title: Immunomodulatory Role of the Stem Cell Circadian Clock in Muscle Repair [RNA-Seq]

city: Chicago

first: Pei

last: Zhu

address: 420 E. Superior St

institute: northwestern university

summary: The circadian clock orchestrates vital physiological processes such as metabolism, immune function, and tissue regeneration, aligning them with the optimal time of day. This study identifies an intricate interplay between the circadian clock within muscle stem cells (SCs) and their capacity to modulate the immune microenvironment during muscle regeneration. We uncover that the SC clock provokes time-of-day (TOD)-dependent induction in inflammatory response genes following injury, particularly those related to neutrophil activity and chemotaxis. These responses are driven by rhythms of cytosolic regeneration of the signaling metabolite NAD+. We demonstrate that genetically enhancing cytosolic NAD+ regeneration in SCs is sufficient to induce robust inflammatory responses that significantly influence muscle regeneration. Furthermore, using mononuclear single-cell sequencing of the regenerating muscle niche, we uncover a key role for the cytokine CCL2 in mediating SC-neutrophil crosstalk in a TOD-dependent manner. Our findings highlight a crucial intersection between SC metabolic shifts and immune responses within the muscle microenvironment, dictated by the circadian rhythms, and underscore the potential for targeting circadian and metabolic pathways to enhance tissue regeneration.

overall_design: Pax7-zsgreen mice, which were sequentially perfused with 50 ml of ice-cold PBS, followed by 50 ml mild fixative (0.5% paraformaldehyde), and subsequently quenched with 50 ml 2M glycine. SCs were extracted from the hindlimb muscles of Pax7-zsgreen mice, both uninjured and following cardiotoxin-induced injury at ZT16, on day 1 post-injury, and subjected to RNA sequencing for transcriptome analysis.

first: Eric

last: Pfrender

first: Adam

last: Steffeck

first: Collen

middle: R

last: Reczek

first: Yalu

last: Zhou

first: Abhishek

last: Thakkar

first: Neha

last: Gupta

first: Ariana

last: Kupai

first: Amber

last: Willbanks

first: Richard

last: Lieber

first: Ishan

last: Roy

first: Navdeep

middle: S

last: Chandel

first: Clara

last: Peek


title: (RNA-seq-SHSY5Y) Hao-Fountain syndrome protein USP7 mediates neuronal differentiation via BCOR-ncPRC1.1

status: Public on Mar 12 2025

city: Belfast

first: Yaser

last: Atlasi

address: Lisburn Road

department: patrick G Johnston Centre for Cancer research

country: United Kingdom

institute: Queen's University Belfast

type: Expression profiling by high throughput sequencing

summary: Pathogenic variants of ubiquitin-specific protease 7 (USP7) cause the neurodevelopmental disorder Hao-Fountain syndrome. However, which of its pleiotropic substrates are relevant for neurodevelopment has remained unclear. Here, we present a combination of quantitative proteomics, transcriptomics and epigenomics to define the core USP7 circuitry during neurodifferentiation. USP7 activity is required for the transcriptional programs that direct the differentiation of human ESCs to neural stem cells, and neuronal differentiation of SHSY5Y neuroblastoma cells. In addition to other substrates, including TRIM27, USP7 controls the dosage of the Polycomb H2AK119ub1 ubiquitin ligases ncPRC1.1 and ncPRC1.6. We found that BCOR-ncPRC1.1, but not ncPRC1.6 or TRIM27, is a key effector of USP7-dependent neuronal differentiation. Indeed, BCOR-ncPRC1.1 mediates the majority of USP7-dependent gene regulation during this process. Besides providing a detailed map of the USP7 regulome during neuronal differentiation, our results suggest that Hao-Fountain syndrome and ncPRC1.1-associated neurodevelopmental disorders involve dysregulation of a shared epigenetic network.

overall_design: RNA-seq in SHSY5Y neuroblastoma treated with USP7 inhibitor, or deleted for p53, BCOR, or USP7

first: Joyce

middle: W

last: van der Meer

first: Axelle

last: Larue

first: Jan

middle: A

last: van der Knaap

first: Gillian

middle: E

last: Chalkley

first: Ayestha

last: Sijm

first: Leila

last: Beikmohammadi

first: Aniek

last: van der Vaart

first: Karel

last: Bezstarosti

first: Dick

last: Dekkers

first: Wouter

last: Doff

first: P.

middle: J

last: van de Wetering-Tieleman

first: K

last: Lanko

first: T

last: Barakat

first: Tim

last: Allertz

first: A

last: van Haren

first: Jeroen

last: Demmers

first: C

middle: P

last: Verrijzer


title: Hao-Fountain syndrome protein USP7 mediates neuronal differentiation via BCOR-ncPRC1.1

first: Yaser

last: Atlasi

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: (ChIP-seq-SHSY5Y) Hao-Fountain syndrome protein USP7 mediates neuronal differentiation via BCOR-ncPRC1.1

overall_design: ChIP-seq for BCOR, H2AK119Ub, H3K27me3 in SHSY5Y neuroblastoma, with USP7 inhibitor in neural differentiation media

first: Joyce

last: van der Meer

first: Axelle

last: Larue


title: Transcriptomic Analysis of adah-1 and pnp-1 RNAi treated  C. elegans

city: La Jolla

first: Emily

last: Troemel

state: CA

address: 9500 Gilman Dr, 4205 Bonner Hall

department: Cell and Developmental Biology

country: USA

institute: UC San Diego

summary: RNA-seq was used to identify gene expression changes in C. elegans upon adah-1 and pnp-1 RNAi treatment

overall_design: Ten C. elegans N2 at L4 stage (P0) were picked onto RNAi plates seeded with adah-1, pnp-1, or L4440 cultures in E. coli HT115 background and incubated at 20°C until their progeny (F1) became gravid adults, which were bleached to obtain synchronized L1 progeny. 1500 L1 progeny (F2) were plated on two 10cm RNAi plates seeded with the respective RNAi culture. These animals were incubated at 20°C for 56 hours, at which point animals were adults and collected for RNA extraction.

first: Nicole

middle: D

last: Wernet

first: Eillen

last: Tecle

first: Mario

middle: B

last: Sarmiento

first: Cheng-Ju

last: Kuo

first: Crystal

last: Chhan

first: Ian

last: Baick

first: Latisha

last: Franklin

first: Wendy

last: Hanna-Rose


title: (RNA-seq-H9) Hao-Fountain syndrome protein USP7 mediates neuronal differentiation via BCOR-ncPRC1.1

overall_design: RNA-seq in H9-hESCs treated with USP7 inhibitor in expansion or neural differentiation media

first: Jan

last: van der Knaap

first: Gillian

last: Chalkley

first: Ayestha

last: Sijm

first: Leila

last: Beikmohammadi

first: Aniek

last: van der Vaart

first: Karel

last: Bezstarosti

first: Dick

last: Dekkers

first: Wouter

last: Doff

first: P.

last: van de Wetering-Tieleman

first: K

last: Lanko

first: T

last: Barakat


title: A novel role of Acyl-CoA Thioesterase 12 in the pathogenesis of renal fibrosis

city: Seoul

first: Ee Hyun

last: Kim

state: State...

address: 52 Ewhayeodae-gil, Seodaemun-gu

country: South Korea

institute: Ewha University

summary: Lipid mal-metabolism, particularly fatty acid oxidation (FAO) dysfunction, is a major driver of renal fibrosis. However, detailed regulatory mechanisms underlying this process remain unclear. In this study, we demonstrated that acyl-CoA thioesterase 12 (Acot12) is a key regulator of lipid metabolism in fibrotic kidneys. A significantly decreased level of ACOT12 was observed in a kidney sample of human patients with chronic kidney disease as well as in mouse kidney injury. Acot12 deficiency induces lipid accumulation and fibrosis in mice subjected to unilateral ureteral obstruction (UUO). Fenofibrate administration does not reduce renal fibrosis in Acot12-/- mice with UUO. Moreover, restoration of peroxisome proliferator-activated receptor (PPAR in Acot12-/- Ppar-/- kidneys with UUO exacerbated lipid accumulation and renal fibrosis, whereas restoration of Acot12 in Acot12-/- Ppar-/- kidneys with UUO significantly reduced lipid accumulation and renal fibrosis suggesting, mechanistically, Acot12 deficiency exacerbates renal fibrosis independently of PPAR. In Acot12-/- kidneys with UUO, a reduction in the selective autophagic degradation of peroxisomes and pexophagy with a decreased level of ACBD5 was observed. In conclusion, our study demonstrates the functional role and mechanistic details of Acot12 in the progression of renal fibrosis, provides a preclinical rationale for regulating Acot12 expression and presents a novel means of preventing renal fibrosis.

overall_design: C57BL/6N mice (6-7 weeks old, male) underwent unilateral ureteral obstruction (UUO) surgery and the kidneys were collected on the seventh day. Wildtype and Acot12-/- mice were used.

first: Ee

middle: H

first: Mi-kyung

first: Mi-Sun

last: Choe

first: Ji

last: Ryu

first: Eun

last: Pak

first: Hunjoo

last: Ha

first: Eun-Jung

last: Jin


title: NRF2 activation by cysteine as a mechanism of survival for Triple Negative Breast Cancer cells

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

country: Germany

institute: Universitätsklinikum Schleswig-Holstein

summary: Triple-negative breast cancer (TNBC) is a highly aggressive and heterogeneous group of cancers, and there is an urgent need to identify the subtype-specific molecular mechanisms underlying TNBC progression and resistance to chemotherapy in order to develop effective therapeutic strategies. TNBC cells are highly dependent on exogenous cystine to proliferate and survive, and overexpress the cystine/glutamate antiporter SLC7A11/xCT to fuel glutathione synthesis and promote an oxidative stress response required by high metabolic demands. Here we show that TNBC cells of the mesenchymal stem-like (MSL) subtype utilize forced cystine uptake to induce activation of the transcription factor NRF2 and promote a glutathione-independent mechanism of oxidative stress defense. Mechanistically, we demonstrate that NRF2 activation is mediated by direct cysteinylation of the inhibitor KEAP1 at sensor cysteine residues 226 and 613. Furthermore, we show that cystine-mediated NRF2 activation induces the expression of important genes involved in the response to oxidative stress (GCLM, TXNRD1, SRXN1, AKR1B10), but also in the epithelial-to-mesenchymal transition and stem-like phenotype (IGF2BP3, TGFBR3, POLR3G). Remarkably, four upregulated genes (OSGIN1, RGS17, SRXN1, AKR1B10) are poor prognostic markers for TNBC, and the expression of OSGIN1 correlates positively with the expression of SLC7A11 and negatively with claudin 3 and 7 as well as the expression of E-cadherin in the MSL subtype. Furthermore, exogenous expression of OSGIN1, similar to NRF2, is able to prevent cystine depletion-dependent death of MSL TNBC cells. The results suggest that the cystine/NRF2/OSGIN1 axis is a potential target for effective treatment of MSL TNBCs.

