title: Red blood cell-tumour cell interactions promote tumour cell progression

city: Santiago de Compostela

first: Clotilde

last: Costa

address: Travesia da Choupana sn

institute: FIDIS

summary: One critical step in the metastatic cascade is the survival of circulating tumour cells (CTCs) within the bloodstream. While numerous interactions between CTCs and various hematopoietic cells have been described, the role of red blood cells (RBCs) in this process remains underexplored. This study investigates the interactions between tumour cells and RBCs from breast and lung cancer patients, revealing significant phenotypic and functional changes in the tumour cells. In vitro co-culture of cancer cell lines with RBCs from metastatic cancer patients resulted in increased cell attachment accompanied by morphological changes. Additionally, RBCs-primed tumour cells showed increased adhesion and disruption of the endothelial barrier in vitro and increased invasiveness both in vitro and in vivo. Transcriptomic analysis showed that RBCs from metastatic breast cancer patients induce significant gene expression changes, notably upregulating PAK4, which enhances migration and epithelial-mesenchymal transition (EMT). PAK4 inhibition reduced these effects. Proteomic studies revealed substantial remodelling, including actin-related changes and the accumulation of VASP at cell edges, promoting directional migration. Clinically, higher RBC distribution width (RDW) in metastatic breast cancer patients is associated with increased CTC counts and worse outcomes. This study highlights the previously unrecognized role of RBCs in promoting metastatic behaviours in cancer cells and suggests potential therapeutic targets, such as PAK4, to counteract these effects. Further exploration of RBCs-tumour cell interactions could provide new insights into metastatic mechanisms and improve cancer prognosis and treatment strategies.

overall_design: MDA-MB-231 breast tumour cells were co-cultured with Red blood cells from healthy donors (HD), and metastatic (M1) breast cancer patients for 24 hours. Non-primed cells were included as a negative control. Additionally, cells were cultured with liposomes to check whether the lipid content could affect gene expression.

first: Thais

last: Pereira-Veiga

first: Celso

last: Yáñez-Gómez

first: Aleksi

last: Pekkarinen

first: Carmen

last: Abuín

first: Christine

last: Blechner

first: Miriam

last: González-Conde

first: Alexander

middle: T

last: Bauer

first: Sabine

last: Vidal-y-Sy

first: Ayham

last: Mustafa

first: Bente

last: Siebels

first: Ana

last: Dávila-Ibáñez

first: Pablo

last: Cabezas-Sainz

first: Maider

last: Santos

first: Laura

last: Sánchez

first: Joao

last: Gorlgulho

first: Julian

last: Goetz

first: Kira

last: Meißner

first: Juan

last: Cueva

first: Patricia

last: Palacios

first: Alexia

last: Cortegoso

first: Teresa

last: Curiel

first: Carmela

last: Rodríguez

first: Marta

last: Carmona

first: Sven

last: Paine

first: Milena

last: Schmidt

first: Nadine

last: Heuer-Olewinski

first: Martin

last: Reck

first: Mustafa

last: Abdo

first: Rafael

last: López-López

first: Klaus

last: Pantel

last: Windhorst

first: Harriet

last: Wikman


title: Noncoding RNA, ncRNA-a3, epigenetically regulates TAL1 transcriptional program during erythropoiesis (RNA-Seq)

status: Public on May 07 2025

city: Hershey

first: Meghana

last: Matur

state: PA

address: 500 University Drive

country: USA

institute: Penn State

type: Expression profiling by high throughput sequencing

summary: Here, we showed that a long non-coding RNA (lncRNA), ncRNA-a3 that is transcribed from TAL1 erythroid +51kb enhancer, is required for TAL1 activation during EPO-induced lineage commitment and formation of erythroblasts. ncRNA-a3 regulates long-range chromatin interactions between +51 enhancer, promoter and other regulatory elements in the TAL1 locus to maintain the erythroid interaction hub. By binding and recruiting p300/BRG1 to the TAL1 locus ncRNA-a3 facilitates chromatin accessibility in the TAL1 locus and activates TAL1 transcription program, including subsequent epigenetic and transcriptional activation of erythroid specific TAL1 target genes.

overall_design: We performed the RNA-seq, ATAC-seq, Cut&Run, NG Capture-C for WT and ncRNA-a3 KD in K562 cell lines and primary CD34+ cord blood hematopoietic cells to investigate ncRNA-a3 function during erythropoiesis


title: Impact of temozolomide on gene expression of LN-229 cells

city: Mainz

first: Christian

last: Schwarzenbach

address: Obere Zahlbacher Str. 67

department: Institute of Toxicology

country: Germany

institute: University medical center Mainz

summary: Transcriptomic gene expression analysis of LN-229 cells stimulated for 48 h or 144 h with temozolomide is compared to unexposed cells for the characterisation of the glioblastoma senescence phenotype

overall_design: To investigate the gene expression profile of LN-229 cells upon exposure to  50 µM temozolomide (TMZ), LN-229 cells were exposed for 48 h, 144 h or unexposed  to TMZ. We then performed comparative gene expression profiling analysis using RNA-seq data obtained from 3 independent experiments.

first: Birgit

last: Rasenberger

first: Maja

last: Tomicic

first: Markus

last: Christmann

first: Sergi

last: Sayols Puig


title: STAT3 inhibitors synergize with KRAS G12C inhibitors in NSCLC by restricting adaptive resistance of STAT3 signaling and augmenting NK cell cytotoxicity

city: Nanjing, Jiangsu

first: Zehao

last: Pan

state: Please Select

address: Baiziting No.42

country: China

institute: Nanjing Medical University Affiliated Cancer Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: KRASG12C inhibitors have demonstrated clinical efficacy in KRASG12C-mutant non-small cell lung cancer (NSCLC), yet adaptive resistance limits their sustained therapeutic benefit. Through high-throughput screening of a pharmacological library, we identified a potent synergistic interaction between the KRASG12C inhibitor sotorasib and the signal transducer and activator of transcription 3 (STAT3) inhibitor napabucasin in KRASG12C-mutant NSCLC models. This combination exhibited superior anti-neoplastic activity compared to monotherapy in vitro and across diverse in vivo models. Mechanistically, KRASG12C inhibitor induced compensatory STAT3 activation, leading to adaptive resistance to sotorasib, which was abrogated by napabucasin. Notably, we elucidated a novel function of STAT3 in regulating HLA-B expression, an inhibitory ligand for natural killer (NK) cells, upon KRASG12C inhibition. The combination therapy enhanced NK cell-mediated cytotoxicity by disrupting the direct binding of phosphorylated STAT3 to the HLA-B promoter to downregulate its expression on neoplastic cells. Our findings unveiled an unexpected immunomodulatory mechanism underlying the synergism between KRAS and STAT3 inhibition, highlighting the potential of concurrently targeting oncogenic signaling cascades and the tumor microenvironment. This study provides a compelling rationale for the clinical evaluation of combined KRASG12C and STAT3 interruption in KRASG12C-mutant NSCLC patients, potentially offering a novel therapeutic strategy to overcome resistance and improve clinical outcomes.

overall_design: Chromatin accessibility of different NSCLC cell lines were assessed using ATAC-sequencing under different treatments.

first: Xuming

last: Song

first: Gaochao

last: Dong

first: Feng

last: Jiang


title: Noncoding RNA, ncRNA-a3, epigenetically regulates TAL1 transcriptional program during erythropoiesis (CUT&Run)


title: Noncoding RNA, ncRNA-a3, epigenetically regulates TAL1 transcriptional program during erythropoiesis (ATAC-Seq)


title: Mapping effective microRNA pairing beyond the seed using abasic mutations

city: Solna

first: Emma

middle: R

last: Andersson

address: Solnavägen 9

department: Department of Cell and Molecular Biology

country: Sweden

institute: Karolinska Institute

summary: MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression by base-pairing to complementary sites in mRNAs. The most important element for site recognition is the seed region (nucleotides 2-8 in the miRNA), but for a minority of sites pairing outside the seed increases efficiency, with the supplementary region (nucleotides 13-16) typically having the greatest impact. However, it is not clear how large an effect supplementary pairing has on target site efficiency, or which sites are most affected by it. Here, we use abasic modified nucleotides to disrupt pairing to residues 13 and 14 of miR-34a and measure the effect of this mutation compared to wild-type miR-34a on the cellular transcriptome using RNA-seq. We find that a subset of sites with predicted supplementary pairing are affected 24 hours after miRNA overexpression, with up to two-fold decreases in site repression. We show that miR-34a 3'-pairing is sensitive to GU wobble pairs in a position-specific manner and favors bulges in the miRNA over the target. These results were validated with luciferase reporter assays. Overall, this study demonstrates a novel methodological approach for elucidating the role of specific miRNA residues in target site selection, advancing our understanding of miRNA-mediated gene regulation.

overall_design: To investigate the impact of supplementary pairing on microRNA targeting, we compared the effects on gene expression of wild-type miR-34a (miR-34a-WT) and a variant where miR-34a residues g13 and g14 were replaced by rSpacer abasic residues (miR-34a-RS). HEK293T cells were transfected with miR-34a-WT duplex, miR-34a-RS duplex or AllStars negative control (Qiagen). Total RNA was collected 24 h post-transfection and samples were analyzed for differential gene expression using bulk RNA-sequencing.

first: David

middle: M

last: Kosek

first: Katja

last: Petzold


title: miR-575 in exosomes of vaginal discharge is downregulated in ovarian cancer patients

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary: We collected vaginal discharge from 30 ovarian cancer patients and 29 benign gynecological disease patients, extracted exosomal miRNAs, and examined the expression differences between groups by RT-qPCR.

overall_design: Vaginal discharge were collected from 30 ovarian cancer patients and 29 patients with benign gynecological diseases, and exosomal miRNAs were extracted by using SmartSEC HT EV Isolation System and miRNeasy Mini Kit. The expression differences between groups were examined by RT-qPCR.

first: Maho

last: Azumi


title: TRAIL-induced cytokine production via NFKB2 pathway promotes neutrophil chemotaxis and immune suppression in triple negative breast cancers [MDA-MB-231]

city: Bethesda

first: Stanley

last: Lipkowitz

state: MD

address: 10 Centre Drive

department: Women's Malignancies Branch

institute: NIH

summary: Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is a potential cancer therapeutic that selectively induces apoptosis in cancer cells sparing the non-malignant cells. While the effective cytotoxic effect of TRAIL has been demonstrated in vitro, its efficacy in clinical trials has been limited, suggesting a presence of unknown modulatory mechanisms responsible for lack of TRAIL activity in patients. We hypothesized that TRAIL treatment elicits transcriptional changes in triple negative breast cancer cells (TNBC) cells that alter the immune milieu. To test this, we performed a RNAseq analysis of MDA-MB-231 cells treated with TRAIL, followed by validation in various TNBC cell lines. We found that TRAIL significantly induces expression of multiple cytokines, such as CXCLs 1, 2, 3, 8,11 and IL-6, which are known to affect neutrophil function. Gene set enrichment analysis (GSEA) indicated a significant enrichment of NFKB pathway. Concordantly, we confirmed that the non-canonical NFKB2 pathway is primarily responsible for induction of these cytokines. We further found that induction of these cytokines was predominantly mediated by death receptor 5 and caspase-8 protein, but not caspase-8 enzymatic activity. CXCLs and IL-6 produced by the TRAIL-treated TNBC cells enhanced chemotaxis of neutrophils isolated from healthy human donors, demonstrating the functional relevance of these cytokines. In vivo, TNBC xenograft tumors grown in mice treated with TRAIL showed an activation of the NFKB2 pathways, elevated production of CXCLs and IL-6, and an increased neutrophil recruitment into the tumors. Moreover, pre-incubation of neutrophils from human donor with supernatants from TRAIL-treated TNBC cells significantly impaired the cytotoxic effect against TNBC cells and showed a reduced respiratory burst. Transcriptomic analysis of neutrophils incubated with either TRAIL alone or supernatant of TRAIL-treated TNBC revealed significant enrichment of expression of inflammatory cytokines, immune modulatory genes, and immune checkpoint genes along with genes having implication on delayed neutrophil apoptosis. Functional studies with these neutrophils confirmed their suppressive effect on T cell proliferation and an increase in Treg suppressive phenotype. Collectively, our study proposes the novel role of TRAIL-induced NFKB2-dependent cytokine production that promotes neutrophil chemotaxis and immune suppression. Our finding suggests that targeting innate immune system may be a promising strategy to improve the efficacy of TRAIL treatment in TNBC.

