title: Granuloma Dual RNA-Seq Reveals Composite Transcriptional Programs Driven by Neutrophils and Necrosis within Tuberculous Granulomas

city: DURHAM

first: David

last: Tobin

state: NC

address: Duke University Medical Center

department: Molecular Genetics and Microbiology

institute: Duke University

summary: Mycobacterial granulomas lie at the center of tuberculosis (TB) pathogenesis and represent a unique niche where infecting bacteria survive in nutrient-restricted conditions and in the face of a host immune response. The granuloma’s necrotic core, where bacteria reside extracellularly in humans, is difficult to assess in many experimentally tractable models. Here, using necrotic mycobacterial granulomas in adult zebrafish, we develop dual RNA-seq across different host genotypes to profile transcriptional alterations that enable bacteria to survive and take advantage of host immune responses. Using both pharmacological and genetic interventions, we find that neutrophils within mature, necrotic granulomas promote bacterial growth, in part through upregulation of the bacterial devR regulon. Finally, we identify conserved transcriptional programs related to K+ transport and the rpf genes induced only in the context of this unique necrotic extracellular niche. Analysis of Mycobacterium tuberculosis strains across diverse lineages suggests that these modules represent targets for bacterial genetic adaptation in the context of human infection.

sample_organism:
Mycobacterium marinum
Danio rerio

platform_organism:
Mycobacterium marinum
Danio rerio

overall_design: Dual host-pathogen RNA-Seq profiling of necrotic granulomas containing Mycobacterium marinum (M. marinum) isolated from wild-type and neutrophil deficient Rac2D57N zebrafish. Total RNA isolated from these granulomas was divided into two portions. One portion was processed without any enrichment strategy and used to derive the host (Zebrafish) transcriptome. The second portion was enriched for M. marinum transcripts using oligo-dT beads, which selectively bind and deplete host RNAs. The enriched fraction was further used to derive bacterial transcripts from the granulomas. Additionally, bulk RNA-Seq was performed on in vitro grown log-phase M. marinum cultures. Comparitive analyses were conducted between the host and bacterial transcriptomes of wild-type and Rac2D57N granulomas to identify transcriptional changes under neutrophil depleted conditions. Further, comparisons were made between the bacterial transcriptome from wild-type granulomas and in vitro grown log-phase cultures to identify mycobacterial transcripts specifically required for survival in wild-type granulomas.

first: Gopinath

last: Viswanathan


title: Large-scale tethering of RNA binding proteins discovers alternative splicing regulators

status: Public on Apr 27 2025

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

country: USA

institute: UCSD

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Genome-wide maps of UV damage repair by yeast CPD photolyase

status: Public on Apr 26 2025

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

summary: Here, we describe a genome-wide map of photoreactivation repair of UV-induced cyclobutane pyrimidine dimers (CPDs) in yeast (Saccharomyces cerevisiae) by the endogenous yeast CPD photolyase. CPDs were mapped at single nucleotide resolution across the yeast genome using the CPD-seq method immediately after UV radiation (0min) and following 30 or 60min photoreactivation with UVA light. Photoreactivation repair by photolyase was mapped in both wild-type yeast and rad14∆ cells deficient in nucleotide excision repair (NER). We used these data to analyze CPD repair by photolyase in yeast genes, nucleosomes, and transcription factor binding sites.

overall_design: We used the CPD-seq method to map UV-induced cyclobutane pyrimidine dimers (CPDs) at single nucleotide resolution across the yeast genome, both immediately after UV-radiation of yeast cells (UV 0min) and following 30min or 60min of photoreactivation with UVA light. CPD-seq was used to analyze photolyase repair in both wild-type (WT) and NER-deficient (rad14∆) yeast cells.

middle: J

first: Kaitlynne

last: Bohm


title: Nanog is repurposed after implantation to repress Sox2 and begin pluripotency extinction

city: Guangzhou

first: Man

last: Zhang

state: Guangdong

address: No.9, XingDaoHuanBei Road, Guangzhou International Bio-island, Haizhu District

department: Department of Basic Research

country: China

institute: Guangzhou Laboratory

summary: Loss of pluripotency is an essential step in postimplantation development that facilitates the emergence of somatic cell identities essential for gastrulation. Before implantation, pluripotent cell identity is governed by a gene regulatory network that includes the key transcription factors SOX2 and NANOG. However, it is unclear how the pluripotency gene regulatory network is dissolved to enable lineage restriction. Here we show that SOX2 is required for postimplantation pluripotent identity and cells that lose SOX2 expression in the posterior epiblast are no longer pluripotent. Using in vitro and in vivo analyses we demonstrate anticorrelated expression of Nanog and Sox2 preceding gastrulation, culminating in an early disappearance of pluripotent identity from posterior NANOGhigh/SOX2low epiblast. Surprisingly, Sox2 expression is repressed by NANOG and embryos with post-implantation deletion of Nanog maintain posterior SOX2 expression. Our results demonstrate that the distinctive features of post-implantation pluripotency are underpinned by altered functionality of pluripotency transcription factors, ensuring correct spatio-temporal loss of embryonic pluripotency.

overall_design: EpiLCs were differentiated by culturing naive ESCs for 48 hours in EpiLC conditions (N2B27+ 1%KSR + Activin and Fgf2) . Culturing EpiLCs for 24 hours in the presence of the Wnt/ß-catenin signalling agonist CHIR99021 and Activin, which mimics the signaling environment occurring in the Nanog-positive proximal posterior epiblast, efficiently upregulated Nanog as well as markers of mesoderm and endoderm. Notably, Sox2 mRNA was low and SOX2 was absent from most cells, appearing prominently in cells lacking NANOG and T . These features are reminiscent of posterior epiblast (posterior epiblast-like cells; pEpiLC). Conversely, 24-hour culture of EpiLCs in N2B27 basal media induced neural markers Sox1 and Pax6, mimicking anterior epiblast (anterior epiblast-like cells; aEpiLC). In these conditions, Sox2 was upregulated and Nanog was suppressed.

first: Frederick

last: C. K. Wong


title: The loss of OPA1 accelerates intervertebral disc degeneration and osteoarthritis in aged mice

city: Philadelphia

first: Makarand

middle: V

last: Risbud

state: PA

address: 1025 Walnut Street

department: Department of Orthopaedic Research

institute: Thomas Jefferson University

summary: NP cells of the intervertebral disc and articular chondrocytes reside in avascular and hypoxic tissue niches. As a consequence of these environmental constraints the cells are primarily glycolytic in nature and were long thought to have a minimal reliance on mitochondrial function. Recent studies have challenged this long-held view and highlighted the increasingly important role of mitochondria in the physiology of these tissues. However, the foundational understanding of mechanisms governing mitochondrial dynamics and function in these tissues is lacking. We investigated the role of mitochondrial fusion protein OPA1 in maintaining the spine and knee joint health in mice. OPA1 knockdown in NP cells altered mitochondrial size and cristae shape and increased the oxygen consumption rate without affecting ATP synthesis. OPA1 governed the morphology of multiple organelles, including peroxisomes, early endosomes and cis-Golgi and its loss resulted in the dysregulation of NP cell autophagy. Metabolic profiling and 13C-flux analyses revealed TCA cycle anaplerosis and altered metabolism in OPA1-deficient NP cells.  Noteworthy, Opa1AcanCreERT2 mice with Opa1 deletion in disc and cartilage showed age-dependent disc degeneration, osteoarthritis, and vertebral osteopenia. Our findings underscore that OPA1 regulation of mitochondrial dynamics and multi-organelle interactions is critical in preserving metabolic homeostasis of disc and cartilage.

overall_design: To understand the transcriptome alterations caused by Opa1 gene depletion, the Opa1 gene was selectively (Intervertebral disc compartment and cartilage) deleted in fully matured 3-month-old mice using AcanCre and aged for an additional 9 months. RNA-sequencing was then conducted on RNA isolated from NP tissues from WT and Opa1cKO. Each contains 6 samples, each corresponding to a different mouse.

first: Vedavathi

last: Madhu


title: Effect of zoledronic acid on FOEC cell gene expression

city: kagoshima city

first: Tatsuo

last: OKUI

state: Kagoshima

address: 8-35-1, Sakuragaoka

department: oral surgery

country: Japan

institute: kagoshima university

summary: The effect of zoledronic acid on oral mucosal cells is unknown. We evaluated zoledronic acid-induced changes in gene expression in epithelial cells.

overall_design: Human oral mucosal cell FOEC6 was cultured with or without zoledronic acid(ZOL) for 24h. Cells were collected and RNA were isolated.

first: TATSUO

last: Okui


title: Mucin O-glycans protect host cells by tempering pneumolysin expression in Streptococcus pneumoniae

city: Cambridge

first: Katharina

last: Ribbeck

state: MA

address: 32 Vassar St

department: Biological Engineering

institute: Massachusetts Institute of Technology

summary: The ability of mucosal epithelia to sustain asymptomatic colonization by pathogens, such as Streptococcus pneumoniae (Spn), remains a significant and unresolved scientific question. This study reveals that mucins—the main gel-forming elements of mucus—and their associated glycans, suppress the expression of pneumolysin, a Spn toxin that causes tissue injury and triggers inflammatory responses. These findings highlight a unique protective function of mucins, offering insights into potential therapeutic strategies.

overall_design: Examination of differential gene expression in Streptococcus pneumoniae TIGR4 in response to MUC5AC mucins and MUC5AC glycans in THY medium

first: Jade

last: Bath


title: The stroke risk gene Foxf2 maintains brain endothelial cell function via Tie2 signaling

city: Munich

first: Katalin

last: Todorov-Völgyi

address: Feodor-Lynen-Str 17

department: ISD

country: Germany

institute: LMU Munich

summary: Stroke is a leading cause of death and long-term disability. In up to 30% of cases the underlying etiology is cerebral small vessel disease (SVD), the mechanisms of which are insufficiently understood. Genome-wide association studies have identified FOXF2 as a major risk gene for SVD and stroke. Foxf2 encodes a transcription factor that in the brain is primarily expressed in endothelial cells (ECs) and pericytes but the mechanisms linking Foxf2 to cerebrovascular disease are unknown. Here we show that Foxf2 maintains EC function via Tie2 signaling and limits infarct size in mice after middle cerebral artery occlusion. EC-specific inactivation of Foxf2 in adult mice resulted in blood-brain barrier leakage, which was exacerbated after experimental stroke compared to controls. Proteomic analyses of brain ECs from Foxf2 deficient mice as well as human pluripotent stem cell (iPSC) derived ECs lacking FOXF2 revealed a downregulation of multiple proteins involved in Tie2 signaling. We further found that endothelial Foxf2 deficiency compromises functional hyperemia, reduces endothelial NO production, and increases the size of experimentally induced infarcts via Tie2 signaling. Pharmacological treatment with the Tie2 activator AKB-9778 rescued the effects of Foxf2 deficiency on key outcomes. Moreover, RNA sequencing in combination with chromatin immunoprecipitation sequencing (ChIP-seq) in ECs revealed that FOXF2 functions as a transcriptional activator of Tie2 and other endothelial lineage-specific genes. Collectively, our results highlight the role of endothelial dysfunction and of reduced Tie2 signaling in SVD and stroke, thus offering new perspectives for therapeutic interventions.