overall_design: Hs 578T cells over expressing GFP (Control) or NRF2 were used for this experiment. For cysteine (Cys) depletion, cells were washed with phosphate-buffered saline solution (PBS), pH 7.4, and incubated for the indicated times in DMEM, high glucose, no glutamine, no methionine, no cystine (#21013024, Gibco, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% (v/v) fetal bovine serum (FBS), 0.2 mM L-Methionine, 100 μg/ml streptomycin, 100 U/ml penicillin, and 2 mM L-glutamine. 0.8 mM L-Cystine was added in control cells. Total RNA was extracted from Hs 578T cells and used for RNAseq library prepration.

first: Laura

last: Bottoni

first: Giulia

last: Realini

first: Mahdi

first: Francesco

last: Neri

first: Federico

last: Galvagni


title: The miR-29-IFN-γ-JAK-STAT axis attenuates CD8+ T cell overactivation and differentiation in ulcerative colitis, and delivery of mimics in LMSH-CS hydrogel reduces colitis in mice

city: China

first: Yu qi

last: Wang

address: 17 Haidian District, Beijing

country: China

institute: China agricultural univercity

summary: To investigate the mechanism of miR-29ab in regulation of Tcells , we established miR-29ab1-/- mice and applied dss inflammation model

overall_design:
We then performed gene expression profiling analysis using data obtained from RNA-seq of colon yissue from WT and miR-29ab1-/- mice before and after DSS.
Comparative gene expression profiling analysis of RNA-seq data for WT and miR-29ab1-/- mice.

first: Huiyuan

last: Guo

first: Yingying

last: Lin

first: Yuqi

first: Yuning

last: Zhang


title: Decoding Dengue's Neurological Assault: Insights from Single-Cell CNS Analysis in a Mouse Model

city: Chongqing

first: Jintao

last: Li

address: No.30 Gaotanyan Street

institute: Army Medical University

summary: Dengue encephalitis, as one of the severe neurological manifestations of dengue virus infection, increasingly recognized for its rising incidence and significant public health implications. However, the pathophysiological mechanisms underlying dengue encephalitis remain inadequately elucidated, and effective prophylactic or therapeutic strategies are notably absent. In this study, we employed single-nucleus RNA sequencing to construct a comprehensive atlas of dengue encephalitis, utilizing brain tissues from dengue virus-infected murine models.

overall_design: Brain tissue of the A6 mice were prepasred and analyzed using snRNAseq. There were 3 control samples and 6 infected samples.

first: Minyue

last: Qiu

first: Lixin

last: Zhao

first: Xiaojia


title: N167.Dataset

city: Los Angeles

first: Steve

last: Horvath

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

summary: Cytosine methylation data generated on mammalian methylation platform

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: The data includes 20 Hippocampus of Rattus norvegicus with or without OSKM treatment

first: Rodolfo

last: Goya


city: Sagamihara

first: Makoto

last: Kashima

state: Kanagawa

address: 5-1-16, Fuchinobe

country: Japan

institute: Aoyama Gakuinn University

summary: Time-course indivudal RNA-Seq of zebrafish early development from 6 somites stage to 96 hpf

overall_design: Zebrafish larvas were sacrificed at 6ss, 10ss, 15ss, 20ss, 24 hpf, 32 hpf, 48hpf, 72 hpf, 96 hpf with 8-16 biological replicates.

first: Shujie

last: Liu

first: Junichi

last: Tasaki


title: Targeting USP8 Causes Synthetic Lethality through Degradation of FGFR2 in ARID1A-Deficient Ovarian Clear Cell Carcinoma

city: Chuo-ku

first: Hideaki

last: Ogiwara

state: Tokyo

address: 5-1-1, Tsukiji

department: Division of Cancer Therapeutics

institute: National Cancer Center Research Institute

summary: Over half of ovarian clear cell carcinoma (OCCC) cases exhibit deficiencies in the ARID1A gene, a chromatin remodeling complex component. OCCC is resistant to chemotherapy and challenging to treat, necessitating new drug treatment strategies. This study used a publicly available dependency factor database to identify synthetic lethal targets for ARID1A-deficient cancer. The DepMap portal was used to identify genes on which ARID1A-deficient cancer cell lines are highly dependent. Our analysis limited to ovarian cancer cell lines only identified the deubiquitinating enzyme USP8 as a synthetic lethal target in ARID1A-deficient OCCC cancer cell lines and mouse xenograft models. In addition, USP8 inhibitors were more selective for ARID1A-deficient cells than existing candidate drugs used in promising clinical trials for ARID1A-deficient cancers. Suppression of USP8 in ARID1A-deficient cells led to degradation of FGFR2 via the proteasome. Deficiency of ARID1A causes abnormalities in the STAT3 pathway, which is one of the downstream pathways of FGFR2, but suppression of USP8 attenuates phosphorylation of STAT3 pT705 and induces apoptosis. Taken together, the data suggest that USP8 is a novel therapeutic target for ARID1A-deficient OCCC and that it suppresses FGFR2-STAT3 signaling.

overall_design:
ARID1A-proficient OCCC cell lines and ARID1A-deficient OCCC cell lines were transfected for 96 h with siRNA for Non-targeting (siNT) or USP8 (siUSP8)
ARID1A-proficient OCCC cell lines and ARID1A-deficient OCCC cell lines were treated for 6 h with or without 2μM USP8i (DUB-IN-2)


title: RNA-seq analysis of early T cell progenitors from various gene deficient mice

city: Kyoto

first: Kazuko

last: Miyazaki

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

institute: Institute for Life and Medical Sciences, Kyoto University

summary: Analysis of the gene expressions of early T progenitors in the lymphocyte development.

overall_design: Transcriptome analysis of early T progenitors from various gene targeting mice associated with E-protein activity and Notch singnalling by bulk RNA-seq

first: Masaki

first: Kenta

last: Horie

first: Taishin

last: Akiyama


title: ATAC-seq analysis of early T cell progenitors from various gene deficient mice

summary: Analysis of epigenetics of early T progenitors in the lymphocyte development.

overall_design: Analysis of chromatin accessibilites of early T progenitors from various gene targeting mice associated with E-protein activity and Notch signalling by bulk ATAC-seq.


title: Early T cell progenitors from various gene deficient mice


title: Genome-wide transcriptome differences associated with perceived discrimination in an urban, community-dwelling middle-aged cohort

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Discrimination is a type of social adversity defined as unfair treatment and prejudice against individuals due to membership of a specific group. Discrimination has been linked to several age-related outcomes such as cognitive decline, inflammation, and cardiovascular disease. However, the molecular drivers to these observations are poorly understood. Social adverse factors have been associated with proinflammatory and interferon gene expression, a phenomenon described as Conserved Transcriptome Response to Adversity. It is not known whether there are additional genes whose transcription is associated with exposure to discrimination among both African American and White adults.  In this study, we have examined how perceived discrimination in African American and White adults affects genome-wide transcriptome differences using RNA sequencing. Perceived discrimination was measured based on responses to lifetime discrimination and racial discrimination questionnaires. Differential gene expression and pathway analysis was conducted in a cohort (N=59) stratified by race, sex, and discrimination exposure. We found that there were 28 significantly differentially expressed genes associated with high discrimination exposure in African American adults when compared to White adults with high discrimination exposure. The most significantly upregulated genes among African Americans with high discrimination exposure were related to immune function  immunoglobulin lambda variable 2-11 (IGLV2-11), S100 calcium binding protein B (S100B), immunoglobulin kappa variable 3-20 (IGKV3-20), immunoglobulin kappa variable 4-1 (IGKV4-1); the most significantly downregulated genes were associated with immune modulation and cancer, lung cancer associated transcript 1 (LUCAT1), thrombospondin 1 (THBS1), and actin related protein 2/3 complex inhibitor (ARPIN).  In addition, the most significantly upregulated Gene Ontology (GO) biological process among African American men with high exposure to discrimination compared to White male adults with high exposure to discrimination was regulation of cytokine biosynthetic processes. Conversely, immune response was the most significantly downregulated GO biological process among African American women with high discrimination exposure compared White women with high discrimination exposure. Understanding the biological pathways through which adverse social factors like discrimination affect gene expression will be critical in advancing knowledge of age-related health disparities.

overall_design:
In this study, we have examined how perceived discrimination in African American and White adults affects genome-wide transcriptome differences using RNA sequencing.
Peripheral blood mononuclear cells (PBMCs) were isolated from HANDLS participants that were exposed to either low or high perceived discrimination. Total RNA was isolated from PBMCs and RNA sequencing was performed.

first: Natasha

middle: L

last: Pacheco

first: Nicole

last: Noren Hooten

first: Sharon

middle: F

last: Wu

first: Maame

last: Mensah-Bonsu

first: Yongqing

first: Kumaraswamy

last: Chitrala

first: Nicolle

last: Mode

first: Ngozi

last: Ezike

first: Danielle

last: Beatty-Moody

first: Alan

last: Zonderman

first: Michele

middle: K

last: Evans


title: Switching of OAS1 splicing isoforms mitigates SARS-CoV-2 infection

city: Higashi-Osaka

first: Kei

last: IIDA

state: Osaka

address: Kowakae 3-4-1

institute: Kindai University

summary: We aimed to study impact of CDC-like kinase (CLK) inhibitor CaNDY on OAS1 splicing manipulation. Our data indicates CaNDY treatment induces switching of OAS1 splice isoforms to provide an increased resistance to SARS-CoV-2 infection.

overall_design: PolyA-tailed RNA profiles were obtained for Calu-3 cells infected with SARS-CoV-2 and treated with 10 µM CaNDY (n=3) or 0.1% DMSO (n=3).

last: Iida

first: Masahiko

last: Ajiro

first: Masatoshi

last: Hagiwara


title: Characterization of group I introns in generating circular RNAs as vaccines

city: Singapore

first: Roland

middle: G

last: Huber

address: 30 Biopolis Street

department: Bioinformatics Institute (BII)

country: Singapore

institute: Agency for Science, Technology and Research (A*STAR)

summary: Group 1 introns can be utilized for efficient circularization of RNA molecules.  However different group 1 introns are known to have different properties, including having different efficiencies of circularization and generating different levels of immune response inside cells (reactogenicity).  Here, we investigated generating circular RNAs using permuted intron-exon (PIE) systems of group 1 introns from different organisms. We observed that group 1 intron sequences have variable circularization efficiency that is size dependent and circularize with high accuracy. We also determined the sequence properties of the exon1 and exon2 domains of different group1 introns and showed that we can engineer elements such as S1 tag into this domain for better purification. Structural probing and mutational analysis in group 1 introns and their PIE RNAs showed that structural features in P2 and P9 domains are correlated with circularization efficiency and that swapping sequences can improve circularization efficiency. Lastly, we showed that circular RNAs made by Sd group 1 introns elicit lower amount of reactogenicity and either An or Sd can act as effective RNA vaccines. Our work deepens the understanding of the properties of group 1 introns and their use in circular RNA production and medicine.