overall_design: To determine the transcriptomic response elicited by TRAIL in TNBC cells, we performed a time series RNA-seq analysis with MDA-MB-231, a TRAIL sensitive TNBC cell line. We administered suboptimal dose of TRAIL (45nM) on the MDA-MB-231 cell line to observe the differential gene expression in live cells instead of apoptotic cells. RNA abundance due to TRAIL was observed over 24Hrs at an interval of 0H, 1H, 3H, 6H, 12H and 24H in triplicate.

first: Manjari

last: Kundu


title: Overexpression of human SAMD9 inhibits protein translation and alters MYC signaling resulting in cell cycle arrest

city: NASHVILLE

first: Marisol

last: Ramirez

state: TENNESSEE

address: 2220 Pierce Avenue, 571 Preston Research Building

department: Center for Quantitative Sciences, Department of Biostatisticss

institute: Vanderbilt University Medical Center

summary: Inherited bone marrow failure syndromes (iBMFS) often result from pathogenic mutations in genes that are important for ribosome function, namely, Diamond-Blackfan anemia, Shwachman-Diamond syndrome, and dyskeratosis congenita. Germline mutations in SAMD9 are a frequent genetic lesion resulting in an iBMFS with monosomy 7; some patients have severe multisystem syndromes that include myelodysplasia. The association of germline SAMD9 mutations and bone marrow failure is clear, but to date, there is no reliable method to predict if a novel SAMD9 mutation is pathogenic unless it is accompanied by an obvious family history and/or clinical syndrome. The difficulty with pathogenicity prediction is, in part, due to the incomplete understanding of the biological functions of SAMD9. We used a SAMD9-targeted, inducible CRISPRa system and RNA sequencing to better understand the global transcriptional changes that result from transcriptional manipulation of SAMD9. Supporting recent discoveries that SAMD9 acts as a ACNase specific for phenylalanine tRNA (tRNA-Phe), we confirmed with crosslinking and solid-phase purification (CLASP) that SAMD9 is an RNA binding protein and analyzed how overexpression of tRNA-Phe may reverse transcriptomic changes caused by SAMD9 activation. Our data show that overexpression of SAMD9 from the endogenous locus results in decreased cell proliferation, cell cycle progression, and global protein translation. When SAMD9 contains a gain-of-function mutation (p.E1136Q) these functional phenotypes are exacerbated, but only partially rescued with tRNA-Phe overexpression suggesting additional molecular actions of SAMD9. Additionally, we demonstrate that gene expression pathways important for ribosome biogenesis and MYC signaling are the most significantly impacted by SAMD9 overexpression.

overall_design: Six different K562 cell lines (WT-parental, [VPR]-WT-D9, [VPR]-WT-D9-tRNA-Phe, MUT-parental, [VPR]-MUT-D9, [VPR]-MUT-D9-tRNA-Phe) were analyzed by RNA sequencing. Comparisons were made between no treatment conditions and IFN or doxycycline.

first: Kristen

last: McSweeney

first: Paul

last: Hoover

last: Ramirez-Solano

first: Qi

last: Liu

first: Jason

last: Schwartz


title: Temporal artery biopsy of Giant cell arteritis

city: Setagaya-ku

first: Nobumasa

last: Watanabe

state: Tokyo

address: 2-1-6 Kamikitazawa

institute: Tokyo Metropolitan Institute of Medical Science

summary:
Background
Giant cell arteritis (GCA) is a prevalent, intractable, granulomatous, large-vessel vasculitis. The pathologic features include destruction of the tunica media, infiltrating macrophages and multinucleated giant cells (MNGCs), immune responses associated with CD4+ T cells, accumulation of myofibroblasts, and hypertrophy of the intima.
Objectives
The molecular pathology of GCA has largely remained elusive, while the morphological features are well defined. We aimed to identify key molecules associated with the pathogenesis of GCA.
Method
Arterial lesions were obtained through temporal artery biopsy from 16 patients, including those diagnosed as GCA and not. The obtained samples underwent genome-wide gene expression profiling. The resulting data were examined to reveal specific pathways and genes, and some of the molecules were followed up by immunohistochemistry.
Results
GCA lesions had a distinguishing pattern of gene expression, including enrichment of immune cells and phagocytic pathways related to microglia and osteoclasts. We found MMP12 (macrophage elastase), HLA-DRA, phagocytosis- and osteoclast-associated molecules in infiltrating macrophages and MNGCs. We also found LRRC15-expressing cells in the tunica intima, suggesting a myofibroblast subpopulation that suppresses cytotoxic CD8+ T cells. These molecules were often upregulated in other granulomatous diseases affecting not only arteries but also lymph nodes.
Conclusion
Infiltrating macrophages and MNGCs expressed molecules that contribute to the pathogenetic features of GCA, including degradation of the tunica medium, induction of immune responses, and accumulation of myofibroblasts. The extended list of key molecules provides a solid baseline of elucidating the pathogenesis of GCA and developing therapeutic strategies.

overall_design:
Arterial lesions were obtained through temporal artery biopsy from 16 patients, including those diagnosed as GCA and not. The obtained samples underwent genome-wide gene expression profiling. The resulting data were examined to reveal specific pathways and genes, and some of the molecules were followed up by immunohistochemistry.

Diagnoses:
GCA = giant cell arteritis
MPA = microscopic polyangiitis
PAN = polyarteritis nodosa
PMR = polymyalgia rheumatica
RA = rheumatoid arthritis
Fever of unknown origin

first: Yuichiro

last: Hara

first: Yasumasa

last: Nishito

first: Mai

last: Kounoe

first: Kazunari

last: Sekiyama

first: Eisuke

last: Takamasu

first: Takayasu

last: Kise

first: Naofumi

last: Chinen

first: Kota

last: Shimada

first: Makoto

last: Sugihara

first: Hideya

last: Kawaji


title: TRAIL-induced cytokine production via NFKB2 pathway promotes neutrophil chemotaxis and immune suppression in triple negative breast cancers [neutrophils]

first: Stanley

last: Lipkowitz

overall_design: To characterize the effect of TRAIL therapy on human neutrophils, we performed bulk RNA seq of healthy donor-derived, isolated neutrophils incubated in either T-CM (TRAIL treated on tumor cells followed by media collection) or tumor condition media (CM). Simultaneously, to understand the exclusive effect of TRAIL on neutrophils, we also analyzed transcriptomics of neutrophils incubated in serum free media (SFM) in the presence or absence of TRAIL (SFM-T/SFM) respectively. Briefly, donor isolated neutrophils were either incubated in SFM/SFM-T/CM/T-CM for 18h prior to processing for RNA-seq. Total number of samples collected (n) was 5 for 4 conditions.

first: Manjari

last: Kundu

first: Yoshimi

middle: E

last: Greer


title: Detailed genotype-phenotype analysis of AOSD cohorts

city: Leeds

first: Sinisa

last: Savic

address: St James's University Hospital

country: United Kingdom

institute: University of Leeds

summary: Adult-onset Still’s disease (AOSD) is systemic autoinflammatory disorder of unknown aetiology. Various genetic and environmental factors have been implicated in its pathogenies, but the genetic studies so far have been limited to few selected genes of interest.  We conducted detailed genetic analysis of a large cohort of patients with AOSD, using deep whole exome sequencing to identify rare germline variants and somatic mutations of interest. In parallel, we conducted a comprehensive inflammatory marker profiling from the patients’ sera. We used a bespoke assay to detect NLRP3 inflammasome activation and novel method to measure Type I Interferon (IFN) score. We found a strong genetic connection between AOSD and the presence of rare germline variants and somatic mutations within genes associated with monogenic autoinflammatory disorders and clonal haematopoiesis of unknown significance. Profiling of inflammatory markers showed significantly elevated ASC/NLRP3 speck levels in AOSD compared to healthy controls, whilst cytokine analysis identified several significantly elevated cytokines including IL-18, IL-6, IL-23, IFN and IFN-2. The Type I IFN score was also significantly higher in AOSD compared to healthy and some disease controls. We did not find any correlation between rare genetic variants and somatic mutation burden with selected inflammatory markers (ASC/NLRP3 speck, ASC speck, IL-1IL-18, IL-6 and Type I IFN score). Our study demonstrated considerable genetic complexity within AOSD. Many enriched variants may not be sufficient, individually to cause disease but more likely to contribute to a multiple-hit model for AOSD.

overall_design: Differential gene expression between AOSD cases and healthy controls were investigated using RNA extracted from whole blood samples

first: Joanne

last: Topping

first: Leon

last: Chang

first: Jurgen

last: Rech


title: Targeted Degradation of CDK9 Potently Disrupts MYC Network

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

summary: Cyclin-dependent kinase 9 (CDK9) coordinates signaling events that regulate RNA polymerase II (Pol II) pause-release states. It is an important co-factor for transcription factors, such as MYC, that drive aberrant cell proliferation when their expression is deregulated. CDK9 modulation offers an approach for attenuating dysregulation in such transcriptional programs. As a result, numerous drug development campaigns to inhibit CDK9 kinase activity have been pursued. We validated that CDK9 inhibition triggers a compensatory mechanism that dampens its effect on MYC transcriptional programs and found that this resistance mechanism was absent when the Kinase is degraded. Importantly, CDK9 degradation is more effective than its inhibition for disrupting MYC transcriptional regulatory circuitry likely through the abrogation of both enzymatic and scaffolding functions of CDK9.

overall_design: Three or four replicates each of 3 cell lines (MOLT4, PSN1 or RH1) treated with either DMSO (vehicle control), KB-0742 (CDK9 inhibitor) or KI-CDK9d-32 (CDK9 degrader) for 2hr, 4hr or 8hr.

first: Mohammed

middle: A

last: Toure

first: Keisuke

last: Motoyama

first: Yichen

last: Xiang

first: Julie

last: Urgiles

first: Florian

last: Kabinger

first: Ann-Sophie

last: Koglin

first: Ramya

last: Iyer

first: Katie

last: Gagnon

first: Amruth

last: Kumar

first: Samuel

last: Ojeda

first: Drew

last: Harrison

first: Matthew

last: Rees

first: Jennifer

last: Roth

first: Christopher

middle: J

last: Ott

first: Richard

last: Schiavoni

first: Stuart

middle: S

last: Levine

first: Forest

last: White

first: Eliezer

last: Calo

first: Andre

last: Richters

first: Angela

middle: N

last: Koehler


title: Inhibiting the P2Y12 Receptor in Megakaryocytes and Platelets Suppresses Interferon-Associated Responses

city: New York City

first: Florencia

last: Schlamp

state: New York

address: 435 East 30th Street

institute: NYU Langone Health

summary: Megakaryocytes (MKs) and platelets are recognized mediators of inflammation and altered immunity. While antiplatelet therapies are widely used to prevent cardiovascular events, their role in attenuating platelet-mediated inflammation is uncertain. This study was designed to investigate the transcriptomic effect of APT on MKs and its impact on proinflammatory pathways. We demonstrated a significant effect on the MK transcriptome following P2Y12 receptor inhibition. Specifically, we found a significant downregulation of IFN pathways with P2Y12 receptor inhibition. In conclusion, targeting the P2Y12 receptor modulates MK and platelet inflammatory signaling pathways. P2Y12-mediated suppression of MK IFNα signaling may benefit proinflammatory diseases

overall_design: We used human CD34+-derived MKs from 4 donors that were treated with aspirin, P2Y12 inhibition or both together for 24 hours and performed RNA-seq.