overall_design: scRNA-seq of mouse brain endothelial cells (BEC) that were isolated after conditional Foxf2-KO

first: Judit

last: González-Gallego


title: Irisin ameliorates the progression of intervertebral disc degeneration via LATS/YAP/CTGF signaling.

first: Taiqiu

last: Chen

address: 33, Yinfeng Road

institute: Sun yat-sen university

summary:
Taken together, this study demonstrated that FNDC5 was lost in degenerative NP tissues, while irisin treatment ameliorated the ECM metabolism of NPCs and delay the progression of IDD via LATS/YAP/CTGF signaling.
Taken together, this study demonstrated that FNDC5 was lost in degenerative NP tissues, while irisin treatment ameliorated the ECM metabolism of NPCs and delay the progression of IDD via LATS/YAP/CTGF signaling.

overall_design: Genome‐wide transcriptional sequencing was applied between TNF-α treated groups and TNF-α with irisin treated groups to identify the differential expression levels of RNA.

first: Youxi

last: Lin


title: RNA-seq result of human skin derived from patients with psoriasis and healthy controls.

status: Public on Apr 25 2025

city: Seoul

first: Hye Li

last: Kim

address: 50-1, Yonsei-ro

country: South Korea

institute: Yonsei university

summary: This study aimed to identify disease-specific transcriptomic signatures and compare them with those of psoriasis and healthy controls to distinct molecular markers. Differential expression analysis revealed key genes associated with epidermal barrier function and inflammation, including FLG, SPINK5, LOR, and SERPINB4, highlighting the unique molecular features of psoriasis in Asian populations. This dataset offers a valuable resource for advancing the understanding of psoriasis pathogenesis and exploring potential therapeutic targets.

overall_design: Skin biopsy samples from the lesional areas were obtained from Asian patients with psoriasis. All patients were clinically diagnosed by dermatologists. The study protocol was approved by the Institutional Review Board (N0. 4-2017-0782)

first: Tae-Gyun

first: Chang Ook

last: Park


title: Effect of treatment with Levamisole 1 mM on activated human T-cells

city: Amsterdam

first: Gerarda

middle: Hendrika

last: Khan

address: Chico Mendesstraat 39

department: Pathology

country: Netherlands

institute: Amsterdam UMC - AMC

summary: To investigate the effects of levamisole treatment on in vitro activated human T-cells, we isolated T-cells from buffy coats from 3 donors. All buffy coats were collected from adult anonymous healthy blood donors (Sanquin Blood Supply, Amsterdam, The Netherlands) who provided written informed consent for usage of the remainder of their blood donation in research. Untouched T cells were isolated from PBMCs by negative Magnetic-activated cell sorting (MACS) using the human pan T cell isolation kit (Miltenyi Biotec) according to the manufacturer’s instructions. Purity of the T cell fraction was assessed by flowcytometry for CD3 (>98% for all donors).  To investigate the effects of Levamisole treatment on the T-cell immune response we performed  bulk RNA sequencing on 24-hour and 48-hour aCD3/aCD28 dynabeads activated T-cells (Gibco, Thermo Fisher Scientific). Levamisole samples were treated with levamisole 1 mM while control samples were treated with the appropriate solvent controls. 3 separate donors were included in this experiment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 24-hour and 48-hour activated human isolated pan T-cells from 3 biological donors treated with Levamisole 1 mM or solvent control.

middle: H

first: Jeroen

middle: E

last: Guikema

first: Sandrine

last: Florquin


title: Large-scale bidirectional arrayed CRISPR screens identify OXR1 and EMC4 as modifiers of α-synuclein aggregation

city: Zürich

first: Sandesh

last: Neupane

address: Schmelzbergstrasse 12

country: Switzerland

institute: University Of Zurich

summary: In synucleinopathies, including Parkinson’s disease, α-synuclein (α-Syn) misfolds and forms Ser129-phosphorylated aggregates (pSyn). Mitochondrial and lysosomal dysfunction, along with impairments in protein and organelle trafficking, exacerbate α-Syn pathology through poorly defined molecular mechanisms. We used CRISPR-mediated gene activation and ablation to systematically interrogate mitochondrial, trafficking and motility-related genes to identify pSyn regulators in HEK293 cells exposed to α-Syn fibrils. We found that activation of the mitochondrial protein OXR1 increased pSyn by impairing ATP synthesis and altering the mitochondrial membrane potential, whereas ablation of the endoplasmic reticulum (ER)-associated protein EMC4 reduced pSyn by enhancing ER-driven autophagic flux and lysosomal clearance. Assays with distinct strains of α-Syn fibrils revealed that OXR1 was preferentially synergistic with multiple system atrophy (MSA)-associated fibrils, whereas EMC4 broadly reduced pSyn across diverse α-Syn polymorphs. These findings were validated in human iPSC-derived cortical and dopaminergic neurons, with OXR1 preferentially driving somatic aggregation and EMC4 depleting both somatic and neuritic aggregates. This work identifies OXR1 and EMC4 as organelle-specific regulators of α-Syn proteostasis and underscores the involvement of mitochondrial and ER-lysosomal pathways in synucleinopathies.

overall_design: Summary This study investigates transcriptomic alterations resulting from CRISPR-based modulation of OXR1 and EMC4 in a human cellular model of α-Synucleinopathy. HEK293 cells stably overexpressing human α-Synuclein (α-Syn) were subjected to CRISPRa-mediated activation of OXR1 and CRISPR/Cas9 CRISPRo-mediated ablation of EMC4, respectively. Total RNA was isolated and subjected to bulk RNA-sequencing. Differential gene expression analyses were performed to uncover downstream pathways associated with mitochondrial and ER-lysosomal function in the context of α-Syn accumulation, with relevance to Parkinson’s disease.  Overall Design Two independent bulk RNA-seq experiments were conducted:  CRISPRa: OXR1 activation  Cell line: HEK293 cells stably overexpressing human α-Synuclein  Perturbation: CRISPR activation of OXR1 using a dCas9-VPR system  Control: Non-targeting guide RNA (NTG)  Biological replicates: 3 per condition (OXR1 and NTG)  CRISPRo: EMC4 ablation  Cell line: HEK293 cells stably overexpressing human α-Synuclen Perturbation: CRISPR repression (CRISPRo) of EMC4 using a Cas9 system  Control: Non-targeting guide RNA (NTG)  Biological replicates: 3 per condition (EMC4 and NTG)


title: Total plasma cfDNA methylation in kidney transplant recipients provides insight into acute allograft rejection pathophysiology

city: Madison

first: Benjamin

middle: L

last: Spector

state: WI

address: 600 Highland Ave

department: Pediatrics

institute: University of Wisconsin- Madison

type: Methylation profiling by high throughput sequencing

summary: Acute rejection threatens kidney allograft longevity. Cell-free DNA (cfDNA) is a real-time marker of organ injury and immune response. DNA methylation is an epigenetic marker that regulates gene expression. We aim to elucidate differential methylation of total plasma cfDNA between pediatric kidney transplant recipients in the presence compared to the absence of acute rejection. In doing so, we hope to exploit the property of cfDNA as a real-time biomarker and build on available testing to identify genes and processes participating in acute allograft rejection pathophysiology in kidney transplantation. Twenty plasma cfDNA samples from pediatric kidney transplant recipients were collected at the time of allograft biopsy. Using whole genome bisulfite sequencing (WGBS), differentially methylated cytosines were identified in presence vs absence of acute rejection. Separate analyses were performed comparing those with borderline rejection to those with rejection, and to those without rejection. Differentially methylated cytosines were then assessed for gene associations and pathway enrichments. Acute rejection was present in 7 biopsies, borderline rejection in 4 biopsies, and no rejection in 9 biopsies. In the comparison of acute rejection to non-rejection biopsies, there were 34,356 differentially methylated cytosines corresponding to 1,269 associated genes, and 533 enriched pathways. These numbers were all substantially greater (4x-13x) than the comparisons made between acute rejection against those with borderline rejection, and between non-rejection against borderline rejection. Prominently enriched pathways between samples of individuals with and without acute rejection were related to immune cell regulation, inflammatory response, lipid metabolism, and tryptophan-kynurenine metabolism. Our data suggest methylation plays a role in development of or response to acute kidney allograft rejection. Specifically, differentially methylated pathways associated with acute rejection include those related to immune and inflammatory responses.

overall_design: WGBS was performed on cell-free DNA isolated from plasma of pediatric kidney transplant recipients. Differentially methylated cytosines (DMCs) were compared between individuals with acute allograft rejection, borderline rejection, and no evidence of rejection.

first: Boryana

last: Koseva

first: Drinnan

last: Sante

first: Warren

middle: A

last: Cheung

first: Reid

middle: S

last: Alisch

first: Alexander

last: Kats

first: Phillip

last: Bergmann

first: Elin

last: Grundberg

first: Gerald

last: Wyckoff

first: Laurel

middle: K

last: Willig


title: Gene expression profile of extraocular muscles in the primary inferior oblique overaction

city: Tianjin

first: Yuchuan

last: Wang

address: Gansu Road

institute: Tianjin Eye hospital

summary: To identify the differences in gene expression of primary inferior oblique overaction，the transcriptome sequencing for extraocular muscles (EOMs) was conducted in this study.

overall_design: The gene expression profile was studied by transcriptome sequencing in ten EOMs of primary inferior oblique overaction and ten EOMs of secondary inferior oblique overaction. Differentially expressed genes (DEGs) were filtered by methods of bioinformatics.

first: Rui

last: Hao

first: Wei

last: Zhang


title: BKK1/BAK7 and TCP21 form a positive feedback loop to facilitate submergence tolerance in plants

city: Hangzhou

first: Yiyi

last: Guo

state: China

address: Zijingang Campus, Zhejiang Uni

institute: Zhejiang University

summary: Submergence can be a deleterious threat to plant development and the agricultural production of Brassica napus (B. napus), an important worldwide oil crop. However, the molecular mechanisms underlying submergence tolerance in B. napus remain elusive. Here, through a genome-wide association study, we identify a SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE, BKK1/BAK7, which is indispensable for plant survival after submergence stress. Submergence rapidly activates the expression of BAK7 and induces the accumulation of the kinase part of BAK7 in the nucleus. BAK7 interacts with and phosphorylates class I TCP transcription factor TCP21, stabilizing it. TCP21, along with several other class I TCPs, modulates the transcriptomic reprogramming after submergence to enhance plant tolerance to submergence. Moreover, overexpression of TCP21 rescues the submergence-intolerant phenotype of bak1-3 bkk1-1 mutant. Interestingly, TCP21 directly binds to the promoter regions of BAK7 to activate its expression after submergence. This study provides insights into the molecular mechanism of plant adaptation to submergence stress and offers promising solutions for breeding submergence-resistant B. napus accessions.

overall_design: To illuminate bak1-3 bkk1-1, tcp21 and tcpq sensitive phenotype under submergence treatment, we performed gene expression profilling analysis using data obtained from RNA-seq under mock and submergence treatment.

