title: Deciphering ESR1-driven transcription in human endometrial stromal cells via transcriptome, cistrome, and integration with chromatin landscape [ESR1_Cut_Run]

city: Durham

first: Skylar

last: Montage Redecke

summary: Estrogen (E2) acting through the estrogen receptor alpha (ESR1) is a critical regulator of endometrial growth, differentiation and disease. The endometrial stromal cell (ESC) is a key target of ESR1 action and plays a crucial role in regulating paracrine communication to control uterine function. A mechanistic understanding of the role of ESR1 in ESCs is limited by low levels of expression of ESC lines.   Here we engineered telomerase-immortalized hESC (THESC) to express the CRISPR activation system to activate ESR1. Among six tested guide RNAs, the ESR1-3 gRNA induced robust ESR1 activation, restoring E2 responsiveness in THESC. Bulk RNA-seq revealed ESR1-mediated E2-dependent and E2-independent transcriptional programs, regulating pathways involved in inflammation, proliferation, extracellular matrix organization, and cancer. Notably, 72% of differentially expressed genes (DEGs) overlapped with genes active in human endometrial tissue during the proliferative E2 dominant phase, supporting their physiological relevance. Cut&Run-seq identified genome-wide ESR1 binding sites, with most located at distal regulatory elements. To associate distal ESR1 binding sites with genes, we integrated H3K27ac HiChIP chromatin loops in hESC to identify distal ESR1 binding sites that loop to gene promoters. We identified genes regulated by ESR1/E2 through long-range chromatin looping that are involved in stromal cell decidualization, including FOXO1 and IL6R. Additionally, we identified genes implicated in endometrial cancer, including ERRFI1, NRIP1, and EPAS1, suggesting a role for stromal ESR1 driven endometrial pathologies. Functional assays confirmed that ESR1 promotes cell viability and, in the presence of E2, enhances migration. In this study, we reveal novel insights into ESR1-dependent transcriptional regulation using a newly developed cell culture model that restores ESR1 expression in hESCs to overcome their limited E2 responsiveness. Additionally, we demonstrate the utility of integrating HiChIP chromatin looping data with cistromic data to associate distal ESR1 binding sites to gene promoters.

overall_design: Immortalized human endometrial stroma cells (THESC) were engineered with the CRISPR activation system to activate the Estrogen Receptor Alpha gene. ESR1 activated THESC were then treated with 10nM E2 or vehicle (0.01% ethanol) for 1, 3 or 6 hours and Cut&Run was conducted with an ESR1 Antibody in biological duplicates.

last: Montague Redecke

first: Austin

last: Bell-Hensley

first: Shuyun

first: MyeongJin

last: Yi

first: Akshadha

last: Jain

first: Abdull

middle: J

last: Massri

first: Francesco

last: DeMayo


title: CITE-seq of Neuropilin 2-expressing CD4+ T cells

status: Public on May 02 2025

city: Boston

first: Johannes

last: Wedel

state: MA

address: 300 Longwood Ave

country: USA

institute: Boston Children's Hospital

type: Expression profiling by high throughput sequencing

summary: We report that Neuropilin 2 expressing human CD4+ cells are a unique population of dysfunctional T effector cells.

overall_design: SCID-beige mice were humanized by intravenous transfer of 5x10^7 human PBMC. 7 days post-transfer, human CD4+ T cells were isolated from spleen, stained for NRP2 expression using two DNAoligo-conjugated antibodies and 10^4 cells were loaded onto a 10x controler.

first: Sek

middle: W

last: Kong

first: David

middle: M

last: Briscoe


title: Multi-omic analysis identifies erythroid cells as the major population in mouse placentas expressing genes for antigen presentation in MHC class II, chemokines, and antibacterial immune response

status: Public on May 01 2025

city: Novosibirsk

first: Roman

middle: Yurievich

last: Perik-Zavodskii

state: Novosibirsk region

address: Yadrincevskaya 14

country: Russia

institute: "Research Institute of Fundamental and Clinical Immunology" (RIFCI)

type:
Expression profiling by array
Other

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

overall_design: Refer to individual Series


title: Characterization of the human testicular primary cells

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

summary: In this study, we carried out experiments using commercially available human testicular primary cells - hTPc (Celprogen, CA, USA), obtained from a 25-years old Caucasian man with normal karyotype 46,XY. To characterize the hTP cells, we used the commercial total RNA obtained from normal testicular tissues with preserved spermatogenesis (n=3) (Clontech Laboratories; Agilent Life Technologies, Carlsbad, CA, USA; Ambion Life Technologies, Carlsbad, CA, USA)

overall_design: We performed a comparative analysis of gene expression profiles by RNA-seq between: human testicular primary cells (hTPc) (n=3), the human testicular primary cells from another vial (hTPcIM) (n=3) and human testis with normal spermatogenesis (n=3)

first: Malcher

last: Agnieszka


title: Multi-omics analysis identifies erythroid cells as the major population in mouse placentas expressing the MHC class II antigen presentation, chemokine, and antibacterial immune response genes [Spatial Transcriptomics]

summary: Pregnancy is one of the most important processes for mammals, which is deeply controlled by the immune system. We performed spatial transcriptomics to profile mouse placentas from semi-allogeneic and syngeneic pregnancies at E12.5 to elucidate differences between these types of pregnancies. Our analysis showed that erythroid cells were the major immunoregulatory population in both types of pregnancies.

overall_design: We collected murine placentas at E12.5 from both syngeneic and semi-allogenic pregnancies, froze them in OCT, cut 10mm sections, placed them on a cryoslide, and performed 10X Genomics Visium CytAssist spacial transcriptomic analysis.

first: Olga

last: Perik-Zavodskaia

first: Saleh

last: Alrhmoun


title: Identification of a VHL germline deletion in a family with Von Hippel-Lindau syndrome using MLPA-NGS

status: Public on May 05 2025

city: Shanghai

first: Chaoran

last: Xia

state: Shanghai

address: 800# Dong Chuan Road,  Shanghai, China

country: China

institute: Shanghai Jiaotong University

summary:
Gene chip analysis was performed using the Infinium OmniZhongHua-8 v1.3 BeadChip (Ilumina, Inc.). This method is used to detect ~240 CNV-affected genetic diseases/regions, including uniparental disomy and polyploidy.
To identify copy number and CNV variations on chromosome 3 and in the vicinity of VHL, compared to a new assay called MLPA-NGS, we analysed individual hybridizations conducted on  Infinium OmniZhongHua-8 v1.3 BeadChip (Ilumina, Inc.). Sample types included normal blood.

overall_design: The genotypes of the study samples were determined using Gene chip analysis. IMPUTE2 was utilized to impute supplementary autosomal single nucleotide polymorphisms (SNPs). The genotype assignments were grounded on the phase 3000 Genomes cosmopolitan reference panel.

first: Yongchen

last: Yang


title: Multi-omics analysis identifies erythroid cells as the major population in mouse placentas expressing the MHC class II antigen presentation, chemokine, and antibacterial immune response genes [Nanostring]

summary: Pregnancy is one of the most important processes for mammals, which is deeply controlled by the immune system. We performed NanoString Immune Transcriptome to profile erythroid cells from mouse placentas from semi-allogeneic and syngeneic pregnancies at E12.5 and E19.5 to elucidate the differences between these types of pregnancies.

overall_design: We collected murine placentas at E12.5 and E19.5 from both syngeneic and semi-allogenic pregnancies, extracted Ter-119 Erythroid cells and performed NanoString Immune transcriptome analysis

first: Perik-Zavodskaia

last: Olga

first: Perik-Zavodskii

last: Roman


title: Barcoded viral tracing identifies bi-directional immunosuppressive astrocyte-glioblastoma cross-talk

status: Public on Apr 30 2025

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute


title: MEF2C hypofunction in GABAergic cells alters neurotypical behavior and prefrontal cortex inhibitory synaptic transmission in a sex-dependent manner