first: Marcin

last: Sowa

first: Tricia

last: Wang

first: Hanane

last: El Bannoudi

first: Macintosh

last: Cornwell

first: Hannah

last: Bash

first: Peter

last: Izmirly

first: H

last: Belmont

first: Kelly

middle: V

last: Ruggles

first: Jill

middle: P

last: Buy

first: Deepak

last: Voora

first: Tessa

last: Barrett

first: Jeffrey

last: Berger


title: Synthetic polymer based 3D culture improve naïve properties of human induced pluripotent stem cells

city: Gyeonggi-do

first: Taemook

last: Kim

address: Dongtancheomdansaneop 1-ro

country: South Korea

institute: Deargen Inc.

summary: Human induced pluripotent stem cells were cultured on crosslinked cyclosiloxane based polymer. Gene expression profiling analysis was conducted through data obtained from RNA sequencing to investigate the genetic difference between human induced pluripotent stem cells cultured on vitronectin plate and polymer coated plate.

overall_design: Gene expression pattern analysis of RNA sequencing data for CMC-iPSC-009 cells cultured on vitronectin plate , ultra low attachment plate, and polymer coated plate. Two replicates for each culture condition.

first: Changjin

last: Seo

first: Yoonjung

last: Choi

first: Junhyuk

last: Song


title: Dynamic genome Chromatin accessibility of T lymphocyte under microgravity condition

city: Beijing

first: Li

last: Nuomin

address: No.5 Yard，Zhong Guan Cun South Street Haidian District，Beijing

institute: Beijing Institute of Technology

summary: In space flight,microgravity may be sensed and transmitted through cellular and nuclear structures, thereby altering nuclear plasticity, chromatin organization and openness, which in turn leads to differential gene expression.  Studies on genome-wide chromatin openness under microgravity environments will help to clarify whether the Earth's gravity is stable and maintains the structure and openness of chromatin, as well as the steady-state conditions that constitute genome modification.   At the same time, it will provide a strong scientific basis for astronaut's protection under extreme conditions.

overall_design: By simulating microgravity environments,Genome-wide chromatin openness was assessed based on ATAC-Seq in nuclei prepared from human T lymphocytes (Jurkat).

first: Nuomin

last: Li

first: Shicong

last: Zhao

first: Hao

first: Hong

last: Ma

first: Yulin

last: Deng


title: The dynamic transcriptome of Plasmodium malariae in the mosquito

city: Granada

first: Jose

middle: Luis

last: Ruiz Rodriguez

state: Granada

address: Avda. del Conocimiento 17. P. T. Ciencias de la Salud

country: Spain

institute: IPBLN-CSIC

summary: To survive and multiply in different host niches, malaria parasites require sets of proteins that are expressed during the life cycle in a timely manner. Plasmodium malariae is a human malaria parasite that is present in most malaria-endemic regions. However, this species remains enigmatic because it is very challenging to culture, its low parasitaemia in human infections, and frequent co-infection with other malarias . We investigate the transcriptome of P. malariae during transmission in the vector by analyzing RNA-seq data from midgut and salivary gland parasite stages obtained in two experimental mosquito infections with field P. malariae isolates. Our analysis results in 3,699 expressed genes, of which 263 are developmentally regulated and 1,338 are P. malariae-specific, including genes with unknown functions and without orthologs in other Plasmodium. We detected unique expression patterns of the ApiAP2 family of transcription factors, many of which appear to function as master regulators during sporogony. We found expressed several members of multigene families, like PIR, PHIST, fam-l, and described new families potentially showing transcriptional heterogeneity. Our findings point to the uniqueness of the P. malariae transcriptome, probably related to different transmission traits in the vector, and the lower pathogenicity and virulence in the human.

overall_design: Transcriptome profiling (RNA-seq) of mosquito tissues after experimental infections with P. malariae

first: José

middle: L

last: Ruiz

first: Bárbara

last: Díaz-Terenti

first: Thierry

last: Lefèvre

first: Rakiswendé

last: Yerbanga

first: Thomas

middle: D

last: Otto

first: Elena

last: Gómez-Díaz


title: Noncoding RNA, ncRNA-a3, epigenetically regulates TAL1 transcriptional program during erythropoiesis (NG Capture-C)

first: Meghana

last: Matur


title: Immune checkpoint TIM-3 regulates microglia and Alzheimer’s disease [BulkRNAseq_Dataset1_Batch2_7M]

city: Boston

first: The Gene Lay Institute of

last: Immunology and Inflammation

address: 60 Fenwood Road,

institute: Brigham and Women's Hospital

summary: Microglia are the resident immune cells in the brain and have pivotal roles in neurodevelopment and neuroinflammation1,2. This study investigates the function of the immune-checkpoint molecule TIM-3 (encoded by HAVCR2) in microglia. TIM-3 was recently identified as a genetic risk factor for late-onset Alzheimer’s disease3, and it can induce T cell exhaustion4. However, its specific function in brain microglia remains unclear. We demonstrate in mouse models that TGFβ signalling induces TIM-3 expression in microglia. In turn, TIM-3 interacts with SMAD2 and TGFBR2 through its carboxy-terminal tail, which enhances TGFβ signalling by promoting TGFBR-mediated SMAD2 phosphorylation, and this process maintains microglial homeostasis. Genetic deletion of Havcr2 in microglia leads to increased phagocytic activity and a gene-expression profile consistent with the neurodegenerative microglial phenotype (MGnD), also referred to as disease-associated microglia (DAM). Furthermore, microglia-targeted deletion of Havcr2 ameliorates cognitive impairment and reduces amyloid-β pathology in 5×FAD mice (a transgenic model of Alzheimer’s disease). Single-nucleus RNA sequencing revealed a subpopulation of MGnD microglia in Havcr2-deficient 5×FAD mice characterized by increased pro-phagocytic and anti-inflammatory gene expression alongside reduced pro-inflammatory gene expression. These transcriptomic changes were corroborated by single-cell RNA sequencing data across most microglial clusters in Havcr2-deficient 5×FAD mice. Our findings reveal that TIM-3 mediates microglia homeostasis through TGFβ signalling and highlight the therapeutic potential of targeting microglial TIM-3 in Alzheimer’s disease.

overall_design: All mice were treated with Tamoxifen to induce Tim3 KO under CX3CR1-CreERT2 at the age of 6 weeks. Microglia (7AAD- CD45int CD11b+ Gr1- Tmem119+)  were sorted and analyzed.

first: Kimitoshi

last: Kimura

first: Ayshwarya

last: Subramanian

first: Zhuoran

last: Yin

first: Yufan

last: Wu

first: Danyang

last: He

first: Madhumita

last: Das

first: Karen

last: Dixon

first: Udbhav

middle: K

last: Chitta

first: Ruihan

last: Tang

last: Pertel

first: Aastha

last: Aastha

first: Masashi

last: Nomura

first: Vasundhara

last: Singh

first: Lei

last: Liu

first: Conner

last: Lambden

first: Neha

last: Gupta

first: Yiran

middle: C

last: Cheng

first: Sebastian

last: Silveira

first: Huiyuan

last: Zhang

first: Aamir

last: Suhail

first: Toni

last: Delorey

first: Orit

last: Rosenblatt-Rosen

first: Aviv

last: Regev

first: Dennis

last: Selkoe

first: Mario

last: Suva

first: Oleg

last: Butovsky

first: Vijay

last: Kuchroo


title: Immune checkpoint TIM-3 regulates microglia and Alzheimer’s disease [snRNAseq_5M]

first: The Gene Lay Institute of

last: Immunology and Inflammation

overall_design: All mice were treated with Tamoxifen to induce Tim3 KO under CX3CR1-CreERT2 at the age of 6 weeks. A hemisphere of the brain was snap frozen in dry ice, after transcardial perfusion with cold HBSS, at the age of 5 months.

first: Kimitoshi

last: Kimura

first: Ayshwarya

last: Subramanian

first: Zhuoran

last: Yin

first: Yufan

last: Wu

first: Danyang

last: He

first: Madhumita

last: Das

first: Karen

last: Dixon

first: Udbhav

last: Chitta

first: Ruihan

last: Tang

first: Thomas

last: Pertel

first: Aastha

last: Aastha


title: Efficient profiling of total RNA in single cells with STORM-seq

status: Public on May 06 2025

city: Grand Rapids

first: Benjamin

last: Johnson

state: MI

address: 333 Bostwick Ave NE

institute: Van Andel Institute

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

overall_design: Refer to individual Series


title: DNA methylation analysis in MCF-7 cell line with overexpression of POU1F1

city: Santiago de Compostela

first: Leandro

middle: Avila

last: Concepcion

state: Coruña

address: Ave Barcelona

department: Department of Physiology, Center for Molecular Medicine and Chronic Diseases

institute: University  Santiago de Compostela

type: Methylation profiling by genome tiling array

summary: The transcription factor POU1F1 plays an important role in breast cancer. It has been described that POU1F1 is capable of regulating the expression of different genes involved in cell proliferation, apoptosis and cell plasticity. The mechanism by which POU1F1 carries out these regulations is still unknown, and epigenetics is one of the possible causes. Epigenetics refers to modifications in gene expression that are heritable through cell division and that occur without changes in the DNA sequence. DNA methylation is one of the most important epigenetic mechanisms.

overall_design: Analysis of DNA methylations using MCF-7 cells lines with overexpression of POU1F1

last: Avila

first: Sandra

last: Rodríguez-González

first: Roman

last: Pérez-Fernández


title: COMBINED EXERCISE AND ITS EPIGENETIC SIGNATURES: 8-WEEKS PROTOCOL MODULATED THERMOGENESIS, CARDIOVASCULAR AND LIPID BIOMARKERS RELATED PATHWAYS

city: Ribeirão Preto

first: Guilherme

middle: Da Silva

last: Rodrigues

address: Avenida Bandeirantes, 3900

country: Brazil

institute: Universidade de São Paulo

summary: Background:  Obesity, a health concern shaped by genetic, epigenetic, and environmental factors, has emerged as a global epidemic, particularly with a 60% increment in Brazil from 2006 to 2016. This study explored the effects of an 8-week integrated strength and aerobic training protocol on the DNA methylation patterns in 11 sedentary women with obesity

overall_design: MethylationBrazil Assay

first: Guilherme da Silva


title: Dynamic Multi-omics Profiling Unveils Bimodal Epigenetic Roles of Chromatin O-GlcNAc modification in Premature Senescence Program [BiSulfite-seq]

city: Panjin

first: Yubo

last: Liu

address: Dagong Lu

institute: Dalian University of Technology

type: Methylation profiling by high throughput sequencing

summary: Cellular senescence, a recognized instigator of tumorigenesis and age-associated disorders, can be precipitated by characteristic alterations in gene expression profiles. However, the underlying mechanisms that precise orchestrate the expression of senescence-related genes are still elusive. Here, we employed a time-series approach using a chemical genomics multi-omics strategy to panoramically investigate the role of O-GlcNAc chromatin-associated proteins (OCPs) throughout the process of oncogene-induced senescence (OIS) in human primary fibroblasts. The progression of OIS is associated with the dynamic accumulation of chromatin O-GlcNAc modification, which facilitates cells commitment to senescence. Through the integration of dynamic analyses of transcriptome and epigenome profiles, we can demonstrate that OCPs experience genomic occupation shifts across diverse epigenetic chromatin states, and display bimodal sequential regulatory activity within the senescence transcriptome. Mechanistically, O-GlcNAc aids in the formation of bimodal epigenetic regulatory complexes (TF-SWI/SNF and NuRD), which dictate the gene expression patterns related to both the senescence-associated secretory phenotype (SASP) and cell cycle arrest. Additionally, we pinpointed O-GlcNAc JUN and GATAD2A as key regulators affecting the phenotypes of OIS in both in vitro and in vivo models of senescence and tumorigenesis. Our findings on the dynamic behavior and chromatin organization principles of O-GlcNAc epigenetic factors provide insights into the senescence process and enable potential therapeutic manipulation of the senescence phenotype.

