title: Secreted miRNAs from primary myocytes

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

institute: University of Padova

summary: Amyotrophic lateral sclerosis (ALS) is the most common adult-onset paralytic disorder, characterized primarily by a progressive loss of motor neurons in whose degeneration skeletal muscle involvement has been demonstrated. Skeletal muscle is a plastic tissue that responds to insults through proliferation and differentiation of satellite cells. The process of skeletal muscle degeneration and regeneration are finely regulated by signals that regulate satellite cell proliferation and differentiation. It is known that satellite cell differentiation is impaired in ALS, but little is known about the involvement of miRNAs and their role in intercellular communication in skeletal muscle in ALS. Here we demonstrated impaired differentiation of satellite cells derived from ALS mice related to the impairment of myogenic p38MAPK and PKA/pCREB signaling pathways that can be regulated by miR-882 and -134-5p. These miRNAs participate in autocrine signaling in association with miR-26a-5p, that, secreted from WT and captured by ALS myoblasts, enhances ALS-related myoblast differentiation by repressing Smad4-related signals. These findings underscore the urgency of better understanding the role of intercellular communication and the molecular mechanisms underlying ALS pathogenesis and progression. They also suggest that miRNAs could be targeted as potential therapeutic agents to enhance myofiber regeneration.

overall_design: Primary cultures of myocytes were performed collecting leg skeletal muscle from from different mice. Each sample described in this research represent a biological replicate. Experiments were performed using three different co-cultures to evaluate miRNAs secreted in the culture medium. Performed co-cultures were hSOD1(WT)/hSOD1(WT), hSOD1(WT)/hSOD1(G93A) and hSOD1(G93A)/hSOD1(G93A). Tg mice overexpressing WT hSOD1 (strain B6SJL(Tg-SOD1)2Gur/J, abbreviated as hSOD1(WT) or the G93A mutant of the protein (B6SJL(Tg-SOD1*G93A)1Gur/J mice (model for Amyotrophyc Lateral Sclerosis), here abbreviated as hSOD1(G93A), were from Jackson Laboratories (cat. n. 002297 and 002726, respectively). Colonies were preserved by breeding Tg hemizygote males with wild-type B6SJLF1/J hybrid females. Newborns were genotyped as previously described 80 using the MyTaq Extract-PCR kit (Bioline). Primary myoblasts from newborn (1-3 days) hSOD1(WT) or hSOD1(G93A) mice were prepared as previously described 81. Briefly, the posterior limb muscles were removed, and cells isolated by three successive treatments with 0.1% trypsin in phosphate-buffered saline (PBS; 140 mM NaCl, 2 mM KCl, 1.5 mM KH2PO4, 8 mM Na2HPO4, pH 7.4) for 30 min at 37 °C, seeded at a density of 2.5 × 105 cells onto 13 mm-coverslips coated with collagen (0.1% w/v in PBS) for immunocytochemistry, or at a density of 1 × 106 cells onto 35 mm-collagen-coated plates for biochemical assays, and cultured in proliferation medium (Ham's F12 with 10% foetal bovine serum, 2 mM glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin) for 2 days (2 Days In Vitro: 2 DIV). At this time point, proliferation medium was replaced by differentiation medium (Dulbecco’s Modified Eagle Medium containing 2% horse serum, 2 mM glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin) for myoblast differentiation into myotubes. All reagents for cell culture were from Euroclone.

first: Caterina

last: Peggion

first: Raphael

middle: S

last: Bonadio

first: Roberto

last: Stella

first: Silvia

last: Scalabrin

last: Millino

first: Beniamina

last: Pacchioni

first: Alessandro

last: Bertoli

first: Maria

middle: L

last: Massimino

first: Stefano

last: Cagnin


title: Deciphering the functional impact of Alzheimer’s Disease-associated variants in resting and proinflammatory immune cells [MPRA]

status: Public on Jul 02 2025

city: Chapel Hill

first: Marielle

last: Bond

state: NC

address: 116 Manning Dr

department: Genetics

country: USA

institute: UNC Chapel Hill

summary: Genome-wide association studies have identified loci associated with Alzheimer’s Disease (AD), but identifying the exact causal variants and genes at each locus is challenging due to linkage disequilibrium and their non-coding nature. To address this, we performed a massively parallel reporter assay of 3,576 AD-associated variants in THP-1 macrophages in both resting and proinflammatory states and identified 47 expression-modulating variants (emVars). To understand the endogenous chromatin context of emVars, we built an activity-by-contact model using epigenomic maps of macrophage inflammation and inferred condition-specific enhancer-promoter pairs. Intersection of emVars with enhancer-promoter pairs and microglia expression quantitative trait loci allowed us to connect 39 emVars to 76 putative AD risk genes enriched for AD-associated molecular signatures. Overall, the systematic characterization of AD-associated variants enhances our understanding of the regulatory mechanisms underlying AD pathogenesis.

overall_design: Massively parallel reporter assay (MPRA) on Alzheimer's Disease risk variants in resting and proinflammatory THP-1 monocyte-derived macrophages

first: Yoseli

last: Quiroga-Barber

first: Susan

last: D'Costa

first: Yija

last: Wu

first: Jessica

last: Bell

first: McAfee

last: Jessica

first: Nicole

last: Kramer

first: Sool

last: Lee

first: Mary

last: Patrucco

first: Douglas

last: Phanstiel

first: Hyejung

last: Won


city: Qingdao

first: Yanhai

last: Gong

address: No.189 Songling Road

department: single cell center

country: China

institute: qibebt, cas

type: Expression profiling by high throughput sequencing

summary: Transcriptome analysis of NoPAC4 mutants under low light revealed a novel role of PAC4 that enhances carotenoid synthesis in N. oceanica

overall_design: Cells were cultured in flasks for 5 days to reach the logarithmic phase at 23 °C under continuous light (50 μmol photons m-2 sec-1).

first: Qintao

last: Wang

first: Jian

last: Xu


title: Super-enhancer-driven CACNA2D2 is an EWSR1::WT1 signature gene encoding a diagnostic marker for desmoplastic small round cell tumor (DSRCT) [Affymetrix]

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

country: Germany

institute: German Cancer Research Center (DKFZ)

summary: This dataset comprises transcriptome data of two subcutaneously xenografted desmoplastic small round cell tumor (DSRCT) cell lines (JN-DSRCT-1 and SK-DSRCT2) after posttranscriptional knockdown of EWSR1::WT1 fusion oncogene for 96h.

overall_design: Two desmoplastic small round cell tumor (DSRCT) cell lines were stably transduced with inducible shRNA expressing casettes targeting either the CDS (shWT1-CDS) or 3'-UTR (shWT1-UTR) of the EWSR1::WT1 fusion transcript. One million DSRCT cells harboring either shRNA against WT1-CDS or WT1-UTR were resuspended in PBS and mixed with Geltrex™ LDEV-Free, hESC-Qualified, Reduced Growth Factor Basement Membrane Matrix in 1:1 proportion, and slowly injected subcutaneously in the right flank of 10–12 weeks old NOD/scid/gamma (NSG) mice. When the tumors reached an average volume of 80 mm3, mice were randomized into two groups. 96h prior to the pre-determined end of the experiment, mice were treated with either 2 mg/ml doxycycline (DOX) dissolved in drinking water containing 5% sucrose to induce an in vivo knockdown of EWSR1::WT1 (DOX (+)), or 5% sucrose (control, DOX (−)). At the experimental endpoint the mice were sacrificed by cervical dislocation. Then, subcutaneous xenografted tumors were extracted and used for total RNA extraction. RNA was isolated from 16 xenografts, two xenografts per shRNA and per cell line from mice treated with DOX and from control mice. The transcriptome was profiled on GeneChip™ Human Genome U133 Plus 2.0 Array. Raw data were processed applying the Robust Multi-chip Average (RMA) algorithm, including background adjustment, quantile normalization and summarization. For RMA normalization custom brainarray Chip Description Files (CDF; ENTREZG, v25) were used, yielding one optimized probe set per gene.

first: Florian

middle: H

last: Geyer

first: Florencia

last: Cidre-Aranaz

middle: G

last: Grünewald


title: PABPN1 couples the polyadenylation and translation of maternal transcripts to mouse oocyte meiotic maturation

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

summary: In the process of mammalian maternal-to-zygotic transition (MZT), the degradation of zygotic decay (Z-decay) mRNA is later than that of maternal factor-mediated mRNA decay (M-decay) mRNA. The regulatory mechanism and physiological significance of Z-decay mRNA to maintain stability during meiosis are urgent scientific questions. In this study, we identified that PAPα worked together with poly(A)-bound RNA binding protein PABPN1 to promote the polyadenylation and translation of maternal transcripts, leading to rupture of germinal vesicles in mammalian oocytes. The oocytes specifically knocked out Pabpn1 at the primary follicle stage could develop into the fully grown (FGO) stage, but hardly could enter to the meiotic process. Furthermore, PABPN1 maintains the stability of Z-decay maternal transcripts during oocyte meiotic maturation. A number of Z-decay transcripts and the translational activity in Pabpn1-null oocytes was significantly lower than that of wild-type oocytes during meiosis. Therefore, during meiotic maturation of oocytes, PABPN1 maintains the stability of Z-decay transcripts and promotes the degradation of some M-decay transcripts, ensuring normal GVBD and polar body-1 emission.

overall_design:
The construction of PAIso-seq libraries (WT FGO, WT MII oocytes, zKO FGO and zKO MII oocytes, 100K oocyes per sample) followed the protocol published before[1]
Briefly, total RNA was extracted by TRIzol reagent (Invitrogen, #15596026) and chloroform (Sinopharm, #10006818), and precipitated with isopropanol (Sinopharm, #80109218) and dissolved with nuclease-free water. Purified total RNA were used for templated end extension by dU-containing end-extension oligo[1] and Klenow fragment 3’-5’ exo- (NEB, #M0212L). Then the templated RNA were cleaned by USER enzyme (NEB, #M5505S) and RNA Clean & Concentrator-5 kit (Zymo Research, #R1016). Purified templated RNA were retro-transcripted into cDNA by using SuperScript Ⅱ reverse transcriptase (Invitrogen, #18064-014) and TSO primer. The full-length cDNA were further pre-amplified by using 2×KAPA HiFi HotStart ReadyMix (KAPA Biosystems, #KK2601) and cleaned by SPRIselect beads (Beckman Coulter, #B23318). For each sample, 20 ng purified cDNA were used for final amplification and cleaning as pre-amplification. Finally, cDNAs from different samples were mixed together  according to the concentration and fragments length, and 500ng mixed cDNA were used for SMRTbell template library and sequencing by using Pacbio sequell Ⅱ.

first: Xingxing

last: Dai

first: Yuke

first: Hengyu


title: Multilevel regulation of gene expression in brasilicardin biosynthetic gene cluster