overall_design:
To investigate whether different group 1 introns can enable RNA circularization upon PIE re-arrangement, we tested 8 group 1 intron sequences across a range of different buffers, differing in salt and temperature to identify the condition for efficient circularization (Supp Table 1). These 8 group 1 introns are from T4 phage (T4), Anabaena (An), Scytalidium dimidiatum (Sd), Clostridium botulinum (Cb), Scytonema hofmanni (Sh), Geosmithia virida (Gv), Penicillium oblatum (Po), and Barrmaelia oxyacanthae (Bo) (15-18). PIE constructs were made by splitting these group 1 introns at the P6 region and moving 3’-intron and exon 2 (3’I-E2) sequences to the 5’ end and exon 1 and 5’-intron (E1-5’I) sequences to the 3’ end (Figure 1A, B). For initial testing purpose, a 0.5kb Gaussia luciferase (Gluc) gene is used as an insert between 3’I-E2 and E1-5’I. To test circularization, all T4, An, Sd, Cb, Sh, Gv, Po, Bo PIE Gluc RNAs were in-vitro transcribed using T7 RNA polymerase and were incubated in different buffer conditions at different temperatures for circularization (A to G, Methods).
To determine of exon sequence requirement for circularization,  T4 PIE N60 Gluc, An PIE N60 Gluc, Sh PIE N60 Gluc, and Po PIE N60 Gluc IVT RNA were folded in condition B for 15 minutes or 1 hour. These samples were resolved by agarose gel and the lower band in each sample containing circular RNA was gel extracted for sequencing
To analyze the circular RNA formation accuracy, synthesis of first-stand cDNA from circular Gluc RNA was performed using SuperScript III reverse transcriptase (Thermo Fisher) with primer junction R according to manufacturer’s instructions. Subsequently, this cDNA was used as template for PCR amplification of 6 junction fragments with respective T4, An, Sd, Cb, Sh, and Po junction F and R primers. Each junction PCR fragment was processed using NEBNext Ultra II DNA Library Prep Kit to construct libraries compatible for Illumina sequencing.
To investigate sequences of full circular RNA, same cDNA template was used for full circular PCR amplification with respective T4, An, Sd, Cb, Sh and Po full circle F and R primers. Then these full circle fragments were sequenced using Nanopore ligation sequencing kit.

first: Kuo-Chieh

last: Liao

first: Anston

last: Tan

first: Aixin

last: Yap

first: Xiang

last: Gao

first: Zebin

last: Hong

first: Jian

last: Han

first: Youzhi

last: Cheng

first: You

middle: Z

last: Cheang

first: Wilfried

last: Saron

first: Li

last: Zhang

first: Bhuvaneshwari

last: Shunmuganath

first: Paul

last: Macary

first: Ashley

last: John

first: Yi

middle: Y

last: Yang

first: Sylvie

last: Alonso

first: Haiwei

last: Song

first: Yue

last: Wan


title: Nutrient-driven histone code determines exhausted CD8+ T cell fates

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

summary: Exhausted T cells (TEX) in cancer and chronic viral infections undergo metabolic and epigenetic remodeling, impairing protective capabilities. However, the impact of nutrient metabolism on epigenetic modifications that control TEX differentiation remains unclear. Our study reveals that TEX cells shift from acetate to citrate metabolism by downregulating acetyl-CoA synthetase 2 (ACSS2) while maintaining ATP-citrate lyase (ACLY) activity. This metabolic switch increases citrate-dependent histone acetylation, mediated by histone acetyltransferase KAT2A-ACLY interactions, at TEX signature-genes while reducing acetate-dependent histone acetylation, dependent on p300-ACSS2 complexes, at effector and memory T cell genes. Nuclear ACSS2 overexpression or ACLY inhibition prevents TEX differentiation and enhances tumor-specific T cell responses. These findings unveil a nutrient-driven histone code governing CD8+ T cell differentiation, with implications for metabolic- and epigenetic-based T cell therapies

overall_design: Gene expression profile at single cell level of tumor infiltrating immune cells in MC38 tumor model

first: Shixin

last: Ma

first: Susan

middle: M

last: Kaech


title: Effects on microglial morphology and function following CNS colonization by C. neoformans and its GXM capsule

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Morway RD

department: ICBR

institute: UNIVERSITY OF FLORIDA

summary: Cryptococcus neoformans is an encapsulated basidiomycete fungus that has a predilection for the CNS, causing cryptococcal meningoencephalitis. This disease is most common in immunocompromised individuals such as patients with HIV+ or on immunosuppressive regimens. The fungus is inhaled from pigeon droppings and Eucalyptus tree bark. Once inhaled, the fungus travels from the airway into the bloodstream where it travels systemically into the CNS. It has acquired three main ways of crossing the blood-brain barrier, but questions still exist about the dynamics of how the fungus colonizes the brain and how the host responds to this colonization. The fungus has three main virulence factors that allow it to colonize its hosts: antioxidant melanin production, immune-modulatory GXM polysaccharide capsule, and the ability to withstand physiological temperatures. Focusing on the effect of GXM, we saw that infection with the capsular H99 strain of C. neoformans, there was a decrease in mortality, while fungal burden and microglial migration to the cryptococcoma rose. There were also morphological changes in these microglial, so transcriptomics and functional migration and phagocytosis assays were conducted to evaluate the cellular activities at the site of infection. In summary, although microglia migrated and were recruited to the site of infection by the upregulation of pro-inflammatory pathways, they were unable to exert their functional roles due to a stonewall effect by GXM, as demonstrated by a reduction in migration to and phagocytosis of the fungus.

overall_design: To investigate the impact that polysaccharide capsule has on the microglial response to cryptococcosis and the development of meningoencephalitis.

first: Vanessa

last: Enriquez

first: Claudia

last: Charles-Nino

first: Melissa

last: Munzen

first: Fahong

last: Yu

first: Karina

last: Alvina

first: Luis

last: Martinez


title: Single-nucleus transcriptomic sequencing and cross integration comparison of multiple species revealed new cell composition and specific gene marker in hippocampal aging of tree shrew

city: kunming

first: Rui-ze

last: Niu

address: Chunrong West Road

institute: kunming medical university

summary: The brain of the tree shrew (Tupaia belangeri chinensis, TS) has drawn considerable attention due to its high similarities to that of humans. The hippocampal formation is one of the main brain regions affected in aging and neurological diseases. However, the cellular compositions of the TS hippocampus involving in aging development remain elusive. Here we established the first single-nucleus transcriptomic profiles of TS hippocampus and identified 16 cell subpopulations. The cross-species comparison of multi-species hippocampus revealed the cell landscape and associated specific gene expression patterns at the single-cell resolution. We validated ROBO2 and FGF14 as a TS/primate-specific NB[1] marker and confirmed TS-specific neural stem cells (NSCs) with SOX5/SOX6 high expression. Then, we identified TS cell types and molecular pathways closely associated with human neurological disorders, bridging the gap between gene mutations and pathogenesis. Importantly, we established the first single-nucleus transcriptomic atlas of TS hippocampal aging, in which the dynamics of the neurogenic lineage and the diversity of oligodendrocyte and microglia was revealed and delineated. Specifically, the regulatory continuum from adult NSCs to immature and mature granule cells was addressed in the neurogenic lineage. Meanwhile, in-depth dissection of gene-expression dynamics revealed impaired neurogenesis along the neurogenesis trajectory; additionally elevated pro-inflammatory responses in the aged microglia and endothelial cells may contribute to a hostile microenvironment for neurogenesis. Together, to our knowledge, this is the first time to report a single-cell atlas of TS in hippocampus aging which therefore provides extensive resources in both cell compositions and specific gene map for future research regarding neural science, evolutionary developmental biology, and regenerative medicine, combined with a comprehensive analysis across species.

overall_design: Single-nucleus RNA-sequencing of hippocampus from infancy, adult, and aging tree shrew (Tupaia belangeri chinensis).

first: Liu-Lin

last: Xiong

first: Rui-Ze

first: Yi-Fei

last: Sun

first: Jia

last: Liu

first: Ting-Hua

last: Wang


title: The function of IQGAP3 in gastric cancer

first: Mitsuhiro

last: Shimura

address: 14 Medical Drive

department: Cancer Science Institute of Singapore

institute: National University of Singapore

summary: The first is transcriptional profiling of siRNA-mediated knockdown of IQGAP3 in human gastric cancer cell line AGS, NUGC3, and Hs746T comparing with non-target siRNA transfected AGS, NUGC3, and Hs746T as a control.  The aim of this experiment was to evaluate the functions of IQGAP3 in three different gastric cancer cell lines in vitro. The second is bulk RNA-sequence from subcutaneous tumors, which were injected NUGC3 shIQGAP3 knockdown cells and NUGC shContorl cells into immunodeficient mice (NSG mice). The aim is to evaluate the difference of transcriptional profiling in human cancer cells and mouse stromal cells of shIQGAP3 knockdown tumors compared to shContorol tumors.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Transcriptional profiling of  IQGAP3 knockdown samples compared to control samples using gastric cancer cell lines like AGS, NUGC3, and Hs746T, and bulk tumors from NUGC3.

first: Yoshiaki

last: Ito


title: SARS-CoV-2 proteins inhibit mitochondrial HIGD1A to induce complement-mediated endothelial cell injury

city: Shanghai

first: Shuxun

address: Xiangyin Rd.800

department: Immunology

institute: Naval Medical University

summary: Purpose:  The purpose is to systemically identify the genes regulating CD59 expressed on endothelial cells by Crispr/cas9-gRNA library screening  Methods: We profiled gRNA sequnecing of endothelial cells with significant CD59 changes and those cells without significant CD59 changes  Results: several genes with upregulated or downrgulated were identified as regulators of CD59 in endothelial cells with the edited genome

overall_design: Endothelial cell lines (HMEC-1) were transfected with lentivirus packaged with Cripsr/Cas9-gRNA library at a MOI of 0.3; after puromycin selection, surviving cells were cultured into many wells, two wells were transfected with null plasmid (Mock), some wells were transfected with N protein plasmid, and some wells  were transfected with a pooled plasmids repectively SARS-CoV-2 proteins；half of wells were cultured regularly and half of wells were cultured in high glucose condition. After 48-72h, the expression of CD59 was detected. Cells had significant CD59 changes were subjected into the second screening as the first one. Cells had no significant CD59 changes were pooled as control group, and cells with significant CD59 changes after two cycles of screening were pooled as experiment group. We then performed gRNA sequencing of the two groups.

first: Xuetao

last: Cao


title: RNA-seq and iCLIP-seq of cells that harbor retinitis pigmentosa mutations

city: Frankfurt am Main

first: Michaela

last: Müller-McNicoll

address: Max-von-Laue-Str. 13

institute: Goethe University Frankfurt

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

overall_design: Refer to individual Series


title: Transcriptome-wide mapping of RNA:protein interactions of PRPF8 and SNRNP200 (BRR2) with retinitis pigmentosa (RP) mutations by iCLIP

summary: We used HeLa cells that express GFP-tagged PRPF8 with and without the RP mutations F2314L and Y2334N at physiological levels as well as SNRNP200-GFP with and without the RP mutations S1087L and R1090L and performed iCLIP using anti-GFP antibodies. We also used RPE cells with and without the Y2334N mutation inserted by CRISPR/Cas9 and compared their binding pattern on snRNAs and pre-mRNAs.