overall_design: Whole genome DNA methylation(WGBS) analysis in human primary fibroblasts cells(oncogene induce senescence time D0, D2, D4, D10).

first: Nana

last: Zhang

first: Jianing


title: Transcriptomic profiles of CT26 syngeneic tumor tissues following treatment with the dual EP2/EP4 antagonist TP-18.

city: shanghai

first: Yao

address: No. 500, Dongchuan Road

institute: East China Normal University

summary: To investigate the antitumor mechanisms of the dual EP2/EP4 antagonist TP-18, we conducted RNA-seq-based transcriptomic analysis of CT26 tumors, with or without TP-18 treatment.

overall_design: Female BALB/c mice (6–8 weeks old) bearing subcutaneous CT26 tumors were treated with either vehicle or TP-18 (50 mg/kg, QD, orally) for 3 weeks.  Following treatment, mice were euthanized by cervical dislocation, and subcutaneous tumors were excised and stored in liquid nitrogen for subsequent sequencing.

first: Weiqiang

last: Lu

first: Mingyao


title: Targeted delivery of PGC-1α gene by gas vesicles-assisted ultrasound cavitation for early treatment of acute kidney injury

city: Hangzhou

first: Yuxian

last: Kuai

state: Zhejiang

address: No. 88 Jiefang Road, Shangcheng District

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

summary: Endothelial cell (EC) injury plays a critical part in the occurrence and progression of renal ischemia-reperfusion injury (IRI). PGC-1α, as a master regulator of mitochondrial function, has been identified as a potential therapeutic target for treating injured ECs. Here, fucoidan-plasmid PGC-1α-gas vesicles (Fuc-pPGC-1α-GVs) are synthesized to identify damaged renal ECs at the early stage of renal IRI through the high affinity of fucoidan to P-selectin, and significantly enhance gene transfection efficiency by ultrasound-mediated controlled cavitation, resulting in specific overexpression of PGC-1α in injured renal ECs. In vitro and in vivo evidence reveals that ultrasound-mediated gene transfection with Fuc-pPGC-1α-GVs could ameliorate renal IRI by rescuing the function of ECs, decreasing immune cells infiltration, and alleviating renal tubular injury. Mechanistically, overexpressed PGC-1α in injured renal ECs promotes mitophagy and inhibits ROS production by upregulating BNIP3, BNIP3L and SOD2. This study provides a promising strategy for early and efficient treatment of renal IRI.

overall_design: To investigate the potential therapeutic mechanisms of Fuc-pPGC-1α-GVs combined with ultrasound irradiation treatment for renal ischemia-reperfusion injury (IRI), transcriptomic analysis of renal microvascular endothelial cells (RMVECs) was performed comparing the hypoxia/reoxygenation (H/R) group and the H/R+Fuc-pPGC-1α-GVs+US group.

first: Wen

last: Xu

first: Xue

last: Wang

first: Xiaodan

first: Pintong

last: Huang


title: Population Imaging of Enterochromaffin Cell Activity Reveals Regulation by Somatostatin

city: San Francisco

first: Nathan

middle: Daniel

last: Rossen

state: CA

address: 600 16th Street Genentech Hall Room N-272E Genentech Hall Room N-272E

department: Physiology

institute: University of California, San Francisco

summary: Sensory enteroendocrine cells in the intestinal epithelium detect and relay information about the luminal environment to other cells within and outside the gut. Serotonergic enterochromaffin (EC) cells are a subset of enteroendocrine cells that detect noxious stimuli within the gut lumen, such as chemical irritants and microbial byproducts, and transduce this information to sensory nerve fibers to elicit defensive responses such as nausea and visceral pain. While much has recently been learned about the pharmacological and biophysical characteristics of EC cells, a more broadscale investigation of their properties has been hindered by their relatively low prevalence and sparse anatomical distribution within the gut epithelium. Here, we introduce a method for large-scale parallel analysis of individual EC cell activity within a physiologically relevant epithelial context. Using this approach, we identify somatostatin-28 (SST28) as a potent inhibitor of both basal and stimulus-evoked serotonin release from EC cells and delineate the signaling pathway that underlies this modulatory response. Our analysis suggests that targeting this inhibitory signaling pathway may offer novel therapeutic avenues for treating gastrointestinal disorders associated with EC cell function and dysregulated serotonin signaling. Together with the ongoing development of specific biosensors, this platform provides a template for the efficient characterization of other rare sensory cell types and their pharmacological modulators.

overall_design: To determine differential gene expression in small intestinal enterochromaffin cells, crypt and villus epithelial fractions were seperately collected from the the total small intestine of Tph1-CFP mice.  Following single-cell dissociation, CFP(+) enterochromaffin cells and CFP(-) non-enterochromaffin epithelial cells were FACS sorted from either the crypt or villus epithelium for a total of four experimental groups (Crypts-EC, Crypts-epi, Villi-EC, Villi-epi). N = 4 mice/samples per group. 5000 cells were pooled per sample.

first: Kouki

last: Touhara

first: David

last: Julius


title: Immune checkpoint TIM-3 regulates microglia and Alzheimer’s disease [BulkRNAseq_Dataset3_4M]

first: The Gene Lay Institute of

last: Immunology and Inflammation

first: Kimitoshi

last: Kimura

first: Ayshwarya

last: Subramanian

first: Zhuoran

last: Yin

first: Yufan

last: Wu

first: Danyang

last: He

first: Madhumita

last: Das

first: Karen

last: Dixon

first: Udbhav

last: Chitta

first: Ruihan

last: Tang

first: Thomas

last: Pertel

first: Aastha

last: Aastha

first: Masashi

last: Nomura

first: Vasundhara

last: Singh

first: Lei

first: Conner

last: Lambden

first: Neha

last: Gupta

first: Yiran

last: Cheng

first: Sebastian

last: Silveira

first: Huiyuan

first: Aamir

last: Suhail

first: Toni

last: Delorey

first: Orit

last: Rosenblatt-Rosen

first: Aviv

last: Regev

first: Dennis

last: Selkoe

first: Mario

last: Suva

first: Oleg

last: Butovsky

first: Vijay

last: Kuchroo


title: Reprogramming breast cancer cells to breast cancer stem cells-like by the POU1F1 transcription factor

first: Leandro

last: Concepcion

summary: POU1F1 (also named PIT-1) is a well-known transcription factor involved in embryonic and adult pituitary development that has also been analyzed for its role in breast cancer . This study provides compelling evidence of POU1F1 in reprogramming breast cancer cells into BCSC-like. Our data demonstrates that POU1F1 induces a BCSC-like phenotype in breast tumor cells by deregulating markers such as CD24, CD44, CD133, and ALDH. These phenotypic modifications are correlated with functional changes, i.e. higher clonogenicity, increased mammospheres formation, and increased glycolysis metabolism. In addition, using in vivo immunodeficient mice models we found that a subpopulation of ALDHhigh cells from the POU1F1 overexpressing MCF-7 cells possess high tumor-initiating capacity, high resistance to chemo- and radiotherapy, and reduced overall survival. Mechanistically, POU1F1 induces an increase in IL-6 mRNA expression and raises IL-6 in the culture medium. This activates the IL-6/JAK/STAT3 pathway, which in turn increases ALDH mRNA expression.

overall_design: RNA-seq profiling of wildtype MCF-7 cells and their overexpreesion of POU1F1 transcripcion factor.

last: Avila

first: David

last: Martinez-Delgado

first: Roman

last: Perez-Fernández


title: Study of epithelial-mesenchymal transition induced by POU1F1 in normal breast cells

first: Sandra

last: Rodríguez González

address: Campus Vida Avenida Barcelona, s/n, 15782, A Coruña

institute: CiMUS

summary: The failure of treatment to deal with intractable cancer cells has raised the question of whether there is a special population of cells in tumor heterogeneity that exhibit resistant phenotypes that favor micrometastasis and have the potential to cause recurrence. One of the current points of view is that most solid cancers, including breast cancer, are stem cell diseases, and that these CSCs are critical to dissemination and metastasis. Our objective is to study the role of POU1F1 in breast cancer cell plasticity. Specifically, we will evaluate whether POU1F1 could modify the phenotype of normal -epithelial- cells to induce its transformation into CSCs/BCSCs

overall_design: RNA-seq profiling of HMEC control and HMEC with POU1F1 overexpression

last: Rodríguez-González


title: MiR-126-driven Vascular Remodeling of Aging Bone Marrow: A Correctable Cause of Age-related Loss of Hematopoietic Activity

city: Duarte

first: Hsun

middle: Teresa

last: Ku

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

summary: We describe here how inflammation-mediated depletion of miR-126 in endothelial cells (ECs) of aging bone marrow niche contributes to vascular remodeling and reduced supply of EC miR-126 to hematopoietic stem cells (HSCs) and causes age-related decrease of HSC self-renewal capacity.

overall_design: RNA-seq were performed with lineage-Sca-1+c-Kit+CD150+CD48- hematopoietic stem cells (HSCs) sorted from 2 month-old young or 20 month-old aged mice (n=3 young HSC samples were pooled from 30 young mice; n=3 aged HSC samples were pooled from 4 aged mice).

first: Bin

last: Zhang

first: Min-Hsuan

last: Chen


title: Rice B2 and B3 RAFs play central roles in both ABA and osmotic stress signaling

city: Shenzheng

first: Xinyong

last: Wang

address: 1088 Xueyuan Avenue, Shenzhen 518055, P.R. China

institute: South University of Science and Technology of China

summary: Rice (Oryza sativa L.) is one of the most important crops worldwide. In the field, rice always faces low humidity, salinity, or drought in various growth stages, which largely limit seedling growth, tillering, filling, and yield of rice. Here, we generated B RAF high-order mutants by CRISPR/Cas9 mediated genome editing.  By RNA-seq analysis, we found rice B2 and B3 RAFs play central roles in osmotic stress responses, the mannitol-induced expression genes are largely impaired. Our findings uncovered the central role of B2 and B3 RAFs in rice's osmotic stress responses and ABA signaling.

overall_design: To investigate the impact of B2 and B3 RAFs on osmotic stress-induced gene expression in rice, we performed a transcriptomics analysis in WT/NIP and raf-b2/3 seedlings with or without 6 hours of 800 mM mannitol treatments. Total RNA was isolated from 5-day-old seedlings of WT/NIP and raf-b2/3 mutant with and without mannitol treatment, and library preparation. All libraries were sequenced in paired-end 150 bases protocol (PE150) on an Illumina Nova sequencer.

first: Guanquan

last: Lin

first: Hongliang

first: Pengcheng


title: Dynamic Multi-omics Profiling Unveils Bimodal Epigenetic Roles of Chromatin O-GlcNAc modification in Premature Senescence Program [RNA-seq]

first: Yubo

last: Liu

overall_design: Gene expression profiling of  human primary fibroblasts cells were performed by RNA-seq(oncogene induce senescence time D0, D2, D4, D6, D8, D10).