first: Jie

last: Dong


title: GSK3 acts as a switch for transcriptional programs in a model of low-grade gliomagenesis

city: Heidelberg

first: Sevin

last: Turcan

address: Im Neuenheimer Feld 420

institute: University Hospital Heidelberg

summary: Mutations in isocitrate dehydrogenase (IDH)-1/2 are defining drivers of low-grade gliomagenesis. However, mutant IDH alone is not sufficient for malignant transformation, and additional events are required for the development of low-grade glioma. While specific genetic lesions have been identified to contribute to low-grade gliomagenesis, less is known about the signaling pathways involved in acquiring malignancy. To identify prerequisites of IDH mutant tumorigenesis, we modulated pathways previously implicated in glioma initiation using a tractable in vitro model system for early IDH1R132H-dependent gliomagenesis. Through the use of chemical compounds, we targeted WNT/GSK3, TGF-β and NOTCH-signaling, assessing their functional, transcriptional, and translational impacts. Expression of LGG-related marker L1CAM was affected by perturbation of all pathways, though only modulation of WNT/GSK3-signaling resulted in profound molecular transformation, including glioma-associated genes and programs regulating cellular architecture and cell replication. This was accompanied by altered cell morphology, migration capacity, and enhanced proliferation. Transcription factor RUNX2 was identified as a potential downstream effector, whose inhibition abrogated cell proliferation. Disrupted WNT/GSK3 signaling in a model system of early low-grade gliomagenesis fundamentally impacted cell fate, as demonstrated by a reshaped transcriptional landscape, aberrant transcription factor activity, ECM restructuring, and altered proliferation capacity. Our data suggests that GSK3 may play a central role during low-grade gliomagenesis, warranting further investigation.

overall_design: RNA-seq profiling of immortalized IDH1R132H human astrocytes treated with CHIR99021, Repsox or YO-01027 resp. mock and RNA-seq profiling of immortalized IDH1R132H human astrocytes treated with CHIR99021 and siRUNX2 or siControl


title: Microcystin-LR prenatal exposure induces coronary heart disease through macrophage polarization imbalance mediated by trophoblast-derived extracellular vesicles.

city: Nanjing

first: Meihong

state: None Selected

address: 南京市鼓楼区汉口路22号南京大学

institute: Nanjing University

type: Non-coding RNA profiling by high throughput sequencing

summary: Trophoblast-derived extracellular vesicles (T-EVs) increase during pregnancy and act as a critical signal in macrophage polarization. However, MC-LR significantly affected the miRNA expression profile of T-EVs. Upon internalization into macrophages, T-EVs-derived miR-377-3p specifically targets the 3’UTR region of NR6A1 to inhibit the gene expression. Silencing of transcription suppressor NR6A1 leads to abnormal activation of the downstream mTOR/S6K1/SREBP pathway, inducing metabolic reprogramming and ultimately leading to M1 polarization of macrophages.

overall_design: HTR-8/Svneo cells cultured in exosomes free medium were treated with 0 or 1 μM MC-LR (A-LR-M001, TAIWAN ALGAL SCIENCE INC) for 24 h, after which the cell culture medium was collected for T-EVs extraction by differential centrifugation (300 g/10 min, 2000 g/20 min, 10000 g/30 min and 100000 g/70 min).Then the RNA was extracted for miRNA sequencing


title: WUSCHEL-dependent cis-regulation in maize inflorescence development at single-cell resolution

city: Athens

first: Robert

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

type: Genome binding/occupancy profiling by high throughput sequencing

summary: WUSCHEL (WUS) is a key transcription factor essential for the homeostasis of stem cells in the inflorescence meristem. In maize, ZmWUS1 is expressed in the central zone harboring stem cells, and its overexpression induces significant phenotypic alterations during the early stages of ear development. Here, single-cell ATAC-seq analyses revealed that ZmWUS1 overexpression alters chromatin accessibility exclusively in the central zone. This alteration includes both open and closed chromatin regions, with a notable predominance of the CAATAATGC motif observed in the open chromatin regions. Conversely, the TGAATGAA motif, identified through ZmWUS1-DNA interactions genome-wide, is not prevalent in these open chromatin regions and exhibits lower activity in the central zone compared to other cells. Furthermore, we observed the closed chromatin regions in the central zone involved in regulating auxin response factors genes, illustrating its negative impact on auxin signaling. These findings suggest that ZmWUS1 employs central zone-specific motif utilization and cis-regulation.

overall_design: Comparing the chromatin accessibility between wild type and Bif3 of maize immature ear.


title: Gene expression prolifes at single cell levels of neural crest cells with augmented bone morphogenetic protein (BMP) signaling.

city: Ann Arbor

first: Hiroki

last: Ueharu

state: Michigan

address: 1011 N. Univ. Ave.,

department: Biologic and Material Sciences & Prosthodontics

institute: The University of Michigan School of dentistry

summary: Transgenic mice expressing constitutively activated BMP type 1 receptor (caAcvr1) in neural crest cells (NCCs)(P0-Cre;caAcvr1 mice, hereafter, caAcvr1 mut mice) develop ectopic cartilage in the face but not in trunk region despite both facial and trunk region composed of NCCs. This study was aimed to identify genes that expressions are changed only in cranial NCCs by BMP signaling, but not in trunk NCCs. The genes were candidate genes involved in BMP-induced ectopic cartilage formation in the face.

overall_design: We isolated cranial NCCs (from the first branchial arch) and trunk NCCs (from the trunk regions) of control and caAcvr1 mut mice at E10.5, respectively. By comparing comprehensive gene expression profiles between four groups, genes significantly changed only in cranial NCCs of caAcvr1 mut mice were candidates involved in ectopic cartilage formation.

first: Haichun

last: Pan

first: Sher

last: Khehra

first: Shigeki

last: Iwase

first: Sundeep

last: Kalantly

first: Yuji

last: Mishina


title: Immunologic adaptation following recombinant amphiregulin ( rAREG) exposure in high grade serous ovarian cancer cell lines

city: Providence

first: Payton

last: De La Cruz

state: Rhode Island

address: 200 Chestnut St

department: Division of Biology and Medicine

institute: Brown University

summary:
770 genes as well as pathways were deternined in high grade serous ovarian cancer cell lines, OVCAR8WT and PEA1 cells stimulated with either BSA control or recombinant AREG (rAREG)
n/a

overall_design: A total of 12 samples were included in this experiment; OVCAR8WT cells stimulated with BSA control , OVCAR8WT cells stimulated with rAREG, PEA1 cells stimulated with BSA control, PEA1 cells stimulated with rAREG. All treatments were performed at 2 hour timepoints, with 3 biological replicates for each treatment.

first: Nicole

last: James

first: Jasmine

last: Ebott

first: Christoph

last: Schorl


title: Immune-based changes in gene expression determine clinical efficacy of CDK4/6i in metastatic breast cancer

city: Badalona

first: Cristina

last: Gálvez

state: Barcelona

address: Ctra. de Canyet s/n

department: Data Management

country: Spain

institute: IrsiCaixa

summary: By using standardized tissue-based transcriptomic analysis in pre-treatment tumor samples, we identified and characterized immunological and molecular pathways associated with different treatment outcomes, identifying putative tissue-based biomarkers that might be used in clinical settings. Importantly, we show that high intratumorally expression of Treg and IFNgamma signatures is significantly associated with poor clinical response and shorter progression-free survival.

overall_design: 63 tumor samples, stratified in good/bad efficacy based on criteria from pivotal clinica trials that led to CDK4/6 inhibitor approval

first: Eudald

last: Felip

first: Mireia

last: Margelí

first: Anna

last: Martínez-Cardús

first: Ester

last: Ballana

first: Adrià

last: Bernat


title: Gene expression profiles at single cell level of nucleotides optimized WT or S449A PTPN22 in J.Lck WT or J.Lck Y192F Jurkat cells

city: Los Angeles

first: Richard

last: Ainsworth

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

summary: Protein Tyrosine Phosphatase Non-receptor type 22 (PTPN22) is encoded by a major autoimmunity gene and is a known inhibitor of T cell receptor (TCR) signaling. PTPN22 Ser449 is a novel phosphorylation site. Here we used optimized coding sequences (CDS) of PTPN22 WT or S449A eukaryotic expression vectors with N-terminal mEGFP and electroporated into either J.Lck WT or J.Lck Y192F cells to analyze the relationship between PTPN22 Ser449 phosphorylaion and Lck Tyr192 phosphorylaion by CITE seq.

overall_design: Electroporated cells were stimulated by 0.5ug/ml antibodies aginst human CD3/CD28 for 12 h and stained by Totalseq anti-human CD69 antibody. mEGFP+ T cells were sorted out and subjected to CITE- seq.

first: Nunzio

last: Bottini

first: Shen

last: Yang


title: Multisensory gamma stimulation enhances adult neurogenesis and improves cognitive function in male mice with Down Syndrome

first: Li-Huei

last: Tsai

address: 43 Vassar Street

summary: Multisensory Gamma Stimulation (MGS) has previously been linked with improved cognitive performance in mouse models and patients with Alzheimer´s Disease (AD). In this study, we aimed to investigate the effects of chronic exposure to MGS in Ts65Dn mice, a mouse model of Down Syndrome (DS). For three weeks, mice were exposed daily to one hour of multisensory audiovisual stimulation or, as a control, one hour of ambient light and sound. Mice receiving MGS showed improved object recognition and spatial working memory. To gain mechanistic insight into how MGS improves cognitive function in Ts65Dn mice, we conducted single-nuclei RNA-seq (snRNA-seq) of hippocampal samples from control and treated mice. We found upregulation of genes related to synaptic organization and downregulation of genes related to aging and AD.  Moreover, we detected upregulation of neurogenesis-related genes in the dentate gyrus.  We validated these observations by demonstrating increased adult neurogenesis following MGS treatment. A potential mechanism underlying this MGS-mediated increase in adult neurogenesis is increased mitochondrial fusion.  Together, our data indicate that MGS can ameliorate cognitive impairment in DS mice through modulation of conserved gene regulatory signatures and enhanced neurogenesis in hippocampal regions. These findings suggest that multisensory 40 Hz stimulation may have potential as a therapeutic approach to boost cognitive performance in individuals with Down Syndrome.

overall_design: We exposed one group of Ts65Dn mice (ST group) to one hour of 40 Hz auditory and visual stimulation per day, while a parallel control group of Ts65Dn mice (NS group) was exposed to ambient light and sound. After three weeks of treatment period, hippocampal nuclei were subjected to single nuclei RNAseq using 10x Genomics.

first: Md Rezaul

last: Islam

first: Brennan

last: Jackson


title: HIF transcriptome in clear cell renal carcinoma cells

status: Public on Apr 24 2025

city: Dallas

first: Weibo

last: Luo

state: Texas

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: Global gene changes by HIF-1/2alpha loss or VHL expression in cancer cells

overall_design: Parental, HIF-1/2alpha double knockout, VHL reconsituted RCC10 cells were subjected to mRNA-seq.

first: Yong

last: Wang


title: Description and functional analysis of the transcriptome from malting barley

first: Sarah

last: Whitcomb

address: 502 Walnut St

department: Cereal Crops Research Unit

institute: USDA-ARS

summary: The present study aimed to establish an early model of the malting barley transcriptome, which describes the expression of genes and their ontologies, identify the period during malting with the largest dynamic shift in gene expression for future investigation, and to determine the expression patterns of all starch degrading enzyme genes relevant to the malting and brewing industry. Large dynamic increases in gene expression occurred early in malting with differential expressed genes enriched for cell wall and starch hydrolasesamongst many malting related categories. Twenty-five of forty starch degrading enzyme genes were differentially expressed in the malting barley transcriptome including eleven α-amylase genes, six β-amylase genes, three α-glucosidase genes, and all five starch debranching enzyme genes. Four new or novel α-amylase genes, one β-amylase gene (Bmy3), three α-glucosidase genes, and two isoamylase genes had appreciable expression that requires further exploration into their potential relevance to the malting and brewing industry.