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street, BE208

institute: MUSC

summary: Heterozygous loss-of-function mutations or deletions of the MEF2C gene cause a neurodevelopmental disorder, termed MEF2C Haploinsufficiency syndrome (MCHS), that is characterized by autism spectrum disorder, intellectual disability, seizures, and other neurological symptoms. In mice, global Mef2c heterozygosity produces numerous behavioral phenotypes reminiscent of MCHS. MEF2C is highly expressed in multiple cell populations in the developing brain, including GABAergic inhibitory neurons. While MEF2C hypofunction in excitatory neurons or microglia alter neurotypical behaviors and brain circuit function, the impact of MEF2C heterozygosity in GABAergic neurons remains unknown.

overall_design: We employed GABAergic cell type-specific manipulations to study mouse Mef2c heterozygosity in a battery of MCHS-like behaviors. We also performed single cell transcriptomics and patch-clamp electrophysiology and optogenetics to assess intrinsic excitability and synaptic transmission.

first: Yongjoo

last: Cho

first: Chirstopher

last: Cowan


title: Transcriptomic profiling of Neuropilin 2-expressing CD4+ T cells

summary: We report a novel Neuropilin 2-expressing CD4+ T cell subset that modulates immune responses in vivo.

overall_design: Human CD4+ T cells were isolated from venous blood and in vitro activated with 3 mcg/ml phytohemagglutinin for 16 hours. NRP2pos and NRP2neg cells were subsequently FACS-sorted and gene expression profiling was performed on 4 biological replicates.


title: Chromation accessibility profiles of cKit positive bone marrow cells from six genotype mice - WT, Idh1R132, Npm1c, Flt3ITD, Idh1R132+Npm1c, and Idh1R132+Flt3ITD

city: New York

first: Cem

last: Meydan

state: New York

address: 1305 York

department: Physiology & Biophysics

institute: Weill Cornell Medical College

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Here we show that the combination of Idh1R132 plus Npm1c mutations cooperatively induced overt AML in vivo, using genetically engineered mouse model. In contrast, the combination of Idh1R132 plus Flt3ITD led to myeloid proliferation disease, but not AML. The mice harboring both of Idh1R132 and Npm1c mutations got fatal (median survival, 254 days) due to AML, which demonstrated rapid lethality on recipient mice in secondary transplantation experiments. We analyzed cKit-positive bone marrow cells from six genotype mice - WT, Idh1R132, Npm1c, Flt3ITD, Idh1R132+Npm1c, and Idh1R132+Flt3ITD. We isolated cKit positive BM cells from the mice of the two different ages (3 and 6 months old), and subjected to RNA-seq, bisulfite-seq, and ATAC-seq.

overall_design: We examined gene-wide chromatin accessibility profiles of cKit positive BM cells from six genotype mice - WT, Idh1R132, Npm1c, Flt3ITD, Idh1R132+Npm1c, and Idh1R132+Flt3ITD, with 3-4 biological replicates for each genotype. We examined the cells from mice of the two different ages (3 and 6 months old).

first: Takashi

last: Sakamoto

first: Jonathan

last: Foox

first: Julie

last: Leca

first: Christopher

middle: E

last: Mason

first: Ari

last: Melnick

first: Tak

last: Mak


title: Super Pol II Domains enhance minor ZGA through 3D-interaction to ensure the integrity of major transcriptional waves in ZGA delayed mammals (HiC)

city: Yangling

first: zhang

last: yong

state: Shanxi

address: No.3 Taicheng Road

institute: Northwest A&F University

summary: Zygotic genome activation (ZGA) represents the inaugural post-fertilization transcription event. In mouse, RNA polymerase II (Pol II) initiates embryonic transcription through a step-wise transition, but the ZGA initiation process remains unclear in non-rodents. Here, Pol II profiling in bovine and porcine embryos, combined with multi-omics data across four mammalian species, revealed strong intergenic Pol II clusters, termed super Pol II domains (SPDs), that boost minor ZGA gene expression via chromatin interactions in bovine. Intriguingly, a similar strategy was found in human embryos, which also exhibit delayed ZGA followed by rapid up-regulation of minor ZGA genes. By contrast, these genes are precociously activated in porcine and mouse gametes before fertilization. Moreover, disruption of SPD structure, which decreases two minor ZGA genesKLF17orDUXAexpression, and knockdown them in bovine, leads to aberrant gene activation and impeded embryogenesis. Our findings highlight SPD enhancement as a species-specific evolutionary adaptation for initiating transcription in bovine and human embryos, thus illustrating previously underappreciated diversity in mammalian reproductive developmental strategies.

overall_design: The multiomics data (methylation, ChIP-seq,RNA-seq and Hi-C) on gametes and early embryos in bovine and porcine.

first: Jingcheng

last: Zhang

first: Hengkuan

first: Linmi

first: Jie

last: Wu

first: Linjie

last: Song

first: Xin

last: Liu

first: Wenying

first: Zixiao

first: Mei

last: Jiao

first: Mingyang

last: Hu

first: Hexu

first: Zhangyuan

last: Pan

first: Binqiang

last: Shi

first: Yong

last: Wang

first: Debao

first: Yunxia

last: Zhao

first: Gang

last: Ren

first: Shuhong


title: Evolution of Mycobacterium tuberculosis transcription regulation is associated with increased transmission and drug resistance [RNA-seq]

first: Peter

last: Culviner

address: 677 Huntington Ave

department: IID

institute: Harvard School of Public Health

summary: Mycobacterium tuberculosis (Mtb) has co-evolved with humans for thousands of years leading to variation in clinical virulence, transmissibility, and disease phenotypes. To identify bacterial contributors to this phenotypic diversity, we developed new RNA-seq and phylogenomic analysis tools to capture hundreds of Mtb isolate transcriptomes, link transcriptional variation to genetic variation, and find associations between variants and epidemiologic traits. Across 274 Mtb clinical isolates, we uncovered unexpected diversity in expression of virulence genes which could be linked to known and previously unrecognized regulators. Surprisingly, we found that many isolates harbor variants associated with decreased expression of EsxA (Esat6) and EsxB (Cfp10), which are virulence effectors, dominant T cell antigens, and immunodiagnostic targets. Across >55,000 isolates, these variants associate with increased transmissibility, especially in drug resistant Mtb strains. Our data suggest expression of key Mtb virulence genes is evolving across isolates in part to optimize fitness under drug pressure, with sobering implications for immunodiagnostics and next-generation vaccines.

overall_design: Clinical isolates from Vietnam and Peru were grown to the same OD in rich media. RNA-Seq libraries were captured to compare in vitro transcriptomes across clinical isolates to determine if transcriptional regulation plays a role in disparate phenotypes between Mtb clinical isolates.

middle: H

first: Sarah

last: Fortune


title: Evolution of Mycobacterium tuberculosis transcription regulation is associated with increased transmission and drug resistance [IDAP-seq]

overall_design: To identify binding of Rv0042c (slfR) transcription factor, slfR was purified and added at a 300 nM final concentration to an in vitro binding reaction with sheared Mycobacterium tuberculosis gDNA (IDAP-Seq). Enrichment of genomic regions was compared to a control reaction where no protein was added.


title: DNA methylation profiles of cKit positive bone marrow cells from six genotype mice - WT, Idh1R132, Npm1c, Flt3ITD, Idh1R132+Npm1c, and Idh1R132+Flt3ITD

first: Cem

last: Meydan

type: Methylation profiling by high throughput sequencing

overall_design: Using Bisulfite-Seq, we profiled gene-wide DNA methylation patterns of cKit positive BM cells from six genotype mice - WT, Idh1R132, Npm1c, Flt3ITD, Idh1R132+Npm1c, and Idh1R132+Flt3ITD, with 3-5 biological replicates for each genotype. We examined the cells from mice of the two different ages (3 and 6 months old).