first: nana

last: zhang

first: Jianing


title: RNA sequencing data of OTUB1-knockdown in PDGF-BB-treated HASMCs

city: Shanghai

first: Fei

last: Xu

state: Shanghai

address: 1609 Xietu Road

institute: Zhongshan Hospital, Fudan University

summary: We report the high-throughput RNA sequencing on human aortic smooth muscle cells (HASMCs) transfected with siRNA targeting OTUB1 (si-OTUB1) or control siRNA (si-NC). Cells were treated with PDGF-BB for 48 hours.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for cultured primary HASMCs transfected with siRNA (si-NC and si-OTUB1).

first: Han

first: Changyi

last: Zhou


title: Impact of Short term exposure of HFD on gut immune cells

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Prolonged exposure to a high-fat diet (HFD) exacerbates intestinal disease pathology, yet the early events preceding the development of gut inflammation remain poorly understood. Here we show that within 48 hours, HFD impairs intestinal group 3 innate lymphoid cells (ILC3) and their capacity to produce interleukin-22 (IL-22), critical for maintaining gut homeostasis. This loss of function was associated with rapid dysbiosis, increased gut permeability, and reduced production of antimicrobial peptides, mucus, and tight junction proteins. While saturated fatty acids metabolized through oxidation impaired ILC3 function, unsaturated fatty acids sustained IL-22 secretion by ILC3 through the formation of lipid droplets using DGAT enzymes. Upon inflammation, saturated fatty acids significantly impaired IL-22 production by ILC3 and increased the susceptibility of the gut to injury. Our findings reveal the differential acute impact of saturated and unsaturated fatty acids on gut homeostasis through distinct metabolic pathways in ILC3.

overall_design: CD45+ cells from the small intestine of wild-type mice fed with either a regular diet or 36% high fat diet (HFD) were sorted for scRNA-seq. Each group contains 3 biological replicates.

first: Peter

last: Hickey

first: Cyril

last: Seillet


title: innate immune cell memory induced by endogenous and exogenous triggers

city: Oxford

first: Amélie

middle: M

last: Julé

address: Roosevelt Drive, Headington

institute: Kennedy Institute of Rheumatology (KIR)

summary: Innate memory is a key defence mechanism against infection, enhancing protective immunity and limiting unnecessary collateral tissue damage.  Inflammation triggered by endogenous stimuli that signal cellular stress or tissue injury, must also be tightly controlled to balance robust response to intrinsic danger whilst avoiding catastrophic autoimmunity.  Here, we assess the contribution of innate memory to this balance.  The extracellular matrix protein tenascin-C, a damage-associated, toll-like receptor 4 (TLR4) agonist, reprograms monocyte response to subsequent threat, inducing concomitantly suppressed and enhanced responses to rechallenge.  Comparative analysis of memory evoked by tenascin-C and the pathogenic TLR4 agonist, LPS, revealed both common and distinct gene expression signatures, effects that were controlled transcriptionally, These data highlight how intrinsic and extrinsic innate re-programming exerts control over dysregulated inflammatory networks driving either infectious or chronic ‘sterile’ inflammatory diseases.

overall_design: Primary human monocytes from healthy individuals were stimulated for 24hours with LPS (100 ng/mL) or the FBG domain from tenascin-C (FBG-C). Cells were then washed, rested for 5 days, and restimulated for 4 hours with LPS, FBG-C or POLY-I:C (TRIGGER) on day 6 (7D Protocol), or cells washed and immediately restimulated for 2 hours with LPS or FBG-C (24H Protocol). After restimulation with the TRIGGER cells were lysed and transcriptomic changes analyzed by bulk RNAseq. 5 independent donors were analysed.

first: Anja

last: Schwenzer

first: Kim

last: Midwood

first: Amelie

last: Jule

first: Anna

last: Marzeda

first: Bogdan

last: Didov

first: Kieran

last: Woolcock

first: Libby

last: Jennings

last: Yang

first: Jean-Baptiste

last: Richard

first: Steve

last: Sansom

first: Adam

last: Cribbs

first: Wyatt

middle: W

last: Yue

first: Carl

last: Goodyear

first: Karim

last: Raza


title: Chemical genetic interaction linking eIF5A hypusination and mitochondrial integrity

city: Wako-shi

first: Tilman

last: Schneider-Poetsch

email: tilman@cal.berkeley.edu, tsp@riken.jp

state: Saitam

address: 2-1 Hirosawa

department: Center for Sustainable Resource Science

institute: RIKEN

summary: The eukaryotic translation factor eIF5A plays an important role in translation elongation, especially across stretches of prolines and charged amino acids, and in translation termination. eIF5A undergoes hypusination, a post-translational modification unique to this protein, although the role of hypusination in the function of eIF5A remains elusive. Here, we investigated the cellular defects induced by the hypusination inhibitor GC7 (N1-guanyl-1,7-diaminoheptane). Proteome, translatome, and transcriptome analyses indicated that GC7 downregulated a subset of mitochondrial proteins and DNA, causing mitochondrial stress and eliciting the integrated stress response. Chemical genomic screening using barcoded shRNA libraries identified genes encoding proteins involved in polyamine metabolism/transport and MPV17L2, a mitochondrial disease gene homologue whose product regulates mitochondrial translation. Depletion of MPV17L2 caused hypersensitivity to GC7 and phenocopied the effects of GC7 treatment. These results suggest that eIF5A hypusination and MPV17L2 synthetically regulate mitochondrial molecular synthesis and integrity.

overall_design: RNA sequencing  of human cells treated with GC7

first: Ken

last: Matsumoto

first: Rumi

last: Kurokawa

first: Megumi

last: Takase

first: Feng

last: Ling

first: Takehiro

last: Suzuki

first: Makoto

last: Muroi

first: Peixun

last: Han

first: Taisei

last: Wakigawa

first: Masato

first: Kyohei

last: Higashi

first: Hiroyuki

last: Osada


title: Single-cell RNA sequence analysis of fibrotic mouse liver.

first: Yuan

last: Li

address: 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing

department: Post-translational modification

institute: Beijing Proteome Research Center

summary: In this study, we investigated the composition of lymphocytes in the livers of fibrotic mice by single-cell RNA sequence analysis.

overall_design: To induce liver fibrosis, all mice were injected intraperitoneally every two days for 12 weeks with CCl4. Then sorted CD45+ cells were analysed by sc-RNA-seq.

first: Ping

last: Xu

first: Tao

last: Zuo


title: Fibrosis Like Phenotype in TP53KO Hepatic Organoids within a Pro Carcinogenic Tumor Microenvironment (pc-TME)

city: Izmir

first: Mustafa

last: Karabicici

address: Mithatpasa Cad. 58/5 Balcova, Izmir/TURKEY

department: Molecular Biology and Genetic

country: Turkey

institute: Dokuz Eylul University(Izmır Biomedicine and Genome Center)

summary: The main obstacle to understanding the early stage of HCC is the lack of reliable models that mimic precancerous HCC in humans, leading to delayed diagnoses. In this study, we developed a CRISPR/Cas9-mediated TP53 knockout (TP53KO) human iPSC-derived endodermal hepatic organoid model (eHEPO) to simulate the early stage of liver cancer. Transcriptome analysis confirmed that TP53KO eHEPOs have an enrichment score across various signaling pathways, including inflammation, extracellular matrix (ECM) modification, fibrosis, and tumorigenesis as well as altered proliferation and differentiation balance. Furthermore, we observed enrichment in key regulatory elements, including HIF1A, IFNA, and STAT3, alongside discernible alterations in the Wnt/TGFB signaling pathways. Moreover, the histopathological analysis highlighted the presence of atypical cells with altered morphology, pseudo-glandular-tubular rosettes, inflammatory areas reminiscent of steatohepatitis, and hepatocytes displaying ballooning-like features. In conclusion, our in vitro eHEPO model confirms a faithful representation of human physiological and genomic landscapes, harmonizing closely with the current scientific discourse on the complications of liver cancer initiation, fibrogenesis, and disease progression. It proves to be a valuable tool for examining the impact of TP53-like first-hit genes and inflammation on the transformation of protumorigenic hepatic progenitor cells in diverse environments. We envision that this in vitro model holds promise for exploring the interactive effects of distinct microenvironments and gene knockouts. Additionally, it emerges as a potential platform for identifying candidates for early-stage drug development.

overall_design: To investigate the role of TP53KO effect on early stage of hepatic differantiation we collect WT and TP53KO organoids at Day12 in differentiation medium and isolate RNA for RNA-seq.

first: Gokan

last: Karakulah

first: Leman

last: Binokay

first: Soheyl

last: Akbari

first: Esra

last: Erdal


title: Immune checkpoint TIM-3 regulates microglia and Alzheimer’s disease [BulkRNAseq_Dataset1_Batch1_3M]

first: The Gene Lay Institute of

last: Immunology and Inflammation

address: 60 Fenwood Road,

institute: Brigham and Women's Hospital

summary: Microglia are the resident immune cells in the brain and have pivotal roles in neurodevelopment and neuroinflammation1,2. This study investigates the function of the immune-checkpoint molecule TIM-3 (encoded by HAVCR2) in microglia. TIM-3 was recently identified as a genetic risk factor for late-onset Alzheimer’s disease3, and it can induce T cell exhaustion4. However, its specific function in brain microglia remains unclear. We demonstrate in mouse models that TGFβ signalling induces TIM-3 expression in microglia. In turn, TIM-3 interacts with SMAD2 and TGFBR2 through its carboxy-terminal tail, which enhances TGFβ signalling by promoting TGFBR-mediated SMAD2 phosphorylation, and this process maintains microglial homeostasis. Genetic deletion of Havcr2 in microglia leads to increased phagocytic activity and a gene-expression profile consistent with the neurodegenerative microglial phenotype (MGnD), also referred to as disease-associated microglia (DAM). Furthermore, microglia-targeted deletion of Havcr2 ameliorates cognitive impairment and reduces amyloid-β pathology in 5×FAD mice (a transgenic model of Alzheimer’s disease). Single-nucleus RNA sequencing revealed a subpopulation of MGnD microglia in Havcr2-deficient 5×FAD mice characterized by increased pro-phagocytic and anti-inflammatory gene expression alongside reduced pro-inflammatory gene expression. These transcriptomic changes were corroborated by single-cell RNA sequencing data across most microglial clusters in Havcr2-deficient 5×FAD mice. Our findings reveal that TIM-3 mediates microglia homeostasis through TGFβ signalling and highlight the therapeutic potential of targeting microglial TIM-3 in Alzheimer’s disease.

overall_design: Dead neurons labeled with a fluorescnece were injected into the brain of Tim3 flox/flox, and Tim3 flox/flox Cx3cr1 Cre mice. Marker+ (phagocytosing) microlgia (live CD45 int CD11b + Ly6C - 4D4+) and nonphagocytosing microglia were sorted and analyzed.