overall_design: Five samples of Conrad, a North American 2-row spring malting cultivar, were obtained from the USDA-ARS Cereal Crops Research Unit (CCRU) in Madison, WI that originated from 2014 and 2015 crop years grown in four different barley producing regions (two in Montana, one in Idaho, and one in North Dakota). These five samples were pooled together equally (120 g w/w) and homogenized. Three micromalting replications were drawn from the pooled sample and each replication was micromalted using 110 g dry weight. Micromalting was performed using the CCRU's Traditional Malting System, which consists of steeping (4 h water immersion [16 °C] followed by 4 h air rest [18 °C] repeated until final moisture is at 45% [Total steep = 38 h]), germinating (120 h [17 °C] while rotating for 3 min every 30 min, and kilning (lowers moisture to ~4% using increasingly hotter air). Kilning was only performed to obtain malt quality data on the remaining samples after collections were finished. Dry samples were unmalted mature grain and out of steep samples were considered 0 days of germination (0 DoG). Remaining samples (1–5 DoG) were collected every 24 h after steeping (0 DoG). Samples were collected at the same time every day, flash frozen in liquid nitrogen, and stored at −80 °C. Total RNA was isolated from all seven micromalting time points (Dry, 0–5 DoG) with three micromalting replications.

first: Marcus

last: Vinje

first: Cynthia

last: Henson

first: Stanley

last: Duke

first: Carl

last: Simmons

first: Khoa

last: Le

first: Evan

last: Hall

first: Cory

middle: D

last: Hirsch


title: Large-scale tethering of RNA binding proteins discovers alternative splicing regulators [microarray]

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: To elucidate the role of large sets of RBPs, we developed a comprehensive and diverse plasmid resource3 of 765 RBPs fused to the MS2 bacteriophage coat protein. When systematically tethered to an intronic 4 MS2 hairpin downstream of an alternative exon, we identified 55 RBPs that significantly induced exon 5 retention.

overall_design: RBPs were exogeneously expressed or depleted and alternative splicing events were assessed by splicing-sensitive microarrays.

first: Tomas

last: Bos

first: Thai

last: Nguyen

first: John

last: Lapek

first: Brian

last: Yee

first: J

middle: P

last: Donahue


title: TLE3 function in rhabdomyosarcoma tumor xenografts.

city: Faridabad

first: Sam

last: Mathew

state: Haryana

address: NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway,

department: Developmental Genetics

country: India

institute: Regional Centre for Biotechnology

summary: mRNA from control and Tle3 knockout RD (embryonal rhabdomyosarcoma) and SJRH30 (alveolar rhabdomyosarcoma) cell lines xenografted into NOD/SCID mice were subjected to sequencing.

overall_design: Identify differentially expressed mRNAs upon loss of Tle3 in RD and SJRH30 rhabdomyosarcoma cell line xenografts in mice. 5 replicates each were sequenced for control and Tle3 knockout tumor xenografts for both RD and SJRH30 cell lines.

first: Bhargab

last: Kalita

first: Anushree

last: Bharadwaj

first: Subhashni

last: Sahu


title: TAT-CRE inhalation enables tumor induction corresponding to adenoviral Cre-recombinase in a lung cancer mouse model

city: Erlangen

first: Lydia

last: Meder

address: Glückstraße 6

department: Department of Experimental Medicine 1

summary: Cre-recombinase inducible model systems are extensively used in cancer research to manipulate gene expression in specific tissues and induce autochthonous tumor growth. These systems often involve the cross-breeding of genetically engineered organisms containing loxP-flanked alleles with those expressing Cre-recombinase. This approach, while effective, has the challenge of requiring high numbers of animals due to breeding requirements. Other frequently used tumor induction methods in cancer research involve the direct application of viral Cre-recombinase vectors. This approach presents the challenge of the accessibility of facilities that meet the necessary safety level. In this context, we performed a comprehensive comparison between TAT-CRE (biosafety level S1) and adenoviral Cre-recombinase induced (biosafety level S2) lung adenocarcinomas driven by KrasG12D expression and Trp53 depletion. We used in vivo lung tumor monitoring via computed tomography, single-cell RNA sequencing, immunohistochemistry and flow cytometry to elucidate similarities and differences between TAT-CRE and adenoviral Cre-recombinase induced lung adenocarcinomas.  TAT-CRE induced lung tumors presented differences in micro-vessels and macrophages but with corresponding tumor onset and growth characteristics compared to adenoviral-Cre recombinase induced lung tumors. Taken together, TAT-CRE is a valuable genetic engineering safety level S1 alternative for cancer induction and may be implemented in other cancer models than lung cancer.

overall_design: Lung tumors of genetically male B6.129-Krastm4Tyj Trp53tm1Brn/J mice were induced by Cre-recombinase inhalation. Two Cre-constructs were compared: TAT-CRE and adenoviral CRE (AD-CRE).

first: Tabea

last: Gewalt

first: Anna

middle: M

last: Dmitrieva

first: Felix

last: Elsner

first: Xinlei

last: Zhao

first: Daniel

last: Sieber

first: Ilayda

middle: G

last: Kocak

first: Qian

last: Yang

first: Claudia

last: Orschel

first: Naja

last: Eckert

first: Bianca

last: Goebel

first: Marieke

last: Nill

first: Franziska

last: Peter

first: Arndt

last: Hartmann

first: Filippo

last: Beleggia

first: Margarete

last: Odenthal

first: Hans

middle: C

last: Reinhardt

first: Roland

middle: T

last: Ullrich

first: Frederik

last: Graw


title: SMARCA4-loss increases RNA Polymerase II pausing and elevates R-loops to inhibit BRCA1-mediated repair in ovarian cancer

city: Montreal

first: Sidong

last: Huang

address: McIntyre Medical Sciences Building 3655 promenade Sir-William-Osler

country: Canada

institute: McGill University

summary: Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is a rare and aggressive cancer mainly affecting young women. It is driven by inactivating mutations in SMARCA4 (BRG1), a key SWI/SNF chromatin remodeling gene. To reveal its druggable vulnerabilities, we perform a compound screen and find that SCCOHT cells and tumors are sensitive to PARP inhibitors. Paradoxically, SCCOHT displays BRCA-deficient traits while retaining wild-type BRCA1 expression. This is caused by elevated R-loop accumulation in SCCOHT cells and tumors, which sequesters BRCA1 limiting its availability for DNA damage repair. Through proximity-dependent biotin identification approach using pathogenic SMARCA4 variants that retain protein expression, we uncover that SMARCA4 promotes RNA polymerase II (Pol II) elongation by mediating the assembly of the polymerase-associated factor 1 (PAF1) complex and its association with Pol II.  Thus, SMARCA4 loss increases Pol II pausing, resulting in elevated R-loops and BRCA1 redistribution. This leads to the sensitivity of SCCOHT cells and tumors to PARP inhibitors, which is further enhanced by addition of a CDK9 inhibitor targeting Pol II elongation. Our findings reveal a link between SMARCA4 loss and perturbed Pol II elongation causing hampered BRCA1 repair, which can be exploited therapeutically to target SCCOHT. (These studies were supported by Canadian Institute of Health Research (CIHR) grants PJT-156233 and PJT-438303).

overall_design: FT190 cells expressing shRNA against SMARCA4 or PLKO control were collected. Chromatin immunoprecipitation DNA-sequencing (ChIP-Seq) for BRCA1;PolII2 and S2PolII was performed.

first: Xianbing

last: Zhu

first: Jutta

last: Steinberger


overall_design: FT190 cells expressing shRNA against SMARCA4 or PLKO control were collected. CUT&RUN for BRCA1 and DRIP (DNA:RNA Immunoprecipitation)-seq for Rloop was performed in indiucated cells.

first: Giulio

last: Aceto


summary: Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is a rare and aggressive cancer mainly affecting young women. It is driven by inactivating mutations in SMARCA4 (BRG1), a key SWI/SNF chromatin remodeling gene. To reveal its druggable vulnerabilities, we perform a compound screen and find that SCCOHT cells and tumors are sensitive to PARP inhibitors. Paradoxically, SCCOHT displays BRCA-deficient traits while retaining wild-type BRCA1 expression. This is caused by elevated R-loop accumulation in SCCOHT cells and tumors, which sequesters BRCA1 limiting its availability for DNA damage repair. Through proximity-dependent biotin identification approach using pathogenic SMARCA4 variants that retain protein expression, we uncover that SMARCA4 promotes RNA polymerase II (Pol II) elongation by mediating the assembly of the polymerase-associated factor 1 (PAF1) complex and its association with Pol II. Thus, SMARCA4 loss increases Pol II pausing, resulting in elevated R-loops and BRCA1 redistribution. This leads to the sensitivity of SCCOHT cells and tumors to PARP inhibitors, which is further enhanced by addition of a CDK9 inhibitor targeting Pol II elongation. Our findings reveal a link between SMARCA4 loss and perturbed Pol II elongation causing hampered BRCA1 repair, which can be exploited therapeutically to target SCCOHT. (These studies were supported by Canadian Institute of Health Research (CIHR) grants PJT-156233 and PJT-438303).

overall_design: To investigate the gene expression program that can be affected by inhibition of SMARCA4, RNA from FT190 cells expressing shRNA against SMARCA4 or PLKO control were collected. Gene expression profiling analysis was performed using the RNA-Seq data generated in these cells.

first: Judy

last: Liu


title: Lysine Pyruvylation Mediated by HAT1/p300-SIRT3 Couples Glycolytic Flux to Epigenetic Regulation [RNA-Seq]

city: HANGZHOU

first: xiaohan

last: song

address: No.1 XIANGSHAN ROAD

institute: University of the Chinese Academy of Sciences Hangzhou Institute for Advanced Study

summary: Post-translational modifications (PTMs) serve as critical regulatory mechanisms connecting metabolism and protein functions. Following our prior discovery of lysine lactylation (Kla), we herein report the identification and characterization of lysine pyruvylation (Kpy), a previously undescribed PTM driven by the central glycolytic hub metabolite pyruvate. Through integrated biochemical and proteomic strategies, we established the existence and specificity of Kpy. Proteomic profiling revealed Kpy sites across both histones and non-histone proteins, implicating its broad physiological significance. Notably, our investigations demonstrated that Kpy abundance fluctuates in respond to alterations in glycolytic flux and pyruvate concentration, providing a direct mechanism by which metabolic alterations influence protein functions. Additionally, we identified Sirtuin 3 (SIRT3) as the "eraser" enzyme for Kpy removal, while Histone acetyltransferase 1 (HAT1) and p300 (EP300) function as "writer" enzymes responsible for Kpy deposition. Initial mechanistic studies suggested Kpy's regulatory role in transcriptional control. Together, the elucidation of Kpy expands our understanding of metabolite-protein crosstalk through PTMs, providing mechanistic insights into pathophysiological processes and facilitating the development of targeted therapeutic interventions for metabolic disorders.

overall_design: RNA-seq profiling of control and 20 mM 2-Deoxy-D-glucose(2-DG)-treated HEK293T cells.