first: Takashi

last: Sakamoto

first: Jonathan

last: Foox

first: Julie

last: Leca

first: Christopher

last: Mason

first: Ari

first: Tak


title: Gene expression profiles of cKit positive bone marrow cells from six genotype mice - WT, Idh1R132, Npm1c, Flt3ITD, Idh1R132+Npm1c, and Idh1R132+Flt3ITD

overall_design: Using RNA-Seq, we examined gene expression profiles of cKit positive BM cells from six genotype mice - WT, Idh1R132, Npm1c, Flt3ITD, Idh1R132+Npm1c, and Idh1R132+Flt3ITD, with 4-5 biological replicates for each genotype. We examined the cells from mice of the two different ages (3 and 6 months old).

last: Melnick

last: Mak


title: Cancer-associated snaR-A noncoding RNA interacts with core splicing machinery and disrupts processing of mRNA subpopulations

status: Public on Apr 28 2025

city: Urbana

first: Sihang

last: Zhou

state: IL

address: 601 S Goodwin Ave

institute: University of Illinois Urbana-Champaign

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA polymerase III (Pol III) transcription in cancer is linked with the emergence of snaR-A (small NF90-associated RNA isoform A), a hominid-specific ncRNA shown to enhance cell proliferation, migration, and invasion. Here, we investigate snaR-A-protein interactions to delineate its role as a putative driver of cancer progression. At the molecular level, we discover that snaR-A interacts with mRNA splicing factors, including SF3B2 - a core component of the U2 small nuclear ribonucleoprotein (snRNP) - and localizes to subnuclear foci enriched for splicing factors. Ectopic snaR-A overexpression leads to increased intron retention, a hallmark of inefficient splicing, whereas depletion of endogenous snaR-A reduces intron retention in mRNA subpopulations associated with 3’ intron-exon U2 snRNP residency and nuclear speckle proximity. We further show that high levels of snaR-A promotes cell migration in cells linked with increased intron retention, consistent with evidence supporting snaR-A as a negative prognostic factor in cancer. Taken together, these findings establish snaR-A as a molecular disruptor of splicing. We propose that snaR-A-related splicing disruption may phenocopy previously reported splicing defects and consequences attributed to mutations in U2 snRNP in cancer, eliciting an alternate, non-mutational pathway during tumorigenesis.

overall_design: To investigate the effect of SSB on snaR-A, we performed SSB knockdown in HEK293T and sequenced the samples. The experiment included three biological replicates for scramble and SSB knockdown. Raw mRNA signal counts were extracted.

first: Kevin

last: Van Bortle


title: Intersecting impact of CAG repeat and Huntingtin knockout in stem cell-derived cortical neurons [cortical_bulkRNASeq]

status: Public on Apr 29 2025

city: Irvine

first: Ricardo

last: Miramontes

address: 845 Health Sciences Rd

institute: UC Irvine

summary: Huntington’s Disease (HD) is caused by a CAG repeat expansion in the gene encoding Huntingtin (HTT). While normal HTT function appears impacted by the mutation, the specific pathways unique to CAG repeat expansion versus loss of normal function are unclear. To understand the impact of the CAG repeat expansion, we evaluated biological signatures of HTT knockout (HTT KO) versus those that occur from the CAG repeat expansion by applying multi-omics, live cell imaging, survival analysis and a novel feature- based pipeline to study cortical neurons (eCNs) derived from an isogenic human embryonic stem cell series (RUES2). HTT KO and the CAG repeat expansion influence developmental trajectories of eCNs, with opposing effects on the growth. Network analyses of differentially expressed genes and proteins associated with enriched epigenetic motifs identified subnetworks common to CAG repeat expansion and HTT KO that include neuronal differentiation, cell cycle regulation, and mechanisms related to transcriptional repression and may represent gain-of-function mechanisms that cannot be explained by HTT loss of function alone. A combination of dominant and loss-of-function mechanisms are likely involved in the aberrant neurodevelopmental and neurodegenerative features of HD that can help inform therapeutic strategies.

overall_design: Profiling an isogenic embryonic stem cell line series containing two expanded repeat lines (56 and 72 CAG repeats in exon 1 of HTT), two control length repeat lines (20 and 22 CAG repeats in exon 1 of HTT), and one HTT knockout line differentiated down a cortical nueron lineage.

first: Jennifer

middle: T

last: Stocksdale

first: Matthew

last: Leventhal

first: Keona

middle: Q

first: Charlene

last: Smith

first: Jie

last: Wu

first: Ernest

last: Fraenkel

first: Leslie

last: Thompson


title: Mutant IDH1 cooperates with NPM1c or FLT3-ITD to drive distinct myeloid diseases and molecular outcomes

first: Cem


title: CNOT7 Promotes Radiation Resistance in Colorectal Cancer via XRCC6-Mediated NHEJ DNA Repair Pathway

city: Harbin

first: Binbin

last: Cui

state: Heilongjiang

address: Baojian Road

institute: Harbin Medicial University

summary: In this study, we identified CNOT7 as a key protein influencing the radiotherapy sensitivity of rectal cancer through proteomic sequencing of patient tissues. Patients with high CNOT7 expression often exhibit poorer prognoses during radiotherapy. We explored the potential mechanisms by which CNOT7 affects radiotherapy sensitivity in CRC. CNOT7 reduces polyubiquitination of K48 linked lysine 526 on XRCC6 by regulating TRIM21. This enhances DNA damage repair primarily mediated by the NHEJ pathway, thereby conferring radiotherapy resistance to colorectal cancer cells. Our study suggests that targeting CNOT7 could serve as a potential therapeutic strategy for rectal cancer patients

overall_design: To investigate the function of CNOT7 in the CCR4-Not complex, we established a stable CNOT7 knockdown cell line in the CRC cell line SW480 using shRNA, and performed RNA-seq to identify downstream differentially expressed target genes.

first: Yien

last: Li

first: Luying


title: Changes in nucleus accumbens core translatome accompanying incubation of cocaine craving

city: Portland

first: Alex

middle: B

last: Kawa

state: OR

address: 3181 SW Sam Jackson Park Rd, L470

department: BEHN

institute: OHSU

summary: In the ‘incubation of cocaine craving’ model of relapse, rats self-administer cocaine and then experience a prolonged abstinence period. After this prolonged abstinence period, rats exhibit a progressive intensification (incubation) of cue-induced craving, and the expression of incubated craving depends on plasticity of excitatory synaptic transmission in nucleus accumbens (NAc) core medium spiny neurons (MSN). Previously, we found that the maintenance of this plasticity depends on ongoing protein translation, and that regulation of translation is altered after incubation of cocaine craving. Here we used male and female rats that express Cre recombinase in either dopamine D1 receptor- or adenosine 2a (A2a) receptor-expressing MSN to express a GFP-tagged ribosomal protein in a cell-type specific manner, enabling us to use Translating Ribosome Affinity Purification (TRAP) to isolate actively translating mRNAs from both MSN subtypes for analysis by RNA-Seq. We compared rats that self-administered saline or cocaine. Saline rats were assessed on abstinence day (AD) 1, while cocaine rats were assessed on AD1 or AD40-50. For both D1 and A2a MSN, there were few differentially translated (DT) genes between saline and cocaine AD1 groups. In contrast, a pronounced divergence was observed between cocaine rats on AD1 and AD40, and this was far more robust in D1 MSN. Finally, all comparisons revealed sex differences in translating mRNAs. This study, the first to combine TRAP-seq, transgenic rats, and a cocaine self-administration paradigm, identifies translating mRNAs specifically linked to incubation of cocaine craving in D1 and A2a MSN of the NAc core.

