues of HFD-WT and HFD-Cotl1-/- mice predicted complicated relationships between Cotl1, differentiation of adipocytes, obesity and organization of actin cytoskeleton. Particularly, peroxisome proliferator-activated receptor gamma (Pparg) emerged as a central player, with Cotl1 influencing Pparg expression, consequently regulating adipocyte differentiation. These findings suggest Cotl1 as a pivotal regulator of terminal adipocyte differentiation by modulating adipogenic genes.

overall_design: Wild-type and Cotl1 knockout mice were fed a high-fat diet for 12 weeks, and adipose tissues were isolated for RNA-Seq analysis.

first: Eunkuk

last: Park

first: Hyoju

last: Jeon

first: Kang-Il

last: Oh

first: Junhwan

first: Do-Wan

first: Hyun-Seok

last: Jin


title: Endometrial assembloid model reveals endometrial adenogenesis regulation by estradiol-driven WNT7B expression

city: Hong Kong

first: Yimeng

last: Li

address: 21 Sassoon Road, Pokfulam Hong Kong

institute: The university of Hong Kong

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

overall_design: Refer to individual Series


title: TFEB and TFE3 regulate STING1-dependent immune responses by controlling type I interferon signaling [AM_NIH_RNASeq_50538]

city: Bethesda

first: Pablo

last: Tapia

state: Maryland

address: 50 South Dr

department: Cell Biology and Physiology Center, National Heart, Lung, and Blood

institute: National Institutes of Health

summary: STING1 is an essential component of the innate immune defense against a wide variety of pathogens. Whereas induction of Type I interferon (IFN) responses is one of the best-defined functions of STING1, our transcriptomic analysis revealed IFN-independent activities of STING1 in macrophages, including transcriptional upregulation of numerous lysosomal and autophagic genes. This upregulation was mediated by the STING1-induced activation of the transcription factors TFEB and TFE3, and led to increased autophagy, lysosomal biogenesis, and lysosomal acidification. TFEB and TFE3 also modulated IFN-dependent STING1 signaling by controlling IRF3 activation. IFN production and cell death were increased in TFEB and TFE3 depleted iBMDMs. Conversely, TFEB over-expression led to reduced IRF3 activation and an almost complete inhibition of interferon synthesis and secretion, resulting in decrease caspase-3 activation and increased cell survival. Our study reveals a key role of TFEB and TFE3 as regulators of STING1-mediated innate antiviral immunity.

overall_design: To investigate the role of TFEB and TFE3 in the innate immune response, we used CRISPR-Cas9 to delete TFEB and TFE3 in immortalized bone marrow-derived macrophages (iBMDMs), using a negative control for comparison. Both the negative control and TFEB/TFE3 KO genotypes were treated with the STING agonist DMXAA (10 µg/mL) for 3 hours.

first: PJ

first: JM

last: Martina

last: Contreras

first: Akriti

last: Prashar

first: Eutteum

first: Dominic

last: De Nardo

first: Rosa

last: Puertollano


title: TFEB and TFE3 regulate STING1-dependent immune responses by controlling type I interferon signaling

overall_design: To investigate the role of TFEB in the innate immune response, chromatin immunoprecipitation sequencing (ChIP-seq) was performed on iBMDM cells treated with the STING agonist DMXAA (10 µg/mL) for 2 hours.

first: P

first: J


title: TFEB and TFE3 regulate STING1-dependent immune responses by controlling type I interferon signaling [Q48645_RNAseq]

overall_design: To investigate the role of TFEB and TFE3 in the innate immune response, we treated immortalized bone marrow-derived macrophages (iBMDMs) with the STING agonist DMXAA (10 µg/mL) for 3 hours.


title: RNA-sequncing in UUO-induced PTC-specific p300 knockout mouse kidneys

city: seoul

first: HYUNSIK

last: KIM

address: 50-1 Yonsei-ro

institute: yonsei univ

summary: p300 was knockout in renal proximal tubule cells of mouse kidney. Mouse was sacrificed 8 days after UUO sugery

overall_design: Total kidneys mRNA was extracted 8 days after UUO operted kidney, in triplicate

first: Ho-geun

last: Yoon

first: Hyunsik


title: Interplay between m6A modification and transcripts quantity:  Impacts on mRNA composition in plant stress granules

city: Poznan

first: Michał

last: Szcześniak

address: Uniwersytetu Poznanskiego 6

department: Institute of Human Biology and Evolution

country: Poland

institute: Adam Mickiewicz University

summary: Stress granules (SGs) are cytoplasmic structures that emerge in response to unfavorable environmental conditions. The mechanisms governing the accumulation of transcripts in SGs are only partially understood. Despite the recognized role of m6A in plant transcriptome regulation, its impact on SGs' composition and assembly remains elusive. In L. angustifolius, SGs display a distinctive bi-zonal structure comprising of a ring and a central area with differences in ultrastructure and composition. Subsequent to the transcriptome analysis, specific mRNA were chosen for investigating their localization within SGs and assessing m6A levels. Transcripts of hypoxia-responsive genes (ADH1 and HUP7) showed significantly lower levels of m6A compared to housekeeping genes, but only ADH1 was absent in SGs. HUP7 mRNA, characterized by a low quantity of m6A, is present both in the SGs and cytoplasm, probably due to extremely high expression level. The high amount of m6A was observed only during the assembly of SGs. In mutants of A. thaliana with reduced levels of m6A, ECT2 was not observed in SGs, and poly(A) RNA levels and the number  of SGs were slightly reduced. In summary, our findings demonstrate a limited impact of m6A modification on SGs assembly. However, the interplay between m6A modification and the overall transcript quantity in the cytoplasm appears to play a regulatory role in mRNA partitioning and assembly of SGs

overall_design: Gene expression profiling analysis using data obtained from RNA-seq of narrow-leafed lupin (L.angustifolius) roots grown under physiological conditions, 15-hour submergence, 15 hour submergence followed by 6 hour reoxygenation

first: Dawid

last: Kubiak

first: Michal

middle: W

last: Szczesniak

first: Janusz

last: Niedojadlo


title: Per- and Polyfluoroalkyl Substances Cause Changes in Gene Expression within HepG2 Cells Individually and as Equimolar Mixtures in Concentration-Response

city: Chapel Hill

first: Julia

last: Rager

state: NC

address: 135 Dauer Drive, CB 7431

institute: UNC

summary:
This study set out to evaluate the hypothesis that PFAS exposure alters EV regulation via upstream molecular mediators of EV-based alterations through cellular transcriptomics assessment in a concentration-response manner. To evaluate this hypothesis, HepG2 liver cells were treated in concentration-response with individual PFOS, PFOA, or PFHxA, in addition to an equimolar PFAS mixture. Global gene expression was measured.
These analyses set out to evaluate concentration-dependent changes in mRNA signatures within HepG2 immortalized liver cells exposed to individual PFOS, PFOA, PFHxA or an equimolar mixture containing all three PFAS.

overall_design:
Gene expression data from HepG2 immortalized liver cell line following 24 hr PFAS exposures
We tested an equimolar mixture containing three PFAS compounds: PFHxA, PFOA, and PFOS; with each individual chemical at a concentration of 2.5uM, 10uM, 25uM, or 35uM. We additionally tested PFOS, PFOA, and PFHxA individually at concentrations of 2.5uM, 10uM, 25uM, or 35uM. These PFAS conditions were used to treat HepG2 cells with a 24 hour time-point. RNA was subsequently isolated from HepG2 cell lysates. mRNA expression was measured using an array to evaluate changes in expression associated with exposure.

first: C

middle: K

last: Carberry

middle: E


title: Pharmacogenomic characterisation of a large collection of primary cell lines identifies novel therapeutic options for pleural mesothelioma

city: Paris

first: Sandrine

last: Imbeaud

address: 15 rue de l'Ecole de Médecine

department: INSERM UMRS1138-EQUIPE 28, Sorbonne Université-Inserm-Université de Paris

country: France

institute: Centre de Recherche des Cordeliers

type: Methylation profiling by genome tiling array

summary: Background: Pleural mesothelioma (PM) urgently requires novel effective treatments. Drug repurposing is a relevant strategy to discover new therapeutic options among well-known drugs used in clinical practice. This study aimed to identify new therapies in the context of molecular heterogeneity of PM.  Methods: We performed a multi-omics study of the largest cohort of patient-derived primary PM cell lines (n=58) to date, using whole exome sequencing, RNA sequencing and methylome analysis. We also conducted a large-scale drug screening of over 1300 compounds on a subset of cell lines (n=11), as well as an extension screen (n=48) for selected drugs of interest. The best candidates were validated using 3D culture and mouse models.    Results: We demonstrated that the molecular landscape of the cell lines cohort recapitulates the main findings in tumours and revealed new specific features of PM. The large-scale drug screening and subsequent validations highlighted notably strong sensitivity to entinostat and fluvastatin. Importantly, both compounds displayed same efficacy in 2D and 3D culture models and single treatment prolonged survival in vivo similarly or even better than standard chemotherapy. Strikingly, combining entinostat treatment with anti-PD1 led to cures in some mice and immunized them against tumour cells.  Conclusions: Among several candidates, we identified entinostat, notably in combination with immune checkpoint inhibitor, and to a lesser extent fluvastatin, as promising therapeutic options for patients. We believe our study provides a valuable resource that could contribute to advances in the field and warrants further clinical investigation.