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

institute: Institute for Bioinformatics and Medical Informatics

summary: Brasilicardin A, BraA, is a secondary metabolite produced by the bacterium Nocardia terpenica, and a promising drug due to potent immunosuppressive activity and low cytotoxicity. Currently, a semisynthetic approach confers production of a complete compound but suffers from insufficient biosynthesis of BraA intermediates used in the chemical synthesis steps leading to only lab scale quantities of the compound. A better understanding of gene expression regulatory pathways within the brasilicardin biosynthetic gene cluster, Bra-BGC, is a prerequisite to further improvements in the biosynthesis titers. However, a transcriptional regulation in Bra-BGC has only been superficially analyzed, till now. In this study, we comprehensively analyze the functions of several unstudied transcriptional regulators, KstR, SdpR and OmpR, encoded within the close vicinity of the Bra-BGC, and delve the role of the previously described cluster-situated activator Bra12. We present, that the Bra12 and the novel regulator SdpR, bind several DNA sequences located in the promoter regions of the genes essential for BraA biosynthesis. Subsequently, we demonstrate complex regulatory network through which both regulators are capable of controlling activity of those gene promoters and thus gene expression in Bra-BGC. Furthermore, using heterologous producer strain Amycolatopsis japonicum, we present, that Bra12 and SdpR regulators play opposite roles in brasilicardin congeners biosynthesis in. Finally, we propose a comprehensive model of multilevel gene expression regulation in Bra-BGC and propose the roles of locally encoded transcriptional regulators

overall_design: Differential whole transcriptome shotgun sequencing of Nocardia terpenica IFM 0406  was performed in duplicates at two time points of growth.

first: Tobias

last: Schwarz

first: Dilek

last: Dere

first: Harald

last: Gross

first: Marcin

last: Wolański


title: Decades-long elevation of interferon-alpha can initiate and drive Sjogren syndrome II

city: Bonn

first: Rayk

last: Behrendt

address: Venusberg-Campus 1

department: Institute for Clinical Chemistry and Clinical Pharmacology

institute: University Bonn

summary: Sjogren syndrome (SS) is a chronic inflammatory disease with no effective targeted treatments. There is a pressing need to identify targetable pathways which drive disease. Here we combine ultrasensitive detection of IFN-α with proteomic approaches in two cohorts including UK Biobank to demonstrate that IFN-α is elevated in the majority of individuals with SS, and this elevation can precede diagnosis by 15 years and persists for 30 years. We identify a distinct immunological phenotype associated with elevated IFN-α characterised by peripheral blood cytopenias, hypergammaglobulinaemia and SS-specific autoantibody formation. To address a causal role for chronic interferon elevation in initiating and driving these immunological features we created a novel model of systemic chronic IFN-α elevation upon overexpression of Ifna4 in conventional dendritic cells type 1 of mice. This model recapitulates the key IFN-α -associated features we identified in clinical studies and can be effectively treated by IFNAR1-blocking monoclonal antibodies. In summary chronically elevated IFN-α can initiate and drive immunopathological features of SS and represents a therapeutic target.

overall_design: Transcriptomic investigation of whole spleen in wild-type and Clec9a-Cre IFNa4KI mice.

first: Deborah

last: Forbes

first: Ivana

last: Jorgacevic

first: Kilian

last: Kleemann

first: Jessica

last: Tarn

first: David

last: Hunt

first: Fai

last: Ng


title: The effect of Sars CoV2 on 3d endometrial spheriods

first: Jakob

last: Admard

address: Calwerstr. 7

department: Institut für Medizinische Genetik und Angewandte Genomik

institute: Universitätsklinikum Tübingen

summary: Expression prolifing by high throughput sequencing

overall_design: Endometrial cancer (ishikawa) and benign endometrial stromal cells (HESCs) mRNA profiles of control (CN), control infected (CI), decidualised non infected (DN) and decidualisen infected (DI)  for 48h were generated by deep sequencing, in  quadruplicate using Illumina

first: M

last: Salker

first: Y

last: Singh

last: Camarena Sainz

first: J


title: Gene expression data to identify molecular characteristics of mucinous colorectal cancer

city: Daejeon

first: Jeewoo

last: Seo

address: 125, Gwahak-ro

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology, KRIBB

summary: Mucinous adenocarcinoma (MuC), a subtype of colorectal cancer (CRC), exhibits distinct molecular features and a poorer prognosis compared to non-mucinous CRC (NMuC). Standard CRC treatments often fail to address MuC's unique characteristics, especially in stage II, where the benefit of adjuvant chemotherapy is unclear. Biomarkers that improve risk assessment and guide personalized treatment are needed. Based on RNA-seq data and Cox regression models, we developed a signature reflecting the characteristics of MuC which showed a strong prediction ability and clinical utility in both MuC and NMuC. Our signature represents a valuable tool for predicting recurrence and guiding personalized treatment in CRC.

overall_design: RNA-seq data of 140 fresh frozen tissues of mucinous colorectal cancer tissues (n = 140) were generated. Total RNA was isolated by RNeasy Plus Mini Kit (Qiagen, CA, USA), following the manufacturer’s protocol. The quality and integrity of the RNA were confirmed by RNA Integrity Number (RIN) measurements, with only samples achieving RIN value > 8 were selected for further analysis. Sequencing library was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina, CA, USA) according to the provided protocol. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented and converted into cDNA. Then adapters were ligated and the fragments were amplified on a PCR. Sequencing was performed in paired end reads (100PE) using Novaseq 6000 platform (Illumina, CA, USA).

first: Jeong-Hwan

last: Kim

first: Ye-Jin

last: Ha

first: Jee-Woo

first: Seon-Kyu

first: Jong-Lyul

last: Lee

first: Seon-Young


title: Expression data from early zebrafish embryo

city: Saitama

first: Kyo

last: Yamasu

state: Saitama

address: 255 Shimo-Okubo, Sakura-ku

department: Division of Life Science

country: Japan

institute: Saitama University Graduate School of Science and Technology

summary:
Zebrafish pou5f3 regulates various developmental processes, including neurogenesis and brain formation.
We used microarrays to detail the global program of gene expression regulating isthmus development around the end of gastrulation. To this aim, we employed transgenic (Tg) embryos harboring a heat-inducible dominant-interference pou5f3 gene (en-pou5f3) that functionally suppresses pou5f3 (Tg(hsp-en-pou5f3)).

overall_design: en-pou5f3 was induced by heat shock in Tg embryos at 90% epiboly or 3-somite stage (3-ss). The transcriptomes were compared on Affymetrix microarrays to know the gene profiles specific to each developmental stage.

first: Yukiko

last: Nakayama


title: Myeloid-specific deficiency of ribosomal protein L13a alters macrophage polarity and diversity during differentiation from bone marrow

city: Cleveland

first: Peng

last: Jiang

address: 2399 Euclid Avenue, FH468

institute: Cleveland State University

summary: Macrophages show substantial plasticity, leading to a diverse population of these cells with different states of polarization during differentiation from bone marrow. However, the mechanistic insights into this process are not well understood. Here, we identified a novel role of ribosomal protein L13a previously shown to be engaged in the physiological control of inflammation regulating macrophage diversity and polarity. Using an ex-vivo differentiation model of bone marrow-derived macrophages (BMDM) from the control (L13aflox/flox) and myeloid-specific L13a KO (L13aflox/flox LysMCre+) mice (L13a-KO) we presented compelling evidence of the role of L13a in regulating macrophage polarization that goes beyond the M1-M2-based binary concept. We show that macrophages from L13a-KO mice lead to enhanced expression of classical markers of both M1 and M2 and surprising deviation from the expected response under known inducers of polarity. The phosphorylation-dependent activation of a number of signaling molecules played a role in this process. Bulk RNA and single-cell RNA sequencing of the BMDM from the L13a-KO mice show widespread change in overall gene expression and robust differences in the diverse populations of the bone marrow-derived cells from the control and KO mice. In addition, this study also shows a substantial increase of Th1 and Th2 signature genes in naïve CD4+ T cells isolated from the L13a-KO animals. Together, our studies provide new insights into the regulations of macrophage polarization by L13a-driven novel intermediate effectors or mediators.

overall_design: Bone marrow-derived macrophages (BMDM) were isolated from the femurs of control and L13a KO mice

first: Antara

last: Roy

first: Barsanjit

last: Mazumder


title: Damage sensing through TLR9 Promotes Viral Clearance and Recovery During Influenza Infection

city: NEW HAVEN

first: Yifan

last: Yuan

state: CT

address: 10 Amistad st, 314

institute: yale university school of medicine

summary: Toll-like receptor-9 is a pattern-recognition receptor that binds to the unmethylated CpG sequences in DNA. Its role in influenza infection is not well understood. Using mice deficient in TLR9, we demonstrated that these animals mounted a reduced inflammatory response during early infection on day 7, driven by the myeloid cells and associated cytokine responses. However, despite this diminished inflammation, TLR9-/- mice had increased viral burden on day 7 post-infection. To understand the cellular specificity and underlying mechanism of increased infection susceptibility in TLR9-/- mice, we performed single-cell RNA sequencing of lung tissues. scRNA sequencing data indicate that TLR9-/- immune cells, especially those of myeloid origin are highly susceptible to influenza infection. This susceptibility of TLR9-/- cells appeared to be independent of type I interferon signaling as the type I interferon pathway appeared the most upregulated pathway in TLR9-/- immune cells. We confirmed increased susceptibility of TLR9-/- myeloid cells using ex vivo murine alveolar macrophage and human peripheral blood monocyte cells. Despite the initial amelioration of the lung injury, the widespread infection of immune cells in TLR9-/- lungs upregulated both influenza and inflammatory responses in myeloid cells. This persistent inflammatory response manifested as the accumulation of both myeloid and lymphoid cells in the airways and increased injury markers in TLR9-/- on day 14. Elevated injury on day 14 delayed the weight loss recovery in TLR9-/- mice. Finally, we demonstrate elevated levels of TLR9 ligands during influenza infection in humans. These data demonstrate a key role of TLR9 in regulating host response to influenza infection.

first: Amy

last: Zhao

first: Lokesh

last: Sharma


title: Super-enhancer-driven CACNA2D2 is an EWSR1::WT1 signature gene encoding a diagnostic marker for desmoplastic small round cell tumor (DSRCT) [scRNA]

first: Thomas

last: Grunewald

summary: This dataset comprises single-cell RNA-sequencing data of two orthotopically xenografted desmoplastic small round cell tumor (DSRCT) cell lines (JN-DSRCT-1 and SK-DSRCT2) after posttranscriptional knockdown of EWSR1::WT1 fusion oncogene.

overall_design: Two desmoplastic small round cell tumor (DSRCT) cell lines were stably transduced with inducible shRNA expressing casettes targeting either the CDS (shWT1-CDS) or 3'-UTR (shWT1-UTR) of the EWSR1::WT1 fusion transcript. One million DSRCT cells harboring either shRNA against WT1-CDS or WT1-UTR were resuspended in PBS and mixed with Geltrex™ LDEV-Free, hESC-Qualified, Reduced Growth Factor Basement Membrane Matrix in 1:1 proportion, and slowly injected in the peritoneum of 10–12 weeks old NOD/scid/gamma (NSG) mice. Seven-weeks after injection, mice were randomized in two groups and they were treated with either 2 mg/ml doxycycline (DOX) dissolved in drinking water containing 5% sucrose to induce an in vivo knockdown of WT1 (DOX (+)), or 5% sucrose (control, DOX (−)) for 96h. At the experimental endpoint mice were sacrificed by cervical dislocation.

first: Florian

last: Geyer

first: Tobias

last: Faehling

last: Grünewald

first: Florencia

last: Cidre-Aranaz


title: FABP7 expression modulates the response of astrocyte to induced endotoxemia.

city: Madison

first: Marcelo

last: Vargas

state: WI

address: 600 Highland Avenue

institute: UW-Madison

summary: To investigate the effect of knocking down FABP7 expression in a mouse model of endotoxemia

overall_design: Differencial gene expression analysis of RNA-seq data from the cerebral cortex of shScramble-LPS and shFABP7-LPS  treated mice.