overall_design: Nucleus accumbens punches from adult male and female D1:Cre and A2a:Cre rats that self-administered cocaine or saline and were euthanized 1 or 40 days later. Translating RNA affinity purification (TRAP) was run on the tissue to collect TRAP RNA selectively from D1 or A2a (D2) expressing medium spiny neurons.

first: A

first: J

middle: G

last: Hashimoto

first: M

last: Beutler

last: Guizzetti

last: Wolf


title: Bi-directional immunosuppressive interactions between astrocytes and glioblastoma cells identified by barcoded viral tracing [Human Single Cell Dataset]

first: Zhaorong

summary: Glioblastoma (GBM) is the most lethal primary brain malignancy. Immunosuppression in the GBM tumor microenvironment (TME) presents a major barrier to immune-targeted therapies. However, our understanding of mechanisms of immunomodulation in the GBM TME is still limited. To address this challenge, we developed a viral barcode interaction tracing approach for the analysis of cell-cell communication in the TME in GBM samples and preclinical models with single-cell resolution, which we combined with single-cell and bulk RNA-seq analyses of GBM clinical samples and pre-clinical models, human organotypic GBM slice cultures, in vivocell-specific CRISPR/Cas9-driven genetic perturbations and human and mousein vitroexperimental systems to identify a novel bi-directional communication pathway between ANXA1 expressed inastrocytes and its receptor FPR1 expressed by GBM cells that limits anti-tumor immune responses. ANXA1 expression in astrocytes and FPR1 expression in cancer cells are associated with shorter survival and earlier recurrence in GBM patients. The inactivation of astrocyte-glioma ANXA1/FPR1-signaling enhanced tumor specific CD4+ and CD8+ T-cell responses, increasing tumor infiltration by neoantigen-specific CD8+ T cells while limiting transcriptional modules linked to T-cell exhaustion; ANXA1/FPR1-signaling inactivation also boosted tumor-associated macrophage responses. Using pre-clinical models and human GBMin vitroexperimental systems, we established that FPR1 inhibits immunogenic necroptosis in tumor cells, while ANXA1 retrograde signaling suppresses NF-kB and inflammasome activation within astrocytes. In summary, we developed a new barcoding approach to analyze TME cell-cell interactions with single-cell resolution in clinical samples and pre-clinical models, and used it to identify a novel pathway of bidirectional ANXA1–FPR1 astrocyte-GBM communication which promotes immunoevasion and cancer progression.

overall_design: Single Cell RNA-Seq dataset which includes 12 samples obtained from 3 patients

first: Brian

last: Andersen

first: Camilo

middle: F

last: Akl

first: Francisco

last: Quintana


title: Bi-directional immunosuppressive interactions between astrocytes and glioblastoma cells identified by barcoded viral tracing [Mouse Single Cell Dataset]

overall_design: Single Cell RNA-Seq dataset which includes 6 samples obtained from 6 Mice.


title: Polycomb repressive complex 2 regulates sexual development in Neurospora crassa

status: Public on May 12 2025

city: Athens

first: Zachary

middle: A

last: Lewis

state: GA

address: 120 E. Green St.

department: Microbiology

institute: University of Georiga

summary: In most branches of the fungal kingdom  sexual development marks a dramatic shift from simple multicellular hyphae to complex fruiting bodies composed of multiple tissues and cell types. It is essential to tightly regulate development to prevent unnecessary energy investment into building these structures. Polycomb Repressive Complex 2 (PRC2) is a highly conserved regulator of development in multicellular organisms. In plants  animals  and some fungi  PRC2 represses genes by depositing histone H3 lysine 27 tri-methylation (H3K27me3) in promoters and gene bodies of conditionally activated genes. In Neurospora crassa  H3K27me3-associated genes are poorly conserved and stably repressed in most RNA-seq datasets. Through analysis of publicly available RNA-seq experiments  we found that PRC2-methylated genes are broadly and uniquely activated during sexual development. PRC2-methylated genes comprise a distinct subset of developmentally induced genes (DIGs) characterized by an exceptionally high degree of cell-type specificity. Loss of PRC2 activity results in the precocious formation of perithecia-like structures (dubbed false perithecia)  even in the absence of a compatible mating-type partner. These structures show a unique gene expression profile with activation of both PRC2-methylated and unmethylated DIGs  showing evidence of a transcriptional reprogramming event. Together  these data suggest that PRC2 is part of a developmental checkpoint that restricts fruiting body development to the appropriate conditions.

overall_design: isogenic siblings were isolated from a backcross between FGSC11182 (set-7) and wild-type N. crassa. Individual wild-type and set-7 progeny were inoculated on plates containing SCM agar overlain with cellophane and grown at room temperature in constant darkness for 12 days. Tissue was harvested from the cellophane surface and then snap frozen and ground in liquid nitrogen. RNA was isolated using TRIzol reagent  using methods optimized for solid fungal tissue.

first: Abigail

last: Deaven

middle: R

last: Ameri


title: Single-cell transcriptomic analyses unveil exercise-induced changes in murine skin vascular endothelial cells

city: Montreal

first: Guillaume

last: Lettre

state: Quebec

address: 5000 Belanger

country: Canada

institute: Montreal Heart Institute

summary: Physical activity (PA) is a fundamental aspect of preventive medicine, offering profound benefits for cardiovascular health and overall well-being. Despite its widespread benefits, the molecular mechanisms underlying PA-induced improvements in microvascular functions remain poorly understood. The skin microvasculature is uniquely affected by exercise-induced shear stress, especially during thermoregulation. Using single-cell RNA sequencing, we investigated how voluntary exercise influences the transcription profile of endothelial cells in the skin microvasculature of mice. We assigned 20 mice to either a sedentary group or a 1-month voluntary exercise program involving running wheels. Post-intervention, we collected skin biopsies from twelve mice for transcriptomic analyses. The differential expression analysis showed a significant increase in the expression of the Zbtb16 gene in vascular endothelial cells (vECs). The expression of Zbtb16 in vECs was correlated with genes involved in angiogenesis. Additionally, Gene Set Enrichment Analysis (GSEA) with nominally differentially expressed genes in vECs highlighted the suppression of pathways related to oxidative stress, cell proliferation and metabolism in the exercise group. This suggests an exercise-triggered transition towards improved metabolic efficiency and enhanced homeostasis in vECs. These results begin to reveal how exercise induces molecular changes in vECs of the skin microvasculature, highlighting PA's role in influencing endothelial function.

overall_design: Single cells were isolated from mice subjected to physical activity and from sedentary controls. Libraries were prepared using the 10x Genomics Chromium single-cell RNA-sequencing (scRNA-seq) protocol.