overall_design: 58 patient-derived primary pleural mesothelioma cell lines were analyzed either with the Infinium HumanMethylation450 Beadchip (Illumina) or with the Infinium MethylationEPIC BeadChip Kit (Illumina) or both after bisulfite conversion of 500 ng of genomic DNA using the Zymo EZ DNA Methylation Kit (Ozyme)

first: Clément

last: Meiller

first: Didier

last: Jean


title: Effects of overexpression of MrgD on human pulmonary artery smooth muscle cells.

city: Jinan

first: hongyu

last: zhong

address: 07 Wenhua xi road, Jinan, Shandong

institute: Qilu hospital Shandong University

summary: MrgD is a new member of the RAS system and belongs to a group of G protein-coupled receptors.  The main function of these receptors is to sense and generate itching or pain signals.  In recent years, more and more cardiovascular research has been conducted, and it may have anti-fibrosis resistance.  inflammation and other functional effects.  The RAS system can maintain homeostasis in pulmonary hypertension, but the role of MrgD in pulmonary hypertension is unclear and how it affects downstream signaling pathways.  Taken together, our data provide a molecular framework for the role of MrgD in pulmonary hypertension.

overall_design: To study the function of MrgD in smooth muscle cells in pulmonary hypertension, we used adenovirus to overexpress MrgD in pulmonary artery smooth muscle cells.  After 24 hours, 3% hypoxia stimulation was given.  After 24 hours, we collected the RNA of the cells and performed downstream KEGG and GO analysis on the data obtained by cellular RNA-seq.

first: Hongyu

last: Zhong


title: CUT&Tag sequencing analyses target genes directly bound by transcription factors

city: jinan

first: Jiabei

last: Lian

state: Shandong

address: No.44, Wenhauxi Road, Lixia District, Jinan, China

department: College of Basic Medical Sciences

institute: Shandong University

summary: TF occupancy within or near a gene promoter or enhancer region is often assumed to be sufficient evidence for the gene to be classified as a direct TF target. We identified the TF ATF3 and ONECUT2 occupancy sites and direct target candidate genes using the CUT&Tag  in hepatocyte organoids.

overall_design: We isolated hepatocytes from C57BL/6 adult male mice for organoids culture, and genomic DNA of hepatocyte organoids was extracted and applied to CUT&Tag.

first: Xuena

last: Chen

first: Huili

last: Hu


title: Tumor-derived arachidonic acid reprograms neutrophils to promote immune suppression and therapy resistance in triple-negative breast cancer

city: Houston

first: Xiang

last: Zhang

state: TEXAS

address: One Baylor Plaza, Alkek N1130

department: Breast Center

institute: Baylor College of Medicine

summary: The combination of immune checkpoint blockade and chemotherapies is the standard-of-care for triple negative breast cancer (TNBC). However, initially responsive tumors can still develop recurrences, suggesting acquired resistance mechanisms that remain poorly understood. Herein, we discovered that TNBC cells surviving anti-PD-1 and chemotherapy treatment accumulated neutral lipids. Disrupting lipid droplet formation in cancer cells reversed resistance and mitigated the immunosuppressive microenvironment. Single-cell RNA sequencing revealed a subset of neutrophils exhibiting a lipid-laden phenotype similar to adjacent tumor cells. Mechanistically, tumor-derived extracellular vesicles carrying lipids including arachidonic acid (AA) mediated neutrophil reprogramming. Blocking dietary intake of omega-6 fatty acids or inhibiting fatty acid elongation for AA synthesis restored antitumor immunity and re-sensitized the resistant tumors to anti-PD-1 and chemotherapy treatment. In human patients, AA metabolism-related pathways correlated with neutrophil enrichment. Overall, we demonstrate how lipid accumulation in TNBC cells leads to immune suppression and therapy resistance.

overall_design: Eighteen days after tumor implantation, three tumors from 2208L, 2208L-Res1 and 2208L-Res2 group were collected, and CD45+ immune cells were sorted out for single cell sequencing.

first: Fengshuo

last: Liu

first: Yichao

last: Shen

first: Liqun

last: Yu


title: Chromatin accessibility profiles of mouse liver following PHx and Hepatocyte organoid

summary: The ATAC-Seq experiment was designed to map chromatin accessibility at different stages of regeneration in 70% partial hepatectomy and at different periodss of liver organoid formation.

overall_design: We collected tissues from the undamaged and the initiation phase (6, 12 h), the maintenance phase (24, 48 h) after PHx, and the Hep-Orgs culture for 4 days (T1, initiation phase) and 13 days (T2, maintenance phase) for ATAC-seq analysis to study the chromatin characteristics at different stages.


title: Multi-omics approaches for identification of novel dynamic regulators in transcriptional landscape and chromatin accessibility changes in liver regeneration and hepatocyte organoid formation


title: TBX3 advances the developmental chromatin landscape towards the hepatic fate [ChIP-seq]

city: Vancouver

first: Tabea

last: Stephan

address: 2329 West Mall

institute: University of British Columbia

summary: Hepatocytes differentiate from definitive endoderm in response to external signaling cues, however it is unclear how the hepatic lineage is specified and how transcription factors shape the chromatin to allow gene expression. By mapping histone modifications using a human stem cell model of hepatic differentiation, enhancers were found to exhibit dynamic, stage specific regulation, with many primed at the definitive endoderm stage. While hepatic enhancers gained active histone modifications, non-hepatic enhancers lost H3K4me1 after hepatic specification. TBX3, and to lesser extend HNF4A, bound to the hepatic enhancers and formed an interdependent transcription factor network. TBX3 bound both hepatic enhancers and promoters with low levels of H3K4me1 and a strong TBX3 motif. However, TBX3 binding was transient and upon eviction from TBX3-bound regions, H3K4me1 increased at enhancers, while H3K4me3 was established at promoters. This suggests that TBX3 plays a role in identifying hepatic enhancers and promoters during specification, which will then be activated to drive cell idenity.

overall_design: ChIPseq for the histone modifications H3K4me3, H3K4me1, H3K27me3, H3K27ac, H3K36me3 and transcription factors TBX3 and HNF4a in SV20 cells differentiated into hepatic cells. Samples were taken at Mesendoerm stage, Definitive endoderm stage, heaptic endoderm stage and hepatoblast stage.

first: Rebecca

last: Cullum

first: Sibyl

last: Drissler

first: Bettina

last: Fuglerud

first: Jeremy

last: Lotto

first: Makenna

last: Clement-Ranney

first: Stephen

last: Duncan

first: Pamela

last: Hoodless


title: TBX3 advances the developmental chromatin landscape towards the hepatic fate


title: mRNAseq profiles of gastrocnemius of 24-day-old Nnt-wt male mouse exposed to hypoxia

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

summary: Gene expression profiles from gastrocnemius of fasted Nnt-wt male mice exposed to hypoxia (12%O2) or normoxia for 6 hours  (n=12 per group). Result showed that the FOXO1 was the main transcription factor regulated by hypoxia. FOXO1 activation induces regulation of gene expression related to protein degradation (ubequitin-proteasome system) (atrophy), autophagy and apoptosis inhibition.

overall_design: Gastrocnemiuse muscle mRNA-seq profiles of 24-day-old Nnt-wt male mice after 6-hour hypoxia or normoxia (control) exposure (n = 12 per group). The mouse strain is B6JRccHsd(B6J)-Nnt<+>/Wuhap.

first: Jingyi

last: Song

first: Jaap

last: Keijer

first: Sander

last: Grefte


title: Biologic characteristics of B-lymphoblastic leukemia correspond to immunoglobulin gene diversity [array]

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

summary: We tested the relationship between IgH subclone diversity in B-ALL and the number of resolved chromosomal breaks as assessed by chromosome microarray analysis (CMA).

overall_design: Given the role of off-target recombination activating gene (RAG) activity at non-IgH sites in promoting copy number aberrations (CNA) in B-ALL, we conducted CMA to test whether patients with RAG-mediated IgH subclone diversity demonstrate greater karyotypic variability.

first: Carol

last: Fries

first: Janice

last: Spence

first: Aayush

last: Poudel

first: John

middle: P

first: Philip

last: Rock

first: Bin

first: Anwar

last: Iqbal

first: Hongyue

last: Wang

first: Diana

middle: G

last: Adlowitz

first: Cal

last: Palumbo

first: Helene

middle: R

last: McMurray

first: Andrew

last: McDavid

first: Richard

last: Burack


title: RNA sequencing of undamaged, PHx liver and Hepatocyte organoids

first: Jiabei

last: Lian

summary: To investigate the cellular and molecular mechanisms that initiate liver regeneration and liver organoid formation, we performed RNA sequencing in the following cell types: hepatocytes from undamaged livers of mice as well as 6 h, 12 h, 24 h, 48 h, 72 h, 7 d, 14 d, 21 d of liver regeneration after PHx.  Hep-Orgs were  isolated from adult male mice hepatocytes and cultured for passages.