title: DMM inhibited obstruction-induced renal fibrosis by blunting inflammation and activating PPAR signaling

city: Quanzhou

first: wei

last: zhang

address: NO. 1028 Anji South Road, Fengze District

institute: quanzhou first hospital affiliated to fujian medical university

summary: To understand the roles and mechanisms of DMM in unilateral ureteral obstruction (UUO)-induced renal fibrosis, we performed RNA sequencing of UUO kidneys from mice treated with or without dimethyl malonate (DMM). DMM administration led to metabolic reprogramming in obstructed kidneys, the genes associated with the metabolism of fatty acid, organic acid, cellular amino acid, and mitochondrial function were significantly upregulated. Conversely, the downregulated genes in DMM-treated mice were involved in inflammation, including T cell immunity. Moreover, the upregulated genes in DMM-treated mice were associated with PPAR signaling. The RNA-seq analysis suggests that DMM activated PPAR and metabolic pathways while inhibited inflammatory signalings.

overall_design: Bulk RNA sequencing was performed in UUO kidneys from mice treated with or without DMM.

first: Wei

last: Zhang

first: Yuandong

last: Tao


title: Effects of high cholesterol diet on liver small RNA expression profile utilizing two different RNA-seq methods

city: Riverside

first: Xiuchun

last: Li

address: 900 University Avenue

institute: UCR

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: To  reveal the small RNA profiles in the liver using traitional and PANDORA-seq methods
Methods: 8 week old C57BL/6 male mice were fed a high cholesterol or low cholesterol diet for 4 weeks. Liver RNA was extracted by injecting Trizol into the aorta and collecting the flow through for further processing
Results: PANDORA-seq revealed an abundant amount of tsRNA and rsRNA that were undetected by traditional-seq. Importantly, PANDORA-seq revealed that many differentially regulated sncRNAs also undetected with traditional-seq

overall_design: Liver small RNA were sequenced from C57BL/6 male mice after 4 weeks of low cholesterol or high cholesterol feeding

first: Tong

last: Zhou

first: Changcheng


title: Gene expression profile at single cell level of pulmonary endarterectomy surgical specimens from chronic thromboembolic pulmonary hypertension (CTEPH)

city: Toronto

first: Hon-Sum

middle: Jeffrey

last: Man

state: ON

address: 209 Victoria Street

department: Medicine

country: Canada

institute: University of Toronto

summary: Endothelial cells are implicated in delayed thrombus resolution. We use single cell RNA sequencing of CTEPH surgical specimens to assess endothelial cell phenotypes that contribute to delayed thrombus resolution.

overall_design: Pulmonary endarterectomy specimens were collected from CTEPH patients who underwent pulmonary endarterectomy

middle: J

first: Yidan

first: Marc

last: de Perrot


title: Multi-omic Landscape of Extracellular Vesicles in Human Carotid Atherosclerotic Plaque Reveals Endothelial Communication Networks

first: Sneha

last: Raju

address: 101 College Street, PMCRT 3-309

summary: Background: Carotid atherosclerosis is a multifaceted disease orchestrated by a myriad of cell-cell communication that drives progression along a clinical continuum (asymptomatic to symptomatic). Extracellular vesicles (EVs) are lipid bilayer membrane-enclosed cell-derived nanoparticles that represent a new paradigm in cellular communication. Little is known about their biological cargo, cellular origin/destination, and functional roles in human atherosclerotic plaque.    Methods: EVs were enriched via size exclusion chromatography from human carotid endarterectomy samples dissected into plaque and marginal zones (n= 29 patients, paired plaque and marginal zone; symptomatic n=16, asymptomatic n=13), with further density gradient ultracentrifugation for proteomic analysis. EV cargoes were assessed via whole transcriptome miRNA sequencing and mass spectrometry-based proteomics. EV multi-omics were integrated with publicly available bulk and single cell RNA-sequencing (scRNA-seq) datasets to predict EV cellular origin and ligand-receptor interactions and multi-modal biological network integration of EV-cargo was completed. EV functional impact was assessed with endothelial angiogenesis assays.  Results: Human carotid plaques contained greater quantities of EVs than adjacent marginal zones. EV-miRNA and protein content was different in diseased plaque versus adjacent marginal zones, with differential functions in key atherogenic pathways. EV cellular origin analysis suggested that tissue EV signatures originated from endothelial cells (EC), smooth muscle cells (SMC), and immune cells. Furthermore, EV signatures from SMCs and immune cells were most enriched in the marginal and plaque zones, respectively. Integrated tissue vesiculomics and scRNA-seq indicated complex EV-vascular cell communication strategies that changed with disease progression and plaque vulnerability (symptomatic disease). Plaques from symptomatic patients, but not asymptomatic patients, were characterized by increased involvement of endothelial pathways and more complex ligand-receptor interactions, relative to their marginal zones. Plaque-EVs were predicted to mediate communication with ECs and together with pathway enrichment analysis delineated a strong endothelial signature with potential roles in angiogenesis and neovascularization – well-known indices of plaque instability. This was corroborated functionally, wherein human carotid symptomatic plaque EVs induced sprouting angiogenesis (number and length of sprouts) in comparison to their matched marginal zones.   Conclusion: Our findings indicate that EVs may drive dynamic changes in plaques through EV-vascular cell communication and effector functions that typify vulnerability to rupture, precipitating symptomatic disease. The discovery of endothelial-directed processes mediated by EVs creates new avenues for novel therapeutics in atherosclerosis.

overall_design: To understand the EV-miRNA transcriptome, we enriched EVs from carotid plaque and adjacent marginal zones. Whole transcriptome miRNA sequencing was completed using HTG sequencing technologies.

first: Kathryn

last: Howe


title: Divergent FOXA1 mutations drive prostate tumorigenesis or therapy-resistant intra-luminal plasticity [RNA-Seq]

city: Ann Arbor

first: Arul

last: Chinnaiyan

state: MI

address: 1500 East Medical Center Dr

department: MCTP

institute: University of Michigan

summary: FOXA1 is recurrently altered in hormone-driven malignancies, with activating hotspot mutations detected in 10-40% of primary prostate cancers based on ethnicity. Yet, the tumorigenic potential and pathobiology of FOXA1 remain unexplored in vivo. Here, we generated and characterized knock-in mouse models harboring FOXA1 mutant transgenes that represent distinct classes of activating mutations. Our findings reveal that FOXA1 class 1 mutations (i.e., wing 2 alterations) in a Trp53-null background, drive high-grade, invasive luminal adenocarcinoma with full penetrance by 40 weeks of age. These hyperproliferative lesions retain luminal characteristics, gain expression of NSD2, and regress upon androgen withdrawal—mirroring features of primary human prostate adenocarcinomas. Mechanistically, class 1 mutants aberrantly activate mTORC1/2 signaling and reprogram androgen receptor (AR) activity by expanding the enhancer landscape at non-canonical chimeric AR-half elements enriched in patient tumors. In contrast, FOXA1 class 2 mutations (i.e., C-terminal truncations) do not drive transformation but induce intra-luminal plasticity in androgen-intact normal tissues, which is otherwise triggered in response to castration. Class 2 mutants lead to a 10- to 20-fold expansion of Ar+/Ck8+ luminal epithelia expressing stem/progenitor markers such as Trop2, Ck4, and Psca. Mechanistically, class 2 mutants maintain AR activity while de-compacting over 40,000 new cis-regulatory elements bound by Klf5 and AP-1 transcription factors to activate stemness and WNT gene programs. Class 2-mutant-expressing prostate epithelial cells resist castration-induced atrophy, remain proliferative in androgen-deprived conditions, and form organoids and allografts at higher frequencies. Additionally, metastatic prostate tumors from patients harboring class 2 mutations show elevated KLF5 expression and stemness signatures. Collectively, our data establish FOXA1 as a critical oncogene in both primary and advanced AR-dependent prostate cancers, revealing its functional versatility in driving either tumor initiation or therapy resistance depending on the mutation class.

overall_design: Comparative DNA binding profiles of noted proteins in FOXA1 Class 1 and class 2 mouse prostate organoids.

first: Sanjana

last: Eyunni

first: Eleanor

last: Young

first: Yuping

first: Abhijit

last: Parolia


title: Decades-long elevation of interferon-alpha can initiate and drive Sjogren syndrome I

first: Rayk

last: Behrendt

overall_design: Transcriptomic investigation of whole spleen in anti_IFNAR1 and isotype treated Clec9a-Cre IFNa4KI mice.

first: Deborah

last: Forbes

first: Ivana

last: Jorgacevic

first: Kilian

last: Kleemann

first: Jessica

last: Tarn

first: David

last: Hunt

first: Fai

last: Ng


title: Single-cell transcriptomics predict novel potential regulators of acute epithelial restitution in the ischemia-injured intestine

first: Yuliya

last: Pylayeva-Gupta

state: North Carolina

address: 450 West Dr

institute: University of North Carolina at Chapel Hill

summary: This original research article outlines the successful isolation and characterization of the transcriptomic profile of post-ischemic restituting epithelial through a translational pig model.

overall_design: Superficial mucosal epithelial cells collected from recovering ischemic jejunum of juvenile pigs were processed for single cell RNA sequencing.

first: Elizabeth

middle: C

last: Rose

first: Jeremy

middle: M

last: Simon

first: Ismael

last: Martinez

first: Scott

middle: T

last: Magness

first: Jack

last: Odle

first: Anthony

last: Blikslager

first: Amanda

last: Ziegler


title: The RNA binding protein Bcas2 is necessary for antibody class switch in mammalian genomes

city: Beijing

first: changchang

last: cao

state: China

address: Datun, 15

institute: IBP

summary: In children, hyper-IgM syndrome type 1 (HIGM1) is a type of severe antibody disorder, the pathogenesis of which remains unclear. Here we report for the first time that breast cancer amplified sequence 2 (BCAS2), known as an RNA-binding protein, regulates the antibody class transition processes through alternative splicing (AS). Based on integrated analysis of the whole genome sequence and CLIP-seq data, we revealed that BCAS2 regulates AS through binding to the GAAGAA motif of target genes in B cells. Besides, BCAS2 can interact with SRSF7/DHX15 proteins and form spliceosomes that regulates AS and mRNA levels of target genes. In HIGM2 patients, BCAS2 affected the AS and expression of key target genes, and consequently the serum antibody levels. Collectively, the results in this study show that Bcas2 forms a complex with factors such as SRSF7 to regulate AS of key genes, thereby affecting the antibody production. The deletion or reduced expression of BCAS2 may lead to the HIGM2 phenotype. The present study reveals for the first time the pathogenesis of HIGM2, providing a potential molecular target for treatment of the disease.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: BCAS2 CLIP-seq was performed with naïve spenic B cells and LPS-activated B cells, and two biological replications were labeled as Rep1 and Rep2 respectively. Two biological repeats of mouse IgG CLIP-seq in LPS-activated B cells were labeled as Rep1 and Rep2. Meantime,  BCAS2 RNA-seq was performed with or without the depletion of BCAS2 in activated B cells. The RNA-seq of peripheral blood mononuclear cells from two healthy person and HIGM1 patients was also performed. Two biological replications were labeled as Rep1 and Rep2 respectively.