first: Xiaohan

last: Song

first: Panan

last: Peng

first: Haonan

last: Zheng

first: Yanan

first: Qianjing

last: Wang

first: Yu

last: Ge

first: Doudou

last: Tan

first: He


title: Thioridazine induces pyrolysis and autophagy in epithelial ovarian cancer

city: Nanchong

first: Min

last: Yong

state: Sichuan

address: Wen hua Road

department: Center for Reproductive Medicine, Department of Obstetrics and Gynecology

institute: Affiliated Hospital of North Sichuan Medical College,

summary: Thioridazine exhibits inhibitory effects on various tumors, including epithelial ovarian cancer, but the mechanisms remain unclear. Proliferation and invasion were assessed using CCK8 and Matrigel invasion assays. Autophagy and pyroptosis-related markers were detected via Western blot. Autophagy flux was tracked using the mRFP-GFP-LC3 reporter. Autophagy inhibitors 3MA andBufA1 were used to confirm whether autophagy flux was functioning properly. RNA sequencing was performed to identify differentially expressed genes, and Co-IP was used to detect interacting proteins. A subcutaneous tumorigenesis experiment in nude mice was conducted to evaluate the effect of thioridazine in vivo. As a result, thioridazine inhibited proliferation and invasion of EOC while promoting autophagy and pyroptosis. The upregulation of the pyroptosis marker NLRP3 may be attributed to DRD2 inhibition. Inhibition of autophagy enhanced NLRP3 expression, and the autophagy inhibitor CQ increased the tumor-inhibiting effects of thioridazine. In conclusion, thioridazine inhibited EOC proliferation and invasion by inducing pyroptosis and autophagy, with autophagy playing a protective role in thioridazine treatment. Thioridazine combined with the autophagy inhibitor CQ may be an effective treatment for EOC.

overall_design: After being treated with 15μM thioridazine for 24h, the SKOV3 cells were lysed with Trizol and collected for RNA sequencing.


title: HIF-1 ChIP-seq in hypoxic breast cancer cells

first: Weibo

last: Luo

summary: The genome-wide HIF-1alpha binding to chromatin under hypoxia

overall_design: MDA-MB-231 cells were exposed to 1% O2 for 24 hrs and subjected to HIF-1alpha ChIP-seq.

first: Lei

last: Bao


title: The pioneer transcription factor PBX as a downstream target of MNX1 [ATAC]

city: Gothenburg

first: Eric

last: Malmhäll-Bah

address: Bruna stråket 16

department: Laboratory Medicine

country: Sweden

institute: University of Gothenburg

summary: Recently we have identified the upregulation of the homebox domain protein MNX1 associated with the paediatric t(7;12) AML as the initiating event for Leukaemia in mice. We demonstrated that MNX1 triggers abnormal histone modifications, specifically H3K4me3 and H3K27me3, by interacting with SAM-dependent methyltransferases. In the current study our aim was investigate downstream targets of MNX1 and the relationship with histone modification. Employing TMT Mass spectrometry and RNA-Seq integrative analysis identified the pioneer transcription factor PBX1 as a downstream target of MNX1. We observe that MNX1 binds to the promoter region of PBX1, leading to increased expression of PBX1. This binding of MNX1 to the PBX1 promoter was associated with enhanced H3K4me3 and decreased H3K27me3 in the same promoter region. Interestingly, this binding of MNX1, but not the histone modification on the PBX1 promoter was transient and diminishes as MNX1-FL cells progress to leukaemia in mice. To gain further insight, we conducted a comparative analysis of H3K4me3 using ACT-Seq and RNA-Seq data between MNX preleukemia FL cells and leukaemia MNX1 BM blasts. Our results indicate that this phenomenon is not limited to PBX1 but is rather widespread throughout the genome, identifying several downstream targets for MNX1 mediated H3K4me3 modification. Investigating the PBX1 and 4 motifs identified from Chip-Seq, revealed a significant enrichment in MNX1 H3K4me3 and ATAC-seq peaks. This suggest that PBX family might play an important role in the function of MNX1, which was further confirmed by showing MNX1 induced PBX1 expression to be downregulated using the sinefungin inhibitor, which we have previously reported to inhibit leukemia induction by MNX1.

overall_design: ATAC-seq of fetal liver cells, transduced with MNX1 or empty vector control.

first: Lars

last: Palmqvist

first: Ahmed

last: Waraky

first: Dieter

last: Weichenhan

first: Christoph

last: Plass


title: IGF2BP1 stabilizes OTX2 mRNA in an m6A-dependent manner to restrict human germ cell fate by repressing TFAP2C [CUT&Tag]

city: Jiaxing

first: Yashi

last: Gu

address: No.718, HaiZhouEastRoad

institute: zje

summary: N6-methyladenosine (m6A) is the most abundant and reversible modification on messenger RNAs. The differential m6A profiles in different cell types are installed by writers (such as METTL3) and removed by erasers (such as FTO). The m6A-modified RNAs are recognized by readers to trigger downstream regulation of RNA metabolism, eventually contributing to the regulation of cell fates. Primordial germ cells (PGCs) are specified early during embryogenesis and establish the germ cell lineage for transmitting genetic and epigenetic information from parents to offspring. Defects in the establishment of germline may lead to infertility, germ cell tumors, and birth defects. Despite extensive research, the m6A-mediated epigenetic regulation of the specification of PGCs remains elusive. In this study, we discovered that knock-out of m6A writer or over-expression of erasers leads to increased percentage of human PGC-like cells (hPGCLCs) induced from embryonic stem cells. We identified the m6A reader IGF2BP1 as the key factor for restricting hPGCLC fate induction by stabilizing OTX2 mRNAs in an m6A-dependent manner. Moreover, we discovered that OTX2 suppresses TFAP2C during germ cell lineage specification. In summary, we characterized the m6A-IGF2BP1-OTX2-TFAP2C axis in restricting the specification of human germ cell fate.

overall_design: To study the function of m6A related components in the regulation of hPGCLCs induced from hESCs，we established H1 hESCs cell line in which each target gene has been knocked out by CRISPR Cas9 and overexpressed. CUT&TAG for OTX2 in iMeLC stage is performed. m6A-seq for detecting m6A profile in hESCs is performed.

first: Jin

last: Zhang

first: Lingling

last: Tong

first: Boshi

last: Feng

first: Ziqi

first: Qizhe

last: shao

first: Yanxi

last: Chen

first: Huanchang

last: Tu

first: Shenghua

last: Dong

first: Honglin

last: Yu

first: Xiang

last: Li

first: Yueqi

first: Ziying

last: Lin

first: Xueting

first: Zhipeng

last: Ai

first: Yangquan

last: Xiang

first: Peng

last: Xia


title: The pioneer transcription factor PBX as a downstream target of MNX1 [ACT]

first: Eric

last: Malmhäll-Bah

overall_design: Antibody-guided chromatin tagmentation sequencing (ACT-seq) fot histone variants H3K4me3, H3K4me1 and transcription factor MNX1 as well as IgG control, in bone marrow and non-transplanted fetal liver cells, transduced with MNX1 or empty vector control.

first: Lars

last: Palmqvist

first: Ahmed

last: Waraky

first: Dieter

first: Christoph


title: IGF2BP1 stabilizes OTX2 mRNA in an m6A-dependent manner to restrict human germ cell fate by repressing TFAP2C [m6A-seq]

first: Yashi

last: Gu

first: Jin

first: Lingling

first: Boshi

first: Ziqi

last: Wang

first: Qizhe


title: Transcriptome induced by DNMT degrader in ccRCC cells

first: Weibo

last: Luo

summary: Global gene changes by DNMT degrader SGI1027 in VHL-deficient ccRCC cells

overall_design: RCC10 cells were treated with vehicle or SGI1027 for 2 days and subjected to mRNA-seq.

first: Yong


title: High throughput screening of patient's iPSC-derived neurons identifies gut microbial metabolites as a potential treatment for Alzheimer's disease.

status: Public on Apr 23 2025

city: CLEVELAND

first: Feixiong

last: Cheng

state: OH

address: 9620 Carnegie Ave.

department: Genome center

institute: The Cleveland Clinic Lerner Research Institute

summary: Altered gut microbial composition observed in Alzheimer’s disease patients drive microbial metabolome changes associated with AD pathogenesis; however, key microbial metabolites involved in this process and their functional roles are unknown. Here, we  screened library of 352 gut metabolites in AD patient iPSC derived neurons for their ability to reduce phosphorylation of tau. We identified 4-methylcatechol, menaquinone-4 and agmatine as candidate metabolites associated with decreased tau phosphorylation and chose agmatine for further validatory studies. We demonstrated that Agmatine significantly reduce tau hyperphosphorylations (pTau181, pTau205 and pTau231) in AD patient iPSC-derived neurons and cerebral organoids. We also observed that agmatine treatment enhances learning and memory, reduces amyloid burden and neuroinflammation in a 5xFAD mouse model. Transcriptomics analysis from patient iPSC derived brain organoids suggested decreased expression of complement system pathway genes (e.g. C1S, C2, C3AR1, C5AR1) by agmatine treatment. The study also highlights agmatine as an important modulator of AD pathology via regulating C3aR-STAT3 axis and implicates it as a novel therapeutic target for AD.

overall_design: We screened library of 352 gut metabolites in AD patient iPSC derived neurons for their ability to reduce phosphorylation of tau. We performed comparative transcriptomics analysis from patient iPSC derived brain organoids treated with DMSO and 100 µM agmatine at day 1 and day 3, in triplicates..

first: Dhruv

last: Gohel

first: Amit

last: Gupta


title: Integrated transcriptomic and metabolomic analysis of Jinggang honey pomelo Yellow Spot Disease to reveal the disease defence mechanism

city: Ji an

first: huimin

last: sun

state: Jiangxi

address: No. 28 Xueyuan Road, Qingyuan District

department: College of Life Sciences

institute: Jinggangshan University

summary: Jinggangshan honey pomelo, branded with "Jinggangshan," is a specialty fruit, but yellow spot disease severely affects its yield and quality. This study employed an integrated analysis of metabolomics and transcriptomics to investigate key differential metabolites (DAMs) and differentially expressed genes(DEGs) in two pomelo varieties, Jinlan (af) and Jinsha (js).

overall_design: A total of 1,681 DAMs were identified in the af variety, while 1,233 DAMs were identified in the js variety. The upregulated DAMs in both af and js were primarily flavonoid compounds. In the transcriptome analysis, there were 1,714 common DEGs between af and js. KEGG enrichment analysis indicated that these DEGs were significantly enriched in Plant hormone signal transduction, Plant-pathogen interaction, Phenylpropanoid biosynthesis, MAPK signaling pathway in plants, and flavonoid biosynthesis pathways. The joint analysis showed that the metabolic pathways commonly involved by DEMs and DAMs in both af and js were significantly enriched in Phenylpropanoid biosynthesis. The results revealed that in two varieties (af and js) of Jinggang honey pomelo infected with yellow spot disease, both metabolomic and transcriptomic data were enriched in the flavonoid metabolic pathway, suggesting that flavonoids may play a significant role in the defense mechanisms against this disease in Jinggang honey pomelo.

first: Huimin

last: Sun

first: Zexia


title: The gut microbiota regulates the vascular inflammatory phenotype in mesenteric ischemia-reperfusion injury via endothelial Toll-like receptor-2 signaling

city: Mainz

first: Hristo

last: Todorov

address: Duesbergweg 6

institute: University Medical Center Mainz

summary: Here, we set out to study the impact of gut commensals and TLR2 signaling on the vascular inflammatory phenotype of acute mesenteric I/R injured venules. Taking advantage of gnotobiotic experimentation and an endothelial-specific Tlr2-deficient mouse model, we dissect whether I/R-induced NETosis is also supported by endothelial TLR2 activation. To resolve the engagement of microbiota-induced TLR2 signaling on neutrophil function, based on agonist-treatment, we pinpoint the role of TLR2/1 vs TLR2/6 signaling in ex vivo NETosis induction.