overall_design:
We generated transciptome datas from undamaged livers of mice as well as 6 h, 12 h, 24 h, 48 h, 72 h, 7 d, 14 d, 21 d of liver regeneration after PHx. Hep-Orgs were  isolated from e hepatocytes and cultured for passages.
This is our second submission of transcriptomic data from the liver regeneration process following PHx (partial hepatectomy). The data submitted this time covers time points at 6h, 12h, 24h, 48h, 72h, 7d, 14d, and 21d. This dataset serves as a supplement and extension to the previously submitted data, further refining the comprehensive landscape of gene expression dynamics during liver regeneration.

first: Xuena

last: Chen

first: Huili

last: Hu


title: Menin-MLL complex cooperates with NF-Y to promote HCC survival [RNA-seq]

status: Public on Apr 07 2025

first: Jesse

last: Raab

address: 120 Mason Farm Rd

department: Genetics

institute: University of North Carolina Chapel Hill

summary: Identification of new therapeutic targets in liver cancer remains critical. Chromatin regulating complexes are frequently mutated in liver cancer suggesting dysregulation of chromatin environments is a key feature driving liver cancer. We applied a focused CRISPR library targeting all genes involved in chromatin regulation to determine if the altered chromatin state of hepatocellular carcinoma cells could be targeted. The focused approach allowed us to test multiple cell lines in both 2D and 3D growth conditions which revealed striking differences in the essentiality of genes involved in ubiquitination and uncovered multiple chromatin regulators that are essential in 2D but whose loss promotes growth in 3D. We found the menin-MLL complex as among the strongest essential genes in all screens and deeply characterized the mechanism menin-MLL uses to promote hepatocellular carcinoma growth. Inhibition of menin-MLL led to global changes in occupancy of the complex and concomitant decreases in H3K4me3 and gene expression. A surprising increase in chromatin accessibility at sites not bound by menin-MLL was associated with recruitment of the pioneer transcription factor complex NF-Y. A screen of chromatin regulators in the presence of the menin-MLL inhibitor SNDX-5613 revealed a synergy between NF-YB loss and menin-MLL inhibition. Together these data show that menin-MLL is necessary for cell survival in HCC and cooperates with NF-Y to regulate transcription.

overall_design: RNA-seq on HLF and PLC/PRF/5 liver cancer cell lines following treatment with 5uM menin inhibitor (SNDX-5613) or DMSO or with menin knockout

first: Margarita

last: Dzama


title: AI-generated MLH1 small binder improves prime editing efficiency

city: Seoul

first: Heesoo

last: Uhm

address: 103 Daehak-ro

summary: The prime editing (PE) system consists of a Cas9 nickase fused to a reverse transcriptase, which introduces precise edits into the target genomic region guided by a prime editing guide RNA. However, PE efficiency is limited by mismatch repair. To overcome this limitation, transient expression of a dominant-negative MLH1 (MLH1dn) has been used to inhibit key components of mismatch repair. Here, we designed a de novo MLH1 small binder (MLH1-SB) that binds to the dimeric interface of MLH1 and PMS2 using RFdiffusion and AlphaFold 3. The compact size of MLH1-SB enabled its integration into existing PE architectures via 2A systems, creating a novel PE-SB platform. The PE7-SB system significantly improved PE efficiency, achieving an 18.8-fold increase over PEmax and a 2.5-fold increase over PE7 in HeLa cells, as well as a 3.4-fold increase over PE7 in mice. This study highlights the potential of generative AI in advancing genome editing technology.

overall_design: RNA-seq profiling of Mock, PuroR, MLH1dn, SB, PE7, and PE7SB treated sample to investigate off-target effects on transcriptome level after gene editing

first: Ju-Chan

last: Park

first: Yong-Woo

last: Kim

first: Ye Eun

last: Oh

first: Jang Hyeon

last: Lee

first: Jiyun

last: Yang

first: Kyoungmi

first: Sangsu

last: Bae


title: A novel regulator of the fungal phosphate starvation response revealed by transcriptional profiling and DNA affinity purification sequencing

city: Ithaca

first: Lori

middle: B

last: Huberman

address: 236 Tower Rd.

department: Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science

institute: Cornell University

summary: Cells must accurately sense and respond to nutrients to compete for resources and establish growth. Phosphate is a critical nutrient source necessary for signaling, energy metabolism, and synthesis of nucleic acids, phospholipids, and cellular metabolites. During phosphate limitation, fungi import phosphate from the environment and liberate phosphate from phosphate-containing molecules in the cell. In the model filamentous fungus Neurospora crassa, the phosphate starvation response is regulated by the conserved transcription factor NUC-1. The activity of NUC-1 is repressed by a complex of the cyclin-dependent kinase MDK-1 and the cyclin PREG when phosphate is plentiful. When phosphate is limiting, NUC-1 repression by MDK-1/PREG is relieved by the cyclin-dependent kinase inhibitor NUC-2. We investigated the global response of N. crassa to phosphate starvation. During phosphate starvation, NUC-1 directly activated expression of genes encoding phosphatases, nucleases, and a phosphate transporter and directly repressed genes associated with the ribosome. Additionally, NUC-1 indirectly activated the expression of an uncharacterized transcription factor, which we named nuc-3. NUC-3 directly repressed the expression of genes involved in phosphate acquisition and liberation after an extended period of phosphate starvation. Additionally, NUC-3 directly repressed expression of the cyclin-dependent kinase inhibitor nuc-2. Thus, through the combination of NUC-3 direct repression of genes in the phosphate starvation response and nuc-2, an activator of the phosphate starvation response, NUC-3 serves to act as a brake on the phosphate starvation response after an extended period of phosphate starvation. This braking mechanism could reduce transcription, a phosphate-intensive process, in conditions when phosphate is limiting.

overall_design: mRNA-seq profiling of Neurospora crassa wild type exposed to 7 mM phosphate or phosphate starvation and nuc-1 deletion and nuc-3 deletion strains exposed to phosphate starvation for 4 h or 12 h. Each experiment was performed in biological triplicate.

first: Vincent

last: Wu

first: David

last: Kowbel

first: Juna

first: Chris

last: Daum

first: Igor

middle: V

last: Grigoriev

first: Ronan

middle: C

last: O'Malley

first: N

last: Glass


title: ARMC5 selectively degrades SCAP-free SREBF1 and is essential for fatty acid desaturation in adipocytes.

city: Suita

first: Akifumi

last: Uota

state: Osaka

address: 2-2 Yamadaoka

country: Japan

institute: Department of Metabolic Medicine, Osaka University Graduate School of Medicine

summary: Background: Armadillo repeat containing 5 (ARMC5)-CUL3 complex was recently identified as an E3 ubiquitin ligase of full-length SREBF. Although ARMC5 was involved in SREBF2 pathway in the adrenocortical cells and might participate in the development of primary bilateral macronodular adrenal hyperplasia (PBMAH), the role of ARMC5 in adipocytes has not been investigated.  Methods and Results: Adipocyte-specific Armc5 knockout mice were generated. In the white adipose tissue (WAT) of these mice, all the stearoyl-CoA desaturase (Scd) were drastically downregulated under refed condition and high fat-high sucrose diet. Consistently, unsaturated fatty acids were decreased, while saturated fatty acids were increased in the WAT of these mice. Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-Seq) peaks at the SREBF1-binding sites were markedly diminished around the Scd1 locus in the WAT of adipocyte-specific Armc5 knockout mice. Armc5-deficient 3T3-L1 adipocytes also exhibited downregulation of Scd. Mechanistically, disruption of Armc5 restored decreased full-length SREBF1 in the CHO cells deficient for Scap, an escort protein required for the transport of SREBF from the ER to the Golgi. In HEK293T cells, overexpression of Scap inhibited ARMC5-mediated degradation of full-length SREBF1, and overexpression of Armc5 increased nuclear SREBF1/full-length SREBF1 ratio in the presence of exogenous Scap in HEK293T cells.  Conclusions: ARMC5 exerts selective removal of SCAP-free SREBF1 and stimulates SCAP-mediated SREBF1 processing, hence is essential for fatty acid desaturation in vivo.

overall_design: ATAC-Seq of epididymal WAT from control flox and adipocyte-specific Armc5 KO.