first: Yu

last: Chen

first: Siyuan

last: Sun

first: Changchang

last: Cao

first: Juan


title: Autophagy inhibition induced by EM-2 augments apoptosis via ROS-mediated ATM-Chk2-p53-p21 and MAPK pathway in lung and breast carcinoma

city: Shenzhen,Guangdong

first: Jinxia

last: Cheng

address: No.66,Gongchang Road,Guangming District

department: School of Medicine

institute: Sun Yat-sen University

summary: Lung cancer (LC) and breast cancer (BC) are two common malignant tumors with the highest incidence rate in men and women worldwide, respectively. As the treatment effect of currently available therapies for LC and BC is unsatisfied, searching for new therapeutic drugs has become an urgent need to be addressed. EM-2, a natural sesquiterpene lactone isolated from Elephantopus mollis H.B.K., has been previously documented to exert anti-tumor effects on many cancers. However, the underlying molecular mechanisms have not been clearly elucidated. Thus, in the present study, we further investigated the anticancer effect of EM-2 on LC and BC with focusing on the involved molecular mechanisms. Our results suggest that  EM-2 induces the impaired autophagy, which subsequently promotes ER stress-mediated apoptosis as well as ROS generation. ROS accumulation induced by EM-2 further simultaneously induces G2/M cell cycle arrest through ATM-Chk2-p53-p21 pathway and augments cell apoptosis via MAPK-mediated mitochondrial signaling pathway in LC and BC cells. These results may provide the experimental basis for future clinical application of EM-2 in the treatment for LC and BC.

overall_design:
To further uncover the molecular mechanism of EM-2's anti-cancer effect, transcriptome profiling by RNA sequencing (RNA-Seq) was conducted.
We separately treated A549 cell lines with DMSO and 6 μM EM-2 for 24 hours. We then extracted total RNA from A549 cells using TRIzol Reagent (Invitrogen Corporation) in accordance with the manufactuere's protocol.
RNA libraries for RNA-Seq were constructed using MGIEasy RNA library preparation kit as described in the manufacturer's protocol. RNA-Seq was then performed on BGISEQ-500 by Beijing Genomic Institution.

first: Jianwei

last: Jiang

first: Yuechun

last: Wang


title: Modified Y RNA-derived fragments form a complex with YBX1 and PARP1 to promote DNA repair

city: Oxford

first: Monika

last: Gullerova

address: S Parks Rd

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

summary: To protect genome integrity from pervasive threats of damage and prevent diseases like cancer, cells employ an integrated network of signalling pathways called the DNA damage response. These pathways involve both protein and RNA components which can act within the damaged cell or be transferred intercellularly to influence population-wide responses to damage. Here, we show that radioprotection can be conferred by damage-derived exosomes and is dependent on YBX1-packaged Y3-derived ysRNA. These ysRNA enter the nucleus of bystander cells upon DNA damage to become methylated by NSUN2. This allows interaction with YBX1 at double strand break (DSB) sites to promote efficient DNA repair and cell survival through complex formation with PARP1. YBX1 facilitates increased PARP1 auto-modification and ADP-ribosylation of ysRNA, promoting increased PARP1 residency at DSBs. We therefore highlight a new role for these under-studied species of small non-coding RNA in DNA repair.

overall_design: To investigate the importance of exosomal RNA in DNA Damage Response, we emplyed small RNA sequencing to quantify small RNA speces (< 200 nucleotides) in RNA isolated from exosomes emanatinf from irradiated cells.

first: Annabelle

last: Shaw

first: Kamal

last: Ajit


title: KPNA2 promotes osteosarcoma by regulating the alternative splicing of DDX3X mediated by YBX1

city: Wuhan

first: Li

state: Hubei

address: Hangkong Road 13, Wuhan, China

department: Wuhan Union Hospital

institute: Huazhong University of Science and Technology

summary: Osteosarcoma (OS) is a rapidly progressive primary malignant bone tumor that usually occurs in adolescents between 15 and 19 years old and adults over 60 years old. Over the past 20 years, limited progress has been made in neoadjuvant chemotherapy and surgery aimed at curing OS. It is well known that alternative splicing (AS) changes caused by abnormal splicing factors contribute to tumor progression. But at present, there is a lack of extensive and in-depth AS research on OS. Gene expression analysis and AS analysis were performed on the sequencing data of 44 patients with osteosarcoma in order to construct a co-expression network among RNA-binding proteins, AS events, and AS genes in the whole genome. The gain or loss of functional osteosarcoma cell model was made, and the osteosarcoma phenotype was proved by in vitro and in vivo experiments. Interactive network analysis and enrichment analysis were carried out to define the internal mechanism.We screened the RBP of Karyopherin Subunit Alpha 2 (KPNA2), which was highly expressed in osteosarcoma cells and negatively correlated with patient survival. KPNA2 transports splicing factor Y-box Binding Protein 1 (YBX1) into the nucleus and promotes the proliferation, migration, and invasion of osteosarcoma. Using RNA-seq, we comprehensively screened and identified multiple AS events affected by YBX1. Specifically, YBX1 accelerates the degradation of ATP-dependent RNA helicase DDX3X (DDX3X) through the Nonsense-mediated decay (NMD) pathway by promoting the intron retention of the DDX3X gene, thus reducing the level of DDX3X protein. The changes in DDX3X in OS will affect significant changes in cell cycle-related proteins, including p53, p21, and AKT1. The KPNA2/YBX1 axis can regulate the stability of DDX3X mRNA and then affect the progress of the cell cycle. YBX1 promotes the proliferation, migration, and invasion of osteosarcoma by regulating the AS event of DDX3X. KPNA2/YBX1 axis activation is an important factor driving abnormal AS in OS. Importantly, we demonstrated that therapeutic targeting of the KPNA2/YBX1/DDX3X axis can inhibit OS proliferation and disease progression. It integrates the AS control of DDX3X into the progression of OS and represents potential prognostic biomarkers and targets of OS therapy.

overall_design: We constructed a YBX1 knock down model in U2 OS and MNNG/HOS cell line by lentivirus, coupled with RNA-seq sequences, to comprehensively reveal the biological function of YBX1 in osteosarcoma cell lines and analyze the alterations of alternative splicing. overexpression.

first: Wei

last: Wu

first: Zengwu

last: Shao


title: Transcriptional Regulation by PHGDH Modulates Pathological Progression in a Human Brain Organoid Model of Late-Onset Alzheimer’s Disease

city: La Jolla

first: Sheng

last: Zhong

state: CA

address: 9500 Gilman Dr

institute: University of California, San Diego

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Phosphoglycerate Dehydrogenase (PHGDH), prominently expressed in brain astrocytes, exhibits heightened levels in the early stages of late-onset Alzheimer’s Disease (LOAD). We demonstrate that alterations in PHGDH expression within astrocytes in a human brain organoid model of LOAD induce pathological changes, independent of PHGDH’s canonical enzymatic role. Remarkably, PHGDH functions as a transcriptional regulator by binding to chromatin, as evidenced by ChIP-seq, snRNA-seq, knockdown, and mutation experiments. Our analysis identifies IKKa and HMGB1, regulators of NFκB and autophagy, as pivotal transcriptional targets of PHGDH. Dual knockdown of IKKa and HMGB1 in astrocytes effectively mitigates PHGDH-induced LOAD pathological changes in brain organoids, reducing Aβ aggregates, cell death, and NFκB activation while enhancing synaptic puncta and autophagy. These findings unveil a novel pathological pathway in LOAD, elucidating PHGDH’s role as a transcriptional regulator in disease progression.

overall_design: To explore PHGDH's role as a transcriptional regulator, we conducted PHGDH ChIP-seq and scRNA-seq analyses in brain organoids. Our samples included normal cultured organoids, serum-induced sporadic AD brain organoids, and sporadic AD brain organoids with astrocyte-specific PHGDH knockdown.

first: Junchen

first: Fatemeh

last: Hadi

first: Xingzhao

last: Wen

first: Pei

last: Lin

first: Riccardo

last: Calandrelli

first: John

last: Charles Richard

first: Xu


title: Temporal multi-omic profiling reveals chemoradiotherapy-specific dualistic metabolic rewiring that supports glioblastoma tumor recurrence (Bulk RNA-Seq)

city: Winnipeg

first: Tanveer

last: Sharif

state: MB

address: 727 McDermot Avenue

institute: University of Manitoba

summary: Tumor recurrence afflicts over 95% of glioblastoma (GBM) patients, contributing to the disease's high fatality rates. To unravel the molecular mechanisms behind post-therapy recurrence, we employed a clinically-relevant chemoradiotherapy model, studying the temporal molecular metabolic evolution of patient-derived GBM samples in vitro and in vivo. Leveraging unbiased multi-omics methods, including single-cell and bulk transcriptomics, untargeted metabolomics, and stable isotope tracing, we revealed a dynamic metabolic rewiring favoring one-way anaplerotic pyruvate metabolism via carboxylation across GBM samples. This conserved adaptation, confirmed in independent datasets, resulted in reduced glucose-derived acetyl-coA production, hindering histone acetylation and silencing neural-differentiation genes NEUROD1 and DCX. Pharmacological intervention targeting this metabolic shift reduced recurrent GBM cell aggressiveness, prolonging survival in preclinical GBM xenograft tumors treated with chemoradiotherapy. These findings illuminate a potential metabolic therapeutic avenue to enhance current strategies, addressing disease recurrence and offering much-needed improvements in survival outcomes for GBM patients suffering from this dismal disease.

overall_design: GBM cells received 25 µM of temozolomide and controls received equal volumes of DMSO vehicle. Immediately following TMZ treatment, cells were exposed to 1 Gy of X-ray irradiation using the Rad Source 2000 and incubated at 37°C in a 5% CO2 incubator for 1 hour. To mimic the exposure time of chemotherapy received by patients, where the half-life of TMZ is approximately 1-2 hours in circulation, the drug treatment was washed out of the patient-derived GBM cells after 1 hour and replaced with fresh media. The concurrent chemoradiotherapy treatment regimen was repeated daily for 5 consecutive days. After the 5th treatment day, patient-derived GBM cells received a 2-day treatment holiday prior to collection and subsequent analysis. Chemoradiotherapy naive or TMZRT-resistant GBM cells received 100 µM of UK-5099 or equal volumes of DMSO vehicle. Total RNA samples were submitted for Next Generation sequencing at the UBC Sequencing + Bioinformatics Consortium, Vancouver, BC.

first: Sharif

last: Tanveer


title: Evalation of Vitamin D and Doxercalciferol Effect on Uterine Fibroid Growth

city: Valencia

first: Ana

last: Corachán

state: València

address: Avenida Fernando Abril Martorell, 106, torreA, Planta 7

country: Spain

institute: Universidad de Valencia - IVI Foundation

summary: Uterine fibroids (UF) are the most common pelvic tumor in women of reproductive age. Despite its high prevalence, there is an unmet need in the field for a non-hormonal fertility-friendly anti-fibroid treatment. Vitamin D deficiency has been linked to a higher risk of UF, and its efficiency as a treatment to reduce UF size has been demonstrated in vitro and in vivo. However, long-term vitamin d treatments could induce hypercalcemia, and vitamin D analogs have been proposed as an alternative since they show less calcemic activity. Our study aims to describe the signaling pathways and molecular mechanisms by which Vitamin D (VD3) and Doxercalciferol (a Vitamin D analog) (DCL) reduces UF size in a UF patient-derived xenograft (PDX).