first: Pegah

last: Hejazi

first: Pauline

last: Mury

first: Éric

last: Thorin


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

status: Public on Apr 26 2025

city: DURHAM

first: David

last: Tobin

state: NC

address: Duke University Medical Center

department: Molecular Genetics and Microbiology

institute: Duke University

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

sample_organism:
Mycobacterium marinum
Danio rerio

platform_organism:
Mycobacterium marinum
Danio rerio

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

first: Gopinath

last: Viswanathan


title: Bi-directional immunosuppressive interactions between astrocytes and glioblastoma cells identified by barcoded viral tracing [Mouse Bulk RNA-Seq Dataset of Monocytes, T Cells and Astrocytes 5OLJ]

last: Li

overall_design: Bulk RNA-Seq dataset which includes 33 samples from 4 different cell types sorted from Mice


title: Using a modular massively parallel reporter assay to discover context-specific regulatory grammars in type 2 diabetes - Kyono library

status: Public on Apr 27 2025

city: Ann Arbor

first: Adelaide

middle: Erin

last: Tovar

state: Michigan

address: 100 Washtenaw Ave

department: Computational Medicine & Bioinformatics

institute: University of Michigan

summary: Recent genome-wide association studies have established that most complex disease-associated loci are found in noncoding regions where defining their function is nontrivial. In this study, we leverage a modular massively parallel reporter assay (MPRA) to uncover sequence features linked to context-specific regulatory activity. We screened enhancer activity across a panel of 198-bp fragments spanning over 10k type 2 diabetes- and metabolic trait-associated variants in the 832/13 rat insulinoma cell line, a relevant model of pancreatic beta cells. We explored these fragments’ context sensitivity by comparing their activities when placed up- or downstream of a reporter gene, and in combination with either a synthetic housekeeping promoter (SCP1) or a more biologically relevant promoter corresponding to the human insulin gene (INS). We identified clear effects of MPRA construct design on measured fragment enhancer activity. Specifically, a subset of fragments (n = 702/11,656) displayed positional bias, evenly distributed across up- and downstream preference. A separate set of fragments exhibited promoter bias (n = 698/11,656), mostly towards the cell-specific INS promoter (73.4%). To identify sequence features associated with promoter preference, we used Lasso regression with 562 genomic annotations and discovered that fragments with INS promoter-biased activity are enriched for HNF1 motifs. HNF1 family transcription factors are key regulators of glucose metabolism disrupted in maturity onset diabetes of the young (MODY), suggesting genetic convergence between rare coding variants that cause MODY and common T2D-associated regulatory variants. We designed a follow-up MPRA containing HNF1 motif-enriched fragments and observed several instances where deletion or mutation of HNF1 motifs disrupted the INS promoter-biased enhancer activity, specifically in the beta cell model but not in a skeletal muscle cell line, another diabetes-relevant cell type. Together, our study suggests that cell-specific regulatory activity is partially influenced by enhancer-promoter compatibility and indicates that careful attention should be paid when designing MPRA libraries to capture context-specific regulatory processes at disease-associated genetic signals.

sample_organism:
Rattus norvegicus
synthetic construct

platform_organism:
Rattus norvegicus
synthetic construct

overall_design: We obtained a pool of 79,511 full-length 230-bp fragments spanning variants associated with type 2 diabetes and related metabolic traits from Agilent. We cloned these sequences into the STARR-seq backbone plasmid and inserted 16-bp random barcodes into this library. We electroporated 10 ug of barcoded library into 25 million INS-1/832/13 rat insulinoma cells and harvested the cells 24 hours later. We isolated total RNA and enriched for mRNA using oligo(dT) beads. We generated sequencing libraries and performed paired-end sequencing on the Illumina HiSeq instrument.

first: Yasuhiro

last: Kyono

first: Kirsten

last: Nishino

first: Maya

last: Bose

first: Arushi

last: Varshney

first: Stephen

middle: C

last: Parker

first: Jacob

middle: O

last: Kitzman


title: RNA seq of human colon cancer cell line HT29 treated with nanocurcumin

status: Public on May 13 2025

city: Tabriz

first: Esmaeil

last: Babaei

state: East Azerbaijan

address: 29th Bahman Blvd.,

department: Biology

country: Iran

institute: University of Tabriz

summary: This study explores the transcriptomic effects of Gemini-curcumin (Gemini-Cur), a nano formulated version of curcumin, on HT-29 colorectal cancer cells. RNA sequencing was performed on treated and control samples to identify differentially expressed RNAs. The dataset provides insights into the molecular mechanisms of Gemini-Cur and its potential in modulating gene expression.

overall_design: Four total samples were analyzed, including two biological replicates of untreated HT-29 cells (Control) and two replicates of Gemini-Cur treated cells (Treatment). Cells were treated for 48 hours, after which total RNA was extracted for sequencing.

first: Hewa

last: Jalal Azeez

first: Zohre

last: Zibaei


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

status: Public on Apr 23 2025

first: Kris

last: Kahle

address: 55 Fruit Street

institute: MGH

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

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

first: Kristopher

first: Duy

last: Phan

first: Emre

last: Kiziltug


title: Cancer-associated snaR-A noncoding RNA interacts with core splicing machinery and disrupts processing of mRNA subpopulations II

first: Sihang

last: Zhou

overall_design: To investigate the effect of snaR-A on splicing of mRNAs, we performed snaR-A overexpression and SF3B2 overexpression in HEK293T and A549 cells and deep sequenced the samples. The experiment included three biological replicates for scramble, snaR-A, GFP, and SF3B2 overexpression. Raw mRNA signal counts were extracted.

first: Kevin

last: Van Bortle


title: Bi-directional immunosuppressive interactions between astrocytes and glioblastoma cells identified by barcoded viral tracing [Mouse Bulk RNA-Seq Dataset of Monocytes, T Cells and Astrocytes 63FG]

first: Zhaorong

first: Brian

last: Andersen

first: Camilo

last: Akl

first: Francisco

last: Quintana


title: TKTL1: a new candidate gene in nonobstructive azoospermia

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

institute: University of Bergen

summary: The genetic background of the non-obstructive azoospermia (NOA) remains poorly known. However, recent studies employing next generation sequencing techniques were able to uncover some NOA causative genes, among which was the TKTL1 gene. In this article we aim to understand the function of the TKTL1 gene in human spermatogenesis by inducing its overexpression in human testicular primary cells (hTPc), which we verified in male gonad tissue samples collected from NOA patients by uncovering the genes cluster regulated by TKTL1. Successful overexpression of the TKTL1 gene was achieved in hTP cells, the TKTL1 gene expression level was significantly higher in modified cells compared to both control groups (p<0.01). Using RNA-seq, we selected 20 genes which expression levels significantly differed in the modified hTP cells overexpressing TKTL1 gene in comparison to both controls. Male gonad tissue samples collected from NOA patients harbouring a mutation in the TKTL1 gene showed a significant downregulation (p<0.05) in HERC5, CSF3, HES1 and HSPA1B genes, compared to both controls, which was in accordance with the results obtained for hTPc cells, as the overexpression of the TKTL1 gene correlated with an increased expression level of the named genes compared to control groups.

overall_design: The comparative analysis of gene expression profiles by RNA-Seq between modified human testicular primary cells (hTPc) with overexpressed TKTL1 (n=3) compared to WT cells (n=3) and negative control with expression of GFP (n=3)

first: Malcher

last: Agnieszka


title: Single-cell RNA-sequence of the resolution phase of lung inflammation in LPS-induced ARDS model

city: Bunkyo-ku

first: Kensuke

last: Miyake

state: Tokyo

address: 1-5-45, Yushima

department: Institute of Integrated Research

country: Japan

institute: Institute of Science Tokyo

summary: Acute respiratory distress syndrome (ARDS) is a serious lung failure with a high mortality rate and no effective pharmacological therapies. While the cellular and molecular mechanisms underlying the induction of ARDS have been extensively studied, those controlling its resolution remain poorly understood. Recent human cohort studies have implied the correlation between the severity of ARDS and the paucity of blood basophils. To examine the causative relationships between basophils and the pathogenesis of ARDS, we assessed the effect of basophil depletion in an LPS-induced mouse model of ARDS and explored the possible role for basophils in the induction and resolution of ARDS by using genetically engineered mice and single-cell RNA-sequencing (scRNA-seq) analyses.  Intratracheal LPS administration induced severe lung inflammation with massive neutrophil accumulation, followed by the recovery to homeostatic conditions. Basophil depletion impaired the recovery but not induction of lung inflammation, demonstrating the crucial role for basophils in the resolution phase of ARDS. scRNA-seq analysis identified that basophils accumulating in the lung were predominant sources of cytokine IL-4. Mice with basophil-specific IL-4 deficiency failed to resolve the lung inflammation. This was also the case in mice with neutrophil-specific IL-4 receptor deficiency. scRNA-seq analysis suggested that basophil-derived IL-4 acts on neutrophils to suppress their expression of anti-apoptotic genes and pro-inflammatory mediators. Thus, the present study demonstrated that basophils play a crucial role in the resolution phase of a mouse model of ARDS through the production of IL-4 which in turn acts on neutrophils to restrict lung inflammation.