overall_design: For each GFP-tagged protein, 3 biological replicates were subjected to the iCLIP procedure with UV-crosslinking at 254 nm. Non-crosslinked samples were used as controls.


title: Effect of chemical chaperone lumacaftor (VX-809) on gene expression in HEK-293 cells expressing hERG/A561V

city: Ning bo

first: Jiangfang

last: Lian

address: No. 57 Xingning Road, Yinzhou District, Ningbo, Zhejiang Province, China

department: cardiology

institute: Lihuili Hospital Facilitated to Ningbo University, Ningbo University.

summary:
To investigate the molecular effect of lumacaftor in the regulation of mutatant hERG protein expression, we established HEK-293 cell lines expressing hERG/A561V, 15μM lumacaftor treatment as experimental group (HAL) and DMSO treatment (HA) as control group.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different groups.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HEK-293 cells with and without lumacaftor (HA, HAL).

first: Zequn

last: Zheng


title: ASH1L regulates gene expression in lung cancer

city: Houston

first: Yue

last: Lu

state: TX

address: 1881 East Road

department: Epigenetics & Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

summary: ASH1L is frequently amplified and mutated in various human cancers, including lung adenocarcinoma, liver, uterine and balder cancers. We used two shRNAs to knockdown endogenous ASH1L proteins in A549 cells, and carried out RNA-seq analysis to identified the genes regulated by ASH1L. We found that compared with the control cells, 541 genes were upregulated in both ASH1L knockdown cells, whereas 398 genes were upregulated. Ingenuity Pathway Analysis (IPA) revealed that the downregulated genes are enriched in fundamental cellular activities, including cell cycle, replication, cell death and survival, and cell growth, and are important for caner and some other diseases . Gene Ontology (GO) analysis also revealed similar cellular pathways that the downregulated genes are involved, whereas the upregulated genes are not enriched in any specific pathways that are statistically significant. Taken together, these data suggest that ASH1L has an oncogenic role in lung adenocarcinoma promoting cancer cell growth, therefore may serve as a potential therapeutic target for the treatment of lung adenocarcinoma patients that have ASH1L amplifications.

overall_design: A549 cells were transduced with two shRNAs targeting ASH1L and one control non-targeting shRNA and selected with puromycin for 4-6 days. RNA-seq was then performed to identify differentially expressed genes among different conditions.

first: Kevin

last: Lin

first: Chih-Chao

last: Hsu

first: Xiaobing

last: Shi


title: Switching of OAS1 splicing isoforms mitigates SARS-CoV-2 infection [Caco-2]

first: Kei

last: IIDA

overall_design: PolyA-tailed RNA profiles were obtained for Caco-2 cells, treated with 10 µM CaNDY (n=3) or 0.1% DMSO (n=3).

last: Iida

first: Masahiko

last: Ajiro

first: Ken-ichiro

last: Kamei

first: Masatoshi

last: Hagiwara


title: Transcriptomic analysis reveals the importance of sugar metabolism and export for positive mycorrhizal growth responses in soybean

city: Guangzhou

first: Shaopeng

last: Zhao

state: Guangdong

address: Tianhe District, Wushan Road

department: College of Natural Resources and Environment

institute: South China Agricultural University

summary: To elucidate molecular mechanisms controlling differential growth responses to root colonization by arbuscular mycorrhizal (AM) fungi varying in colonization and cooperative behavior, transcriptome analyses were carried out using two soybean genotypes and three AM inocula. The results showed that inoculation by cooperative Rhizophagus irregularis (Ri) or less-cooperative Glomus aggregatum with high AM colonization (Ga-H) significantly promoted plant growth compared with inoculation by Glomus aggregatum with low AM colonization (Ga-L). A large number of soybean genes, especially those involved in metabolism, transport and regulation of lipids were significantly up-regulated by these three AM inoculations compared with un-inoculated control plants. However, genes encoding two SWEET transporters and one invertase were only up-regulated in response to Ri and Ga-H inoculation, which coincided with positive growth responses in these two inoculation treatments. Promoter analyses in transgenic soybean plants further demonstrated that GUS driven by the GmSWEET6 promoter was highly expressed in arbuscule-containing cortical cells. Additionally, Ri and Ga-H inoculation increased the contents of sucrose, glucose and fructose in both shoots and roots. These results imply that positive mycorrhizal growth responses in plants may mostly be due to the stimulation of photosynthate metabolism and transport by AM fungal inoculum with high colonization capabilities.

overall_design: Transcriptome analyses were carried out using three AM inocula and a NM as control, every treatment had three replicates.

first: Xiurong


title: RNA-seq of RPE cells that harbor a C-terminal GFP-tag on the splicing factor PRPF8 and the retinitis pigmentosa mutation Y2334N

summary: RPE cells were edited using CRISPR/Cas9 to fuse a GFP-tag at the C-terminus of PRPF8 and additionally mutate amino acid 2334 from Y to N.

overall_design: RPE cells with WT and Y2334N loci were subjected to RNA-seq in 2 biological replicates each.

first: Zuzana

last: Cvackova


title: The Role of BAZ2-dependent Chromatin Remodeling in Suppressing G4 DNA Structures and Associated Genomic Instability [INDUCE-seq]

status: Public on Mar 11 2025

city: Boston

first: Tovah

middle: A.

last: Day

state: MA

address: 330 Huntington Avenue, Northeastern University Mugar Life Science Building, Room 134

department: Biology

institute: Northeastern University

summary: DNA G-quadruplexes (G4s) are secondary structures with significant roles in regulating genome function and stability. Dysregulation of the dynamic formation of G4s is linked to genomic instability and disease, but the underlying mechanisms are not fully understood. In this study, we conducted a screen of chromatin-modifying enzymes and identified nine potential inhibitors of G4 formation, including seven that were not previously characterized. Among these, we highlight the role of BAZ2 chromatin remodelers as key suppressors of G4 DNA and G4-related genome instability. Depletion of BAZ2 subunits led to increased G4 formation, especially at transcriptional regulatory elements. BAZ2B was found to associate with G4 loci, suggesting that it plays a direct role in suppressing G4s. While BAZ2-deficient cells exhibited modest genomic instability, treatment with the G4-stabilizing ligand BRACO19 exacerbated double-strand breaks (DSBs), highlighting its utility as a tool to study G4-dependent genome instability. DSB profiling using INDUCE-seq uncovered distinct breakage patterns around G4s, further underscoring the impact of G4s on genome integrity. Notably, we found that within G4s, G repeats were more susceptible to DSBs than loops. These results establish BAZ2 chromatin remodeling complexes as direct regulators of G4 dynamics and provide new insights into G4-dependent genome instability.

overall_design: INDUCE-seq performed on A549 cells following different siRNA treatments and BRACO19 treatment.

first: Adrianna

last: Vandeuren

first: Kierney

last: O'Dare

first: Rosemary

last: Wilson

first: Patrick

last: van Eijk

first: Simon

last: H. Reed


title: Development and Characterization of Chicken Lung Organoids for Future In Vitro Modeling of Avian Influenza Virus-Host Cell Interaction [bulk RNA-seq]

city: Ames

first: Christopher

last: Zdyrski

state: Iowa

address: 1800 Christensen Dr, Bms 1072 Vet Med, Bms 1072 Vet Med

institute: Iowa State University

summary: High pathogenicity avian influenza viruses pose a growing threat to poultry, livestock, wildlife, and humans as they undergo accelerated expansion of host and geographical ranges. Since 2020, these viruses have driven a panzootic characterized by extensive viral diversification and spillover into species previously considered to be resistant. There is currently a lack of physiologically relevant in vitro models that can be used to screen the rapidly changing viral landscape. To address this need, we describe the first chicken lung organoids derived from adult stem cells of specific pathogen free White Leghorns. We analyze their gene expression with bulk RNA sequencing, confirm their cellular heterogeneity via single-nuclei RNA sequencing, and provide basic morphological characterization using hematoxylin and eosin (H&E) staining, immunohistochemistry, immunofluorescence, and transmission electron microscopy. The results indicate that the organoids contained several cell types, including non-ciliated columnar, cuboidal, squamous, and mucin-producing cells, representative of different regions of the avian respiratory system. Furthermore, expression of genes relevant to influenza A virus replication appeared to be conserved across different samples. These organoids have the potential to effectively and efficiently model viral infection of the chicken lung, enabling the investigation of viral pathogenesis and evolutionary potential, virus-host interactions, and discovery of targets for antiviral treatments.

overall_design: RNA-seq profiling of three SPF White Leghorn chicken organoids and corresponding tissues.

first: Hannah

last: Nicholson

first: Karin

last: Allenspach

first: Jonathan

last: Mochel

first: Silvia

last: Carnaccini


title: Development and Characterization of Chicken Lung Organoids for Future In Vitro Modeling of Avian Influenza Virus-Host Cell Interaction [scRNA-seq]


title: Targeting eRNA-producing super-enhancers regulates TNFα expression and mitigates chronic inflammation in mice and patient-derived immune cells [CUT&RUN]

city: Seoul

first: Su Min

last: Kim

state: Gangnam-gu

address: Dogok-ro 237

institute: Severance Hospital

summary: Chronic inflammatory diseases are driven by immune cell dysregulation and overproduction of pro-inflammatory molecules, such as tumor necrosis factor alpha (TNFα). Super-enhancers (SEs) and their enhancer RNAs (eRNAs) are critical gene expression regulators and offer therapeutic potential beyond protein-targeting approaches. We hypothesized that targeting eRNAs could reduce chronic inflammation by modulating TNFα expression. We generated TNF-9 knockout (KO) mice by deleting a Tnfα-regulating enhancer region. These mice exhibited significantly reduced Tnfα levels, improved disease outcomes, and diminished immune cell activation in models of rheumatoid arthritis (RA), psoriasis, and lipopolysaccharide (LPS)-induced sepsis. Integrative epigenomic and transcriptomic analysis identified additional LPS-responsive, eRNA-producing enhancers as therapeutic targets. Antisense oligonucleotide (ASO)-mediated knockdown of TNF-9 eRNA in mouse macrophages demonstrated decreased Tnfα expression and alleviated RA symptoms. Furthermore, ASO-mediated inhibition of the eRNA of the human homolog of TNF-9 similarly reduced TNFα levels. These findings support eRNA-targeted interventions as potential treatment for chronic inflammatory diseases.

overall_design: CUT and RUN seq of BMDM from C57BL/6 mouse with or without LPS 1hr stimulation (with LPS stimulation : LPS, without LPS stimulation : UT). Chromatin profiling was conducted using three antibodies : H3K4me1 (me1), H3K27Ac (ac), and input control (IgG).

first: Minjeong

last: Cho

first: Jiyeon

last: Lee

first: Wonjin

last: Woo

first: Hyo Jin

last: Park

first: Eunji

first: Lark Kyun


title: Targeting eRNA-producing super-enhancers regulates TNFα expression and mitigates chronic inflammation in mice and patient-derived immune cells [RNA-KO]

overall_design: RNA-seq profiling of BMDM from HSS9 KO mouse (KO) and littermate control mouse (WT), with or without LPS 6hr stimulation (with LPS stimulation : LPS, without LPS stimulation : UT).