overall_design: MED12-mutant human uterine fibroids (UF) were collected from African American women undergoing hysterectomy or myomectomy for symptomatic UF (n=10). Female NOD-SCID mice (n=14) were used to generate the PDX mouse model. Mice were hormonally supplemented with 60-day release pellets with 17ß-estradiol (0.2 mg) and progesterone (50 mg). One week after the xenograft surgery, animals were treated for 6 weeks with the bioactive form of Vitamin D3 (VD3), 1α,25(OH)2D3 and the synthetic Vitamin D2 analog Doxercalciferol (DCL). According to the treatment two different studies were conducted: 1) VD3 0.5 µg/kg/day (n=3) and 2) DCL 0.3 µg/kg/day (n=4). Each study had her own control group, in which animals were treated with the corresponding drug vehicle. At the end of the treatment, animals were euthanized and UF xenografts were collected. Each study had her own control group, in which animals were treated with the corresponding drug vehicle.

first: Maria

middle: V

last: Bariani

first: Mohamed

last: Ali

first: Qiwei

last: Yang

first: Hortensia

last: Ferrero

first: Ayman

last: Al-Hendy


title: Temporal multi-omic profiling reveals chemoradiotherapy-specific dualistic metabolic rewiring that supports glioblastoma tumor recurrence (scRNA-Seq)

overall_design: GBM cells received 25 µM of temozolomide and controls received equal volumes of DMSO vehicle. Immediately following TMZ treatment, cells were exposed to 1 Gy of X-ray irradiation using the Rad Source 2000 and incubated at 37°C in a 5% CO2 incubator for 1 hour. To mimic the exposure time of chemotherapy received by patients, where the half-life of TMZ is approximately 1-2 hours in circulation, the drug treatment was washed out of the patient-derived GBM cells after 1 hour and replaced with fresh media. The concurrent chemoradiotherapy treatment regimen was repeated daily for 5 consecutive days. After the 5th treatment day, patient-derived GBM cells received a 2-day treatment holiday prior to collection and subsequent analysis. At days 0 (Naïve), 1, 3, 5, and 7 (Resistant), during this treatment protocol, samples were collected and living persisting cell populations were isolated by eliminating dead cells through magnetic bead sorting. Cellular populations consisting of living single cells were submitted for Single cell 3’ RNA-Seq using 10X Genomics Chromium (10X Genomics) and Illumina next generation sequencing technologies (Illumina Nextseq 500 Sequencer).


title: Notch3 Directs a Regulatory T Cells-Microglia axis to Promote Autoimmune Neuroinflammation

city: Boston

first: KLaus

last: Schmitz-Abe

state: MA

address: 300 Longwood Avenue

department: Asthma, Allergy and Immunology

institute: Children's Hospital Boston

summary: Deciphering the mechanisms that promote central nervous system inflammation in multiple sclerosis is critical for developing precision therapies. We show that a specific regulatory T (Treg) cell subpopulation expressing Notch3 was increased in the peripheral blood and cerebrospinal fluid of individuals with multiple sclerosis (MS) and in the central nervous system (CNS) of mice with experimental autoimmune encephalomyelitis (EAE). Notch3 expression was upregulated by mechanisms involving the gut microbiota and Treg cell-specific toll-like receptor (TLR) signaling to promote EAE severity. Notch3 interaction with delta-like ligand 1 (DLL1) on microglia subverted Treg cells into T helper 17 (Th17) cells by Hippo pathway-dependent mechanisms while also inducing an inflammatory microglial response. Its deletion inhibited EAE by preventing Treg cell destabilization into Th17 cells while simultaneously promoting the expansion of a novel brain-protective neuropeptide receptor 1 (NPY1R)+ Treg cell population that suppressed pathogenic IFN+ and GM-CSF+ effector T cells. Our studies thus identify Notch3-mediated immune tolerance subversion as a fundamental mechanism that licenses autoimmune neuroinflammation.

overall_design: Treg cell and microglia were cell sorted from CNS of Foxp3YFPCRE and Foxp3YFPCre Notch3Fl/FL mice post EAE induction

first: Mehdi

last: Benamar

first: Klaus

first: Talal

middle: A

last: Chatila


title: Temporal multi-omic profiling reveals chemoradiotherapy-specific dualistic metabolic rewiring that supports glioblastoma tumor recurrence

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

overall_design: Refer to individual Series


title: The bovine oviductal environment and composition are negatively affected by elevated body energy reserves

city: Québec

first: Ricardo

middle: Perecin

last: Nociti

state: Québec

address: 2425, Rue de l'Agriculture

department: Animal Science

institute: Université Laval

summary: To analyze the effects of high body energy reserve (BER) within the oviductal environment and its composition, Nellore cows were fed two different nutritional plans to obtain animals with moderate BER (MBER) and high BER (HBER). After obtaining the groups with different BERs, all animals were subjected to oestrus synchronization and artificial insemination, and 120 hours after ovulation induction, the cows were slaughtered, the reproductive tract was removed, and the ipsilateral oviduct to the corpus luteum was collected and dissected. Analyses were performed only for animals that had an 8-cell embryo in the isthmus. After embryo identification, we evaluated the molecular profiles of extracellular vesicles from oviductal flushing (OF-EVs) and luminal epithelial cells (OV-Cell) and performed histomorphological analysis of oviductal tissue from the ampullary and isthmic oviductal regions. The HBER group presented higher concentrations of ampullary extracellular vesicles (AMP-EVs) and larger sizers of isthmic extracellular vesicles (IST-EVs). The miRNA profile of AMP-EVs showed that the differentially expressed miRNAs were predicted to regulate pathways associated with cell growth, migration, differentiation and metabolism, with the HBER group being more susceptible to insulin modulation. The MBER animals showed greater ampullary vascularization than the HBER animals did. Additionally, the miRNA profile and differential gene expression (DEG) data obtained for ampullary (AMP-Cell) and isthmic (IST-Cell) luminal epithelial cells revealed pathways related to insulin metabolism. Thus, elevated BER may lead to oviductal insulin resistance, affecting normal functioning and, probably, embryo metabolism during early development, thus impacting gestational rates in these animals.

overall_design: Nellore cows (n=21) were randomly divided into two experimental groups and subjected to two different nutritional plans: moderate (n=9) or high (n=12) body energy reserve (BER), as previously described by Bastos et al. Upon slaughter the reproductive tract was removed and immediately transported to the laboratory. Briefly, the ipsilateral oviducts to the corpus luteum were collected and dissected, and the oviductal portions of the ampulla and isthmus were separated through the ampullary-isthmic junction before oviductal flushing. The cows from MBER and HBER that presented an 8-cell embryo within the flushing had their ampulla and isthmus used for RNA-seq.

first: Natália

last: Bastos

middle: P

first: Juliano

last: da Silveira


title: Trajectory analysis reveals an uncommitted neuroblastic state in MYCN-driven neuroblastoma development

city: Nagoya

first: Shoma

last: Tsubota

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Department of Molecular Biology

institute: Nagoya University Graduate School of Medicine

summary: We analyzed the transcriptomic features of spontaneous regression in pre-cancerous neuroblasts using Th-MYCN mice, an animal model that closely resembles human neuroblastoma. Single-cell transcriptomic analysis of ganglion tissues from Th-MYCN mice was conducted to elucidate the cellular and molecular underpinnings. Trajectory analysis of pre-cancerous neuroblasts revealed a distinct subtype we designated as "uncommitted" cells, characterized by the expression of neuronal genes, indicative of a semi-differentiated state. Samples with predicted failed tumorigenesis had a greater proportion of these uncommitted cells, hinting at their association with spontaneous regression.

overall_design: To investigate the cellular and molecular mechanisms underlying the fate determination of neuroblastoma cells in Th-MYCN+/-mice, we performed scRNA-seq of SMG tissues from 3-week-old wild-type (WT, n = 1), 3-week-old Th-MYCN+/- (n = 10), and 6-week-old Th-MYCN+/- mice (n = 1)

first: Daniel

middle: R

last: Carter

first: Janith

last: Seneviratne


title: Provoking the Immunotherapy Efficacy of Renal Medullary Carcinoma

city: Houston

first: Haoqiang

last: Ying

state: Texas

address: 1515 Holcombe Blvd

institute: M. D. Anderson Cancer Center


title: Addressing human astrogliosis in a human iPSC-derived 3D CNS model

city: Oeiras

first: Catarina

middle: Monteiro

last: Gomes

state: Lisboa

address: Av. República, Qta. do Marquês

country: Portugal

institute: iBET

summary: Astrogliosis is an inflammatory process by which astrocytes undergo morphological, transcriptional, and functional changes that primarily contribute to tissue healing and restore CNS homeostasis as a response to neuroinflammation. However, excessive astrocyte activation causes neuronal death, immune cell activation and infiltration, and chronic neuroinflammation. The advent of human induced pluripotent stem cell (hiPSC)-derived three-dimensional (3D) models has aided research of complex CNS processes by generating complex structures of neural cells able to decode the molecular mechanisms that trigger and sustain astrocyte activation and drive microenvironment remodeling in the human CNS. Despite depicting interactions between different brain cell types and their microenvironment, the lack of reproducibility, and immature/activated cell phenotypes typical of these models limit their utility to address neuroinflammation mechanisms. Here we establish a hiPSC-derived model of neuroinflammation to dissect cellular crosstalk along the neuroinflammatory axis. A methodology pioneered by our team was used, in which hiPSC-derived neural progenitors were cultured in perfusion stirred-tank bioreactors and differentiated into 3D neurospheroids composed of neurons, astrocytes, and oligodendrocytes. This model recapitulates specific features of the brain microenvironment, such as human brain-like ECM deposition and neuron-glia functional interactions. The neurospheroids were challenged with prototypical inflammatory factors reported to induce activation of astrocytes in mice models, namely TNF-α, IL-α, and C1q. By performing whole transcriptome analysis (RNAseq), we observed an upregulation of several inflammatory-related genes associated with TNF and NF-kB signaling (e.g., CXCL5, CCL2, TNAIP3, and NFKB2). Whole proteome analysis (SWATH-MS) also depicted the enrichment of proteins involved in cell response to stress and cytokine regulation, namely TXLNA, DCTN5, and NOLC1. Concomitantly, time course analysis of conditioned media from the stimulated neurospheroids exhibited increased secretion of inflammation-related cytokines (e.g., CCL2, CXCL10, IL-6, and IL-8). Astrocytes in challenged neurospheroids displayed an impaired capacity for clearance of extracellular glutamate and secretion of glutamine compared to the unstimulated control, indicating functional impairment and known molecular effects of TNF signaling. Together, these results further demonstrate astrocyte functionality within the neurospheroids, which undergo canonical astrogliosis events that are considered hallmarks of neuroinflammation. The human neurospheroid model described may contribute to better understand the mechanisms governing human astrogliosis and be used as a platform to study glial-neuron mature interactions during acute stimulation and inflammation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for quiescent and activated hiPSC-derived astrocytes from four independent experiments

first: Carolina

last: Gonçalves

first: Beatriz

last: Painho

first: Gabriela

last: Silva

first: Paula

last: Alves

last: Brito

last: Simão


title: Changes in gene expression in L-02 cells after treatment with PBAT material

city: Guangzhou City

first: congying

last: chen

state: Guangdong Province

address: Tianhe District

department: COLLEGE OF FOOD SCIENCE

institute: South China Agricultural University

summary: We report the application of sequencing technology based on the reference transcriptome in L-02 cells. After using Cutadapt to filter out unqualified sequences (sequencing junctions, low quality sequences, etc.) from the raw data to obtain valid data (Clean Data), a reference genome alignment was performed using Hisat2. Based on the Hisat2 alignment results, transcripts were reconstructed using Stringtie and the expression levels of all genes in each sample were calculated. We found multiple down- and up-regulated genes in L-02 cells of the PBATc treatment group.  Cluster heat maps were used to demonstrate differential gene expression patterns, and GO and KEGG pathway enrichment analyses were performed for differentially expressed genes. The results of GO functional annotation analysis showed that the largest number of differential genes were localized in biological processes, mainly including signal transduction, regulation of transcription and DNA-templated. In terms of cellular components, differential genes were mainly concentrated in In terms of cellular components, the differential genes are mainly in membrane, cytoplasm and nucleus, and the common Molecular Functions are protein binding, metal ion binding and DNA binding.  The results of KEGG pathway analysis showed that there were differential genes in AMPK and mTOR pathways. Among them, AMPK, mTOR, SIRT1 and PGC-1α protein expression levels were down-regulated. Based on the above results, we examined each pathway protein.  This study provides a strong reference for detecting the mechanism of cell damage after PBAT material treatment study.