overall_design: Cells isolated from inflamed lungs of WT and IL-4 KO mice on day 6 post-LPS inhalation were analyzed by scRNA-seq.

first: Seiko

last: Takasawa

first: Jun

last: Sugihara

first: Tomoya

last: Tateishi

first: Sho

last: Shibata

first: Sachiko

first: Hajime

last: Karasuyama

first: Yasunari

last: Miyazaki


title: Intersecting impact of CAG repeat and Huntingtin knockout in stem cell-derived cortical neurons

first: Ricardo

last: Miramontes

overall_design: Profiling an isogenic embryonic stem cell line series containing two expanded repeat lines (56 andd 72 CAG repeats in exon 1 of HTT), two control length repeat lines (20 and 22 CAG repeats in exon 1 of HTT), and one HTT knockout line at the pluripotent stage by RNAseq.

first: Jennifer

last: Stocksdale

first: Matthew

last: Leventhal

first: Keona

last: Wang

first: Charlene

last: Smith

first: Jie

last: Wu

first: Ernest

last: Fraenkel

first: Leslie

last: Thompson


title: CDA HFD mice analysed for hepatic gene expression after treatment with semaglutide

status: Public on Apr 25 2025

city: Maaloev

first: Jenny

last: Norlin

state: Denmark

address: Novo Nordisk Park 1

department: Translational Leads Department

country: Denmark

institute: Novo Nordisk

summary:
Metabolic dysfunction-associated steatohepatitis (MASH) is a chronic liver disease strongly associated with cardiometabolic risk factors. Semaglutide, a glucagon-like peptide-1 receptor agonist, improves liver histology in MASH, but the underlying signals and pathways driving semaglutide-induced MASH resolution are not well understood. We show that, in two preclinical MASH models, semaglutide improved histological markers of fibrosis and inflammation, and reduced hepatic expression of fibrosis- and inflammation-related gene pathways.
NOTE: dose is 20 µg/kg QD as stated in the publication, not 10 nmol/kg as stated in the fastq file names!

overall_design: CDA HFD mice were analysed for hepatic gene expression after treatment with semaglutide. Male C57BL/6JRj mice (7–8 weeks old) were obtained from Taconic (Ejby, Denmark) and housed in a controlled environment (12-h light/dark cycle, lights on at 6 AM, 21 ± 1.0°C, humidity 45–65%). Mice had ad libitum access to tap water and either chow or a high-caloric CDA-HFD diet (kcal %; fat 60%, carbohydrates 20%, 5.2 kcal/g, #A06071302, Research Diets, New Brunswick, NJ, USA) for 6 weeks prior to treatment start. CDA-HFD mice were randomly allocated to groups and treated with vehicle or semaglutide 20 µg/kg  for 6 (called 6-12w) or 12 weeks (called 6-18w). A group of CDA-HFD mice were terminated at treatment start to determine baseline levels of NASH ( baseline group). Vehicle-dosed chow-fed mice and mice switched to chow and does with vehicle served as additional controls.  Vehicle-dosed chow-fed mice and mice switched to chow and dosed with vehicle served as additional controls. Dosing was performed subcutaneously once daily in a volume of 5 ml/kg. To reduce initial gastric discomfort, the dose was increased through daily increments until reaching the target dose on treatment day 5.

first: Kasper

last: Almholt

first: Nikos

last: Sidiropoulos


title: Leucegene: AML sequencing (part 1-6, GRCh38 reference)

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

summary: RNA sequencing of human leukemia

overall_design:
The goals of this project are to obtain a comprehensive study of mutations and gene expression in human acute myeloid leukemia (AML). Methods: AML cells were thawed. DNA and RNA (polyA) was extracted and sequences were obtained with an illumina HiSeq 2000 sequencer.
**Re-analysis/re-quantification with new methods and updated reference genome of samples already found in the following Series: GSE49642, GSE52656, GSE62190, GSE66917, GSE67039 and GSE106272**

first: Camille

last: Simon

first: Jalila

last: Chagraoui

first: Jana

last: Krosl

first: Patrick

last: Gendron

first: Geneviève

last: Boucher

first: Pierre

last: Chagnon

first: Simon

last: Drouin

first: Raphaëlle

last: Lambert

first: Claude

last: Rondeau

first: Annie

last: Bilodeau

first: Sylvie

last: Lavallée

first: Martin

first: Caroline

last: Pabst

first: Anne

last: Bergeron

first: Vincent

first: Jonathan

last: Yeh

first: Eric

last: Deneault

first: Jessica

last: Simard

first: Giovanni

last: D'Angelo

first: Bernhard

last: Lehnertz

first: Radia

last: Johnson

first: Clarisse

last: Thiollier

first: Tara

last: McRae

first: Miriem

last: Marquis

first: Frédéric

last: Barabé

first: Brian

last: Wilhelm

last: Marinier

first: Sébastien

last: Lemieux

first: Josée

last: Hébert


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

city: Los Angeles

first: Richard

last: Ainsworth

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

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

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

first: Nunzio

last: Bottini

first: Shen

last: Yang


title: Lymphoid subsets in the AML bone marrow microenvironment following chemotherapy induction

status: Public on Apr 21 2025

first: Stefano

last: Berto

address: 68 President Street, BE208

institute: MUSC

summary: Using scRNA-seq, bone marrow (BM) aspirates, collected post-induction, from 12 complete responders (CR) and 10 refractory patients were compared for lymphoid cells subpopulations.

overall_design: AML patients’ bone marrow (BM) samples and information were collected after obtaining consent in accordance with institutional review board-approved studies at Fred Hutchinson Cancer Research Center (FHCRC). One vial of BM from each of the 22 patients was thawed with standard protocol. Then, cells were counted, and viability was evaluated with Trypan blue staining. 50,000 cells were directly sent to the Center for Medical Genomics of the Indiana University School of Medicine to be processed on the 10x Genomics while the leftover cells were stained for multicolor flow cytometry.

first: Suganya

last: Subramanian

first: Sophie

last: Paczesny


title: Copy number variants in autism spectrum disorders

status: Public on Apr 22 2025

city: Cairo

first: Amal

last: Mohamed

address: El-Bohooth

department: Human Cytogenetics

country: Egypt

institute: National Research Centre

type:
Genome variation profiling by SNP array
Genome variation profiling by array

summary: Our cohort comprised 40 non-syndromic ASD children.We conducted genome wide analysis using Affymetrix Cytoscan-HD microchips. We identified pathogenic CNVs in 7 patients (17.5%), other variant classified as variants of uncertain significance (VUS) or benign.

overall_design: Our design of the project aimed to identify and assess CNVs and their associated gene impacts in Egyptian ASD patients. Correlate the pathological CNVs to the ASD diagnostic parameters. Also we aimed to identify if ASD with pathological CNVs has certain clinical manifestations in comparison to other ASD patients.