first: Kimitoshi

last: Kimura

first: Ayshwarya

last: Subramanian

first: Zhuoran

last: Yin

first: Yufan

last: Wu

first: Danyang

last: He

first: Madhumita

last: Das

first: Karen

last: Dixon

first: Udbhav

last: Chitta

first: Ruihan

last: Tang

first: Thomas

last: Pertel

first: Aastha

last: Aastha

first: Masashi

last: Nomura

first: Vasundhara

last: Singh

first: Lei

last: Liu

first: Conner

last: Lambden

first: Neha

last: Gupta

first: Yiran

last: Cheng

first: Sebastian

last: Silveira

first: Huiyuan

last: Zhang

first: Aamir

last: Suhail

first: Toni

last: Delorey

first: Orit

last: Rosenblatt-Rosen

first: Aviv

last: Regev

first: Dennis

last: Selkoe

first: Mario

last: Suva

first: Oleg

last: Butovsky

first: Vijay

last: Kuchroo


title: Efficient profiling of total RNA in single cells with STORM-seq [cell lines]

first: Benjamin

last: Johnson

address: 333 Bostwick Ave NE

institute: Van Andel Institute

summary: Despite significant advances, current single-cell RNA sequencing (scRNA-seq) technologies often struggle with accurately detecting non-coding transcripts, achieving full-length RNA coverage, and/or resolving transcript-level complexity. Many are also difficult to implement or inaccessible without specialized liquid handlers, further limiting their utility. We present Single-cell TOtal RNA-seq Miniaturized (STORM-seq), a random-hexamer primed, ribo-reduced single-cell total RNA sequencing (sc-total-RNA-seq) protocol using standard laboratory equipment. Adapted as a kit, STORM-seq constructs sequence-ready libraries in one working day, producing the highest complexity scRNA-seq libraries to-date, robustly measuring transcript isoforms and clinically relevant gene fusions in single cells. STORM-seq faithfully reconstructs expression profiles of locus-level transposable elements (TEs), and provides high-resolution profiling of transient, low-abundance enhancer RNAs (eRNAs), offering a powerful tool to dissect single-cell gene regulatory networks in unprecedented detail. Applied to human fallopian tube epithelium, the improved transcriptional resolution reveals a putative progenitor-like population and intermediate cell states, shaped by TEs and non-coding RNAs.

overall_design: Benchmarking and investigation of coding and non-coding RNA across cell types (K-562, HEK293T, and RMG-2) using STORM-seq.

first: Mary

middle: F

last: Majewski

first: H. Josh

last: Jang

first: Rebecca

middle: A

last: Siwicki

first: Marc

last: Wegener

first: Ayush

last: Semwal

first: Jacob

last: Morrison

first: Kristin

last: Gallik

first: Michael

last: Hagemann-Jensen

first: Kelly

last: Foy

first: Larissa

last: Rossell

first: Emily

last: Siegwald

first: Dave

last: Chesla

first: Jose

last: Teixeira

first: Marie

last: Adams

first: Ronny

last: Drapkin

first: Corinne

last: Esquibel

first: Rachael

last: Sheridan

first: Ting

last: Wang

first: Rickard

last: Sandberg

first: Timothy

last: Triche Jr.

first: Hui

last: Shen


title: Single-cell gene expression profiles of mice lung tissue under PM2.5 exposure

city: Beijing

first: Guoqing

last: Feng

address: No. 30 Shuangqing Road, Haidian District

institute: Tsinghua University

summary: Numerous epidemiological studies have demonstrated a significant association between PM2.5 exposure and pulmonary diseases. PM2.5 may contribute to epithelial injury and immune dysregulation in lung cells. In this study, we provide single-cell level gene expression profiles of mouse lungs under PM2.5 exposure, offering insights into the microenvironmental alterations and physiological responses induced by PM2.5.

overall_design: C57BL/6 mice were housed and managed at the animal facility. Airborne PM2.5 was collected by air PM sampler and multi-nozzle cascade impactor (MCI) (Tokyo Dylec Co.). The collected airborne PM2.5 was exposed to mice via respiratory tract. The duration of ambient PM2.5 exposure was one month to investigate the relatively long-term physiological effects. Subsequently, fresh lung tissue of mice was cleaned and placed in tissue preservation solution. C57BL/6 mice were randomly assigned to the PM2.5 exposure group and the control group to minimize batch effects in the single-cell experiment.

first: Yu

last: Li

first: Bencheng

last: Lin

first: De

last: Hao

first: Weilai

last: Zhou

first: Wenke

last: Yuan

first: Yuwei

last: Chen

first: Qian

last: Di

first: Miao

last: He

first: Huaiyong


title: Differential analysis of transcriptome of different Trichophyton mentagrophytes strains

city: hangzhou

first: xiao

middle: chen

last: wen

address: desheng_road NO.298

institute: Zhejiang Academy of Agricultural Sciences

overall_design: The CDR1 gene of Trichophyton beardii was knocked out and replenished by ATMT technology. The effect of CDR1 gene on the gene expression profile of Trichophyton beardii was studied by high-throughput sequencing, all the strains were cultured on SDA  plates with  10 days. Then collect the colonies and store them in liquid nitrogen. Perform the next step of high-throughput sequencing.

first: Xiao

last: Chenwen

first: Liang

last: Siyuan

first: Wang

last: Jiaoyu

first: Lin

last: Fucheng


title: Potential of Bezafibrate for Combination with Nivolumab in Treatment of Advanced Non-Small Cell Lung Cancer

city: Kyoto

first: Kenji

last: Chamoto

state: Kyoto

address: Yoshida Konoe-cho, Sakyo-ku

department: Department of Immunology and Genomic Medicine

institute: Graduate School of Medicine, Kyoto University

summary: Background. Novel combination therapies with PD-1/PD-L1 inhibitors are needed to overcome resistance to these drugs. Bezafibrate, a ligand of PGC-1a/PPAR complexes, has shown a synergistic antitumor effect with PD-1 blockade in mice that is mediated by activation of mitochondria in T cells. We have therefore now performed a phase I trial of bezafibrate with nivolumab in previously treated patients with advanced non-small cell lung cancer. The primary end point was the percentage of patients who experience dose-limiting toxicity, and this combination regimen was found to be well tolerated. Preplanned comprehensive analysis of plasma metabolites and gene expression in peripheral cytotoxic T cells indicated that bezafibrate promoted T cell function through upregulation of mitochondrial metabolism including fatty acid oxidation and may thereby have prolonged the duration of response. This combination strategy targeting T cell metabolism thus has the potential to maintain antitumor activity of immune checkpoint inhibitors and warrants further validation.

overall_design: 28 samples, PBMC CD8+T cells, before (-1) and after (-2) the treatment of nivolumab and bezafibrate, R: responder, NR: nonresponder

first: Kentaro

last: Tanaka

first: Sho

last: Saeki

first: Yuki

last: Ikematsu

first: Kazuko

last: Sakai

first: Nobuhisa

last: Ando

first: Ryusuke

last: Hatae

first: Kazuhiro

last: Sonomura

first: Shinsuke

last: Kojima

first: Sidonia

last: Fagarasan

first: Masanori

last: Taketsuna

first: Young

middle: H

last: Kim

first: Hironori

last: Yoshida

first: Hiroaki

last: Ozasa

first: Yuichi

last: Sakamori

first: Fumihiko

last: Matsuda

first: Toyohiro

last: Hirai

first: Kazuto

last: Nishio

first: Takuro

last: Sakagami

last: Fukushima

first: Yoichi

last: Nakanishi

first: Tasuku

last: Honjo

first: Isamu

last: Okamoto


title: A genome-wide CRISPR/Cas9-based functional screen uncovers the KLF4-Survivin/BIRC5 signaling pathway as a key regulator of cell fate following endoplasmic reticulum stress: Implications for tumor growth and therapeutic targeting

city: Philadelphia

first: Constantinos

last: Koumenis

state: PA

address: 13400 Civic Center Blvd

department: Radiation Oncology

institute: University of Pennsylvania

summary: The growth and spread of tumors involve intricate interactions with the surrounding tissue microenvironment. As a tumor develops, it faces various stresses from its microenvironment, including hypoxia, nutrient deficiency, and acidosis. In response to these challenges, cancer cells can hijack existing cytoprotective mechanisms, such as the Unfolded Protein Response (UPR). The UPR activates signaling pathways at the translational and later transcriptional levels to alleviate cellular stress and prevent cell death. However, under unresolved or chronic endoplasmic reticulum (ER) stress, the UPR may paradoxically promote cell death. The precise mechanisms through which the UPR influences cellular fate during ER stress remain poorly understood. To address this knowledge gap, we employed a functional CRISPR-based genetic knockout screen to identify novel regulators of the UPR. Using a lentiviral genome-wide CRISPR-Cas9 knockout library, we identified over-represented sgRNAs (associated with pro-apoptotic genes) and underrepresented sgRNAs (associated with pro-survival genes) following ER stress induced by Thapsigargin and Tunicamycin. One of the top candidates identified was Survivin/BIRC5, a protein with anti-apoptotic and cell cycle regulatory activities and which is overexpressed in tumor cells compared to healthy tissues. Functional studies revealed that genetic or pharmacological inhibition of Survivin expression enhanced ER stress-induced apoptosis, but not apoptosis in response to other forms of stress. These findings were validated in multiple cancer cell lines, ruling out off-target effects. Mechanistically, ER stress led to PERK-dependent downregulation of Survivin, and overexpression of Survivin blocked Thapsigargin-induced apoptosis. In vivo xenograft models showed that combining Survivin ablation with PERK inhibition significantly delayed tumor growth and improved overall survival. Through a combination of bioinformatics analysis and loss-of-function studies, we identified the transcription factor KLF4 as a mediator of PERK-dependent effects on Survivin repression. Notably, CRISPR-mediated KLF4 knockout successfully rescued Survivin levels post-ER stress. Additionally, an analysis of TCGA data across various tumor types provided supporting evidence of a negative correlation between KLF4 and Survivin expression. In summary, this study unveils a novel regulatory axis, PERK-KLF4-Survivin, as a key determinant of cell fate in the cellular responses to ER stress. Targeting Survivin in conjunction with PERK inhibition showed promising antitumor effects in vivo. The growth and spread of tumors involve intricate interactions with the surrounding tissue microenvironment. As a tumor develops, it faces various stresses from its microenvironment, including hypoxia, nutrient deficiency, and acidosis. In response to these challenges, cancer cells can hijack existing cytoprotective mechanisms, such as the Unfolded Protein Response (UPR). The UPR activates signaling pathways at the translational and later transcriptional levels to alleviate cellular stress and prevent cell death. However, under unresolved or chronic endoplasmic reticulum (ER) stress, the UPR may paradoxically promote cell death. The precise mechanisms through which the UPR influences cellular fate during ER stress remain poorly understood. To address this knowledge gap, we employed a functional CRISPR-based genetic knockout screen to identify novel regulators of the UPR. Using a lentiviral genome-wide CRISPR-Cas9 knockout library, we identified over-represented sgRNAs (associated with pro-apoptotic genes) and underrepresented sgRNAs (associated with pro-survival genes) following ER stress induced by Thapsigargin and Tunicamycin. One of the top candidates identified was Survivin/BIRC5, a protein with anti-apoptotic and cell cycle regulatory activities and which is overexpressed in tumor cells compared to healthy tissues. Functional studies revealed that genetic or pharmacological inhibition of Survivin expression enhanced ER stress-induced apoptosis, but not apoptosis in response to other forms of stress. These findings were validated in multiple cancer cell lines, ruling out off-target effects. Mechanistically, ER stress led to PERK-dependent downregulation of Survivin, and overexpression of Survivin blocked Thapsigargin-induced apoptosis. In vivo xenograft models showed that combining Survivin ablation with PERK inhibition significantly delayed tumor growth and improved overall survival. Through a combination of bioinformatics analysis and loss-of-function studies, we identified the transcription factor KLF4 as a mediator of PERK-dependent effects on Survivin repression. Notably, CRISPR-mediated KLF4 knockout successfully rescued Survivin levels post-ER stress. Additionally, an analysis of TCGA data across various tumor types provided supporting evidence of a negative correlation between KLF4 and Survivin expression. In summary, this study unveils a novel regulatory axis, PERK-KLF4-Survivin, as a key determinant of cell fate in the cellular responses to ER stress. Targeting Survivin in conjunction with PERK inhibition showed promising antitumor effects in vivo. The growth and spread of tumors involve intricate interactions with the surrounding tissue microenvironment. As a tumor develops, it faces various stresses from its microenvironment, including hypoxia, nutrient deficiency, and acidosis. In response to these challenges, cancer cells can hijack existing cytoprotective mechanisms, such as the Unfolded Protein Response (UPR). The UPR activates signaling pathways at the translational and later transcriptional levels to alleviate cellular stress and prevent cell death. However, under unresolved or chronic endoplasmic reticulum (ER) stress, the UPR may paradoxically promote cell death. The precise mechanisms through which the UPR influences cellular fate during ER stress remain poorly understood. To address this knowledge gap, we employed a functional CRISPR-based genetic knockout screen to identify novel regulators of the UPR. Using a lentiviral genome-wide CRISPR-Cas9 knockout library, we identified over-represented sgRNAs (associated with pro-apoptotic genes) and underrepresented sgRNAs (associated with pro-survival genes) following ER stress induced by Thapsigargin and Tunicamycin. One of the top candidates identified was Survivin/BIRC5, a protein with anti-apoptotic and cell cycle regulatory activities and which is overexpressed in tumor cells compared to healthy tissues. Functional studies revealed that genetic or pharmacological inhibition of Survivin expression enhanced ER stress-induced apoptosis, but not apoptosis in response to other forms of stress. These findings were validated in multiple cancer cell lines, ruling out off-target effects. Mechanistically, ER stress led to PERK-dependent downregulation of Survivin, and overexpression of Survivin blocked Thapsigargin-induced apoptosis. In vivo xenograft models showed that combining Survivin ablation with PERK inhibition significantly delayed tumor growth and improved overall survival. Through a combination of bioinformatics analysis and loss-of-function studies, we identified the transcription factor KLF4 as a mediator of PERK-dependent effects on Survivin repression. Notably, CRISPR-mediated KLF4 knockout successfully rescued Survivin levels post-ER stress. Additionally, an analysis of TCGA data across various tumor types provided supporting evidence of a negative correlation between KLF4 and Survivin expression. In summary, this study unveils a novel regulatory axis, PERK-KLF4-Survivin, as a key determinant of cell fate in the cellular responses to ER stress. Targeting Survivin in conjunction with PERK inhibition showed promising antitumor effects in vivo.