overall_design: Examination of differential gene expression in L-02 cells in PBAT material treatment versus control.

first: Congying

last: Chen


title: Epigenetic Reactivation of CNS Endothelial Developmental Programs Triggers Adult Brain Angiogenesis, Promotes Post-Stroke Revascularization and Neuroregeneration.

status: Public on Jul 01 2025

first: Peeyush Kumar

last: Thankamani Pandit

state: TEXAS

address: 6431 Fannin St,

department: Neurosurgery

institute: University of Texas Health Science Center Houston

summary: We identified the role of brain endothelial cell Hdac2 and Ezh2 mediated epigenetic mechanism in maintaining blood brain barrier in adult mice. Also, we we studied the impact of reactivation of brain endothelial cell Wnt/β-catenin signaling in adult mice.We evaluated derepression of Hdac2 mediated epigenetic mechanism in imice model of schemic stroke.

overall_design: Ultra-low mRNA sequencing of FACS sorted CD31+ve/CD41-ve/CD45-ve adult mice brain cortical endothelial cells isolated from WT, Hdac2 ECKO, Ezh2 ECKO and β-catenin GOF mice. For endothelial specific deletion of Hdac2 and Ezh2, or β-catenin constitutive activation, Hdac2lox/lox:Cdh5CreERT2, Ezh2lox/lox:Cdh5CreERT2 and Ctnnb1lox/lox:Cdh5CreERT2 mice were  treated with five doses of Tamoxifen (75mg/Kg body weight) and brains were harvested after 2 months.

first: Peeyush

last: Kumar

first: Sithara

last: Thomas


title: Micro RNA expression in rodent skeletal muscle mitochondria

city: Burwood

first: Jessica

last: Silver

address: 221 Burwood Highway

country: Australia

institute: Deakin University

summary: MiRNAs are non-coding RNAs that regulate gene expression. MiRNAs mostly localise within the cytosol but are also found in the mitochondria where they can regulate the expression of mitochondrial-encoded transcripts. Aberrant miRNA expression is linked to mitochondrial dysfunction in chronic metabolic conditions. However, the role of miRNAs in the regulation of mitochondrial function in healthy tissue, such as in response to endurance exercise training, is not known. The aim of this study was to use a small RNA library preparation approach to profile the entire population of miRNAs in rat skeletal muscle mitochondria and investigate if mitochondrial miRNA expression was altered following4 weeks of endurance training

overall_design: Male Wistar-Kyoto (WKY) rats were obtained from the Australian Resource Centre (Murdoch, WA, Australia) at 4 weeks of age. At 5 weeks of age, the rats were randomly allocated to one of two groups: sedentary (n=12) or endurance trained (n=13). The endurance training protocol consisted of treadmill running 5 days per week for 4-weeks. Sedentary rats were handled identically and were placed on a stationary treadmill for the same amount of time as their trained counterparts during the 4-week training protocol.

first: Stella

last: Loke

first: Larry

last: Croft

first: Adam

last: Trewin

first: Danielle

last: Hiam

first: Severine

last: Lamon

first: Glenn

last: Wadley


title: Priming adult human hepatocytes as organoids for liver tissue engineering

city: Seattle

first: Kelly

last: Stevens

state: WA

address: 850 Republican St

department: Bioengineering

institute: University of Washington

summary: While human hepatocytes in the adult liver perform hundreds of life-sustaining functions, culture methods to support their phenotype and function in vitro remain elusive.  Here, we describe establishment of an organoid culture system for adult human hepatocytes and demonstrate its robustness by generating organoids from eight different adult donors. Organoids accurately model the phenotype and morphology of hepatocytes in the adult liver, express a mature liver transcriptome distinct from fetal hepatocytes, and exhibit mature functions such as inducible cytochrome activity. Finally, hepatocyte organoids efficiently engraft in vivo in engineered tissues, exhibiting up to 25-fold greater functionality after engraftment compared to previous adult hepatocyte models. Furthermore, organoids negate the need for inclusion of exogenous non-parenchymal cells in engineered tissues to support engraftment, an important translational milestone. These results demonstrate the potential of adult human hepatocyte organoids for basic and translational applications such as pharmaceutical screening and hepatic regenerative medicine.

overall_design:
Adult human hepatocytes organoids were grown, digested to single cells after 5 or 15 days of growth, and analyzed using scRNAseq.
-----------------------------------------
Authors state "Unfortunately the raw data files were lost when our server crashed recently."

first: Sarah

last: Saxton

first: Tara

middle: N

last: McCray


title: Identifying Macrophage-specific L13a Knockout Transcriptomic Signatures

city: Cleveland

first: Peng

last: Jiang

address: 2399 Euclid Avenue, FH468

institute: Cleveland State University

summary: The goal of this study is to identify Macrophage-specific L13a Knockout Transcriptomic Signatures. We treated Macrophages (L13a KO and WT) with M1/M2 cytokines , and identified L13a KO specific transcriptomic changes.

overall_design: WT and L13a knockout samples

first: Antara

last: Roy

first: Narsanjit

last: Mazumder


title: c-Jun binding profile in Cal-33 cells

city: papagou, athens

first: THEODOROS

last: RAMPIAS

state: N/A = Not Appli

address: 4 SORANOU EPHESIOU STR, PAPAGOU, BRFAA

department: Systems Biology

country: Greece

institute: Biomedical research foundation Academy of Athens

summary: ChIP-seq profilling was conducted in order to identify DNA repair factors that are transcriptionaly regulated by cJun

overall_design: Chromatin was prepared from Cal-33 cells with the SimpleChIP® Enzymatic Chromatin IP Kit (Cell Signaling, #9003) according to the manufacturer's instructions. The cJun -ChIPed DNA fragments were sequenced in NextSeq 500.

first: Theodoros

last: Rampias

first: Lorena

last: Hoxhallari

first: Marios

last: Agelopoulos

first: Marialena

last: Pouliou


title: KLF5 controls subtype-independent highly interactive enhancers in pancreatic cancer to regulate cell survival [RNA-Seq]

city: Stuttgart

first: Steven

last: Johnsen

address: Auerbachstrasse 112

institute: Robert Bosch Center for Tumor Diseases

summary: Pancreatic ductal adenocarcinoma (PDAC) remains a highly lethal cancer with a 5-year survival rate of 13%. Despite recent molecular stratification of tumors into distinct classical and basal-like cell states, most tumors are heterogeneous contain of both subtypes. Therefore, therapeutic approaches targeting one subtype may not be suitable for PDAC therapy. Here, we integrated chromatin accessibility (ATAC-seq), genome-wide occupancy (ChIP-seq) for epigenetic status (H3K27ac) and H3K4me3-anchored chromatin topology (HiChIP) to uncover subtype-independent highly interactive enhancers that interact with essential genes in PDAC. Motif analysis revealed these common enhancers were bound by KLF5 with subsequent depletion leading to decreased cell viability via induction of apoptosis. To elucidate the transcriptional and epigenetic mechanisms by which KLF5 functions in PDAC, we employed rapid depletion of KLF5 with dTAG technology and profiled the effects on the open and active chromatin landscape and transcription with nascent RNA and mRNA-seq over time. Enhancer inactivation via KRAB domain Zim3-dCas9 fusion protein confirmed KLF5-bound enhancers regulate target genes, including the anti-apoptotic gene BCL2L1. Multiplex immunofluorescence confirmed co-staining of KLF5 and Bcl-xL in patient samples and overexpression of Bcl-xL rescued the induction of apoptosis after KLF5 depletion. Taken together, this study provides new insights into common mechanisms to target highly heterogeneous PDAC tumors.

overall_design: To investigate KLF5-dependent mechanisms of cell survival in pancreatic cancer, we performed RNAseq after dTAG treatment in clonal L36pl cells with endogenous knockin of GFP-FKBP12 into the KLF5 locus.

first: Thomas

last: Ekstrom


title: KLF5 controls subtype-independent highly interactive enhancers in pancreatic cancer to regulate cell survival [ChIP-Seq]

overall_design: To investigate KLF5-dependent mechanisms of cell survival in pancreatic cancer, we performed ChIPseq after dTAG treatment in clonal L36pl cells with endogenous knockin of GFP-FKBP12 into the KLF5 locus.


title: The role of endothelial Zeb2 in the progression of non-alcoholic fatty liver disease

city: Rotterdam

first: Eskeatnaf

last: Mulugeta

address: Wytemaweg 80

department: Cell Biology

country: Netherlands

institute: Erasmus University Medical Center Rotterdam (Erasmus MC)

summary: Zinc-Finger E-Box-binding Homeobox (Zeb)2 has an anti-angiogenic and anti-fibrotic role in liver endothelial cells, but its role in non-alcoholic fatty liver disease remains unknown. We performed RNA sequencing on endothelial cells sorted from wild-type mice and mice lacking Zeb2 specifically in endothelial cells kept on a western or standard diet to identify RNA expression changes and gene ontology terms affected by knock-out of endothelial Zeb2, western diet challenge, or the combination of both challenges.

overall_design: Endothelial cells were isolated by density centrifugation and FACS from livers of wild-type and endothelial-specific Zeb2 knock-out mice (n=6 per group) kept on regular chow or challenged by a western diet.  RNA was isolated using Reliaprep (Promega) and was sequenced according to the Smart-seq2 method.

first: Wouter

last: Dheedene

first: Aernout

last: Luttun


title: KLF5 controls subtype-independent highly interactive enhancers in pancreatic cancer to regulate cell survival [ATAC-seq]

overall_design: To investigate KLF5-dependent mechanisms of cell survival in pancreatic cancer, we performed ATACseq after dTAG treatment in clonal L36pl cells with endogenous knockin of GFP-FKBP12 into the KLF5 locus.


title: Next Generation Sequencing Facilitates Quantitative Analysis of Hypertrophic Cardiomyopathy/Healthy control Left Ventricular Transcriptomes

city: Guangzhou

first: Rui

last: Wang

address: 2rd ZhongShan Road

institute: Guangdong Provincial Hospital

summary: In the present study, we performed the whole transcriptome resequencing in left ventricular samples from HCM patients and healthy controls. Quantitative real-time PCR (qRT-PCR) was used to validate circRNA expression. By analysing the differentially expressed circRNAs and mRNAs, we constructed the ceRNA networks based on ceRNA theory. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed of target mRNAs of differentially expressed circRNA.