first: Yosuke

last: Okuno


title: Menin-MLL complex cooperates with NF-Y to promote HCC survival [CRISPR]

first: Jesse

last: Raab

overall_design: HLF or PLC/PRF/5 cells were infected with lentiviral guide RNA library targeting chromatin regulators (737 genes). gDNA from cells was harvested at an initial time point and again after 28 days grown in 2D or 3D culture conditions. For some samples, either DMSO or SNDX-5613 was added to growth. gRNAs were then sequenced and compared either to the initial time point or to between two endpoint conditions (2D vs 3D ; DMSO vs SNDX-5613)

first: Margarita

last: Dzama


title: Biologic characteristics of B-lymphoblastic leukemia correspond to immunoglobulin gene diversity

first: Cameron

last: Baker

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

overall_design: Refer to individual Series


title: Argonaute 15 controls MITE-generated sRNAs in potato: implications on plant defense

city: Uppsala

first: Kristian

middle: Erik

last: Persson Hodén

address: Almas allé 5

department: Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: Canonical ribonucleases like Argonautes (AGOs) participate in RNA-based gene regulatory processes. They are important for the small RNA association and formation of the RNA-induced RNA silencing complexes (RISCs). Potato (Solanum tuberosum, St) has 14 AGO-encoding genes, among those is the Solanum-specific StAGO15, which is activated upon infection by filamentous pathogens. Here, we analyzed sRNAs associated to StAGO15 during leaf infection with the aim to clarify its role in plant immunity

overall_design: Leaves with lesion sizes between 8 and 12 mm from a potato line harboring p35S:StAgo15-GFP inoculated with P. infestans (Pi) strain 3928A were collected 5 days post inoculation (dpi). In parallel, leaf materials from water inoculated potato Desirée were prepared. Three replicates for each sample consisting of 2 g of pooled leaf material were used for co-immunoprecipitation as earlier described (Åsman et al., 2016). Six libraries were prepared at the SciLifeLab (Solna, Sweden).  The libraries were designed for Illumina NextSeq 2000 P2 (2x50bp), with a 51nt (Read1, R1)-6nt (Index1)-51nt (Read2, R2) setup using Illumina TrueSeq small RNA Kit. The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite applying the Sanger / phred33 / Illumina 1.8+ quality scale. Data analysis was performed as earlier outlined (Persson Hodén et al., 2021), except the Illumina R2 FASTA files were reversely complemented using fastx_reverse_complement in the FASTX-Toolkit (Hannon, 2010). Resulting R1 and R2 FASTA files were combined followed by prediction of cleavage sites by applying the smartPARE pipeline (Persson Hodén et al., 2021). Comparisons between datasets of infected and control materials were performed to generate increased or decreased normalized fragment abundance (NFA) datasets.

first: Shailja

last: Singh

first: Xinyi

last: Hu

first: Zhen

last: Liao

first: Christina

last: Dixelius


title: The role of Cd24a in the post natal lens

city: Newark

first: Melinda

middle: K.

last: Duncan

state: DE

address: 327 Wolf Hall

department: Biological Sciences

institute: University of Delaware

summary: This trancriptome analysis reports genes that are differentially expressed as the result of Germline deletion of the gene Cd24a.

overall_design: Lenses were isolated from 7 week old Wild Type (WT) and Cd24a Germline Knockout mice by microdissection (2 lenses/sample, three biological replicates/genotype) and total RNA was isolated. cDNA libraries were constructed using SMARTer Stranded Total RNA-Seq - Pico Input Mammalian, and sequenced using an Illumina NextSeq 500 (DNA Link USA, Inc) in an attempt to undestand the role of Cd24a in the post natal lens.  Each library was sequenced accross 4 flow cell lanes.

first: M

middle: H

last: Shihan

first: A

last: Faranda


title: Albumin treatment transcriptionally reprograms circulating immune cells in patients with acutely decompensated cirrhosis

city: Barcelona

first: Ferran

last: Aguilar

state: Barcelona

address: Travessera de Gràcia, 11

country: Spain

institute: EF-CLIF

summary:
BACKGROUND AND AIMS: The effects of intravenous albumin on lymphocyte perturbations and defective neutrophil anti-microbial functions that characterize patients with acute-on-chronic liver failure (ACLF) are unknown.
METHODS: Forty-nine patients admitted for severe acutely decompensated cirrhosis without ACLF were investigated with the use of whole-blood RNA sequencing (RNA-seq) on admission and after a median period of 15 days once they had developed ACLF. Such patients were selected because they follow a steady systemic inflammation course. Thirty patients had received albumin during the progression to ACLF but not the 19 others. Single-cell RNA-seq (scRNA-seq) in peripheral blood mononuclear cells (PBMCs) exposed ex vivo to albumin or vehicle for 2 hours, and assessment of the anti-microbial capacity of neutrophils exposed ex vivo to albumin were performed in additional patients with acutely decompensated cirrhosis.
RESULTS: Analysis of whole-blood RNA-seq data revealed that patients who had received albumin exhibited specific upregulation of signatures related to B cells, plasma cells and immunoglobulins; CD4 T cells; myeloid cells; mismatch repair, cell cycle and mitosis; and transcription factors such as c-Myc and E2F family members. The use of scRNA-seq to analyze patients' PBMCs exposed ex vivo to albumin showed increases in signatures related to B cells, myeloid cells, and CD4 T cells. Neutrophils exposed ex vivo to albumin exhibited increased chemotactic and degranulation responses, enhanced phagocytosis, and increased pathogen-destroying swarming functions.
CONCLUSIONS: In patients with severe acutely decompensated cirrhosis, albumin rewires transcription in B cells, CD4 T cells and mononuclear myeloid cells, and resets neutrophil anti-microbial functions to normal.

overall_design:
RNA Preparation for Whole-Blood RNA-seq
RNA was isolated from blood stored in Tempus tubes using the Tempus™ Spin RNA Isolation Kit (reference 43802 Applied Biosystems, Foster City, CA). Preparation for RNA-seq is detailed in the Methods section of the Supplementary Appendix. Importantly, using the HUGO Genome Nomenclature Committee, which is a resource for approved human gene nomenclature, we designed a comprehensive protocol that included not only protein-coding genes, but also genes among other gene locus types, such as immunoglobulin genes, and T-cell receptor genes, resulting in a total of 14,615 genes for analysis. Genes brought by sexual chromosomes and mitochondrial DNA were not included in the analysis.

ScRNA-seq in PBMCs
Peripheral venous blood (8 ml) was collected by venipuncture into EDTA-coated sterile pyrogen-free tubes (Becton Dickinson, East Rutherford, NJ) from 9 patients and 4 age-matched healthy subjects. PBMCs were immediately isolated as previously described.27 PBMCs were seeded at a density of 1.5x106 cells/ml and incubated with either albumin (Albutein®, Grifols, Barcelona, Spain) (15 mg/ml) or vehicle (culture medium) for 2 hours at 37ºC in a 5% CO2 incubator. At the end of the culture, cells were rapidly (within 30 min) transferred to ice at the Single Cell Genomics platform from the CNAG. The protocol used for scRNA-seq and analysis of data are detailed in the Methods section of the Supplementary Appendix.

Experiments in Neutrophils
Neutrophils were isolated from peripheral venous blood (20 ml) obtained from 6 patients and 5 age-matched healthy subjects using the Ficoll-Hypaque method or negative depletion (StemCell neutrophil purification kit). Isolated neutrophils were immediately used for different experiments that assessed major anti-microbial functions of neutrophils such as degranulation assay, phagocytosis assay, swarming, and chemotaxis. For more details, see the Methods section in the Supplementary Appendix.

first: Joan

last: Clària

first: Juan-José

last: Lozano

first: Laura

last: Jiménez-Gracia

first: Juan

last: Nieto

first: Holger

last: Heyn

first: Vicente

last: Arroyo

first: Richard

last: Moreau


title: Improving genome-scale metabolic model simulations by measuring exchange fluxes during exponential growth phase

city: Nijmegen

first: Cyriel

last: Huijer

address: Houtlaan 4

department: Molecular Developmental Biology

institute: Radboud University Nijmegen

summary: With the state-of-the-art techniques currently available, measuring all metabolic reactions in a cell remains impossible. Therefore, systems biology approaches such as genome-scale metabolic models (GEMs) should be used to get a holistic view of metabolism. To reduce the solution space in GEM simulations, models are often constrained with exchange fluxes. However, previous literature that used exchange flux constraints violate the steady-state assumption necessary for GEMs, by inferring the flux from a single metabolomic sample. Here, we present the regression during exponential growth phase (REGP) method, which calculates exchange fluxes only during the log phase, thereby assuring measurements are conducted during metabolic steady-state. The REGP method was tested this method using MCF10A breast epithelial cells. We report that exchange fluxes are generally higher using the REGP method, highlighting the importance of measuring exchange fluxes during steady-state. Even changes in flux direction were observed, which indicates a metabolic shift between the lag phase and the exponential growth phase. While models constrained with previously reported exchange fluxes were infeasible or failed to predict the experimental growth rate, the REGP-constrained GEM accurately predicted the correct growth rate. Flux variability analysis revealed that even with constraints on the exchange of metabolites in central carbon metabolism and amino acid metabolism, these pathways still have intermediate variability in reaction flux. The results of this study suggest that future research should use the REGP method to determine exchange fluxes when these are used as constraints for GEMs, this will provide a better understanding of the complex mechanisms involved in metabolism.