first: Ola

last: Eid

first: Nagwa

last: Meguid


title: Leucegene: AML sequencing (GRCh38 reference)

first: Guy

last: Sauvageau

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

overall_design: Refer to individual Series


title: MUC1-C IS ESSENTIAL FOR INFLAMMATORY MEMORY OF TYROSINE KINASE INHIBITOR RESISTANCE IN NSCLC CELLS

city: Boston

first: Atrayee

last: Bhattacharya

state: Massachusetts

address: 450 Brookline Avenue

department: Medical Oncology

institute: DFCI

summary: This study identifies the oncogenic protein MUC1-C as a key driver of resistance to the EGFR tyrosine kinase inhibitor osimertinib in non-small cell lung cancers (NSCLCs).MUC1-C promotes resistance by activating STAT1 and type I/II interferon pathways, creating an inflammatory memory of the resistant phenotype. This memory is maintained via MUC1-C/STAT1 interaction at one enhancer region (pELS-1) and MUC1-C/JUN/PBAF at another (pELS-2) in the MUC1 gene. MUC1-C also mediates resistance to combination EGFR/MET inhibitors and a fourth-generation EGFR TKI (TQB3804). Importantly, targeting MUC1-C with an antibody-drug conjugate (M1C ADC) is effective both in vitro and in a patient-derived xenograft model, making MUC1-C a promising therapeutic target for TKI-refractory NSCLC.

overall_design: ATAC-seq for WT  H1975 and revertant H1975 (H1975-RT) cells ( cells were treated with Osimertinib for 12 weeks to acquire resistance and then left untreated to make them sensitive to Osi)  and ATAC seq for H1975-RT with Control guide RNA(csgRNA) and MUC1-C guide RNA (MUC1-CsgRNA).

first: Naoki

last: Haratake

first: Shinkichi

last: Takamori


title: Leucegene: AML sequencing (part 7)

summary: RNA sequencing of human leukemia

overall_design: The goals of this project are to obtain a comprehensive study of mutations and gene expression in human acute myeloid leukemia (AML). Methods: AML cells were thawed. DNA and RNA (polyA) was extracted and sequences were obtained with an illumina NovaSeq 6000 sequencer.


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

city: Heidelberg

first: Johannes

last: Betge

address: Im Neuenheimer Feld 580

department: Signaling and Functional Genomics

country: Germany

institute: German Cancer Research Center (DKFZ)

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

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

first: Philipp

last: Albrecht

first: Kyrhatii

last: Trikhirhisthit


title: Nuclear 2′-O-methylation regulates RNA splicing through its binding protein FUBP1 (Nm-mut-seq)

status: Public on Apr 20 2025

city: Chicago

first: Boyang

last: Gao

address: 929 E 57th Street

department: Chemistry

institute: University of Chicago

summary: 2′-O-methylation (Nm) is an abundant RNA modification exists on different mammalian RNA species. However, potential Nm recognition by proteins has not been extensively explored. Here, we employed RNA affinity purification followed by mass spectrometry to identify Nm-binding proteins. The candidates exhibit enriched binding at known Nm sites. Interestingly, some candidates display nuclear localization and functions. We focused on the splicing factor FUBP1. Electrophoretic mobility shift assay (EMSA) validated preference of FUBP1 to Nm-modified RNA. As FUBP1 predominantly binds intronic regions, we profiled Nm sites in chromatin-associated RNA (caRNA) and found Nm enrichment within introns. Depletion of Nm led to increased exon skipping, suggesting Nm-dependent splicing regulation. The caRNA Nm sites overlap with FUBP1 binding sites, and Nm depletion reduced FUBP1 occupancy on modified regions. Furthermore, FUBP1 depletion induced exon skipping in Nm-modified genes, supporting its role in mediating Nm-dependent splicing regulation. Overall, our findings identify FUBP1 as an Nm-binding protein and uncover previously unrecognized nuclear functions for RNA Nm modification.

overall_design: Nm-mut-seq of HepG2 chromatin-associated RNA (caRNA)

first: Chuan

last: He


title: Nuclear 2′-O-methylation regulates RNA splicing through its binding protein FUBP1 (CLIP-seq and PAR-CLIP)

overall_design: PAR-CLIP of FUBP1 in HepG2 cells and CLIP-seq of FUBP1 in HepG2 cells with siFBL


title: Nuclear 2′-O-methylation regulates RNA splicing through its binding protein FUBP1 (RNA-seq and RIP-seq)

overall_design: RNA-seq of HepG2 cells with siFUBP1 controled with siCtrl2, U3KD controled with GFP ASO, and RIP-seq of HepG2 cells with siFBL controled with siCtrl


title: Identification and characterization analysis of the different  genes in Rag1-/- mouse injected with CD8+TSCM cells induced by CUS using RNA-seq

status: Public on Apr 18 2025

city: Nanjing

first: Xiaoyu

last: Yu

state: Jiangsu

address: Dingjiaqiao 87

institute: Southeast univeristy

summary: Whole RNA-sequencing analysis was performed and analyzed by Lc. Biotech Co. Ltd. (Hangzhou, China). hippocampus tissue from the PBS_WT group, PBS_Rag1-/- group, Ctr CD8+TSCM_Rag1-/- group, and  CUS CD8+TSCM_Rag1-/-  group were collected in TRIzol. Total RNAs were extracted from Trizol. UMI technology was used to label each sequence fragment with sequence tags, which minimized the interference of duplication caused by PCR amplification on the quantitative accuracy of the transcriptome. RNA sequencing reads were aligned to the mouse genome (GRCh37/hg19) using the software Hisat2 (2.0.4). Transcript abundance was evaluated by calculating fragments per kilo base of exon per million fragments mapped (FPKM).

overall_design: Examination of different genes by injection of CD8+TSCM cells in Rag1-/- mouse  by RNA-seq.

first: Honghong

last: Yao


title: Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize

status: Public on Apr 16 2025

city: Duesseldorf

first: Thomas

last: Hartwig

address: University Street 1

institute: Heinrich-Heine University

summary: Comprehensive maps of functional variation at transcription factor (TF) binding sites (cis-elements) are crucial for elucidating how genotype shapes phenotype. Here, we report the construction of a pan-cistrome of the maize leaf under well-watered and drought conditions. We quantified haplotype-specific TF footprints across a pan-genome of 25 maize hybrids and mapped over two hundred thousand (epi)genetic variants (termed binding-QTL) linked to cis-element occupancy. Three lines of evidence support the functional significance of binding-QTL: i) coincidence with causative loci that regulate traits, including VGT1, ZmTRE1, and the MITE transposon near ZmNAC111 under drought; ii) bQTL allelic bias is shared between inbred parents and matches ChIP-seq results, iii) partitioning genetic variation across genomic regions demonstrates that binding-QTL capture the majority of heritable trait variation across ~72% of 143 phenotypes. Our study provides an auspicious approach to make functional cis-variation accessible at scale for genetic studies and targeted engineering of complex traits.

overall_design:
MOA-seq was performed in leaf blades of 25 maize F1 hybrids under well-watered and drought conditions.

Please note that each processed data file was generated from multiple replicates and thus linked as Series supplementary file. The sample_to_processed_data.readme.txt list which samples each file belongs to. We further note that all F1 MOA/RNA data was mapped to diploid genomes created by concatenating the B73 V5 genome with the respective paternal genome (NAM v1 / 2 genomes18, Mo17 CAU v1, W22 v220, A188 v119, and A619) with the accession ID added as prefix to the chromosome name.