overall_design: Left ventricular circRNA and mRNA profiles of hypertrophic cardiomyopathy patients and healthy controls

first: Cheng

last: Huang


title: Provoking the Immunotherapy Efficacy of Renal Medullary Carcinoma [RNA-seq II]

first: Haoqiang

last: Ying

summary: Renal medullary carcinoma (RMC) predominantly afflicts young individuals of African descent harboring sickle hemoglobinopathies such as sickle cell disease (SCD) or sickle cell anemia (SCA).  RMC is refractory to targeted and immune therapy strategies used for other renal cell carcinomas. We have demonstrated that RMC is resistant to immune checkpoint inhibition despite harboring an inflamed tumor immune microenvironment. Hence, novel therapeutic strategies are urgently needed to reverse this resistance. We discovered that CD8+ T cells under SCD condition exhibit altered genomic architecture and ferroptosis, which significantly impairs the anti-tumor immunity of effector T cells. These observations may underscore a fundamental mechanism behind the distinct resistance of RMC resistance to immune checkpoint therapies. By leveraging the use of both mouse SCD model and humanized mice phenotypically representing SCD/SCA, as well as primary CD8+ T cells isolated from patients with SCA, we identified that the SLC7A11 gene is transcriptionally downregulated in the CD8+ T cells of SCA donors via genomic architecture alteration. The reduced expression of SLC7A11 partially accounts for the ferroptosis observed in the CD8+ T cells of SCD disease, via impairing the cystine transportation and synthesis of Glutathione (GSH).  Our findings also demonstrated that treatment using a hydrogen sulfide slow-releasing donor restored the expression of SLC7A11, antagonized the ferroptosis of CD8+ T cells under SCD/SDA condition and restored anti-tumor immunity in vivo. Hence, our research findings provide novel mechanistic insights into SCD and RMC and pave the way to develop innovative therapeutic strategies to sensitize RMC to immune therapies.

overall_design: MSRT1 cell line were used in a mouse model to generate renal carcinomas under different treatment conditions (vehicle vs GYY, IgG vs PD1) and total RNA were extracted for sequencing

first: Zilong

last: Zhao

first: Benxia

last: Hu

first: Yalan

last: Deng

first: Melinda

last: Soeung

first: Jun

last: Yao

first: Tina

middle: K

last: Nguyen

first: Yaohua

last: Zhang

first: Zhou

first: Jian

last: Gao

first: Shuang

last: Peng

first: Bora

last: Lim

first: Linghua

first: Qing

first: Li

last: Ma

first: Leng

last: Han

first: Dihua

last: Yu

first: Michael

last: Curran

first: Giannicola

last: Genovese

first: Boyi

last: Gan

first: Wenbo

last: Li

first: Palvos

last: Msaouel

first: Liuqing

last: Yang

first: Chunru

last: Lin


title: KLF5 controls subtype-independent highly interactive enhancers in pancreatic cancer to regulate cell survival [EU-RNAseq]

first: Steven

last: Johnsen

overall_design: To investigate KLF5-dependent mechanisms of cell survival in pancreatic cancer, we performed EU-based nascent RNAseq after dTAG treatment in clonal L36pl cells with endogenous knockin of GFP-FKBP12 into the KLF5 locus.

first: Thomas

middle: L

last: Ekstrom


title: p63 and its co-binding factor Znf148 cooperate to control squamous cell carcinoma proliferation

city: Rome

first: Giacomo

last: Corleone

address: via chianesi 43

country: Italy

institute: IRCCS Regina Elena National Cancer Institute

summary: Head and neck squamous cell carcinoma (HNSCC) are common and aggressive malignancies, and little progress has been made in improving outcomes for patients. HNSCC exhibit frequent overexpression of the p53-related transcription factor TP63. Here, we show that ZNF148 is an important partner in p63-driven tumorigenesis. Mechanistically, while ZNF148 alone binds CCND1 gene promoter, the p63-ZNF148 complex co-binds a CCND1 upstream enhancer leading to an enhancer-derived RNAs (eRNA3) acting as cis-regulatory elements for CCND1 transcription. The eRNA3 p63/ZNF148-dependent transcription is required to support high-rate proliferation in HNSCC. Interestingly, p63/ZNF148, eRNA3 and cyclin D1 expression is highly co-correlated in primary HNSCC, including laryngeal squamous cell carcinoma (LSCC). Their co-expression correlated to tumor stage and lymph nodes positivity. These results revealed a strong cooperation of the two transcription factors, p63 and ZNF148, as HNSCC oncogenic drivers.  Altogether, these findings provide a framework to facilitate categorization of HNSCC sub-types, prognostic/diagnostic biomarkers, and a foundation for development of new therapies.

overall_design: ChIP-seq

first: Rosalba

last: Pecorari

first: Mara

last: Mancini

first: Artem

last: Smirnov

first: Flavia

last: Novelli

first: Anna

last: Lena

first: Michele

last: Caraglia

first: Alessandro

last: Mauriello

first: Maurizio

last: Fanciulli

first: Gerry

last: Melino

first: Eleonora

last: Candi


title: Targeting LINC01711 in FAP+ cancer-associated fibroblasts in lung adenocarcinoma

city: nanjing

first: Qinglin

last: Wang

state: jiangsu

address: Jiangsu Cancer Hospital

institute: Jiangsu Cancer Hospital

summary: The limited response rate to immune checkpoint inhibitors (ICIs) remains a significant challenge in the treatment of lung adenocarcinoma (LUAD). In our study, we identified a lactate-based chemical barrier surrounding FAP+ cancer-associated fibroblasts (CAFs) within the LUAD microenvironment (TME), which may hinder the infiltration and function of CD8+ T cells. Further investigation revealed that FAP+ CAFs specifically overexpress LINC01711. Hence, we performed RNA-seq in FAP+ CAFs, FAP- CAFs and FAP+ CAFs-siLINC01711, FAP+ CAFs-siNC cells.

overall_design: Hence, we performed RNA-seq in FAP+ CAFs vs. FAP- CAFs and FAP+ CAFs-siLINC01711 vs. FAP+ CAFs-siNC cells.

first: Rong

last: Yin


title: Cell-intrinsic Tim-3 is Required for Optimal CD8 Response to Acute LCMV Infection

city: Pittsburgh

first: Lawrence

middle: P.

last: Kane

state: PA

address: 5051 Centre Ave.

department: Immunology

institute: University of Pittsburgh

summary: Tim-3, or transmembrane immunoglobulin and mucin domain-3, is a type I membrane protein expressed by various immune cell types and which is best known as a negative regulator of anti-tumor immunity. However, Tim-3 also has a co-stimulatory role in T cells under some conditions, via enhancement of PI3K signaling. We hypothesize that Tim-3 signaling enhances CD8+ T cell activation during acute infection and contributes to enhanced CD8+ effector function. To test this hypothesis, we used LCMV-specific TCR transgenic (P14) mice expressing a truncated, non-signaling, allele of Tim-3 or CD8-specific deletion of Tim-3. CD8+ T cell effectors were analyzed by flow cytometry after acute infection with LCMV Armstrong. At the effector stage, endogenous Tim-3+ T cells had increased expression of effector CD8 markers, compared with Tim-3 negative cells. Tim-3 knockout mice also showed a significantly lower number of LCMV-specific T cells. Additionally, endogenous Tim-3+ T cells were also significantly better at cytokine production and had increased cytotoxicity. Tim-3 expression correlated with better cell survival in homeostatic conditions after the virus had been cleared. Bulk RNA sequencing and TCR sequencing revealed that Tim-3-expressing effector CD8+ T cells had a distinct pattern of effector gene upregulation, with increased expansion of a subset of TCR clones. Mechanistically, Tim-3 signals enhances phosphorylation of Foxo1, inhibiting its entry into the nucleus, conferring enhanced effector function. Thus, Tim-3 signaling contributes positively to an effective CD8+ T cell response during acute infection. These findings may lead to a better understanding of CD8+ T cell function in different settings, including in tumors.

overall_design: We FACS sorted endogenous Tim-3lo vs. Tim-3hi antigen-experienced (CD44+CD62L-) CD8+ T cells from spleen at day 8 after LCMV armstrong infection. These cells were processed for bulk RNAseq and TCRseq. In the second experiment, P14 TCR Tg (WT, Tim-3 T2 or Tim-3 KO) were transferred into separate cohorts of WT C57BL/6 mice. These mice were infected with LCMV Armstrong and on day 8, P14 cells were FACS sorted and processed for bulk RNAseq,

first: Priyanka

last: Manandhar

first: Lawrennce


title: Transcriptomic analysis of gene expression pathways influenced by toxic chemical exposure on the Caenorhabditis elegans cuticle.

city: Paris

first: Chloé

last: Talarmin-Gas

state: Ile de France

address: 2, rue ambroise Paré

department: Biochemistry

country: France

institute: APHP

summary: Here, we propose that the cuticle of the nematode Caenorhabditis elegans (C. elegans) can be used as a model for human skin to test potentially toxic compounds, in particular, those commonly used in skincare and household products. We examined the effect of toxic chemicals on cuticle morphology and mechanical behavior using atomic force microscopy (AFM) and our findings revealed that two parameters, surface roughness and elastic modulus, are good markers for quantifying cuticle damage caused by chemicals. The damage caused by the chemicals correlated to their toxicity, as expressed in terms of maximum concentration allowed by EU regulations for use in skincare and household products. Transcriptomic analysis showed us that each chemical elicited a specific response in terms of differential gene expression, suggesting the lack of a general response to chemical exposure from the worms in this study. It also showed that a large number of genes involved in the synthesis of cuticle proteins, as well as in metabolism and enzyme activity, were affected by chemical exposure. The number of genes with altered expression levels correlated with chemical toxicity, as well as with level of morphological and mechanical changes in the cuticle. The analysis of affected genes provides a pathway to understand the molecular mechanisms of toxic chemical action. Overall, we show that the cuticle of C. elegans is a good model for human skin for toxicological screening, and this approach will be of particular interest to the cosmetics and household chemical industries.

overall_design: Total RNA was obtained from triplicates of wild-type Caenorhabditis elegans (N2 Bristol) exposed to five different chemicals—Bronopol (BR), Methylisothiazolinone (MIT), Sodium lauryl sulfate (SLS), Formaldehyde (FA), and Phenoxyethanol (POE)—at the L4 larval stage, and compared to wild-type worms grown on standard NGM plates (Normal Growth Medium), named (C, for control).

first: Benjamin

last: Saintpierre

first: Franck

last: Letourneur

first: Chloe

last: Talarmin


title: Effect of myeloid specific rictor knockout on B16-F10 tumors grown in mice

city: Vienna

first: Mario

last: Mikula

address: Währingerstrasse 10

country: Austria

institute: Medical University of vienna

summary: This study investigates the impact of RICTOR knockout macrophages on melanoma development. We hypothesise that the absence of RICTOR in macrophages reduces melanoma growth by inducing an inflammatory phenotype.

overall_design: C57/BL6 floxed Rictor, LysMcre littermates (Rictor WT: Rictor fl/fl +/+ and Rictor KO: Rictor fl/fl cre/+) were injected with B16-F10 cells intradermally into the right and left flank. Tumor growth was observed until the biggest tumor exceeded 1000 mm3. Tumors were harvested from myeloid specific Rictor knockout and wildtype  animals.