overall_design: MCF10A breast epithelial cells were transduced with the empty vector (EV) using the Retro-X™ Tet-One™ Inducible Expression System (Takara, Cat# 634307) and selected with puromycin. No gene-of-interest was incorporated into the plasmid, resulting in no gene overexpression. Cells were harvested without doxycycline treatment.

first: Xiang

last: Jiao

first: Yun

last: Chen

first: Rosemary

last: Yu


title: CHD7 binds to insulators during neuronal differentiation [RNA-Seq]

city: Piscataway

first: Kelvin

middle: Y.

last: Kwan

state: NJ

address: 604 Allison Rd.

department: Cell Biology & Neuroscience

institute: Rutgers University

summary: Spiral ganglion neurons (SGNs) are crucial for hearing, and the loss of SGNs causes hearing loss. Stem cell-based therapies offer a promising approach for SGN regeneration and require understanding the mechanisms governing SGN differentiation. We investigated the chromatin remodeler CHD7 in SGN differentiation using immortalized multipotent otic progenitor (iMOP) cells. We demonstrate that CHD7 knockdown significantly impairs neuronal differentiation. Genome-wide analysis reveals CHD7 enrichment at diverse cis-regulatory elements, with notable enrichment at sites marked by the insulator-binding protein CTCF between topologically associating domains (TADs). Insulators marked by the enrichment of CHD7 and CTCF resided near genes critical for neuronal differentiation, including Mir9-2. Targeting these regulatory regions in iMOPs with CRISPR interference (CRISPRi) and activation (CRISPRa) increased miR9 transcription, irrespective of the method. The occlusion of the regulatory elements suggested that the insulators function to regulate gene expression. The study highlights CHD7 activity at insulators and underscores its importance in promoting neuronal differentiation.

overall_design: We performed RNA-seq to compare the gene expression profiles of proliferating iMOPs and iMOP-derived neurons

first: Jingyun

last: Qiu

first: Azadeh

last: Jadali

first: Julie

last: Ni

first: Edward

last: Martinez

first: Zhichao

last: Song


title: CHD7 marks TAD boundaries during neuronal differentiation [RNA-Seq]

summary: The chromodomain helicase DNA binding protein 7 (CHD7) is a nucleosome repositioner implicated in multiple cellular processes, including neuronal differentiation. We identified CHD7 marked sites at TAD boundaries that regulate neuronal differentiation in an otic stem cell line.  We showed that CHD7 co-occupied CTCF sites genome-wide. We identified CTCF+ CHD7+ sites near an essential transcription factor, Sox11, required for otic neuronal differentiation. The Sox11 promoter and  3’ untranslated region (UTR) showed CHD7 enrichment.  The CHD7-marked sites at the 3’UTR displayed histone marks corresponding to active transcription that resulted in Sox11 antisense transcripts.  Blocking the singular CHD7-marked site with CRISPRi decreased neurite lengths, reduced neuronal marker expression (TUBB3), and attenuated Sox11 antisense transcripts. Sox11 antisense transcripts were previously suggested to form double-stranded RNA and degrade the Sox11 transcript. Surprisingly, the level of the Sox11 sense transcripts remained unaffected after CRISPRi.  We propose that CHD7 at TAD boundaries modulate the chromatin accessibility of CTCF-marked insulators, altering the 3D chromatin organization and ultimately affecting gene expression. Our results implicate a general mechanism of CHD7 in facilitating neuronal differentiation and provide insight into CHD7 dysfunction in CHARGE syndrome, an intellectual developmental disability disorder.

overall_design: Stranded RNA-seq from proliferating iMOPs (immortalized multipotent otic progenitors) and iMOP-derived neurons

first: Anna-Marie

last: Hinman

first: Zhouli

first: Jihyun

last: Kim

middle: Y


title: Menin-MLL complex cooperates with NF-Y to promote HCC survival [ATAC-seq]

first: Jesse

last: Raab

overall_design: ATAC-seq for HLF human liver cancer cells treated for 24 hours with DMSO or 5uM SNDX-5613.

first: Margarita

last: Dzama


title: Ionizing radiation-Induced reprogramming of polarized Macrophages and their exosomes

city: Jeongeup-Si

first: Hyoung-woo

last: Bai

address: 29 Geumgu-gil

institute: Korea Atomic Energy Research Institute (KAERI)

summary: Macrophages play a central role in immune regulation by adopting distinct polarization states—pro-inflammatory M1 and anti-inflammatory M2 phenotypes. Ionizing radiation has emerged as a promising tool for modulating immune cell functions; however, its impact on macrophage polarization and associated molecular changes remains poorly understood. In this study, we investigated the transcriptional and functional alterations induced by gamma irradiation (10 Gy) in M1- and M2-polarized RAW 264.7 macrophages. Transcriptome analysis was performed to identify radiation-induced gene expression changes and to uncover key regulators driving these responses. Additionally, we explored the biological functions of exosomes derived from irradiated macrophages, given their potential as cell-free therapeutic agents that reflect parental cell status. Our findings provide new insights into how ionizing radiation reprograms polarized macrophages and modulates their cytokine signaling and exosomal profiles, highlighting novel targets and strategies for immune modulation and therapeutic development.

overall_design: Transcriptomic profiling of ionizing radiation-exposed M1/M2-polarized macrophages and their exosomes by RNA-seq

first: Hanui

last: Lee


title: TBX3 advances the developmental chromatin landscape towards the hepatic fate [RNA-seq]

first: Tabea

middle: L

last: Stephan

overall_design: Total RNA-seq in SV20 cells differentiated into hepatic cells. Samples were taken at Pluripotent stage, Mesendoerm stage, Definitive endoderm stage, heaptic endoderm stage, hepatoblast stage and hepatocyte-like stage.

first: Rebecca

last: Cullum

first: Sibyl

last: Drissler

first: Bettina

middle: M

last: Fuglerud

first: Jeremy

last: Lotto

first: Makenna

last: Clement-Ranney

first: Stephen

middle: A

last: Duncan

first: Pamela

last: Hoodless


title: Menin-MLL complex cooperates with NF-Y to promote HCC survival [CUT&RUN]

city: Chapel Hill

summary: Identification of new therapeutic targets in hepatocellular carcinoma (HCC) remains critical. Chromatin regulating complexes are frequently mutated or aberrantly expressed in HCC, suggesting dysregulation of chromatin environments is a key feature driving liver cancer. To investigate whether the altered chromatin state in HCC cells could be targeted, we designed and utilized an epigenome-focused CRISPR library that targets all genes involved in chromatin regulation. This focused approach allowed us to test multiple cell lines in both 2D and 3D growth conditions, which revealed striking differences in the essentiality of genes involved in ubiquitination and uncovered multiple chromatin regulators vital for HCC cell survival in 2D but whose loss promoted growth in 3D. We found the core subunits of the menin-MLL1 complex among the strongest essential genes for HCC survival in all screens and thoroughly characterized the mechanism through which menin-MLL1 complex promote HCC cell growth. Inhibition of the menin-MLL1 interaction led to global changes in occupancy of the complex and concomitant decreases in H3K4me3 and gene expression.  We observed that increased chromatin accessibility at sites not bound by menin-MLL1 was associated with the recruitment of the pioneer transcription factor complex NF-Y. A CRISPR/Cas9 screen of chromatin regulators in the presence of the menin-MLL1 inhibitor SNDX-5613 revealed  a synergistic effect on cell death when combining NF-YB loss and menin-MLL1 interaction inhibition. Together, these data show that menin-MLL1 is necessary for HCC cell survival and cooperates with NF-Y to regulate oncogenic gene transcription.

overall_design: CUT&RUN was performed for indicated antibodies following treatment of HLF cells with 5uM SNDX-5613 or DMSO for 24 hours


title: CHD7 marks TAD boundaries during neuronal differentiation [ChIP-Seq]

first: Kelvin

last: Kwan

overall_design: ChIP-seq for CHD7 from proliferating iMOPs (immortalized multipotent otic progenitors) and iMOP-derived neurons.

first: Edward

first: Azadeh

last: Jadali

first: Jingyun

last: Qiu

last: Ni


title: Transcriptional responses of oxyR mutation in Pseudomonas aeruginosa

city: Beijing

first: Qing

last: Wei

address: NO.1 Beichen West Road, Chaoyang District

institute: Institute of Microbiology, Chinese Academy of Sciences

summary: Analysis of Pseudomonas aeruginosa PAO1 (ATCC 15692) transcriptional response by disruption of oxyR. PAO1 cells are evaluated with RNA-seq to understand the genes affected by this mutation. Our results provide new vision on the regulation of oxyR in pathogens.

overall_design: We used two PAO1 replicates and two oxyR replicates to compare the differential gene expression under exponential phase by RNA-seq.