overall_design: RNA-seq profiling transcriptome of liver endothelial cells of conventionally raised (CONV-R) and germ-free (GF) mice.


title: An Integrated Transcriptomic and Metabolomic Analysis of Black Spot Disease in Jinggang Honey Pomelo Reveals Underlying Resistance Mechanisms

summary: The Jinggang honey pomelo is recognized as one of the three major fruit industry brands in Jiangxi Province. However, the crop’s growth and yield have been significantly affected by the black spot disease caused by Diaporthe citri. Despite this impact, the defense mechanisms and underlying molecular responses of the Jinggang honey pomelo to the disease remain poorly understood.

overall_design: In this study, we utilized UPLC-MS/MS and RNA-Seq to conduct a comparative analysis of differentially abundant metabolites (DAMs) and differentially expressed genes (DEGs) in uninfected and D. citri-infected Jinggang honey pomelo fruits 13 days post-infection (dpi) in vivo. Our analysis yielded 1744, 1616, and 1325 DAMs, as well as 3403, 1767, and 453 DEGs from the respective varieties, with 426 DAMs and 66 DEGs common across all three. Kyoto Encyclopedia of Genes and Genomes enrichment analysis demonstrated significant enrichment of these DAMs and DEGs in phenylpropanoid and flavonoid biosynthesis pathways. We also discovered that transcription factors (TFs), specifically MYB and bHLH, related to these pathways, were highly expressed. Our elucidation of the phenylpropanoid and flavonoid biosynthesis pathways surmises that genes (4CL, F5H, HCT, CCR, and CAD) and metabolites (p-coumaryl acetate, pinocembrin, naringin, and neohesperidin) could significantly contribute to the resistivity of Jinggang honey pomelo against D. citri. Our findings suggest that Jinggang honey pomelo activates phenylpropanoid and flavonoid biosynthesis pathways, leading to the accumulation of flavonoid compounds that resist D. citri invasion. This study lays the groundwork for further research into the molecular mechanisms and breeding of Jinggang honey pomelo resistant to black spot disease.

first: Weiwei

last: Li


title: Design and Biological Activity of a Novel Urea Compound Against Glioblastoma [scRNAseq_MXC-017_374_in_vivo]

first: Frank

last: Pajonk

state: CA

address: 10833 Le Conte Ave

institute: UC Los Angeles

summary: Despite advances in surgery and radiotherapy, glioblastoma (GBM) remains the deadliest adult brain cancer with unacceptable low median survival rates. Targeted therapies and biologics have failed to improve outcome and the standard-of-care against GBM has not changed in two decades. GBM, like many solid tumors are thought to be organized hierarchically with a small number of radiation- and chemotherapy-resistant glioma stem cells (GSCs) producing more differentiated progeny and can repopulate tumors after sublethal treatment.In this study we sought to develop novel compounds that cross the blood-brain barrier (BBB), target existing GSCs and interfere with glioma cell plasticity to prevent the induction of GSCs in response to irradiation. We show that novel urea compounds target existing GSCs, prevent the radiation-induced conversion of non-stem glioma cells into GSCs and prolong the median survival in mouse models of GBM with minimal normal tissue toxicity.

overall_design: 300,000 HK-374 cells, engineered to express GFP and firefly luciferase, were implanted intracranially and allowed to engraft for one week. Engraftment was verified by bioluminescent imaging, after which mice received either a single 4 Gy dose of radiation alone or radiation followed by MXC-017 treatment (5 i.p. injections per week, 50 mg/kg) for two weeks. Tumors were then harvested and dissociated into single cells using the Miltenyi Brain Tumor Dissociation Kit (#130-095-942), followed by mouse cell depletion (Mouse Cell Depletion Kit, #130-104-694, Miltenyi). Cells from 2-3 mice were pooled and subjected for sequencing.

first: Ling

last: He


title: MSCs-encapsulated porous microparticle eye drops for autoimmune dry eye disease treatment

city: Nanjing

first: Taige

last: Chen

address: 321 Zhongshan Road

institute: Affiliated Drum Tower Hospital, Medical School of Nanjing University

summary: Dry eye disease (DED) characterizes by chronic inflammation and an unstable tear film. Stem cells have shown potential for DED treatment, but the main challenge lies in improving the effectiveness of cell delivery. Here, we developed novel eye drops for DED treatment by employing porous microcarriers with mesenchymal stem cells. The microcarriers were created by electrospraying the solution of Arginine-Glycine-Aspartic Acid (RGD) peptides-modified sodium alginate with polyethylene oxide and mesenchymal stem/stromal cells (MSCs) into the calcium chloride solution. In vitro experiments based on a hyperosmotic corneal epithelial cell model indicated that porous microcarriers encapsulated with MSCs (RGD-Alg@MSCs) demonstrated notable enhancements in cell viability, reductions in apoptosis and reactive oxygen species (ROS), and diminished expression of pro-inflammatory cytokines. In the DED model using non-obese diabetic (NOD) mice, RGD-Alg@MSCs effectively enhanced tear production, promoted corneal healing, and alleviated inflammation. Additionally, RGD-Alg@MSCs modulated the immune environment in DED by inhibiting dendritic cell (DC) activation and suppressing Th17 differentiation in vitro, effectively disrupting the inflammatory feedback loop characteristic of DED. This immune modulation strategy was further validated through in vivo experiments, confirming its therapeutic potential. Thus, the designed MSCs-encapsulated porous microcarrier system can improve stem cell delivery and DED treatment efficiency.

overall_design: RNA seq of Homo sapiens MSCs cell in Control,  MSCs and RGD-Alg_MSCs group


title: Lysine Pyruvylation Mediated by HAT1/p300-SIRT3 Couples Glycolytic Flux to Epigenetic Regulation

first: xiaohan

last: song

overall_design: CUT&Tag analysis of Kpy modifications in HEK293T cells.

first: Xiaohan

last: Song

first: Panan

last: Peng

first: Haonan

last: Zheng

first: Yanan

first: Qianjing

first: Yu

last: Ge

first: Doudou

last: Tan

first: He

last: Huang


title: Mapping and molecular marker development for the BnaSBT gene controlling inflorescence and plant architectures in B. napus

city: 湖北省 / 武汉市 / 洪山区

first: 京明

last: 李

address: 狮子山街1号华中农业大学

institute: 华中农业大学

summary: Exploring the molecular mechanism underlying plant architecture and breeding new varieties suitable for mechanized harvesting are primary objectives for rapeseed breeders in China. However, few genes controlling plant architecture have been cloned in Brassica napus. In this study, SX3, a scattered-bud B. napus line with a dwarf and compact plant architecture, was characterized. To identify the genes underlying bud arrangement, plant height and branch angle, segregating populations were constructed by crossing SX3 with two clustered-bud lines with a tall and loose plant architecture. Genetic analysis revealed that the scattered-bud trait (SBT) was controlled by a single dominant gene, BnaSBT. BnaSBT is likely a pleiotropic gene that simultaneously controls plant height and branch angle. Using BSA-seq analysis, BnaSBT was mapped to a 4.15 Mb region on ChrA10. Owing to the lack of recombinants within this region, it was infeasible to finely map BnaSBT. RNA-seq analysis of BC2 plants with contrasting inflorescence and plant architectures revealed that the upregulation of genes involved in amino acid and lipid metabolism and genes encoding MADS-box transcription factors is related to the the phenotype of SX3. These findings together with comparative sequencing indicated that BnaA10.SEP1, BnaA10.AGL15, BnaA10.GLN1-4 and BnaA10.AGP15 are candidate genes for BnaSBT. Markers closely linked to the scattered-bud trait were developed for selecting dwarf and compact plants. These findings provide molecular markers and germplasms for breeding new varieties with ideal plant types and lay a theoretical foundation for cloning key genes and elucidating the genetic basis of inflorescence and plant architectures in B. napus.

overall_design: RNA-seq profiling of whole apical meristem from wildtype(ZS11), Natural mutant(SX3), and their BC2 individuals (Zlike and Slike) with contrasting inflorescence and plant architectures at the developmental transition from inflorescence primordium differentiation to floral primordium initiation


title: Curcumin attenuates the progression of hemorrhoids through the inhibition of angiogenesis via miR-190a-5p/TGFBR2

city: Kunming

first: Heng

last: Zhang

state: Yunnan

address: No. 2628 Xiangyuan Street, Chenggong District, Kunming, Yunnan Province, China

institute: Kunming Municipal Hospital of Traditional Chinese Medicine

summary: Background: Hemorrhoids are common diseases of the anorectal system and are usually accompanied by vascular proliferation and edema. Curcumin is a natural molecule with potential anti-inflammatory, antitumor and antioxidant effects. This study aimed to explore the effect and molecular mechanism of curcumin in alleviating angiogenesis in rat hemorrhoids. Methods: A rat model of hemorrhoids was established via glacial acetic acid induction. Human venous endothelial cells were collected to perform cell experiments. The rats received curcumin at 25, 50, or 100 mg/kg/d. The rats were scored for perianal symptoms and inflammation levels, and the expression of angiogenesis-related factors was evaluated by immunofluorescence. Bioinformatics analysis, dual-luciferase, RT‒qPCR and Western blotting were used to verify the molecular mechanism of curcumin in the treatment of hemorrhoids. Results: Curcumin inhibited angiogenesis in endothelial cells and relieved the symptoms of hemorrhoids in rats. The study revealed that the expression of miR-190a-5p was significantly downregulated in hemorrhoids, whereas curcumin promoted the expression of miR-190a-5p. The results revealed that miR-190a-5p could inhibit angiogenesis and inflammation in endothelial cells by targeting TGFBR2, thereby alleviating the development of hemorrhoids. Mechanistically, curcumin inhibits the expression of TGFBR2 by upregulating miR-190a-5p, effectively blocking the angiogenesis ability of endothelial cells and thereby attenuating the progression and development of hemorrhoids in rats. Conclusion: Curcumin effectively inhibits angiogenesis in endothelial cells and relieves inflammation and the progression of hemorrhoids by regulating the miR-190a-5p/TGFBR2 molecular pathway.

overall_design: This study included a total of 6 human samples, comprising 3 hemorrhoid tissue samples (hemorrhoid group) and 3 normal control tissue samples (control group). Both the case and control group samples were pathologically confirmed, and the baseline characteristics, such as age and sex, were not significantly different between the two groups (p > 0.05) on the basis of statistical tests to minimize the interference of confounding factors on the results. For construction of the sequencing library, the TruSeq Small RNA Sample Prep Kit (Illumina, San Diego, USA) was used, which strictly followed the manufacturer’s protocol. After the quality control of the library was passed, high-throughput sequencing was performed using the Illumina HiSeq 2000/2500 platform in single-end mode, with a read length of 50 bp. Differential expression analysis of the miRNAs was conducted using an independent sample t test. The screening criteria for differentially expressed miRNAs were as follows: |log2(fold change)| > 1 (i.e., fold change > 2 or < 0.5) and p value < 0.05.