overall_design: Functional knockout CRISPR/Cas9-based screens were performed in SQ20B and A375 cells to identify new mediators of Endoplasmic Reticulum (ER) stress. The Human GeCKO_v2 sgRNA libraries (AddGene Pooled Library #1000000048, #1000000049) were utilized. 10^8 A375 or SQ20B cells were transduced in 60-well plates both with A and B half-libraries at a MOI of 0.3. After 48h, cells were selected with puromycin for 3 days and an initial pool of 40 million cells was harvested (Qiagen Blood and Tissue extraction kit) for genomic DNA extraction (UT samples). After puromycin selection, cells were left to repopulate the plates and were treated for 24h with 0.5uM of Thapsigargin or Tunicamycin, two ER stress imitators. After 50% of the cells died due to ER stress, the remaining cells were left to grow and treatment with Thapsigargin or Tunicamycin was repeated once more to increase the resistance to ER stress population. Cells were collected for lysing and DNA isolation. After a 72h recovery and expansion, their genomic DNA was extracted and PCR-amplified. A second step PCR was performed to add a specific adaptor sequence to each sample, forming the sgRNA fragment libraries. Next-generation sequencing was performed on an Illumina HiSeq 2500 system to quantify the presence of each sgRNA. After demultiplexing, QC and adapter removal, MAGeCK v0.5.7 was applied to assess gene importance.

first: Nektaria

last: Leli

first: Souvik

last: Dey

first: Hengxi

last: Liu

first: Carlo

last: Salas-Salinas

first: Spyros

last: Tastsoglou

first: Giorgos

last: Skoufos

first: Lauren

last: Brady

first: Victoria

last: Wu

first: Ioannis

last: Verginadis

first: Evangelos

last: Kollettas

first: Crystal

last: Conn

first: Artemis

last: Hatzigeorgiou


title: ILMN_2300_PiganelliJon_totalRNAseq36_Oct2024. RNA Sequessing of Pocinr Kidney Endothelial cells transfected with Control GFP and ST8Sia6 Plasmid

status: Public on May 05 2025

city: Indianapolis

first: Saptarshi

last: Roy

state: Indiana

address: 1210 Waterway Blvd Ste 4100, 16 Tech Innovation Bldg 1

institute: CDMD Indiana University School of Medicine, India

summary: To check the effectes of ST8Sia6 overexpression we performed total RNS sequesnning in porcine kidney endothelial cells to understand the biological functions of DEGs associated with ST8Sia6 overexpression in porcine kidney endothelial cells upon co-culture with human PBMCs, transcriptomic analysis was performed on four independent experimental conditions, including control GFP-expressing cells and ST8Sia6-overexpressing cells.

overall_design: Porcine kidney endothelial cells overexpressing ST8Sia6 and control-GFP cells were collected from four individual experiment after 24 hours transfection for total RNA extraction. Similarly, cells overexpressing ST8Sia6 and control-GFP were collected from co-culturing with four individuals PBMCs as previously described. Cells from different experimental conditions were collected keeping in ice, maintaining temperature at 4°C, washed with cold PBS, and stored as cell pellets at -80°C for total-RNA isolation.

first: Chaitra

last: Rao

first: Jon

last: Piganelli


title: Rebamipide Induces Hair Regeneration through EP4-Driven Lipid Metabolism Remodeling

city: Nanjing

first: Chenjie

last: Feng

state: Jiangsu

address: #24 TongJiaXiang, Gulou District

institute: Cna Pharmaceutical University

summary: Alopecia is a highly prevalent hair loss disorder characterized by abnormality of hair cycling. Induction of autophagy and secretion of growth factors by adipocyte precursors are sufficient to activate quiescent hair follicles. Yet therapies targeting these processes remain limited. Here, we identify rebamipide, a drug initially intended for gastric ulcer treatment, as a promising candidate for hair regeneration by modulating dermal adipocyte metabolism. Topical rebamipide treatment induces autophagy and ATGL-mediated lipolysis in dermal adipocytes. Through primary culture systems, we demonstrate that rebamipide-driven lipolysis triggers adipocyte dedifferentiation, activating HFSCs via elevated PDGFα levels. Mechanistically, computer simulations and target validation experiments confirm that rebamipide directly binds to the prostaglandin E receptor EP4, triggering PI3K/ERK-dependent autophagy and lipolysis. Collectively, our findings highlight EP4 as a novel therapeutic target for alopecia and position rebamipide as an agent that couples lipid metabolism remodeling with HFSC activation.

overall_design: RNA-seq profiling of dorsal skins from C57BL/6 mice treated with vechile or 3% rebamipide at Day 7

first: Hao

last: Dong

first: Liang


title: Type I interferon drives T cell cytotoxicity by upregulation of interferon regulatory factor 7 in autoimmune kidney diseases

city: Hamburg

first: Robin

last: Khatri

address: Falkenried 94

department: Institute of Medical Systems Biology

institute: University Medical Center Hamburg-Eppendorf

summary: In anti-neutrophil cytoplasmic antibody-associated vasculitis (AAV) and systemic lupus erythematosus (SLE), glomerulonephritis is a severe kidney complication driven by immune cells, including T cells. However, the mechanisms underlying T cell activation in these contexts remain elusive. Here we report that in patients with AAV and SLE, type I interferon (IFN-I) induces T cell differentiation into interferon-stimulated genes-expressing T (ISG-T) cells, which are characterized by an elevated IFN-I signature, an immature phenotype, and cytotoxicity in inflamed tissue. Mechanistically, IFN-I stimulates the expression of interferon regulatory factor 7 (IRF7) in T cells, which in turn induces granzyme B production. In mice, blocking IFN-I signaling reduces IRF7 and granzyme B expression in T cells, thus ameliorating glomerulonephritis. In parallel, spatial transcriptomic analyses of kidney biopsies from patients with AAV or SLE reveal an elevated ISG signature and the presence of ISG-T cells in close proximity to plasmacytoid dendritic cells, the primary producers of IFN-I. Our results from both patients and animal models thus suggest that IFN-I production in inflamed tissue may drive ISG-T cell differentiation to expand the pool of cytotoxic T cells in autoimmune diseases.

overall_design: A crescentic glomerulonephritis model was induced in wild-type C57BL/6 mice for 10 days. CD45⁺ cells were isolated from the spleen and blood by FACS for scRNA-seq analysis. From the kidneys of healthy wild-type C57BL/6 mice, CD3⁺ T cells were isolated by FACS for scCITE-seq analysis.

first: Huiying

last: Wang

first: Jonas

last: Engesser

first: Ulf

last: Panzer

first: Nariaki

last: Asada


title: Identification of anti-inflammatory effects of Protaetia brevitarsis seulensis larvae in IL-1β-induced chondrosarcoma cells based on systematic transcriptome analysis

city: Daejeon

first: Su-Jin

last: Baek

address: 1672, Yuseong-daero

institute: KOREA INSTITUTE of ORIENTAL MEDICINE

summary: Osteoarthritis (OA) is a complex degenerative joint and multi-factorial disease. Developing new targeting strategies that can be used to understand its molecular mechanisms is critical owing to the difficulty in treating OA. Protaetia brevitarsis seulensis larvae present high therapeutic value; however, the presence of various active compounds and the multi-factorial risk factors for OA renders the precise mechanisms of action unclear. We screened the key mechanisms of action of P. brevitarsis seulensis larvae aqueous extract (PBSL) and its compounds using systematic transcriptome analysis. Major mechanisms and transcription factors of PBSL were analyzed by profiling gene expression changes in interleukin (IL)-1β-induced human chondrosarcoma cell (SW1353) treated with PBSL. Furthermore, an in vitro assay was perfomed to validate the efficacy of the novel mechanism and targets of PBSL. PBSL exerted anti-inflammatory effects on SW1353 cells by regulating many molecular pathways. The IL-6/JAK/STAT3 pathway was significantly downregulated by PBSL, and STAT3 was identified as a major transcription factor regulating PBSL-induced target gene expression. Furthermore, we found that among the six PBSL compounds, the major compound was regulated by the IL-6/JAK/STAT3 pathway. Our findings reinforce the idea that inhibiting the IL-6/JAK/STAT3 pathway is a therapeutic target for treating OA, providing potential novel mechanisms and transcription factors for PBSL and its active compounds against OA.

overall_design: To investigate the transcriptomic signatures of PBSL, we performed RNA-sequencing data on the untreated cells (NC; n=3), IL-1β-induced SW1353 cells (IL1b; n=3), and IL-1β-induced and PBSL-treated cells (PBSL; n=3).

first: Jin Mi

last: Chun

first: Jun Hong

last: Park

first: Byeong Cheol

last: Moon


title: Signature of NK cells that are enriched for IL-10 production in malaria infection history subjects

city: Minneapolis

first: Geoffrey

middle: Thomas

last: Hart

state: MN

address: 689 23rd Ave SE

department: Medicine

institute: University of Minnesota

summary: Plasmodium falciparum infection can trigger high levels of inflammation that lead to fever and sometimes severe disease. People living in malaria-endemic areas gradually develop resistance and control both parasite numbers and the inflammatory response. Adaptive Natural Killer (NK) cells correlate with reduced parasite load and protection from symptoms. However, additional NK cell immunoregulatory roles may lower inflammation and reduce fever induction. We previously found that murine NK cell production of IL-10 can protect mice from experimental cerebral malaria. Human NK cells can also secrete IL-10, but it was unknown what NK cell subsets produce IL-10 and if this is affected by malaria infection history. Here, we show that NK cells from subjects with malaria history make significantly more IL-10 than subjects with no malaria history. We then determined the proportions of NK cells that are cytotoxic and produce interferon g (IFNg) and/or IL-10 and identified a signature of adaptive and checkpoint molecules on IL-10 producing NK cells. Lastly, we find that co-culture with primary monocytes, Plasmodium-infected RBCs, and antibody induces IL-10 production by NK cells. These data suggest that NK cells may help with protection from malaria because of IL-10 induction.