title: Biologic characteristics of B-lymphoblastic leukemia correspond to immunoglobulin gene diversity [sequencing]

first: Cameron

last: Baker

summary: It remains unclear whether the variable biologic features of B-lymphoblastic leukemia (B-ALL) reflect distinct cells of origin in the hierarchy of early B cell development. Recombination activating genes (RAG) 1 and 2 rearrange the immunoglobulin heavy chain (IgH) locus in B lymphoid progenitors, resulting in unique variable (Vh), diversity (D), and joining (Jh) gene rearrangements. To test whether discrete properties of each B-ALL reflect derivation from distinct developmental B cell stages, we assessed the relationship between IgH variable gene (IGHV) characteristics and gene expression. Using targeted, pre-treatment IgH sequencing of 22 patients’ B-ALL, we discovered 2 distinct groups: leukemias with RAG-mediated intra-clonal IGHV sequence diversification (‘diverse’; N=9, 40.9%) and those lacking diversity (‘homogeneous’; N=10, 45.5%). Three patients (13.6%) lacked a dominant IgH sequence. In the ‘diverse’ cohort, we observed extensive subclone evolution arising from Vh gene recombination after neoplastic transformation (median: 482 subclones; range 2-2600). In the ‘homogeneous’ cohort, all IgH clones lacked subclone evolution. The ‘diverse’ cohort demonstrated enriched expression of genes associated with regulation of a hematopoietic stem cell state, while ‘homogeneous’ cases showed enriched expression of genes involving cell fate commitment. Furthermore, distinct IgH clonotypes within a single patient could be individually diverse or homogenous. Single cell analysis indicated that within a single patient, only occasional IgH clonotypes were expressed; IGHV-expressing leukemia cells were characterized by distinctive phenotypes including RAG1 pathway up-expression. In summary, pre-treatment IgH composition reflects the B cell stage at leukemic initiation and provides insights about the biologic mechanisms of genetic diversity in B-ALL.

overall_design: We evaluated pre-treatment bone marrow (BM) and/or peripheral blood (PB) from 22 patients with newly diagnosed B-ALL. Associated data included age, presenting WBC count, immunophenotype, and cytogenetics. We performed targeted IgH NGS on pre-treatment PB for all 22 cases and on BM for the 16/22 for whom BM was available. Fourteen patients with available viably frozen tissue underwent RNA sequencing (RNAseq), and 7 specimens from 5 patients underwent single-cell RNAseq. Chromosome microarray (CMA) analysis was conducted on the 18/22 cases with available B-ALL DNA after IgH NGS.

first: Carol

last: Fries

first: Janice

last: Spence

first: Aayush

last: Poudel

first: John

first: Philip

middle: J

last: Rock

first: Bin

last: Zhang

first: Anwar

last: Iqbal

first: Hongyue

last: Wang

first: Diana

last: Adlowitz

first: Cal

last: Palumbo

first: Helene

last: McMurray

first: Andrew

last: McDavid

first: Richard

last: Burack


title: Effects of exercise and Phellodendron amurense extract in prostate cancer

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: Oxidative stress, induced by chronic prostatic inflammation, impairs normal protective mechanisms in the prostate and increases the risk for cancer progression. The Phellodendron amurense extract (Nexrutine®) had similar effects as exercise in reducing highly aggressive tumors in the transgenic adenocarcinoma of the mouse prostate (TRAMP) model. In this study, we examined changes in the transcriptome to understand how these two interventions affect prostate cancer.

overall_design: Twenty-four, 8-10 weeks old male TRAMP mice, were randomized to control, exercise, and Phellodendron amurense extract intervention. Mice were maintained in a climate-controlled environment with a 12-hour light-dark cycle with diet and water provided ad libitum. Phellodendron amurense extract was supplied in the diet and running wheel was used as the exercise intervention. The control group mice were group housed had access to AIN-93 diet ad libitum and did not have access to running wheel. Body weight changes, food consumption and distance run on the running wheel were measured weekly for the 12-week intervention. At the end of the study, prostate tumors were excised, weighed, and processed for transcriptome analysis (3 replicates each condition).

first: Darpan

middle: I

last: Patel

first: Paul

last: Rivas

first: Addanki

last: Kumar

first: Rita

last: Ghosh

first: Zhao

last: Lai

first: Ikeno

last: Yuji


title: Transcriptomic profiling of human trophoblast stem cells (hTSCs) and HTR-8/SVneo cells under  normal and MYBL2 knockdown conditions

city: Chongqing

first: Zhihong

last: Wu

state: Chongqing

address: No.1 Yixueyuan Rd, Yuzhong District, Chongqing

institute: Chongqing Medical University

summary: This dataset comprises  the gene expression profiles of human trophoblast stem cells (hTSCs) and HTR-8/SVneo cells under WT and  MYBL2 knockdown conditions. RNA sequencing (RNA-seq) was conducted to examine the effects of MYBL2 depletion on gene expression, with the goal of elucidating its role in trophoblast function, including stemness maintenance, differentiation, and invasion. This dataset offers valuable insights into the molecular mechanisms governed by MYBL2 in trophoblast biology and its potential relevance to pregnancy-related disorders.

overall_design: RNA-seq profiling of MYBL2 knockdown (shMYBL2) and their corresponding control (shNC) in HTR-8/SVneo cells (HTR8) and human trophoblast stem cells (hTSCs).

first: Zhi-Hong

first: Jia-Qi

last: Xu

first: Jing

last: Tang


title: RNA Methylation and Transcriptome Analysis Reveal Key Regulatory Pathways Related to Cadmium-Induced Liver Damage

city: Guangzhou

first: Hao

last: Huang

state: Guangdong

address: No. 1023 Shatai Road

institute: Southern Medical University

type: Methylation profiling by high throughput sequencing

summary: Cadmium (Cd) is a prevalent environmental and industrial contaminant that causes significant damage to liver function. However, the role of m6A methylation─a critical epigenetic modification─in Cd-induced liver injury remains poorly understood. This study aimed to investigate the effects of m6A methylation in Cd-induced liver damage. A mouse model of Cd-induced liver injury was established, and exposure to CdCl2 (20 mg/kg) for 90 days resulted in reduced m6A methylation levels. Using methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-Seq), we characterized the m6A methylation profiles in both control and Cd-exposed groups. A total of 8355 unique m6A peaks and 1,101 unique m6A-modified genes were identified. Among these, 673 genes exhibited differential m6A methylated modifications, including 463 hyper-methylated and 210 hypo-methylated genes. Conjoint analysis of MeRIP-seq and RNA-Seq data unveiled genes that showed both differential methylation and expression. These genes were significantly enriched in the AGE-RAGE and PI3K-Akt signaling pathway. Through bioinformatics screening, five key genes (Il-1β, Ccl2, Tlr2, Itgax, and Ccr2) were identified, and expression validation indicated that Itgax and Ccr2 may play pivotal roles in Cd-induced liver injury. Notably, elevated expression of methyltransferase-like 14 (METTL14) was observed in both in vivo and in vitro models. Inhibition of Mettl14 can regulate Cd-induced liver inflammation through m6A-dependent regulation of Ccr2 expression. Collectively, our findings highlight the crucial role of Mettl14 and Ccr2 in Cd-induced liver injury, providing novel insights into the epigenetic mechanisms underlying liver diseases and potential biomarkers for diagnosis and therapy.

overall_design: Comparative gene expression analysis of MeRIP-seq data from the livers of normal and CdCl2-exposed mice for 90 days.

first: Wei

last: Q. Zhi

first: Huang

last: H.

first: Guo

last: S. Hui

first: Li

last: K. Le

last: W.

first: Zhou

last: Q. Wen


overall_design: Comparative gene expression analysis of RNA-seq data from the livers of normal and CdCl2-exposed mice for 90 days.


title: Th1 cells are critical tissue organizers of myeloid-rich perivascular activation niches

first: Noor

last: Bala

address: 602 Tower Rd

summary: Aggregating immune cells within perivascular niches (PVN) can regulate tissue immunity in infection, autoimmunity and cancer. How cells are assembled at PVNs and the activation signals imparted within remain unclear. Here, we integrate dynamic time-resolved in vivo imaging with a novel spatially-resolved platform for microanatomical interrogation of transcriptome, immune phenotype and inflammatory mediators in skin PVNs. We uncover a complex positive-feedback loop within CXCL10+PVNs that regulates myeloid and Th1 cell positioning for exchange of critical signals for Th1 activation. Th1 cells spend ∼24h in the PVN, receiving initial peripheral activation signals, before redeploying to the inflamed dermal parenchyma. Niche-enriched, CCR2-dependent myeloid cells were critical for Th1 IFNγ-production. In turn, PVN instructional signals enabled Th1s to orchestrate PVN assembly by CXCR2-dependent intra-tissue myeloid cell aggregation. The results reveal a critical tissue organizing role for Th1s, gained rapidly on tissue entry, that could be exploited to boost regional immunity.