title: Targeting eRNA-producing super-enhancers regulates TNFα expression and mitigates chronic inflammation in mice and patient-derived immune cells [RNA B6]

overall_design: RNA seq profiling of BMDM from C57BL/6 mouse with our without LPS 1hr stimulation (with LPS stimulation : LPS, without LPS stimulation : Control).


title: The multifaceted roles of the DNA polymerase subunit Pol32 in maintaining genome integrity

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

institute: College of Life Sciences, Zhejiang University

summary: A total of 40 diploid WYpol32 strains that spontaneously produced red and white colonies were analyzed using a chromosome IV microarray.

overall_design: The diploid strain WYpol32 carries a homozygous ade2-1 mutation, which is partially suppressed by the SUP4-o gene on chromosome IV. A break between the centromere and the SUP4-o insertion site can induce recombination, leading to crossover events and the formation of red-white sectored monoclonal colonies. Analyzing 40 pairs of red-white sectors can reveal the critical role of the Pol32 in recombination.

first: Lei

last: Qi

first: Daoqiog

first: Thomas

last: Petes


city: Birmingham

first: Maria

middle: B.

last: Grant

state: AL

address: 1670 University Blvd, VH490

department: Ophthalmology

institute: University of Alabama at Birmingham

summary:
Hallmark findings in age-related macular degeneration (AMD) include the accumulation of extracellular lipid and vasodegeneration of the choriocapillaris. Choroidal inflammation has long been linked to AMD, but little is known about the immune cells of the human choroid. Using 3D multiplex immunofluorescence, single-cell RNA-sequencing, and flow cytometry, we unravel the cellular composition and spatial organization of the human choroid and the immune cells within it. We identify two populations of choroidal macrophages with distinct FOLR2 expression that account for the majority of myeloid cells. FOLR2+ macrophages predominate in the nondiseased eye, express lipid-handling machinery, uptake lipoprotein particles, and contain high amounts of lipid. In AMD, FOLR2+ macrophages are decreased and functionally attenuated with respect to lipoprotein metabolism. In mice, FOLR2+ macrophages are negative for the postnatal fate-reporter Ms4a3, and their depletion causes an accelerated AMD-like phenotype. Our results show that prenatally-derived resident macrophages decline in AMD and are implicated in multiple hallmark functions known to be compromised in the disease.

Citation: Fortmann, Seth D. et al. 2025. Prenatally-Derived Macrophages Support Choroidal Health and Decline in Age-Related Macular Degeneration. Journal of Experimental Medicine. In Press.

overall_design:
This repository contains reanalyzed single-cell RNA-sequencing (scRNA-seq) data from RPE/Choroid of nondiseased and age-related macular degeneration human donors. There are 99 scRNA-seq samples derived from 7 previously deposited GEO Accessions (GEO Accessions: GSE203499, GSE230348, GSE210543, GSE135922, GSE149100, GSE183320, GSE202735). Each sample is referenced below with its original BioSample identifier per the depositing authors. All scRNA-seq data are 3' 10X Genomics and raw sequencing data are available per the previously deposited BioSample FASTQs.

SCRNA-SEQ PROCESSING
Raw FASTQ files were downloaded from the GEO database (GEO Accessions: GSE203499, GSE230348, GSE210543, GSE135922, GSE149100, GSE183320, GSE202735). Samples were demultiplexed and aligned using CellRanger Count (Version 7.0.2). The prebuilt human reference transcriptome from 10X Genomics, GRCh38, was used for alignment. CellRanger output files were loaded into Scanpy (Wolf et al., 2018), and the scAR package (Sheng et al., 2022) from scvi-tools (Gayoso et al., 2022) was used to identify and remove ambient RNA. To filter out low quality cells, we used the following thresholds: >300 for total genes, >300 for total counts, and <0.35 for mitochondrial proportion. To identify potential doublets we used 2 algorithms, Solo (Bernstein et al., 2020) and DoubletDetection (Gayoso and Shor, 2022), and we removed cells that were identified as probable doublets by both. For size factor normalization of the denoised raw counts, we used scranPY (Fortmann, 2023), a python implementation of r-scran::computeSumFactors (Lun et al., 2016). For dimensionality reduction, we used 3,000 highly variable genes, principal component analysis (PCA) using 20 components, Harmony for batch correction using individual sample identifiers (Korsunsky et al., 2019), nearest neighbor analysis using 80 neighbors, and UMAP with default parameters. For clustering, we used the Leiden algorithm with a resolution of 0.25 (Traag et al., 2019). Lastly, we removed a cluster containing contaminating rods and 3 other small clusters of unknown origin. For subclustering of myeloid cells, we subset the data on the CD14+ cluster and then used the single-cell Variational Inference (scVI) model from scvi-tools to compute a latent space representation for dimensionality reduction. We removed 1 sample from the dataset that contained a large population of unknown cells that did not overlap with the other 98 samples. Cell cycle scores were computed with the Scanpy function score_genes_cell_cycle() using the cell cycle gene list from (Tirosh et al., 2016). The denoised expression matrix was used along with 3 categorical covariates (the individual sample identifier, the donor identifier, and the study identifier) and 3 continuous covariates (the mitochondrial proportion, the G2M score, and the S score). Nearest neighbors were recomputed using the scVI latent space and then UMAP was recomputed using default parameters.

PROCESSED FILES
Scanpy (.H5AD) and Seurat (.RDS) versions of [i] complete RPE/choroid merged dataset and [ii] subclustered myeloid dataset. The processed files contain 3 different gene expression matrices:
[1] scranPY normalized expression ("scranPY"; see GitHub sfortma2/scranPY),
[2] denoised counts ("denoised"; see GitHub Novartis/scar),
[3] raw cell ranger counts ("CR_counts").

These files also contain a variety of metadata:
"GEO_SampleID" = the per sample ID used in this repository,
"GEO_Sample_Title" = the sample title used by the original depositing authors,
"GEO_Donor" = the donor identifier used in this repository; some samples come from the same donor,
"BioSample" = the BioSample identifier of each sample,
"location" = macular vs peripheral,
"diseasegroup" = nondiseased vs AMD,
"diseasetype" = nondiseased vs nvAMD vs atrophic AMD vs early AMD vs intermediate AMD,
"age" = donor age if available,
"sex" = donor sex if available,
"location_diseasetype" = combined location and diseasetype,
"location_diseasegroup" = combined location and diseasegroup,
"barcode" = original barcode,
"clusters" = cell cluster,
"clusters_less" = generalized cell cluster; only in complete RPE/choroid merged dataset,
"clusters_more" = cell clusters plus immune specific clusters; only in complete RPE/choroid merged dataset,
"n_counts" = number of transcripts in cell,
"log_counts" = log number of transcripts in cell,
"n_genes" = number of genes in cell,
"log_genes" = log number of genes in cell,
"size_factors" = scranPY size factor used for normalization,
"percent_mito" = ratio of mitochondrial transcripts in cell,
"percent_ribo" = ratio of ribosomal transcripts in cell,
"count_cutoff" = transcript cutoff used for QC,
"gene_cutoff" = gene cutoff used for QC,
"mito_cutoff" = mitochondrial ratio used for cutoff,
"doublet_score_SOLO" = doublet score calculated using SOLO,
"singlet_score_SOLO" = singlet score calculated using SOLO,
"doublet_labels_SOLO" = doublet vs singlet label per SOLO,
"doublet_score_DoubletDetection" = doublet score calculated using DoubletDetection,
"doublet_labels_DoubletDetection" = doublet vs singlet label per DoubletDetection,
"CR__reads_per_cell" = CellRanger reads per cell for sample,
"CR__total_reads" = CellRanger total reads for sample,
"CR__seq_sat" = CellRanger sequencing saturation for sample,
"CR__Q30_RNA" = CellRanger RNA quality for sample,
"CR__intronic_reads" = CellRanger intronic reads for sample,
"CR__chemistry" = detected chemistry per CellRanger.

first: Seth

last: Fortmann


title: PQM-1 Governs Stress Resilience through DAF-16 and Dietary Cues in C. elegans

city: CHARLOTTE

first: Patricija

last: van Oosten-Hawle

state: NC

address: 9201 University City Blvd, Woodward Hall, Room 246D

department: Biological Sciences

institute: UNC Charlotte

summary: The goal of this study was to identify genes controlled by PQM-1 during heat stress conditions (35 degrees celsius) in young adult C. elegans, independent of DAF-16 and the Insulin-like-signaling pathway.

overall_design: Gene expression profile of Day1 adult C. elegans at 20 degrees celsius and after exposure to 1 hour at 35 degrees celsius (Heat Shock) of a control strain (N2), a daf-16 (mu86) mutant (strain CF1038) and a pqm-1 (ok485) null mutant (strain RB711). Worms were collected after a 2 hour recovery period at 20 degree celsius. 3 biological replicates of each sample.

first: Laura

last: Jones

first: Valeria

last: Uvarova


title: The saponin monophosphoryl lipid A nanoparticle adjuvant induces dose-dependent HIV vaccine responses in non-human primates

city: La Jolla

first: Shane

last: Crotty

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

summary: The induction of durable protective immune responses is the main goal of prophylactic vaccines, and adjuvants play an important role as drivers of such responses. Despite advances in vaccine strategies, a safe and effective HIV vaccine remains a significant challenge. The use of an appropriate adjuvant is crucial to the success of HIV vaccines. Here, we assessed the saponin/MPLA nanoparticle (SMNP) adjuvant with an HIV envelope (Env) trimer, evaluating the impact of adjuvant dose on the establishment of Env-specific memory B cell responses in non-human primates.

overall_design: HIV Env-specific memory B cells from PBMCs were isolated by fluorescence-activated cell sorting (FACS) and analyzed by scRNA-seq, including VDJ and GEX libraries, using the 10X Genomics platform.

first: Parham

last: Ramezani-Rad


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

city: Badalona

first: LUCIA

last: LORENZI

state: Barcelona

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

country: Spain

institute: Josep Carreras Research Institute

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

overall_design: ATAC-seq was performed in duplicates on KO-52 transduced with an empty vector (EV), p42 or p30. Cells were treated with tunicamycin (Tm) for 8h to induce ER stress.

last: Cadefau-Fabregat

first: Gerard

last: Martínez-Cebrián

first: Lucía

last: Lorenzi

first: Sergi

last: Cuartero


title: RNA-sequencing of HCMV-infected ARPE-19 and MCF10A cells

city: Chicago

first: Adam

last: Oberstein

state: IL

address: 835 South Wolcott Ave.

department: Microbiology and Immunology

institute: University of Illinois

summary: In this study, viral and cellular gene expression profiles were acquired after infecting ARPE-19 and MCF10A cells with strain TB40/E-BAC4 of human cytomegalovirus. ARPE-19 cells are permissive for HCMV infection, while MCF10A cells are semi-permissive. This data was acquired to study the effects of epithelial and mesenchymal cell states on HCMV infection. Despite being derived from a primary retinal epithelial explant, ARPE-19 cells require long periods of high confluency to display epithelial characteristics. Under the conditions used in this experiment, ARPE-19 cells are phenotyically mesenchymal, as shown in Golconda et al, Viruses, 2024. MCF10A cells display strong epithelial characteristics under the conditions used here.