first: Chunling

first: Qingsheng

last: Liu

first: Weiping

last: Wan

first: Jian

last: Cheng

first: Xu

last: Han


title: RNA seq of activated CD8 T cells of WT and Card11 mutant mice(E134G/K215M)

city: Shanghai

first: Wei

last: Lu

state: Shanghai

address: 320 YueYang Road

department: CAS Key Laboratory of Tissue Microenvironment and Tumor

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

summary: To investigate the impact of Card11 on TCR downstream signaling, we isolated naive CD8+ T cells from wild-type (WT) mice and Card11 mutant mice (K215M and E134G). These cells were stimulated in vitro with anti-CD3/CD28 for 24 hours, after which RNA was extracted from the stimulated cells for sequencing analysis.

last: Hu

first: Qifan

last: Zhao

first: Yingquan

last: Qin


title: ATAC seq of  CD8 TILs of WT and Card11 mutant mice(K215M)

summary: To investigate the impact of the Card11 on Tex cell differentiation, we isolated Tex cells from tumors of both WT mice and K215M mice and performed genomic library construction and ATAC-seq. Concurrently, Tprime cells from the tumors of WT mice were also sorted out to serve as controls.

overall_design: ATAC seq of Tex from WT and Card11 mutant mice (K215M)


title: Single Cell RNAseq to identify subpopulations of glial progenitors in iPSC-derived oligodendroglial lineage cultures

first: Thomas

last: Durcan

state: Quebec

address: 3801 University Street

department: The Neuro

summary: Cellular heterogeneity is a common issue in differentiation protocols of oligodendrocytes (OLs) from human induced pluripotent stem cells. Our previous work described a novel method to generate OLs and highlighted the presence of glial progenitors. Here, we unravel the glial heterogeneity and characterize the response of isolated subpopulations to differentiation. This study provides a novel tool for studying the dynamics of glial development in vitro and on a transcriptomic level.

overall_design:
iPSCs from two healthy control donors were differentiated into OL-lineage progenitors and expanded. Cells were collected and fixed using the ParseBio fixation workflow and libraries were created from the WT kit.

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
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first: Gabriela

last: Blaszczyk

first: Valerio

last: Piscopo

first: Taylor

last: Goldsmith

first: Alexandra

last: Chapleau

first: Julien

last: Sirois

first: Geneviève

last: Bernard

first: Jack

last: Antel


title: Single-cell elderly blood-CSF atlas implicates peripherally-influenced neuroinflammatory degeneration in normal pressure hydrocephalus

city: New Haven

first: Kristopher

last: Kahle

state: Connecticut

address: 333 Cedar St

institute: Yale University Department of Neurosurgery

summary: Idiopathic normal pressure hydrocephalus (iNPH) is a common, yet enigmatic form of dementia characterized by cerebral ventriculomegaly. In contrast to other types of hydrocephalus, iNPH exhibits normal or even reduced intracranial pressures and infrequent reductions in ventricular size after CSF shunting. Here, we generated the first single-cell RNA sequencing atlas of the peripheral blood and ventricular CSF in elderly iNPH patients totaling 140,207 transcriptomes. Integrated analyses identified a pro-inflammatory signature in peripheral blood and CSF monocytes that was significantly enriched in iNPH subgroups with lower cognitive function. We also identified novel CSF cell populations likely representing the periventricular sloughing of degenerating neuroglial cells. Our findings suggest that immune dysregulation detectable in peripheral blood monocytes contributes to CSF space inflammation, neurodegeneration, and associated cognitive deficits in iNPH. These data shift the paradigm of iNPH from a primary disorder of impaired “brain plumbing” and highlight the potential for non-invasive, immune-based diagnostic and treatment strategies.

overall_design: Investigate the inflammatory features of NPH pathology and their correlation with clinical phenotypes.

first: Duy

last: Phan

first: Emre

last: Kiziltug


title: Non-invasive liquid biopsy based on transcriptomic profiling for early diagnosis of occult peritoneal metastases in locally advanced gastric cancer

city: Shijiazhuang

first: Jia'xiang

last: Wu

address: Shijiazhuang 050011,China

institute: The Fourth Hospital of Hebei Medical University

summary: Gastric cancer (GC) remains one of the leading causes of cancer-related death worldwide, especially in East Asian countries. Despite advances in treatment, patients with locally advanced gastric cancer (LAGC) still have a poor prognosis due to the high incidence of metastasis and recurrence. Peritoneal metastasis is particularly occult and difficult to detect by conventional imaging techniques at an early stage. Existing imaging methods lack high sensitivity and are difficult to detect early metastatic lesions. Although diagnostic laparoscopy has high sensitivity, it is invasive and difficult to use routinely. Therefore, innovative diagnostic methods are urgently needed. Transcriptomics methods can provide a comprehensive understanding of the biological state of cancer, especially showing potential in the early detection of GC and peritoneal metastasis. Our objective is to provide a more sensitive diagnostic method in the latent stage of peritoneal metastasis by identifying the RNA expression pattern of cancer cells.

overall_design: To investigate the RNA expression patterns of GC tissues with or without peritoneal metastasis, we performed RNA sequencing (RNA-seq) analysis on ribosomal RNA-depleted total RNA extracted from GC tissue samples of 17 GC patients (5 with peritoneal metastasis and 12 with primary lesions but without peritoneal metastasis).


title: scRNA and TCR seq of  CD8 TILs of WT and Card11 mutant mice(E134G/K215M)

summary: To investigate the impact of Card11 on TIL differentiation, we isolated TILs from B16-F10 tumors of WT mice, E134G mice, and K215M mice and performed scRNA seq. We also sorted tumor-infiltrating lymphocytes (TILs) from melanoma(B16-F10) of WT mice and conducted scRNA and scTCR sequencing. To further investigate the impact of Card11 on TCR clonal diversity, we sorted CD8 T cells from melanoma WT mice or K215M mice and performed scRNA and scTCR sequencing.

first: Yu


title: Olfactory Receptors as Tumor Suppressors in Cutaneous T-Cell Lymphoma via p38γ Pathway Modulation

city: Duarte

first: Hannah

last: Zhang

address: 1500 E Duarte Rd

department: Research-Rosen, Steven - MC

institute: City of Hope National Medical Center

summary:
We screened 270,000 compounds from an NCI library for the ability to dock with the non-ATP-binding site of p38γ using virtual screen.
The resulting candidate compounds were for cytotoxicity assays to the Hut78 CTCL cell line and identified CSH18 as one of the most promising agents.

overall_design: To show downstream pathway that CSH18-mediated targeting of p38γ, we first isolated RNA and subjected to microarray analysis of treated vs. control cells and observed upregulation of TNF alpha in several top hit  after assesments of its downstream pathways.

first: Xu Hannah

first: Xiwei

first: Steven

last: Rosen


title: Combined MEK and PARP inhibition enhances radiation response in rectal cancer

city: Heidelberg

first: Johannes

last: Betge

address: Im Neuenheimer Feld 580

department: Signaling and Functional Genomics

institute: German Cancer Research Center (DKFZ)

summary:
Rectal cancer is most frequently diagnosed at a locally advanced stage and treated by neoadjuvant chemoradiation. Current efforts to improve treatment outcome are focused on intensifying neoadjuvant chemotherapy, which is however associated with higher levels of toxicity. To discover alternative strategies, we established patient-derived rectal cancer organoids (PDOs) that reflect clinical radiosensitivity and used these organoids to screen 1596 drug-radiation combinations. We found that inhibitors of RAS-MAPK signaling, especially MEK inhibitors, strongly enhance radiation response. Mechanistically, MEK inhibitors suppressed radiation-induced activation of RAS-MAPK signaling, and selectively downregulated RAD51, a key component of the homologous recombination DNA repair pathway. Through testing drug-drug-radiation combinations in organoids and cell lines, we identified that a combined PARP and MEK inhibition can further enhance radiosensitivity of colorectal cancers, which was confirmed in mouse xenograft models. Our data support clinical testing of MEK and PARP combination therapy with radiation in locally advanced rectal cancers as an alternative to chemoradiation
Microarrays were used to investigate the effect of radiation treatment on gene expression in three patient-derived colorectal cancer organoid lines.

overall_design: We measured total RNA from 3 human patient-derived colorectal cancer organoid lines.

first: Philipp

last: Albrecht

first: Kyrhatii

last: Trikhirhisthit


title: Comparative analysis of gene expression upon DMSO-induced differentiation of hepatoma cell lines [Dif]

city: Strasbourg

first: Frank

last: Jühling

address: 3 Rue Koeberlé

country: France

institute: Université de Strasbourg, Inserm, Institut de Recherche sur Les Maladies Virales et Hépatiques UMR_S1110

summary: The liver, and more precisely hepatocytes, can be infected by several viruses such as hepatitis B (HBV), hepatitis D (HDV), hepatitis C (HCV), hepatitis E (HEV) viruses, with chronic infection leading to end-stage liver diseases. Since no in vitro model allowing multi-infections with the four viruses is reported, limited data are available on the interplay between those viruses as well as on the potential cross-reactivity of antivirals in multi-infection cases. Here we showed that HuH7.5-NTCP cells can be partially differentiated into hepatocyte-like cells and genuinely replicate HBV, HDV, HCV and HEV for at least 4 weeks after mono or multiple infections. Additionally, we recapitulated the effect of known antivirals and found that FXR-agonists, also strongly inhibited HEV replication. Using HEV infected HuHep mice, we confirmed the antiviral effect of Vonafexor, the FXR agonist clinical candidate currently tested against HBV and HDV, highlighting FXR-ligands as potential broad acting antivirals. Here, we set-up the first in vitro model allowing multi-infections with hepatitis viruses that can be used for broad drug screening.

overall_design: HuH7-NTCP cells and HuH7.5-NTCP cells were differentiated or not in 2% DMSO-containing medium. Total RNAs were extracted and gene expression was analyzed by RNAseq

first: Eloi

last: Verrier

first: Julie

last: Lucifora


title: The transcriptome sequencing of Galangin treated BGC823 Exosomes

city: Changchun

first: Dongxu

last: Wang

state: Jilin

address: Xi'an Road #5333

department: Laboratory Animal Center, College of Animal Science

institute: Jilin University

summary: Galangin-containing exosomes (Galangin-Exo) were isolated from BGC823 cells treated with Galangin.RNA-seq technology was used to screen differentially expressed MicroRNAs (miRNAs) in Galangin-Exo. BGC823 cells can specifically take up Galangin-Exo. In addition, Galangin-Exo inhibited the growth of gastric cancer cells.

overall_design: RNA-seq screen differentially expressed miRNAs between Con-Exo and Galangin-Exo

first: Qirong

last: Li


title: Comparative analysis of gene expression upon IFNα stimulation in hepatocyte-like cells [IFN]

summary: Patients chronically co-infected by Hepatitis B Virus (HBV) and Hepatitis D Virus (HDV) suffer from the most aggressive form of viral hepatitis leading to severe liver disease such as cirrhosis, hepatocellular carcinoma and liver decompensation. Treatments options are very limited with only two drugs used in clinic (IFN-α and Bulevertide) that rarely allow viral clearance. The molecular mechanisms leading to inhibition of HDV by IFN-α (in patients but also in vitro) are not known and mechanisms behind treatment failures in patients also remain elusive. Here we aimed at the identification of interferon stimulated genes (ISGs) that can specifically inhibit intracellular HDV replication.  IFN-α was  able to inhibit HDV in both co-infected differentiated HuH7.5-NTCP- and HepaRG cells (dHuH7.5-NTCP and dHepaRG, respectively). We hypothesized that ISGs responsible for the antiviral effect of HDV should be upregulated in both dHepaRG and dHuH7.5-NTCP cells upon treatment with IFN-α. To identify these ISGs, dHuh7.5-NTCP and dHepaRG cells were stimulated with IFN-α for 8h, total RNAs were extracted and gene expression was analyzed by RNAseq.