overall_design: Single-cell RNA-Seq analysis was carried out using the ddSEQTM Single-Cell Isolator (Bio-Rad, Hercules, CA) and the SureCellTM WTA 3' Library Prep Kit (Illumina, San Diego, CA). Magnetically enriched NK cells from malaria naïve subjects were treated with cytokines IL-15, IL-21, IL-12 or IL-15 alone prior to capture on the ddSeq Single-Cell Isolator. Library preparation was done using SureCellTM WTA 3' Library Prep Kit. Resulting libraries were analyzed for an appropriate length distribution using an Agilent TapeStation, and initially sequenced on the Illumina MiSeq Nano with read lengths: read 1 = 70 bp, index = 8 bp, R2 = 76 bp. Deeper sequencing was then achieved using an Illumina NextSeq 550 High-ouput 2x75 flow cell  (total = 6 samples). Per-cell gene expression was quantified for each sample using the BaseSpace® SureCellTM RNA Single-Cell Analysis Workflow v1.2.0 from Illumina, which uses Isas v1.2.6-000184develop for analysis, STAR v2.5.2b for read alignment to the Homo sapiens UCSC hg38 genome, and SAMtools v 1.3. Data was processed downstream using the Seurat single-cell analysis pipeline v4 in R v 4.1.0 (https://doi.org/10.1038/nbt.4096  ). Samples were filtered of low quality (number gene Features < 200) cells  before normalization with SCTransform (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1874-1) using 3,000 variable genes, and batch correction using the Seurat integration procedure using the top 30 PCs (Stuart et al., 2019 ; https://www.cell.com/cell/fulltext/S0092-8674(19)30559-8). UMAP visualizations and nearest neighbor clustering (Louvain algorithm) were performed using the top 6 PCs. Purified NK cells were used and single cells that were determined CD3 negative by gene expression were 0 and were labeled as IL10 positive if IL10 raw counts ≥ 1. NK cells that were CD3 negative and IL10 negative were compared to cells that were NK cells that were CD3 neg and IL10 positive (baseline group) with the Wilcoxon rank sum test using their SCT-normalized gene counts (assay=“SCT”, min.pct=0.1, logfc.threshold=0, only.pos=FALSE). Genes were considered differentially expressed if FDR < 0.05. Those DEGs were plotted using the Seurat DotPlot() function.

first: Sarah

last: McNitt

first: Jenna

last: Dick

first: Maria

last: Castaneda

first: Jules

last: Sangala

first: Mark

last: Pierson

first: Marissa

middle: G

last: Macchietto

first: Kristina

middle: S

last: Burrack

first: Peter

last: Crompton

first: Karl

last: Seydal

first: Sara

middle: E

last: Hamilton

middle: T


title: Functional heterogeneity analysis of Vibrio algalinolyticus cells in biofilm based on M20 single-cell sequencing [scRNA-seq]

city: Xiamen

first: qiu

last: li

address: No. 185, Yinjiang Road, Jimei District, Xiamen City, Fujian Province

institute: Jimei University

summary: The heterogeneity of bacterial cells in biofilms is an important property. We performed single-cell sequencing to profile heterogeneous cell populations within Vibrio alginolyticus biofilm. Our analysis has revealed the key functional compartments for the composition and development of biofilms

overall_design: After 60 hours of incubation at 28°C on LB agar, Vibrio algalinolyticus developed mature biofilms, which were collected for single-cell sequencing to investigate the functional heterogeneity of bacterial cells within the biofilm.

first: Qiu

last: Li

first: Lixing

last: Huang


title: RNA sequencing in Atp7b -/- mice under high-fat diet conditions

first: Zixuan

last: Wang

address: 1665 Kongjiang Road, Shanghai, China

institute: Xin Hua Hospital affiliated to Shanghai Jiao Tong University School of Medicine

summary: The aim of this study was to elucidate the impact of ATP7B deficiency on hepatic gene expression profiles in mice fed a high-fat diet. Systemic ATP7B-knockout (Atp7b-/-) mice on a C57BL/6J genetic background were generated via CRISPR/Cas9 technology and subjected to a high-fat, high-fructose, and high-cholesterol diet (abbreviated as high-fat diet, HFD) for 24 weeks to establish a steatohepatitis model. Hepatic gene-expression profiles were analyzed by RNA sequencing (RNA-seq). ATP7B deficiency exacerbated hepatic inflammation and fibrosis in HFD-fed mice, as revealed by RNA-seq data.

overall_design: Liver gene expression signature were compared between wild-type (WT) and Atp7b-/- mice at 24 weeks of HFD feeding.

first: Qingyang

last: Xu

first: Mengyu

first: Jiangao

last: Fan


title: Insights into the target-directed miRNA degradation mechanism in Drosophila ovarian cell culture

city: Moscow

first: Sergei

last: Ryazansky

address: Kurchatov sq., 2

department: Department of Molecular Genetics of Cell

country: Russia

institute: Institute of Molecular Genetics

summary: Target-directed miRNA degradation (TDMD) is a process of post-transcriptional regulation of miRNA stability in animals induced by an extended pairing of Ago-bound miRNAs with specialized complementary RNA targets. As suggested by studies on human cell culture, Ago engaged with the extended duplex is recognized by the ZSWIM8 receptor of the Cullin-RING-ligase complex (CRL3), which also contains Cul3, EloB, and EloC proteins. The CRL activity is accelerated by the neddylation of Cul3 with the involvement of the E2 conjugating protein UbcE2M. The CRL ubiquitinates Ago, resulting in proteolysis of Ago and degradation of the released miRNAs. To date, the molecular mechanism of TDMD has not been studied in other species. To further characterize TDMD in animals, we investigated the protein Dora, the Drosophila ortholog of ZSWIM8, in the culture of Drosophila ovarian somatic cells (OSC). We showed that Dora in OSCs localizes in protein granules unrelated to P- and GW-bodies. The dora knockout resulted in the accumulation of multiple miRNAs, including miR-7-5p, and transcriptome-wide affected the mRNA targets of differentially expressed miRNAs. We also showed that Dora associates with proteins of the CRL3 complex, and the depletion of CRL3 components or inhibition of Cul3 neddylation upregulates miR-7-5p. We concluded that the molecular mechanism of TDMD is conserved in humans and Drosophila. Finally, we found that cells without Dora have an impaired Notch signaling pathway, indicating that TDMD in OSCs may contribute to the modulation of the Notch pathway.

overall_design:
Using Cas9-based techniques, we obtained two Drosophila OSC cell cultures: one with an endogenously HA-tagged Dora gene (OSC[DoraHA]) and one with DoraHA carrying the puromycin resistance gene integrated into it (OSC[DoraHA-KO]).
To compare the contents of mRNAs in OSC[DoraHA]) and OSC[DoraHA-KO], we performed 3’-end RNA-seq using the original protocol. Total RNA from each OSC line was reverse transcribed with oligo-dT primers containing 9 nt UMI and 4 nt sample-specific barcodes. The cDNA from different samples was pooled for further library preparation for paired-end sequencing. Raw R1 reads were demultiplexed according to the sample barcodes, UMI-based deduplicated, and proceeded further for the quantification of mRNA species. The libraries of each genotype were prepared in two biological replicas.
To compare the contents of miRNAs, total RNA from OSC[DoraHA]) and OSC[DoraHA-KO] were separated in PAGE, and gel pieces containing 20-25 nt in length RNA were excised. The library preparation for single-end sequencing was performed with gel eluted fractions of small RNAs according to a randomized splint ligation protocol (https://doi.org/10.1093/nar/gkaa480). The libraries of each genotype were prepared in two biological replicas.

first: Natalia

last: Akulenko

first: Elena

last: Mikhaleva


title: Bisphenol A-induced renal metabolic disruption: Insights into MAPK-mediated steroid hormone dysregulation from transcriptomic and metabolomic analyses

city: Taiyuan

first: Rui

last: Gao

address: Shanxi University of Medical Sciences, 98 University Street, Yuci District, Jinzhong City, Shanxi Province

institute: shanxi medical university

summary: After long-term exposure of BPA, human is probably suffering from invisible renal injury and metabolic disruption, while its linked intricate gene transcriptional mechanisms warrant more conclusive evidence.  Comprehensive analysis utilizing transcriptomics and metabolomics were used to elucidate the transcriptional mechanisms regulating metabolic homeostasis involved in BPA-induced nephrotoxicity. Here, six-week-old male ICR (CD1) mice were randomly divided into vehicle group with 10 mice and BPA exposure group with 10 mice (five mice per cage). The mice in the exposure group received a daily gavage of BPA dissolved in an aqueous solution containing 0.1% ethanol at the dose of 50 μg/kg/d, which is the tolerable daily intake (TDI) dose of BPA. The mice in the vehicle group received the same dose of aqueous solution containing 0.1% ethanol. After 6-week exposure, the mice were euthanized and left kidney were tissues were frozen with liquid nitrogen and used for RNA transcriptome sequencing.

overall_design: RNA-seq profiling of kidney after BPA exposure


title: Nucleosome positioning and sensitivity suggest novel functional organization of the purple sea urchin (Strongylocentrotus purpuratus) genome

city: Tallahassee

first: Jonathan

last: Dennis

state: FL

address: 319 Stadium Drive

department: Biological Science

institute: Florida State University

summary: The eukaryotic nucleosome is the fundamental subunit of chromatin and plays functional roles in DNA templated processes including replication and transcription. In eukaryotic promoters, nucleosome organization is generally thought to be highly structured, with nucleosomes occupying canonical positions flanking the transcription start site (TSS), thereby regulating access of the transcriptional machinery to the underlying DNA. We sought to determine whether this canonical distribution is present in the purple sea urchin, Strongylocentrotus purpuratus, an important developmental model organism.  We used titrations of micrococcal nuclease to produce high throughput maps of nucleosome distribution, sensitivity to digestion, and subnucleosomal footprints from female urchin gonad tissue. Unlike yeast, flies, zebrafish, maize, or humans, urchins lack a nucleosome depleted region over TSSs. Urchin promoters are dominated by strongly positioned and highly occupied +1 and +2 nucleosomes which are most prominent in highly expressed genes. Additionally, urchin promoters exhibit distinct patterns of sensitivity to nuclease digestion, with heightened sensitivity upstream of the TSS and limited resistance to nuclease digestion. Discretely positioned sensitive nucleosomes were enriched in promoters of highly expressed genes, suggesting a relationship between nucleosome sensitivity and transcriptional regulation. Moreover, urchin promoters were enriched for small fragment-protected footprints associated with known regulatory motifs. Collectively, we present a comprehensive overview of the unique interplay between nucleosome positioning, chromatin sensitivity, cis-regulatory interactions, and gene expression in sea urchins. Our study not only provides a reproducible methodology applicable to other organisms, but also advances our understanding of functional chromatin organization and gene regulation in urchins.

overall_design: MNase-seq of wild caught Strongylocentrotus purpuratus female gonad tissue.

first: Jane

last: Benoit

first: Maya

middle: J

last: Munstermann

first: Sam

last: Karelitz

first: Lorea

middle: N

last: Arambarri

first: Daniel

middle: K

last: Okamoto