overall_design: We integrated IV-MPM single cell dynamics with spatially resolved single cell transcriptomics, flow cytometry and immuno-protein profiling to identify key regulators in the choreography and functional programming of lymphocytes specifically in the perivascular niche (PVN). REX3 (Reporter for the EXpression of Cxcr3 ligands) mice were immunized with CFA/OVA and OT-II Th1 cells adoptively transferred, on d5 post-immunization we imaged the tissue by IV-MPM for CXCL10+ aggregates located perivascularly, based on acute CD31 staining immediately prior to imaging. The spatial coordinates for CXCL10+ PVN (niche) and non-niche regions of then inflamed ear pinna were mapped using the microscope user interface. We optimized the size of the biopsy to ensure full niche capture from the imaging coordinates, with a 2mm punch biopsy providing sufficient tissue margins around the PVN for accurate niche isolation, and often capturing 2-3 adjacent niches in the same biopsy. Non-niche regions were identified in a similar fashion, ensuring the absence of CXCL10+ PVN aggregates. Niche-enriched and non-niche region biopsies were analyzed for spatially-restricted differences using single-cell RNA sequencing


title: Assessing the Impact of Cell Isolation Method on B cell Gene Expression using Next-Generation Sequencing

city: Bethesda

first: Amanda

last: Henning

state: MD

address: 9000 Rockville Pike

institute: National Institutes of Health

summary: Transcriptional profiling of PBMCs is a widely explored research approach across multiple fields. Cell populations of interest are generally isolated prior to analysis, especially if low frequency cell populations are desired. B cells, in particular, make up approximately 5-10% of total PBMCs in healthy individuals, thus, isolation of B cell populations is crucial for researchers investigating B cell malignancies. The most widely used cell isolation methods include negative or positive magnetic cell sorting (MCS) and fluorescence-activated cell sorting (FACS). In contrast to negative MCS, it is widely believed that positive MCS and FACS may affect gene expression due to the direct interaction of cell selection antibodies with surface markers. To the best of our knowledge, no specific studies have examined these effects within CD19+ B cell populations. To evaluate this, we have performed RNA-seq on B cells isolated from n=4 healthy donors using three distinct methods: positive and negative MCS using the EasySep StemCell Technologies kits and FACS, performed using the MACSQuant Tyto sorter (Miltenyi Biotec). We report significant gene expression changes following CD19-dependent B cell isolation via either positive MCS or FACS relative to negative MCS, including a general upregulation of genes associated with immune activity and receptor signaling and downregulation of RNA processing genes. These results suggest B cell isolation methods should be taken into consideration when designing experiments or incorporating publicly available sequencing datasets into ongoing research studies, as they may significantly impact the reliability and interpretability of the findings.

overall_design: Primary human B cells were isolated from whole blood of n=4 healthy donors via 3 different methods: positive MCS isolation, negative MCS isolation, and FACS. RNA-seq was performed on matched samples to evaluate impact isolation method has on gene expression.

middle: N

first: Valeria

last: De Giorgi


title: CORONATINE INSENSITIVE 1-mediated repression of immunity-related genes in Arabidopsis roots is overcome upon infection with Verticillium longisporum

city: Göttingen

first: Christiane

last: Gatz

state: Lower Saxony

address: Julia-Lermontowa-Weg 3

department: Plant Molecular Biology and Physiology

country: Germany

institute: Georg-August-University Göttingen

summary: Verticillium longisporum is a soil-borne fungal pathogen causing vascular disease predominantly in Brassicaceae. We have reported previously that the receptor of the plant defense hormone jasmonoyl-isoleucine (JA-Ile), CORONATINE INSENSITIVE 1 (COI1), is required in roots for efficient proliferation of the fungus in the shoot implicating a mobile root-borne signal that influences the outcome of the disease in shoots. This susceptibility-promoting COI1 function is independent from JA-Ile. To explore the underlying mechanism we compared the root transcriptome of coi1 with the transcriptomes of the susceptible JA-Ile-deficient allene oxide synthase (aos) mutant and susceptible wild-type (WT) plants. The biggest difference between the transcriptomes of coi1 versus WT and aos was due to 316 immunity-related genes that were constitutively higher expressed in coi1 as compared to the susceptible genotypes. Interfering with the expression of a subgroup of these genes partially suppressed the coi1-mediated tolerance phenotype. We therefore hypothesize that secreted defense compounds encoded by genes constitutively expressed in coi1 are transported to the shoot with the transpiration stream where they accumulate to interfere with fungal growth. We furthermore report that 149 of the 316 COI1-repressed genes are induced in WT and aos upon infection reaching similar levels as in mock-treated coi1. These were not further induced in coi1 upon infection. Thus, the repressive effect of COI1 is either lifted or overridden upon infection with V. longisporum.

sample_organism:
Arabidopsis thaliana
Verticillium longisporum

overall_design: Segregating populations resulting from COI1 x coi1-t and AOS x aos crosses were genotyped. Twelve single homozygous roots of either WTaos, WTcoi1-t, aos, coi1-t and sid2-2 (mock-treated, V. longisporum-infected at 10 dpi) were combined for one replicate; replicates per genotype and treatment were obtained from four independent infection experiments. For WTcoi1-t, only three replicates were analysed for both mock and 10 dpi treatments.

first: Louisa

last: Ulrich

first: Johanna

last: Schmitz

first: Corinna

last: Thurow


title: Adventitial fibroblasts direct smooth muscle cell-state transition in pulmonary vascular disease

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

summary: Goal of the study was to evalaute gene expression changes in donor PASMC upon co-culture with IPAH PAAF (diseased pulmonary artery adventitial fibroblasts) compared to baseline (co-culture with source-matched donor PAAF).

overall_design: PASMC and PAAF were fluorescently labled and co-plated in 1:1 ratio on a 6well plate in fully supplemented SMC growth medium. After 24h co-incubation cells were trypsinized and single cell suspension sorted for PASMC and PAAF respectively. Sorted cells were processed for RNA isolation and subsequent RNA-Seq or real-time PCR determination of gene expression

first: Grazyna

last: Kwapiszewska

first: Slaven

last: Crnkovic


title: Effects of Klf9 on non-cardiomyocytes in the heart after myocardial infarction

city: Shanghai

first: Sheng

last: Xu

state: Shanghai

address: No. 301, Yanchang Middle Road

institute: The NO.10 People's Hospital of Shanghai

summary: Klf9 deficiency leads to increased mortality and cardiac rupture rate after myocardial infarction(MI) in mice. We use single-cell RNA sequencing (scRNA-seq) to detect differences in non-cardiomyocytes between  WT and Klf9-/- mice after MI.

overall_design: These cells were isolated from left ventricular(LV) tissues from WT and Klf9-/- hearts 3 days  after MI, cell debris was removed  to obtain live cells,  and each cell sample was pooled from LV tissues of 2 mice


title: ERG activates a stem-like proliferation-differentiation program in prostate epithelial cells with mixed basal-luminal identity [scRNA-seq]

city: New York

first: Erik

last: Ladewig

state: New York

address: 435 East 65th Street

institute: MSKCC

summary: Performed scRNA-seq of an autochthonous mouse model at an early stage of disease initiation. Despite broad expression of ERG in all prostate epithelial cells, proliferation was enriched in a small, stem-like population of cells with mixed-luminal basal identity (intermediate cells).

overall_design: A Rosa26-ERGLSL/LSL; Ptenflox/flox;Pb-Cre4 (EPC) mouse model, using single cell  sequencing (scRNA-seq), at an early timepoint to capture changes associated with cancer initiation. At age 3 months EPC mice have small foci of invasive cancer which subsequently progress to highly penetrant glandular invasion within 6 months

first: Weiran

last: Feng


title: RNA-seq between  between FOLFOX chemotherapy sensitivity and insensitivity in colorectal cancer

first: Xi

last: Cheng

state: State...

address: Ruijin er lu 197

institute: Shanghai Institute of Digestive Surgery

summary: 22 cases of advanced stage CRC who had received preoperative neoadjuvant mFOLFOX before radical resection. All enrolled cases were adult patients with cytologically or histologically confirmed colorectal adenocarcinoma by at least two pathologists and with no history of any neoadjuvant anti-tumor therapy. All patients received 2-4 courses of preoperative neoadjuvant mFOLFOX before surgery, after which patients were organized into 2 groups according to TRG. 9 cases (<2 TRG scores) were included in mFOLFOX sensitive group, while the other 13 cases (2~3 TRG scores) were included in mFOLFOX insensitive group.

first: Haoran

first: Zichao

last: Guo

first: Xianze

last: Chen

first: Kun

last: Liu

first: Haosheng

last: Li

first: Changgang

last: Wang

first: Tao

last: Zhang

first: Ren

last: Zhao


title: SARS-CoV-2 nsp13 restricts episomal DNA transcription and hepatitis B virus infection

city: Wuhan

first: Aixin

state: Hubei Province

address: No.299, Bayi Road, Wuchang District, Wuhan City, Hubei Province

department: School of Basic Medical Sciences

institute: Wuhan University

summary: Non-structural protein 13 (nsp13), as the helicase of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been shown to own multiple functions. Here, we reported that nsp13 could restrict episomal DNA transcription without affecting chromosomal DNA. By using different truncated and mutant forms of nsp13, we demonstrated that its NTPase and helicase activities contributed to episomal DNA transcriptional inhibition. This restriction required direct interaction with episomal DNA. By screening nsp13 interacting proteins, we found that structural maintenance of chromosomes 4 was involved. Given the fact that the episomal DNA of hepatitis B virus (HBV) is the major obstacle for antiviral treatment, we investigated and revealed that nsp13 could significantly restrict HBV replication in vitro and in vivo. In conclusion, our findings demonstrated that SARS-CoV-2 nsp13 can specifically inhibit episomal DNA transcription and can be served as a potential antiviral for HBV infection.