overall_design: differentiated HepaRG cells and differentiated HuH7.5-NTCP cells were stimulated or not with IFNα-2a (500 UI/mL) for 8h. Total RNAs were extracted and gene expression was analyzed by RNAseq


title: IGF2BP1 stabilizes OTX2 mRNA in an m6A-dependent manner to restrict human germ cell fate by repressing TFAP2C [RNA-seq]

first: Yashi

last: Gu

summary: N6-methyladenosine (m6A) is the most abundant and reversible modification on messenger RNAs. The differential m6A profiles in different cell types are installed by writers (such as METTL3) and removed by erasers (such as FTO). The m6A-modified RNAs are recognized by readers to trigger downstream regulation of RNA metabolism, eventually contributing to the regulation of cell fates. Primordial germ cells (PGCs) are specified early during embryogenesis and establish the germ cell lineage for transmitting genetic and epigenetic information from parents to offspring. Defects in the establishment of germline may lead to infertility, germ cell tumors, and birth defects. Despite extensive research, the m6A-mediated epigenetic regulation of the specification of PGCs remains elusive. In this study, we discovered that knock-out of m6A writer or over-expression of erasers leads to increased percentage of human PGC-like cells (hPGCLCs) induced from embryonic stem cells. We identified the m6A reader IGF2BP1 as the key factor for restricting hPGCLC fate induction by stabilizing OTX2 mRNAs in an m6A-dependent manner. Moreover, we discovered that OTX2 suppresses TFAP2C during germ cell lineage specification. In summary, we characterized the m6A-IGF2BP1-OTX2-TFAP2C axis in restricting the specification of human germ cell fate.

overall_design: To study the function of m6A related components in the regulation of hPGCLCs induced from hESCs，we established H1 hESCs cell line in which each target gene has been knocked out by CRISPR Cas9 and overexpressed. CUT&TAG for OTX2 in iMeLC stage is performed. m6A-seq for detecting m6A profile in hESCs is performed.

first: Jin

first: Lingling

last: Tong

first: Boshi

last: Feng

first: Ziqi

first: Qizhe

last: shao

first: Yanxi

last: Chen

first: Huanchang

last: Tu

first: Shenghua

last: Dong

first: Honglin

last: Yu

first: Xiang

first: Yueqi

first: Ziying

last: Lin

first: Xueting

first: Zhipeng

last: Ai

first: Yangquan

last: Xiang

first: Peng

last: Xia


title: Dynamic changes of molecular pattern and cellular subpopulation in puncture-induced tendon injury model [scRNA-seq]

city: Hangzhou

first: Dengfeng

last: Ruan

state: China

address: 88 Jie Fang Road

department: Department of Orthopedic Surgery

institute: The Second Affiliated Hospital, Zhejiang University School of Medicine

summary: Tendon degeneration and injury often result in significant pain and functional impairment. Typically, tendon healing occurs through a scar-mediated response and may progress to chronic tendinopathy without timely intervention. However, the molecular mechanisms underlying early tendon repair remain poorly understood. Further investigation is also impeded by the limited availability of early tendon injury samples in clinical settings. In this study, we established a puncture-induced tendon injury model to investigate the molecular patterns and cellular subpopulations involved in early tendon injury across multiple time points. RNA sequencing identified seven gene sets with distinct expression profiles during the early stages of tendon injury. Single-cell RNA sequencing further revealed eight myeloid cell types and seven mesenchymal cell types participating in the tendon repair process. Together, these findings illuminate the molecular and cellular dynamics coordinating early tendon repair, providing insights that could inform future clinical treatments for tendinopathy and tendon injury.

overall_design: After tendon injury in mice, samples were collected at different time points after injury for transcriptome and single-cell transcriptome sequencing.

first: Zizhan

last: Huang

first: Ziyang

first: Tiwen

last: Xu

first: Honglu

last: Cai

first: Hengzhi

last: Liu

first: Haocheng

last: Jin

first: Peiwen

last: He

first: Yang

last: Fei

first: Canlong

first: Xiao

first: Jia

last: Jiang

first: Weiliang

last: Shen


title: Dynamic changes of molecular pattern and cellular subpopulation in puncture-induced tendon injury model

last: Li

last: Wang

last: Chen


title: Development of RelB-Targeting Small Molecule Inhibitors of Non-canonical NF-kB Signaling with Antitumor Efficacy

city: Beijing

first: Cuifeng

address: Qinghua Yuan Street

institute: Tsinghua University

summary: Dysfunction of the non-canonical NF-kB signaling pathway has been causally associated with numbers of cancers and autoimmune diseases. However, specific inhibitors for this signaling pathway remain to be developed. Here we showed that structure-based cell-based screening yielded a potent and specific small molecule targeting RelB to inhibit non-canonical NF-kB signaling pathway, while had no inhibitory effect on canonical NF-kB signaling pathway. Mechanistically, the inhibitor directly interacted with RelB protein and disrupted RelB binding to its target DNA, thus repressing RelB transactivity on target genes. Through blocking oncogenic activity of non-canonical NF-kB signaling pathway in colorectal cancer or B lymphoma, the inhibitor efficiently exerted a potent antitumor effect in vitro and in vivo. Thus, our study provided new RelB-targeting inhibitor that inhibited non-canonical NF-kB signaling pathway and facilitated precise therapeutic applications in cancers and possibly other diseases.

overall_design: BAFF specifically activates the nonclassical nfkb pathway in B-cell lines, and the specificity of the inhibitor was evaluated by testing its effect on BAFF-induced genes


title: Immune regulation mechanism of polysacchride extracted from Acanthopanax senticosus on RAW 264.7 cells through activating the TLR/MAPK/NF-κB signaling pathway

city: ChangChun

first: Dongxia

last: Gou

address: Changchun University, No.8326 Weixing Street

institute: Changchun university

summary: Acanthopanax senticosus is a unique wild resource in Northeast China. Its main active ingredient is polysaccharide, which has prominent immunomodulatory effect. In this study, the purified polysaccharide component of Acanthopanax senticosus leaves (ASPS-A1) with strong immunomodulatory activity was isolated by column chromatography, and its structure and properties were characterized by HPGPC, FT-IR. Results showed that ASPS-A1 is mainly composed of α-1,4-D-GalA, α-1,5-L-Ara, and β-1,4-D-Gal. RT-qPCR experiments and RNA-seq analysis was used to study the immunoregulatory mechanism of ASPS-A1. The results showed that ASPS-A1 could significantly up-regulated the levels of cytokines iNOS, IL-1β, IL-6 and TNF-α activated macrophages through MAPK, NF-κB, and Toll-like receptor signaling pathways. Inhibitory experiments were further confirmed that ASPS-A1 promote the expression of iNOS, TNF-α, and IL-6 via TLR4 receptor, and TNF-α and IL-1β via TLR2 receptor. In order to identify the target of ASPS-A1, molecular docking experiments were conducted. The results demonstrated that ASPS-A1 could bind to both TLR4 and TLR2, forming stable complexes with the cavities on the protein surface through hydrogen bonding and hydrophobic interaction. The docking scores indicated that ASPS-A1 could regulate the immune response through TLR2 and TLR4 signaling pathways, with a particularly strong interaction with TLR4. In summary, this study screened and characterized the most immunoreactive components of Acanthopanax senticosus polysaccharide, disclosed the immunomodulatory mechanism of ASPS-A1, and furnished a research basis for its potential application as a natural immune enhancer.

overall_design: The RNA-seq analysis was performed on RAW 264.7 cells. RAW 264.7 cells were cultured in 6-well plates at a concentration of 2×105 cells/mL for 24 h, then the supernatant was discarded, and the medium containing ASPS-A1 (200 μg/mL) was added. The cells were collected for 24 h, treated with 1 mL Trizol, and immediately placed in a refrigerator at -80 ℃. Fresh Acanthopanax senticosus leaves were taken and extracted with ultrasonic-assisted extraction at a material-liquid ratio of 1:20, rotary evaporation, alcohol precipitation, and lyophilization to obtain Acanthopanax senticosus leaves crude polysaccharide (ASPS). DEAE cellulose-52 column was used to separate and purify ASPS, and the acidic polysaccharide (ASPS-A) and neutral polysaccharide (ASPS-N) were obtained. ASPS-A was further isolated and purified using a Superdex-G100 gel column and eluted by NaCl at a flow rate of 0.15 mL/min. The liquid was collected, dialyzed, and freeze-dried to obtain ASPS-A1.

first: Yufan

first: Lei

first: Hanwen

last: Zhang

first: Peirou

last: Ren

first: Xiaowen

last: Cheng

first: Fandi

last: Hong

first: Jiaxin

first: Ruining

first: Jun

last: Zhao


title: A germline ETV6 mutation disrupts hematopoiesis via de novo creation of a nuclear export signal

city: Dallas

first: Glen

last: Liszczak

state: TX

address: 5641 Southwestern Medical Ave, Suite B200

institute: UT Southwestern Medical Center

summary: Germline mutations in the transcriptional regulator ETV6 are a root cause of familial inherited thrombocytopenia and predispose carriers to myelodysplastic syndromes and acute leukemias. Here, we report that the ETV6 P214L mutation creates an XPO1-dependent nuclear export signal to cause protein mislocalization. Strategies to disrupt XPO1 nuclear export activity fully restore ETV6 P214L protein nuclear localization and transcription regulation activity, establishing XPO1-dependent mislocalization as a critical mechanism underscoring ETV6 P214L dysfunction. Mechanistic insight inspired the design of ‘humanized’ ETV6 mice in which the germline P214L mutation is sufficient to elicit severe defects in thrombopoiesis and hematopoietic stem cell maintenance and survival in animals. These studies define a unique mechanism by which the ETV6 P214L mutation exerts a dominant negative effect on protein function and reveal critical mutation-dependent disruptions to hematopoiesis that underlie disease phenotypes.

overall_design: Low-input RNA sequencing of Etv6 mutant and WT murine HSC and MEPs sorted by Fluorescence-activated cell sorting (FACS)


title: Identifying Putative Targets of Capn15 in Neurodevelopment

city: Montreal

first: Senthilkumar

last: Kailasam

address: 740 Dr. Penfield Avenue, #4200

department: Human Genetics

institute: McGill University

summary: Calpain 15 (CAPN15), part of the non-classical SOL family, plays a key role in neurodevelopment. This study used RNA-seq  in P2 mice (7 KO and 7 WT) to investigate transcriptomic changes after loss of CAPN15. Differential expression analysis identified Pax2 targets as significantly regulated in CAPN15 KO mice. This work provides insight into CAPN15's molecular mechanisms and its potential role in human developmental disorders.

overall_design: Fourteen P2 mouse brains (7 KO, 7 WT) were sequenced using Illumina NovaSeq 6000. RNA-seq analysis involved ribodepletion, Trimmomatic trimming, STAR alignment, and edgeR for differential expression analysis.

first: Congyao

last: Zha

first: Wayne S.

last: Sossin