overall_design: Triplicate cultures of ARPE-19 and MCF10A cells were infected with a recombinant HCMV (strain TB40/E-BAC4) engineered with a GFP-A206K-P2A cassette inserted at the UL83 ATG-codon. Mock cultures were collected at 6 hpi and 96 hpi. Infected cultures were collected at 6, 12, 24, 48, 96, and 144 hpi. ARPE-19 and MCF10A cells were infected at a multiplicity of 3 or 5 infectious units/cell, respectively. RNA was purified from cultures at each time point and subjected to total RNA-sequencing analysis.


title: Novel cell-to-cell communications between macrophages and fibroblasts regulate obesity-induced adipose tissue fibrosis [bulk RNA-seq]

city: Chikusa-ku

first: Hiro

last: Kohda

state: Nagoya

address: Furo-cho

department: Research Institute of Environmental Medicine

institute: Nagoya Univ.

summary: Mincle (Macrophage inducible C-type lectin, clec4e) is a pattern recognition receptor expressed in innate immune cells and can sense cell death, suggesting a role in sterile inflammation. We previously showed that expression of Mincle is induced in adipose tissue macrophages during the development of obesity. Mincle accelerates adipose tissue inflammation and fibrosis, thereby exacerbating ectopic lipid accumulation and insulin resistance in the liver. In this study, we performed single-cell RNA sequencing analysis of the SVF in visceral adipose tissue from diet-induced obese mice to analyze the cell-cell interaction between Mincle-expressing macrophages and activated fibroblasts. We found that Oncostatin M (Osm), a member of the interleukin-6 cytokine superfamily secreted from Mincle-expressing macrophages, acts on fibroblasts to inhibit collagen expression.

overall_design: Adipose tissue–derived fibroblasts were prepared from the SVF of HFD-fed mice using a magnetic cell sorting system (AutoMACS; Miltenyi Biotec) as CD45-, CD31-, and Ter119-negative cells. Adipose tissue–derived fibroblasts were treated with recombinant human transforming growth factor-β1 (TGFß1) (3 ng/mL; BioLegend) or recombinant mouse Osm (3 ng/mL; BioLegend) for 24 h.

first: Miyako

last: Tanaka

first: Takayoshi

last: Suganami


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

city: Nanjing

first: cheng

last: gao

state: Jiangsu

address: Nanjing Agricultural University

institute: Nanjing Agricultural University

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

overall_design: To investigate the functional roles of STM1 and STM2 genes under Cd stress, we performed transcriptome analyses using plants with Col-0, stm1-1, stm2-2, stm2 stm1. Seedlings grown for 12 days were transferred to plates  with or without Cd(70 µM) for 16 h. Roots and Shoots were sampled separately, and later RNA-seq data from the above tissues were used for comparative analysis of gene expression profiles.

first: Cheng

last: Gao

first: Fangjie

last: Zhao


title: V-ATPase-dependent induction of selective autophagy

city: Ann Arbor

first: Yuxiang

last: Huang

state: MI

address: 2214 Stone Road

department: MCDB

institute: University of Michigan

summary: The general consensus is that the vacuolar-type H+-translocating ATPase (V-ATPase) is critical for macroautophagy/autophagy. However, there is a fundamental conundrum because follicular lymphoma-associated mutations in the V-ATPase result in lysosomal/vacuolar deacidification but elevated autophagy activity under nutrient-replete conditions and the underlying mechanisms remain mysterious. Here, working in yeast, we show that V-ATPase dysfunction activates a selective autophagy flux termed the "V-ATPase-autophagy axis". By combining transcriptomic and proteomic profiling, along with genome-wide suppressor screening approaches, we found that the V-ATPase-autophagy axis is regulated through a unique mechanism distinct from classical nitrogen starvation-induced autophagy. Tryptophan metabolism negatively regulates the V-ATPase-autophagy axis via two parallel effectors. On the one hand, it activates ribosome biogenesis, thus repressing the translation of the transcription factor Gcn4/ATF4. On the other hand, tryptophan fuels NAD+ de novo biosynthesis to inhibit autophagy. These results provide a clear explanation for the mutational activation of autophagy seen in follicular lymphoma patients.

overall_design: Trpytophan prototrophic and tryptophan auxotrophic yeast SEY6210 cells are cultured in nutrient-rich YPD medium, then treated with/without 3-IAA to induce temporal degradation of VMA2-AID*-9MYC protein.

first: Daniel

last: Klionsky


title: Short 5’ UTRs serve as a marker for mRNA translation inhibition by the IFIT2-IFIT3 antiviral complex

first: Eric

last: Van Nostrand

state: Tx

address: 1 Baylor Plaza

department: Biochemistry and Molecular Pharmacology

institute: Baylor College of Medicine

summary: Recognition of non-self nucleic acids, including cytoplasmic dsDNA, dsRNA, or mRNAs lacking proper 5' cap structures, is critical for the induction of innate immunity against viruses. Here, we demonstrate that short 5’ untranslated regions (UTRs), a characteristic of many viral mRNAs, can also serve as molecular pattern for innate immune recognition via the interferon-induced proteins, IFIT2 and IFIT3. The IFIT2-IFIT3 heterodimer, formed through an intricate domain swap structure, mediates viral mRNA 5' end recognition, translation inhibition, and ultimately antiviral activity. Critically, 5' UTR lengths <50 nucleotides are necessary and sufficient to sensitize an mRNA to translation inhibition by the IFIT2-IFIT3 complex. Thus, diverse viruses whose mRNAs contain short 5’ UTRs, such as vesicular stomatitis virus and parainfluenza virus 3, are sensitive to IFIT2-IFIT3-mediated antiviral activity. Our work reveals a new size-restricted pattern of nucleic acid innate immune recognition for the selective repression of viral replication.

overall_design: eCLIP was performed as previously described (Blue SB, et al. Nature Protocols 2022), using antibodies against FLAG (M2 / F1804, Sigma) and HA (HA.11 / 901502, Biolegend) for 293T experiments, and IFIT2 (PA3-845, ThermoFisher) and IFIT3 (ABF1048, Millipore) for MEF experiments. Most experiments were performed in biological duplicate, except for uninfected 293T samples (which were single replicates).

first: Dustin

last: Glasner

first: Candace

last: Todd

first: Brian

last: Cook

first: Agustina

last: D’Urso

first: Shivani

last: Khosla

first: Elena

last: Estrada

first: Jaxon

last: Wagner

first: Mason

last: Bartels

first: Pierce

last: Ford

first: Jordan

last: Prych

first: Katie

last: Hatch

last: Yee

first: Sarah

last: Bellout

first: James Brett

last: Case

first: Kevin

last: Corbett

first: Michael

last: Diamond

first: Gene

last: Yeo

first: Mark

last: Herzik Jr

first: Matthew

last: Daugherty


title: Chromatin accessibility contributes to Candida albicans adaptation to echinocandins

city: Rochester

first: Tyler

last: Stahl

state: NY

address: 601 Elmwood Ave

institute: University of Rochester Medical Center School of Medicine and Dentistry

summary: Infections by the major opportunistic pathogen of human Candida albicans are commonly treated with echinocandin (ECN) drugs. However, C. albicans can adapt to grow in the presence of certain amounts of ECNs. Prior studies by several laboratories have defined multiple genes, as well as mechanisms involving induced aneuploidy, that can govern this. Still, mechanisms of ECN adaptation are not fully understood. Here, we use genome-wide profiling of chromatin accessibility by ATAC-seq to determine if ECN adaptation is reflected in changes in the chromatin landscape in the absence of aneuploidy. We find that drug adaptation is coupled with multiple changes in chromatin accessibility genome-wide, which occur predominantly in gene promoter regions. Areas of increased accessibilities in promoters are enriched with the binding motifs for at least two types of transcription factors: zipfinger and b-zipfinger. We also find that chromatin changes are often associated with differentially-expressed genes including genes with functions relevant to the ECN-adapted phenotype, such as cell wall biosynthesis. Consistent with this, we find that the cell wall is remodeled in ECN-adapted mutants, with chitin up and glucan down and increased cell surface exposure. Full understanding of ECN adaptation processes is of critical importance for prevention of clinical resistance.

overall_design: Three independent batches of C. albicans grown in YPD were used for nuclei preparation based on published protocol with minor modifications (Jenull et al., 2020). Tagmentation done as in (Jenull et al., 2020.).  JMC200-2-5 and JMC160-2-5 are caspofungin adapted mutants whereas Parental (JRCT1) samples were used as control samples. gDNA control was used as tagmentation and background control.

first: Sudisht

last: Sah

first: Anshuman

last: Yadav

last: Rustchenko


title: Transient Pharmacological Inhibition of SUMOylation during Pregnancy Induces Craniofacial Malformations in Offspring Mice

city: Paris

first: Yann

last: Loe-Mie

address: 25 rue du Dr Roux

department: Computational Biology

country: France

institute: Institut Pasteur

summary: Cell identity plays a pivotal role in embryo development, guiding the process of cellular differentiation essential for tissue and organ formation. Post-translational modification by the ubiquitin-related SUMO protein acts as a chromatin barrier to cell fate conversions. While SUMOylation deficiency is incompatible with mammalian embryonic development, haploinsufficiency for the SUMOylation machinery's E1 enzyme, UBA2, leads to various phenotypic traits in humans, including craniofacial malformations and aplasia cutis congenita. To investigate SUMO's role in organogenesis, SUMOylation was transiently suppressed using a specific pharmacological inhibitor, TAK981, administered during the early post-implantation embryo stage. A high-concentration injection led to embryonic lethality associated with epigenetic scars and alterations in nuclear and nucleolar integrity observed in treated embryo-derived fibroblasts. Lower-concentration injections resulted in viable mice with craniofacial deformities often accompanied by hydrocephalus, syndactyly and an aplasia cutis-like phenotype. Transcriptomic analysis revealed the repression of genes involved in neural crest differentiation in the TAK981-treated embryos as well as the overexpression of the Fgfr gene family in the adult TAK981 progeny. These genes, expressed in neural crest derivatives, are known for their gain-of-function mutations linked to human craniosynostosis syndromes, suggesting that potential overactivation of the FGF signaling pathway may contribute to the malformations observed in TAK981 progeny. Altogether, disruption of the SUMOylation/deSUMOylation equilibrium during a short embryonic period is sufficient to induce persistent cellular defects and transcriptional alterations, resulting in severe offspring malformations. In conclusion, the SUMO inhibitor TAK981 has teratogenic effects, disrupting normal fetal development and causing congenital disabilities reminiscent of traits observed in UBA2-related syndrome.