last: Gschwendtner


title: Cell-intrinsic Tim-3 is Required for Optimal CD8 Response to Acute LCMV Infection [RNAseq]


title: RUNX1-Induced DNA Demethylation Drives Hematopoietic Stem and Progenitor Cell Development

city: Yokohama

first: Shiori

last: Maeda

state: Kanagawa

address: 1-7-22 Suehiro-cho Tsurumi-ku

department: Center for Integrative Medical Sciences

institute: RIKEN

type: Methylation profiling by high throughput sequencing

summary: This study investigates the role of RUNX1’s DNA demethylation function in hematopoietic differentiation, revealing its necessity for generating hematopoietic stem and progenitor cells (HSPCs). Using CRISPR-edited iPSC lines—TADΔ (truncated transactivation domain) and Runt-VP64 (TAD replaced with VP64)—we demonstrated that RUNX1’s ability to induce DNA demethylation is critical for HSPC emergence. While wild-type RUNX1 enabled robust HSPC production (41.1% efficiency), Runt-VP64 and TADΔ severely impaired differentiation (13.5% and 0.024% efficiency, respectively). Methylome analysis linked RUNX1-binding motifs to differentially methylated regions (DMRs) in wild-type cells, absent in mutants, highlighting RUNX1’s role in site-specific demethylation during progenitor cell emergence. These findings establish RUNX1’s DNA demethylation activity as essential for initiating hematopoietic lineage commitment, providing novel insights into epigenetic regulation of hematopoiesis.

overall_design: EM-seq from cells obtained from different days differentiated from WT, Runt-VP64, Runt-TAD iPSC cells

first: Jing-Ru

last: Li

first: Yuri

last: Nakanishi

first: Erina

last: Furuhata

first: Hajime

last: Nishimura

first: Mami

last: Kishima

first: Harukazu

last: Suzuki


title: HERVHLin modulates pluripotency and protects the genome from active retroelements by rewiring the conserved LIN28A/let-7 pathway [RNA-Seq]

city: Berlin

first: Amit

last: Pande

address: Robert-Rössle-Straße 10

institute: Max Delbruck Center for Medicine

summary: Sequential waves of coding transcript expression mark genome reactivation during embryonic development and reprogramming to pluripotency. We additionally observed two distinct waves of non-coding retrotransposable element (RE) expression: an initial wave of younger, partially active REs (LINE-1, SVA, and Alu), followed by older HERVH elements. These waves are not merely correlative, as HERVH depletion leads to an increase in transposition of L1, Alu, and SVA elements. We identified a great apes-specific subgroup of HERVH (N=101), termed HERVHLin, characterized by a motif with duplicated LIN28 binding sites, which alone inhibits L1 transposition. HERVHLin transcripts bind to LIN28 and allow let-7 microRNA to mature, rewiring the conserved LIN28-let-7 regulatory axis. Full locus HERVHLin knockout (KO) results in increased LINE-1 transposition, rescued by the let-7 mimic. HERVHLin KO presents an EMT-like phenotype, downregulation of RE-defense and pluripotency-specific genes, underscoring the role of HERVHLin in genome protection of pluripotent stem cells.

overall_design: Two orangutan iPSC cell lines (Dokana - replicate 1, Djasinga - repliacte 2), provided by MDC Stem cell facility, were cultured for 3 sequential passages (technical replicates) and collected for RNA isolation. Matched total RNA and small RNA libraries were generated

first: Aleksandra

last: Kondrashkina

first: Egor

last: Semenchenko


title: IL-26 from ILCs regulates early-life gut epithelial homeostasis by shaping microbiota composition III

first: Yazan

last: Salloum

address: 11-13 Rue Pierre et Marie Curie

institute: Institut Curie

summary: Animals host symbiotic microbial communities that shape gut health. However, how the host immune system and microbiota interact to regulate epithelial homeostasis, particularly during early development, remains unclear. Human interleukin-26 (IL-26) is associated with gut inflammation and has intrinsic bactericidal activity in vitro, yet its in vivo functions are largely unknown, primarily due to its absence in rodents. To examine the role of IL-26 in early life, we used zebrafish and found that gut epithelial cells in il26-/- larvae exhibited increased proliferation, faster turnover, elevated  and DNA damage response, and altered cell population abundance. This epithelial dysregulation occurred independently of the IL-26 canonical receptor and resulted from dysbiosis in il26-/-. Moreover, IL-26 bactericidal activity was conserved in zebrafish, suggesting a potential role of this property in regulating microbiota composition. We further identified innate lymphoid cells (ILCs) as the primary source of IL-26 at this developmental stage. These findings establish IL-26 as a central player in a regulatory circuit linking the microbiota, ILCs, and intestinal epithelial cells to maintain gut homeostasis during early life.

overall_design: RNA-seq profiling of dissected guts from 5-day post-fertilization WT zebrafish larvae 1 hour post injection with BSA or recombinant zebrafish IL-26 (rzIl26).

first: Pedro

last: Hernandez


title: Using human urinary-derived renal epithelial cells for deep phenotyping of NPHP1 deletion and determining personalised response to novel therapeutics

city: Newcastle Upon Tyne

first: Juliana

middle: Estefania

last: Arcila-Galvis

state: Selecciona un estado

address: 258A  BAxterwood Court, Newcastle Upon Tyne, Tyne and Wear, NE4 5HW

department: Biosciences Institute

institute: Newcastle University

summary: Nephronophthisis (NPHP) is an autosomal recessive tubulointerstitial nephropathy classified as a renal ciliopathy disorder and recognised as the leading genetic cause of kidney failure in children and young adults. NPHP1 is the most common genetic cause and encodes nephrocystin-1, a protein that plays crucial roles in the primary cilium and cellular junctions. Here we utilise personalised medicine approaches and deep phenotyping, which enable us to explore mechanistic pathways and identify potential therapeutic strategies. In a family where we detected a homozygous NPHP1 whole-gene deletion in three affected siblings, we compared kidney biopsy tissue and human urine-derived renal epithelial cells (hURECs). Both the kidney biopsy and the hURECs demonstrated renal epithelial cells with an elongated and tortuous primary ciliary phenotype. Bulk RNA-seq on patient hURECs revealed disease signatures of the NPHP1 homozygous deletion, which included changes in EGFR signaling, as well as extracellular matrix interactions and adherens junctions, in line with the original description of nephrocystin-1 as an adapter protein at adherens junctions. Treatment of patient hURECs with alprostadil, a recently proposed therapy for NPHP, caused an increase in overall ciliation rate, but also an exaggerated primary ciliary length. In contrast, treatment of patient hURECs with an EGFR kinase inhibitor produced a phenotypic rescue of ciliary length and tortuosity. Following hUREC treatments, alprostadil did not fully restore the disease-associated transcriptional profile, whereas treatment with the EGFR kinase inhibitor AG556 caused a more complete rescue of the transcriptomic disease signature, in keeping with the observed phenotypic rescue. We conclude that patient-derived hURECS enable the deep phenotyping of nephronophthisis, replicate human kidney biopsy findings, and can be used to develop disease pathway signatures and screen candidate drug molecules, providing novel insights into disease pathogenesis and therapies. EGFR inhibition is now a potential therapy for renal ciliopathies, which should be tested within in vivo models of NPHP as a prelude to human studies.

overall_design: RNA-seq profiling was performed on primary urine-derived renal epithelial cells isolated from a male patient with nephronophthisis and an age- and sex-matched healthy control. The dataset includes sequencing of untreated cells, as well as cells treated with a PGE2 receptor agonist, DMSO as a vehicle control, or an EGFR kinase inhibitor.

first: Juliana E.

first: Praveen Dhondurao

last: Sudhindar

first: Marco

last: Trevisan-Herraz

first: John A

last: Sayer


title: Stage-specific extracellular vesicle cargo from Schwann cells orchestrates peripheral nerve regeneration

city: Cincinnati

first: Leyla

last: Esfandiari

state: OH

address: 2600 Clifton Ave

institute: University of Cincinnati

summary: Schwann cells (SCs) play a critical role in peripheral nerve regeneration, undergoing dynamic phenotype transitioning from myelinating to repair stages following injury. While SC-derived extracellular vesicles (SC-EVs) have emerged as key mediators of intercellular communication during nerve repair, their stage-specific molecular cargo and functional roles remained incomplete understood. Here, we delineate protein, microRNA   and lncRNA landscapes of SC-EVs across distinct differentiation stages, including immature, myelinating, and repair phenotypes, using an in vitro model of primary rat SCs. We show that myelinating SC-EVs are enriched with reprogramming factor SOX2 and neurotrophin receptor p75NTR, while repair SC-EVs carry distinct microRNAs predicted to modulate genes involved in myelin ensheathment, neuronal differentiation and neurogenesis.   Moreover, repair SC-EVs contain long non-coding RNAs (lncRNAs) that may regulate miRNA activity. These findings reveal a novel mechanism by which SC-EVs orchestrate neuronal regeneration through stage-specific molecular cargo, and establishes a foundational model for investigating SC plasticity in peripheral nerve repair

overall_design: Schematic of the in vitro differentiation model used to induce Schwann cells (SCs) to induce myelination, followed by reversion to a repair phenotype. Rat primary SCs were treated with 1 mM dbcAMP in rat SC basal media for 72 h to induce differentiation into myelinating SCs, followed by dbcAMP withdrawal to reprogram into repair SCs. Conditioned culture media was used to extract small extracellular vesicles. Total RNA was extracted from cell lysates and EV samples and then sequenced for mRNA, miRNA, and lncRNA.

first: Manju

last: Sharma

first: Supasek

last: Kongsomros

first: Maulee

last: Sheth

first: Somchai

last: Chutipongtanate


title: IL-26 from ILCs regulates early-life gut epithelial homeostasis by shaping microbiota composition II

overall_design: RNA-seq profiling of dissected guts from 5-day post-fertilization WT and il26-/- zebrafish larvae reared germ-free.


title: IL-26 from ILCs regulates early-life gut epithelial homeostasis by shaping microbiota composition IV

overall_design: scRNA-seq profiling of dissected guts from 5-day post-fertilization WT and il26-/- zebrafish larvae.


title: Transcriptomic profiling of adipose tissue in a mouse model of chronic social isolation-induced glucose metabolism dysfunction

city: Shanghai

first: Chao

last: Wu

state: 上海

address: 上海市普陀区真南路500号同济大学

institute: Tongji University

summary: Social isolation is a growing global public health concern, associated not only with mental health disorders but also with metabolic diseases such as type 2 diabetes.  This study investigates the molecular mechanisms by which chronic social isolation disrupts glucose homeostasis via sympathetic nervous system activation.  To elucidate adipose tissue transcriptional responses under socially isolated conditions, inguinal white adipose tissue (iWAT) was collected from male C57BL/6J mice subjected to either standard group housing or single housing for 8 weeks (n = 3 per group).  Bulk RNA sequencing was performed to characterize differential gene expression.  Analysis revealed substantial transcriptional reprogramming in iWAT from isolated mice, including upregulation of thermogenic and lipid metabolic pathways, such as Ucp1, and activation of key transcriptional regulators like Pparg.  These findings suggest that social isolation induces sympathetic-driven metabolic remodeling in adipose tissue.  The dataset provides valuable insight into how psychosocial stress influences peripheral metabolic gene networks and may contribute to stress-related metabolic disorders.

overall_design: Six 8-week-old C57BL/6J mice were evenly divided into two groups and raised separately or in groups, respectively, to simulate social isolation. After 8 weeks, the mice were euthanized, and subcutaneous fat from the inguinal region was collected for RNA-seq analysis.

first: Keran

last: Chen

first: Konglin

last: Huo