overall_design: HEK293T cells were co-transfected with pEF1α-Luc and pHA-NSP13，pHA-NSP13 D374A mutant or empty vector for 24 h, chromosomal gene expression was determined by RNA-seq. This experiment to detect the effect of SARS-CoV-2 NSP13 onchromosomal gene expression.

first: Yuchen

last: Xia


title: Comparative Transcriptome Analyses Reveal the Responses to Hypoxia Challenge of Mactra veneriformis

status: Public on Apr 06 2025

city: Tianjin

first: Gengyin

last: Huang

address: Jinjing road

institute: Tianjin Agricultural University

summary: The transcriptomic analysis of Mactra veneriformis under hypoxia stress was carried out in this paper to explore the response mechanism of M. veneriformis under hypoxia stress from the molecular biological level. The results provided a reference for further study on hypoxia tolerance mechanism and creation of new hypoxia tolerant germplasm of Clams quadricornis. The findings suggest that transcriptome sequencing was performed on M. veneriformis branchial filament tissues under normal and hypoxia conditions by high-throughput sequencing technology, and 54.58Gb of clean data were obtained. There were differences in gene expression between the normal-oxygen group and the hypoxia group. Control group A and hypoxia group B had the most differentially expressed genes (7473 genes), among which 4000 up-regulated genes and 3473 down-regulated genes. Secondly, there were 6407 differentially expressed genes between hypoxia group B and hypoxia group C, with 3535 up-regulated genes and 2872 down-regulated genes. There were 5581 differentially expressed genes in the control group A and the hypoxia group C, 2676 up-regulated genes and 2905 down-regulated genes. According to the enrichment of GO functional annotations, differential genes were mainly concentrated in the membrane of cell components, metabolism in biological processes and binding of molecular functions. The enrichment of KEGG pathway showed that multiple metabolic and genetic information processing pathways were activated.

overall_design: Control group (A), treatment group 1 (B) and treatment group 2(C) were set up with dissolved oxygen concentrations of 7.5 mg/L, 4 mg/L and 2 mg/L, respectively. The water temperature was controlled at 20±1 ℃ and the salinity was 27. There were Mactra veneriformis in each group and 40 clams in each parallel. Hypoxia stress is carried out by continuously filling nitrogen into the aquaculture water, and the experiment is carried out when the dissolved oxygen in the water reaches about 2 mg/L and 4mg/L. At the same time, the water surface is covered with plastic wrap to prevent air exchange at the water-air interface, and the dissolved oxygen in the water is maintained at about 2±0.2 and 4±0.2 mg/L. The oxygen concentration in the water body was measured by the dissolved oxygen meter every 4 h, and the low oxygen level was maintained during the whole experiment by adjusting the ventilation volume. In the control group, DO content in water was 7.5±0.2 mg/L after continuous oxygenation. The experiment period was 72 h without changing the water or feeding. During the experiment, the shellfish were observed every 2 hours, and the dead shellfish were picked out in time. The standard four-horn clam double shell was open, and no reaction was found when it touched the axe foot of the clam. The experimental group underwent vivisection of clams tetragonata after 24 h of stress, collected their gill tissues, put them into frozen tubes and quickly put them into liquid nitrogen, and then transferred the gill tissues to the refrigerator at -80 ℃ for storage. Three replicates were set in each group.

first: Limei

first: Shuai

last: Yu

first: Yongjun


title: Comparative genomic and transcriptomic analysis reveals why Paenarthrobacter strains are specialists in the degradation of the fungicide iprodione

city: Larisa

first: Dimitrios

last: Karpouzas

address: Biopolis

department: Department of Biochemistry & Biotechnology

country: Greece

institute: University of Thessaly

summary: Paenarthrobacter strains effectively degrade the fungicide iprodione, exhibiting a specialization rarely seen amongst bacteria. The transformation of iprodione is controlled by an amidase, a deacetylase and a hydrolase encoded by ipaH, ddaH and duaH respectively. We aimed to elucidate the mechanisms of this catabolic specialization and its evolution in Paenarthrobacters. The genomes of two new iprodione-degrading Paenarthrobacter strains TA1.8 and C1 were sequenced and analyzed comparatively with the genomes of two other iprodione-degrading Paenarthrobacter strains YJN-5 and YJN-D. Comparative genomics revealed different gene organization motifs amongst strains which suggest that the strains are at different stages of pathway evolution, in accord with their prior exposure to iprodione. Strains TA1.8, YJN-5 and YJN-D, all isolated from soils heavily exposed to iprodione, carried multiple copies of ipaH, ddaH and duaH in their chromosomes and plasmids that were assigned to two distinct phylogenetic clusters based on genome topology. Conversely, strain C1, isolated from a pristine soil, carried ipaH, ddaH and duaH in the chromosome. Pangenome analysis of the genus Paenarthrobacter placed ipaH and duaH in the core genome reinforcing their specialization in the degradation of iprodione as they need to acquire only ddaH, the sole gene of the pathway associated with transposable elements in strains C1 and TA1.8, to complete the pathway. We propose an evolution route of the iprodione transformation pathway which involves acquisition of ddaH through horizontal gene transfer, gene duplication of the chromosomally encoded ipaH and ddaH, and further genetic rearrangements for pathway optimization, complementing duaH, a core gene in Paenarthrobacters. Transcriptomic analysis of strain TA1.8 verified the involvement of all copies of ipaH, ddaH and duaH in the transformation of iprodione, and identified hydantoinases, upregulated during iprodione degradation, as potential facilitators of the transformation of the hydantoin-containing intermediate N-(3,-5-dichlorophenyl)- 2,4-dioxoimida-zolidine, a step mediated by DdaH.

overall_design: The experiment investigates the effects of iprodione and succinate on Paenarthrobacter sp. TA1.8 over different time points. Samples were collected at 8, 12, and 24 hours for each treatment, with three biological replicates per condition.

first: Sotirios

last: Vasileiadis

first: Venetios

last: Michelioudakis

first: Stavroula

last: Makri

first: Alexandros

last: Zafranas

first: Christos

last: Myrisiotis

first: Athanasia

last: Katsoula

first: Marco

last: Campos


title: Maternal prenatal stress induces sex-dependent changes in tRNA fragment families and cholinergic pathways in newborns

city: Jerusalem

first: Shani

last: Vaknine Treidel

state: Israel

address: The Safra Campus, Givat Ram

department: Biological Chemistry

country: Israel

institute: The Hebrew University of Jerusalem

summary: Maternal perceived prenatal stress (PPS) is a known risk factor for diverse developmental impairments in newborns, but the underlying molecular processes are incompletely understood. Here, we report that PPS responses altered the birth profiles of blood transfer RNA fragments (tRFs), 16-50nt long non-random cleavage products of tRNAs in a sex-dependent manner. Importantly, comparing stressed versus control maternal and umbilical cord blood serum presented alterations that were not limited to individual tRFs, but rather reflected selective enrichments in particular tRF families grouped by their mitochondrial or nuclear genome origin, parental tRNA coded amino acid, and cleavage type. Supporting a stress- and sex-specific effects, grouped tRF families revealed shared length and expression patterns which were strongest in the female newborns. Of those, several tRFs carried complementary motifs to specific cholinergic mRNAs, indicating possible translational regulation similar to microRNAs. Compatible with the cholinergic regulation of stress reactions, those "CholinotRFs" achieved an AUC of 95% when classifying female newborns according to maternal PPS. Moreover, we found altered catalytic activity of serum acetylcholinesterase, which was particularly elevated in male newborns, marking a second sex-specific effect. Our findings demonstrate an association of tRF families' patterns with newborns' sex-specific stress response to PPS and may lead to better diagnosis and therapeutic tools for these and other stressors.

overall_design: To test the effects of maternal prenatal perceived stress (PPS) on the newborn, we tested short RNA sequencing of maternal and umbilical cord serum from mothers exposed to PPS and their newborn, compared to control dyads.

first: Silvia

last: Lobmaier

first: Ritika

last: Sharma

first: Nimrod

last: Madrer

first: Serafima

last: Dubnov

first: Dana

last: Shulman

first: Pnina

last: Greenberg

first: Estelle

last: Bennet

first: David

middle: S

first: Adi

last: Turjeman

first: Camilla

last: Zelgert

first: Peter

last: Zimmermann

first: Martin

last: Frasch

first: Liran

last: Carmel

first: Marta

last: Antonelli

first: Hermona

last: Soreq