overall_design: bulk RNA-seq was performed on whole embryos at day E13.5, five days after the last injection, compared to control embryos

first: Jorge

last: Mata-Garrido

first: Isabella

last: Zafferri

first: Alice

last: Nordlinger

first: Anne

last: Dejean

first: Jack-Christophe

last: Cossec


title: Spatiotemporal dynamics of the lymph adaptive immune repertoire in response to viral infection

city: Ithaca

first: Shaowen

last: Jiang

address: 237 Tower Rd

institute: Cornell University

summary: The spatial organization of adaptive immune cells within lymph nodes is critical for understanding immune responses during infection and disease. Here, we investigated the spatial and temporal changes in the adaptive immune repertoire (AIR) in the draining lymph node after footpad infection with Vaccinia virus (VACV) in mice. To achieve this, we integrated high-resolution spatial transcriptomics with high-fidelity long-read adaptive immune receptor sequencing of T and B cell receptors. This approach enables simultaneous analysis of whole transcriptomes and AIR in their spatial context. We mapped the spatial distribution and temporal dynamics of immune phenotypes and AIRs at 3, 7, 10, 14, and 21 days post-infection. Our analysis revealed heterogeneous activation niches characterized by Interferon-gamma (IFN-γ) during the early stages of infection. We observed sub-anatomical structures within the germinal center (GC) and provided direct evidence that antibody-producing plasma cells differentiate and exit the GC from the dark zone. Furthermore, we traced the spatial lineage trajectory of B cell clones and found evidence of B cell maturation across multiple GCs. Overall, this method offers valuable insights into the spatial dynamics of immune responses within lymphoid organs, with relevance for spatiotemporal studies of the immune system response to an infectious agent.

overall_design: Six popliteal lymph nodes were collected from 6 individual mice with different conditions including one mock sample as control. We performed spatial transcriptomics on these lymph nodes by using the Curio Seeker platform and followed their protocol to get the complimentary cDNA library from it. Each cDNA library was split into short read (SR) for unbiased spatial trancriptomics or long read (LR) for TCR/BCR transcripts enrichment. So in total we have 12 samples library.

first: Madhav

last: Mantri

first: Iwijn

last: De Vlaminck


title: TRAF3 loss protects glioblastoma cells from lipid peroxidation and immune elimination via dysregulated lipid metabolism

first: Aidong

last: Zhou

address: Shatai North Road

department: Department of Cell Biology

institute: Southern Medical University

summary: Glioblastoma (GBM) is a highly aggressive form of brain tumor characterized by dysregulated metabolism. Increased fatty acid oxidation (FAO) protects tumor cells from lipid peroxidation-induced cell death, although the precise mechanisms involved remain unclear. Herein, we report that loss of tumor necrosis factor receptor-associated factor 3 (TRAF3) in GBM critically regulates lipid peroxidation and tumorigenesis by controlling the oxidation of polyunsaturated fatty acids (PUFAs). TRAF3 is frequently repressed in GBM due to promoter hypermethylation. TRAF3 interacts with enoyl-CoA hydratase 1 (ECH1), an enzyme catalyzing the isomerization of unsaturated fatty acids (UFAs), and mediates K63-linked ubiquitination of ECH1 at Lys214. ECH1 ubiquitination impedes TOMM20-dependent mitochondrial translocation of ECH1, which otherwise promotes the oxidation of UFAs, preferentially the PUFAs, and limits lipid peroxidation. Overexpression of TRAF3 enhances the sensitivity of GBM to ferroptosis and anti-PD-L1 immunotherapy in mice. Thus, the TRAF3-ECH1 axis plays a key role in the metabolism of PUFAs, and is crucial for lipid peroxidation damage and immune elimination in GBM.

overall_design: RNA-seq profiling of patient-derived GBM0709 cells stably transfected with TRAF3 overexpression lentivirus or the control lentivirus.

first: Yu

last: Zeng

first: Liqian

last: Zhao

first: Kunlin

first: Fan

last: Deng

first: Xiaochun

last: Bai

first: Ye

last: Song


title: Molecular Mechanisms Limiting the Therapeutic Window of AAV Gene Therapy in Mouse Models of Blue Cone Monochromacy

city: Morgantown

first: Gangqing

last: Hu

state: WV

address: 64 Medical Center Drive

institute: West Virginia University

summary: Blue cone monochromacy (BCM) is an X-linked retinal disorder caused by mutations in the OPN1LW/OPN1MW gene locus, resulting in impaired cone function and structural degeneration. We conducted a comparative analysis of AAV-mediated gene therapy in Opn1lw/Opn1mw double knockout (DKO) and Opn1mwC198R/Opn1sw-/- (C198R) BCM mouse models and evaluated the therapeutic window, efficacy, and longevity. Our results demonstrate that the AAV8-Y733F capsid achieved superior cone rescue compared to AAV5. While both DKO and C198R models showed similar therapeutic windows and rescue longevity, treatment efficacy decreased markedly in older mutant mice. Structural analysis revealed that aged cones in both models displayed degenerative changes, including mislocalized mitochondria and compromised connecting cilia. At the molecular level, we observed reduced AAV-mediated transgene expression in DKO and C198R older cones, which may result from decreased transduction efficiency, decreased circular episome stability, genome-wide transcription/translation downregulation, targeted mRNA/protein degradation, or overall cone degeneration. Notably, the cone-specific promoters for Pde6c and Cngb3 maintained robust activity in degenerating cones. These findings suggest that combining an efficient AAV serotype with an optimized cone promoter could be a viable approach to extend the therapeutic window and enhance treatment longevity for BCM patients.

overall_design: We generated two mouse models, DKO and C198R, for blue cone monochroamy. we compare gene expression changes in cone photoreceptors between C198R, DKO, and wild-type at 1- and 4- months ages. We also looked for cone genes whose expression remained unchangedenchavenunpregulatedges or evern upregulared in 4 mon vs 1 month in DKO and C198R mice.

first: Wen-Tao

first: Emily

last: Sechrest

first: Li

last: Ma


title: Cancer-cell-derived cGAMP limits the activity of tumor-associated CD8+ T cells

city: Zurich

first: Michael

last: Herbst

address: Winterthurerstrasse 190

country: Switzerland

institute: UZH

summary: To evaluate how CD8+ T-cells are influenced by their STING expression within tumors, we performed single-cell RNA sequencing of reisolated CD8+ T-cells sorted from LLC-cGAStetON-OVA tumors.

overall_design: 3 days after tumor (LLCcGAStetON) injection, STING-expressing and STING-deficient OT-I CD8+ T cells adoptively cotransferred to the mice. 6 days after transfer CD8+ T cells were reisolated by flow cytometric cell sorting (live, CD8+, CD45.1/1+ (STING-deficient) or CD45.1/2+ (STING-expressing)), and subjected to single-cell RNA sequencing.

first: Herbst

last: Michael

first: van den Broek

last: Maries


title: IL-27 producers in a neonatal BCG vaccination model are a heterogenous population of myeloid cells that are diverse in phenotype and function

summary: Tuberculosis (TB) is a serious public health concern in many regions of the world and the only approved vaccine to prevent TB is the live-attenuated BCG vaccine. Despite being widely used, the BCG vaccine fails to prevent pulmonary TB in adults. The BCG vaccine is administered during the neonatal period when levels of the immunosuppressive cytokine interleukin (IL)-27 are elevated, and previous studies have demonstrated that the source of IL-27 can impact downstream immune responses. We therefore sought to characterize the specific subpopulations of myeloid cells that produce IL-27 following BCG vaccination. To investigate this, we administered the BCG vaccine to neonatal IL-27p28eGFP mice that report IL-27 production. Our studies demonstrated that BCG vaccination steadily increased IL-27 production throughout the weeks post-vaccination. We also showed that a predominantly CD11b+ F4/80+population of IL-27 producers increased MHC class II expression following BCG vaccination in both the spleen and the lung. However, producers of IL-27 in these tissues differ, with a population of CD11c+ MHC II+ cells emerging in the spleen and a subset of Ly6G/C+ MHC II+ emerging in the lung. 10x scMultiome analysis further validated the increase in MHC class II expression and demonstrated improved antigen presentation functionality following vaccination. The sequencing analysis also revealed subpopulations of IL-27 producers with immunosuppressive functions such as a population of macrophages with increased Mrc1 expression post-vaccination. Our findings suggest that IL-27 producers are a heterogenous population of myeloid cells that impact the development of protective immune responses induced by the BCG vaccine.

overall_design: Spleens were harvested at 5 weeks post BCG vaccination from IL27p28eGFP mice and the live GFP+ CD3/CD19- negative cells were sorted. Cells from unvaccinated and BCG vaccinated mice were compared to detect differences in cellular producers of IL-27 following BCG vaccination.

first: Ashley

last: Divens


title: Mapping the Evolution of Acinar cell derived Pancreatic Preneoplastic Lesions in a Mouse Model: A Detailed Transcriptomic and Pathological Characterization

city: Munich

first: Thomas

last: Metzler

address: Trogerstr. 18

department: CEP

institute: TU Munich

summary: Background & Aims: Pancreatic ductal adenocarcinoma (PDAC) is among the deadliest cancers with poor prognosis and bad therapy outcome. Therefore, mouse models are frequently used to study PDAC and pancreatic preneoplastic lesions. This study aims to evaluate a proposed progression model from acinar cells via acinar-to-ductal metaplasia (ADM) to mucinous tubular complexes (MTC) at transcriptomic level and to investigate the molecular changes behind acinar-cell derived preneoplastic lesions in a mouse model of PDAC. Methods: Spatial transcriptomics was combined with pathological characterization of preneoplastic lesions in p48Cre/+-LSL-KrasG12D/+ mice (n=5) using the 10x Visium® platform. Integration with the Mouse Cell Atlas (MCA) 2.0 single-cell dataset was performed. Bioinformatic analysis was conducted using different Python toolkits and by calculating a pseudotime along the progression axis. Findings were validated at the protein level using immunohistochemistry (IHC). Results: Transcriptional data aligned well with pathological annotations and single-cell data confirmed a decrease in acinar cells and an increase in ductal cells during ADM. Pseudotime analysis supported the progression from acinar cells via ADM to MTC, with marker gene expression patterns along this axis. Upregulation of Keratin 19 and Tetraspanin 8, and downregulation of Amylase 1 and Claudin 10, were observed. Claudin 18 was upregulated specifically in MTC, while Mesothelin and Cathepsin L peaked during ADM. Validation by IHC confirmed the expression of Keratin 19, Amylase 1, Claudin 18 and Mesothelin on protein level. Conclusions: This study confirms the development of MTC from ADM and identifies novel biomarkers along the preneoplastic progression axis in a mouse model of PDAC, advancing our understanding of early pancreatic cancer development.

overall_design: The pancreata of five p48Cre/+-LSL-KrasG12D/+ mice (age 6 months) were analyzed using combining spatial transcriptomics and pathological annotations of pancreatic preneoplastic lesions.

first: Johannes

last: Wirth

first: Eva-Maria

last: Mayr

first: Shounak

last: Chakraborty

first: Nicole

last: Pfarr

first: Julia

last: Höbart

first: Jürgen

last: Ruland

first: Kaspar

last: Matiasek

first: Katja

last: Steiger


title: Multi-scale chromatin footprinting reveals wide-spread alterations to the structure of DNA regulatory elements [human gDNA]

city: Cambridge

first: Jason

last: Buenrostro

address: 7 Divinity Ave

institute: Harvard University

summary: Cis-regulatory elements (CREs) control gene expression and are dynamic in their structure and function, reflecting changes to the composition of diverse effector proteins over time. However, methods for measuring the organization of effector proteins at CREs across the genome are limited, hampering efforts to connect CRE structure to their function in cell fate and disease. Here, we developed PRINT, a computational method that identifies footprints of DNA-protein interactions from bulk and single-cell chromatin accessibility data across multiple scales of protein sizes. Using these multi-scale footprints, we created the seq2PRINT framework, which employs deep-learning to allow precise inference of transcription factor and nucleosome binding and interprets regulatory logic at CREs. Applying seq2PRINT to single-cell chromatin accessibility data from human bone marrow, we observe sequential establishment and widening of CREs centered on pioneer factors across hematopoiesis. We further discover age-associated alterations in the structure of CREs in murine hematopoietic stem cells, including widespread loss of nucleosomes and gain of de novo-identified Ets composite motifs. Collectively, we establish a method for obtaining rich insights into DNA-binding protein dynamics from chromatin accessibility data and reveal the architecture of regulatory elements across differentiation and aging.

overall_design: Human genomic DNA was first digested by the restriction enzyme SbfI-HF and the size-selected by electrophoresis followed by Tn5 tagmentation.

first: Yan

first: Max

last: Horlbeck


title: Novel cell-to-cell communications between macrophages and fibroblasts regulate obesity-induced adipose tissue fibrosis [scRNA-seq_2]

first: Hiro

last: Kohda

summary: Mincle (Macrophage inducible C-type lectin, clec4e) is a pattern recognition receptor expressed in innate immune cells and can sense cell death, suggesting a role in sterile inflammation. We previously showed that expression of Mincle is induced in adipose tissue macrophages during the development of obesity. Mincle accelerates adipose tissue inflammation and fibrosis, thereby exacerbating ectopic lipid accumulation and insulin resistance in the liver. In this study, we performed single-cell RNA sequencing analysis of the SVF in visceral adipose tissue from diet-induced obese mice to analyze the cell-cell interaction between Mincle-expressing macrophages and activated fibroblasts.

overall_design: Male wild-type and Mincle-deficient mice with a C57BL/6J background were fed a high-fat diet for 15 weeks. Single-cell RNA sequencing analysis was conducted using the SVF prepared from epididymal white adipose tissue.

first: Miyako

last: Tanaka

first: Shigeyuki

last: Shichino

first: Satoshi

last: Ueha

first: Kouji

last: Matsushima

first: Takayoshi

last: Suganami


title: Novel cell-to-cell communications between macrophages and fibroblasts regulate obesity-induced adipose tissue fibrosis [scRNA-seq_1]

overall_design: Male C57BL/6J mice were fed a standard diet (SD) for 16 weeks and  a high-fat diet (HFD)  for 8 and 16 weeks. Single-cell RNA sequencing analysis was conducted using the SVF prepared from epididymal white adipose tissue.


title: Novel cell-to-cell communications between macrophages and fibroblasts regulate obesity-induced adipose tissue fibrosis [spatial transcriptomics]

summary: Mincle (Macrophage inducible C-type lectin, clec4e) is a pattern recognition receptor expressed in innate immune cells and can sense cell death, suggesting a role in sterile inflammation. We previously showed that expression of Mincle is induced in adipose tissue macrophages during the development of obesity. Mincle accelerates adipose tissue inflammation and fibrosis, thereby exacerbating ectopic lipid accumulation and insulin resistance in the liver. In this study, we performed spatial transcriptomic analysis of the visceral adipose tissue from diet-induced obese mice to analyze distribution of Mincle-expressing macrophages and the gene expression around them.

overall_design: Male C57BL/6J mice were fed a standard diet or high-fat diet for 36 weeks. Spatial transcriptomic analysis was conducted using epididymal white adipose tissue.


title: Enforced expression of miR-342 promotes an inflammatory phenotype in liver metastasis-associated macrophages [RNAseq_90]

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

country: Italy

institute: Consiglio Nazionale delle Ricerche

summary: Liver macrophages are crucial to maintain liver homeostasis. However, upon metastatic seeding, cancer cells co-opt these macrophages to act as tumor-associated macrophages (TAMs), facilitating tumor growth and invasiveness. MicroRNAs (miRNAs) are key regulators of TAM pro-tumoral functions, thus modulating their expression in liver macrophages may constitute a novel approach for liver metastasis immunotherapy. In this study, we identify a myeloid specific miRNA, miR-342-3p, and investigate its anti-tumoral function in liver macrophages in the context of colorectal cancer liver metastasis (CRLM). To this aim, we harnessed lentiviral vectors (LV) to infer and modulate miRNA activity in liver macrophages in vitro and in vivo. We found that miR-342-3p was highly active in macrophages in the healthy liver, but downregulated in proximity to CRLM. Rescuing miR-342-3p activity through enforced miRNA expression induced a pro-inflammatory phenotype in liver macrophages, which was associated to reduced CRLM growth. Transcriptomic analysis revealed Slc7a11, a cysteine-glutamate antiporter associated with TAM pro-tumoral functions, as a major miR-342-3p target. Overall, our findings highlight the potential of miR-342-3p in TAM reprogramming to enhance anti-tumoral immunity.

overall_design: To identify genes differentially expressed among iKCs treated with LV for miR-342-3p overexpression, miR-342-3p sponges, or control vectors, we FACS sorted transduced cells (expressing fluorescent marker mOrange+) and performed bulk RNAseq.

first: Chiara

last: Bresesti

first: Marco

last: Monti

first: Stefano

last: Beretta

first: Luigi

last: Naldini

first: Mario

last: Squadrito


title: Multi-scale chromatin footprinting reveals wide-spread alterations to the structure of DNA regulatory elements [in vitro footprinting]

overall_design: Bacterial artificial chromosome DNA was tagmented by Tn5 in the presence or absence of purified recombinant TF.

first: Conrad

last: Hock

first: Rachel

last: Savage

first: Fabiana

last: Duarte

first: Ajay

last: Labade

last: Hu


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

first: LUCIA

last: LORENZI

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

overall_design: RNA was extracted from the mouse cell line HPC-7, mouse primary cells (macrophages and bone marrow progenitors) and the human AML cell line KO-52. LPS was added for 2, 8 or 12 hours.

first: Maria

last: Cadefau-Fabregat

first: Gerard

last: Martínez-Cebrián

first: Lucía

last: Lorenzi

first: Sergi

last: Cuartero


title: Splicing targeting approaches highlight actionable vulnerabilities in triple negative breast cancer

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary: To investigate if pharmacological inhibition of splicing could uncover novel actionable vulnerabilities in TNBC, we profiled the genome-wide transcriptional changes elicited in MDA-MB-231 cells by treatment with Indisulam, that promote degradation of the splicing, and Pladienolide B, that impairs the activity of SF3B1.

overall_design: Poly-A plus RNA-sequencing of MDA-MB-231 cells treated with 10 nM Pladienolide B for 6 hours, Indisulam (3.3µM, 12hrs) or DMSO as control.

first: Cinzia

last: Caggiano

first: Valerio

last: Petrera

first: Miriana

last: Ferri

last: Pieraccioli

first: Eleonora

last: Cesari

last: Naro

first: Claudio

last: Sette


title: Enforced expression of miR-342 promotes an inflammatory phenotype in liver metastasis-associated macrophages [miRNAseq_1510]

first: Ivan

last: Merelli

type: Non-coding RNA profiling by high throughput sequencing

overall_design: To identify genes differentially expressed among cell populations targeted by systemic lentiviral vector (LV) delivery, we injected mice with a PGK.GFP LV and FACS sorted preferentially transduced cell populations, namely Kupffer cells (KCs) and liver sinusoidal endothelial cells (LSECs) from liver and B cells, red pulp macrophages (RPM), classical dendritic cells type 1 and 2 (cDC1, cDC2) from spleen. Bulk RNAseq of small RNA fraction was performed for all samples.

first: Chiara

last: Bresesti

first: Marco

last: Monti

first: Stefano

last: Beretta

first: Luigi

last: Naldini

last: Squadrito


title: Overexpression of RNA polymerase I specific SL1 component TAF1C induces cancer-specific gene expression in BEAS-2B cells

city: ropar

first: srivatsava

last: naidu

state: punjab

address: bhara phool

department: biomedical engineering

country: India

institute: indian institute of technology ropar

summary:
Purpose: Hyperactive RNA Polymerase I (Pol I) transcription and the upregulation of proteins essential for the initiation of Pol I transcription are the common features of a wide range of cancers . However, the role of Pol I transcription in the etiology of cancer remains unclear. Here, we activated Pol I transcription by overexpressing SL1 subunit TAF1C, and performed whole transcriptome analysis by RNA-Seq.
Methods: Non-cancerous lung epithelial  BEAS-2B cellswere transfected with empty vector (eV) and TAF1C expression vector (TAF1C) to generate stable cell lines. Total RNA was isolated from biological triplicates of eV and TAF1C BEAS-2B stable cells and used for RNA sequencing on Illumina platform.
Results: The whole transcriptomics data revealed the upregulation of cancer related genes in BEAS-2B cells stably expressing TAF1C gene. Integration of whole transcriptome data revealed interactive regulatory networks between protein-coding RNAs, lncRNAs and miRNAs associated with various hallmarks of cancer.
Conclusions: For the first time, we provide evidence for the global gene expression changes in response to activated Pol I transcription in the context of cancer. The regulatory networks identified in the study can further be validated as potential drug targets for cancer therapeutics

overall_design: RNA isolated from two eV replicates and three TAF1C replicates were used for long RNA and small RNA sequencing using Illumina platform

first: Sheetanshu

last: Saproo

first: Gouri

last: Dass

first: Suvendu

last: Kumar

first: Gaurav

last: Ahuja

first: Sudhakar

last: Sahoo

first: Srivatsava

last: Naidu


title: Enforced expression of miR-342 promotes an inflammatory phenotype in liver metastasis-associated macrophages [RNAseq_1509]

overall_design: To identify genes differentially expressed among cell populations targeted by systemic lentiviral vector (LV) delivery, we injected mice with a PGK.GFP LV and FACS sorted preferentially transduced cell populations, namely Kupffer cells (KCs) and liver sinusoidal endothelial cells (LSECs) from liver and B cells, red pulp macrophages (RPM), classical dendritic cells type 1 and 2 (cDC1, cDC2) from spleen. Bulk RNAseq of polyA enriched fraction was performed for all samples.

first: Mario


title: MRNA-seq and ChIP-seq identification of unique and overlapping target genes and pathways regulated by TBX4 in human pulmonary fibroblasts and pericytes

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

summary: combined RNA-seq and ChIP-seq results to identify TBX4 direct targets in fibroblast and pericyte; Reactome pathway analysis

overall_design: RNA-seq in fibroblasts and pericytes of  TBX4 KD and control; TBX4 ChIP-seq in fibroblasts and pericytes

first: Ying

last: Cai

first: Rizwan

last: Hamid

first: Eric

last: Austin