first: Julia

last: Engelhorn

first: Samantha

last: Snodgrass

first: Amelie

last: Kok

first: Arun

middle: S

last: Seetharam

first: Michael

last: Schneider

first: Tatjana

last: Kiwit

first: Ayush

last: Singh

last: Banf

first: Duong Thi Hai

last: Doan

first: Merritt

last: Khaipho-Burch

first: Daniel

last: Runcie

first: Victor

last: Sanchez-Camargo

first: Rechien

last: Bader

first: Jorge Vladimir

last: Torres-Rodriguez

first: Guangchao

last: Sun

first: Maike

last: Stam

first: Fabio

last: Fiorani

first: Sebastian

last: Beier

first: James

last: Schnable

first: Hank

last: Bass

first: Matthew

last: Hufford

first: Benjamin

last: Stich

first: Wolf

last: Frommer

first: Jeffrey

last: Ross-Ibarra


title: The non-coding RNA landscape associated with the malignant transformation of endometriosis into endometriosis-correlated ovarian cancer

city: Bologna

first: Gloria

last: Ravegnini

address: via Zamboni 33

country: Italy

institute: Alma Mater Studiorum - Università di Bologna

summary: Background. Endometriosis (EMS) is a chronic, gynecological condition affecting 6-10% of reproductive-age women. While these lesions are benign, ovarian EMS present cancer-like features, and can progress to endometriosis-correlated ovarian cancer (ECOC) through a multistep process. Given the regulatory role of miRNAs in gene expression and biological pathways, we aimed to identify miRNAs associated with the malignant transformation of ovarian EMS, which could serve as a potential diagnostic tool for the early identification of such patients. Methods. Global miRNA profiling was performed in patients with benign ovarian EMS (EMS-b) and  patients with ECOC. Differential expression analysis (DEA) of miRNAs between EMS-b, EMS tissues from patients with ECOC (EMS-k) and ECOC tissues was performed. Receiver Operating Characteristic (ROC) curves were built to evaluate the binary classification performance of significant miRNAs. Results. Comparison between EMS-b and EMS-k revealed 13 significantly deregulated miRNAs. Furthermore, when comparing ECOC and EMS-b we observed significant deregulation of 181 miRNAs. ROC analysis revealed a panel of seven upregulated miRNAs with accuracies above 0.7 in identifying EMS-k and EMS-b. Notably, four miRNAs (hsa-miR-200a-3p, hsa-miR-141-3p, hsa-miR-183-5p, hsa-miR-10a-5p) were consistently upregulated in both EMS-k and ECOC tissues. Conclusions. Our study identified a panel of miRNA biomarkers that may serve as potential candidates for the early detection of ECOC in patients previously diagnosed with ovarian EMS.

overall_design:
Global miRNA profiling was performed in patients with benign ovarian EMS (EMS-b) and  patients with ECOC.
case-control

first: Camelia

last: Coada


title: Metabolic shifts during growth deceleration in Drosophila imaginal wing discs

city: London

first: Gavin

last: Kelly

state: London

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick institute

summary: Growth during development is often characterised by progressive deceleration, as organisms, tissues, and organs approach their final size. Using transcriptomics analysis, we show that, during their two-day period of growth deceleration, wing imaginal discs of Drosophila undergo a progressive metabolic shift away from oxidative phosphorylation and towards glycolysis. We then develop a sensitive reporter of HIF-1a activity (a proxy for hypoxia), which allows us to show that imaginal discs become mildly, though increasingly, hypoxic during normal development, in normoxic conditions. As a result, HIF-1a dampens growth via transcriptional activation of scylla/REDD1, a negative regulator of TOR signalling. We find that overactivation of TOR signalling triggers a marked hypoxia response both cell-autonomously and in surrounding tissues. This suggests that, in wildtype animals, TOR activity imposes increasing pressure on oxygen supplies. Indeed, in the absence of HIF-1a, TOR signalling triggers JNK signalling, a marker of cellular stress. Moreover, TOR-induced stress is alleviated by a small increase is oxygen supplies. Our results suggest that, during normal development, Sima/HIF-1α prevents growth-induced demand from exceeding available supplies, which become increasing scarce as tissue size increases.

overall_design: We performed bulk RNA-Sequencing (RNA-Seq) on precisely timed third larval instar (L3) wing imaginal discs at seven developmental time points, ranging from 80 to 118 hours after egg laying (AEL). For each time point, three biological replicates and two technical replicates were included.

first: Zhao

last: Yifan

first: Alexandre

last: Cyrille

first: Kelly

last: Gavin

first: Perez-Mockus

last: Gantas

first: Vincent

last: Jean-Paul


title: Modeling heart failure by induced pluripotent stem cell-derived organoids.

status: Public on Apr 15 2025

first: Silvia

last: Cetrullo

state: BO

address: Via Irnerio 48

department: DIBINEM

institute: University of Bologna

summary: Cardiac organoids replicate tissue complexity better than 2D models, making them ideal for studying diseases like heart failure (HF). This study developed scaffold-free cardiac organoids from induced pluripotent stem cells (iPSCs) to model HF in vitro. Gene expression analysis confirmed a cardiac phenotype, and endothelin-1 (ET-1) treatment induced HF-like features. Key findings include upregulation of HF markers (ANP, BNP, ACTA1), altered miRNA profiles, reduced contractility, and protein aggregation. Nutraceutical co-treatment mitigated these effects, highlighting the model's utility in understanding HF mechanisms and testing therapies.

overall_design: small RNA-sequencing of scaffold-free cardiac organoids derived from induced pluripotent stem cells (iPSCs) treated or not with endothelin-1 (ET-1) as hypertrophic inducer.

first: Irene

last: Bissoli

first: Francesco

last: Alabiso

first: Cristina

last: Cosentino

first: Aleksandra

last: Seragnoli Chystyakova

first: Fabrizio

last: Ferré

last: Alviano

first: Pasquale

last: Marrazzo

first: Carla

last: Pignatti

first: Giulio

last: Agnetti

first: Romano

last: Regazzi

first: Flavio

last: Flamigni

first: Stefania

last: D'Adamo


title: Synaptic vesicle endocytosis deficits underlie GBA-linked cognitive dysfunction in Parkinson’s disease and Dementia with Lewy bodies

city: New Haven

first: Sreeganga

middle: S.

last: Chandra

address: 295 Congress Avenue

department: Departments of Neurology and Neuroscience

institute: Yale School of Medicine

summary: GBA mutations are major risk factors for Parkinson’s disease (PD) and Dementia with Lewy Bodies (DLB), two common α-synucleinopathies associated with cognitive impairment. Here, we investigated the role of GBA mutations in cognitive decline by utilizing Gba L444P mutant mice, SNCA transgenic (tg), and Gba-SNCA double mutant mice. Notably, Gba mutant mice showed early cognitive deficits but no PD-like motor deficits up to 12 months old. Conversely, SNCA tg mice displayed age-related motor deficits but no cognitive abnormalities. Gba-SNCA mice exhibited exacerbated motor deficits and cognitive decline.  Immunohistological analysis revealed cortical phospho-α-synuclein pathology in SNCA tg mice, which was exacerbated in Gba-SNCA mice, especially in layer 5 cortical neurons. Significantly, Gba mutant mice did not show α-synuclein pathology. Single-nucleus RNA sequencing of cortices instead uncovered selective synaptic vesicle cycle defects in excitatory neurons of Gba mutant and Gba-SNCA mice, via robust downregulation in gene networks regulating synapse vesicle cycle and synapse assembly. Meanwhile SNCA tg mice displayed broader synaptic changes. Immunohistochemical and electron microscopic analyses validated these findings. Together, our results indicate that Gba mutations, while exacerbating pre-existing α-synuclein aggregation and PD-like motor deficits, contribute to cognitive deficits through α-synuclein-independent mechanisms, likely involving dysfunction in synaptic vesicle endocytosis. Additionally, Gba-SNCA mice are a valuable model for studying cognitive and motor deficits in PD and DLB

overall_design: Mice: Gba mutant mice have been previously described in Mistry et al. (2010)1 and Taguchi et al. (2017)2. These mice have a copy of the Gba L444P mutant allele and a Gba KO allele, with Gba expression rescued in skin to prevent early lethality. SNCA tg mice overexpress the human α-synuclein A30P transgene (heterozygous), and have also been previously described. Gba mutant mice were crossed to SNCA tg to obtain Gba-SNCA double mutant mice. Age and sex matched WT mice were used as normal controls. We performed single nucleus RNA sequencing (snRNA-seq) on cortical brain tissue from adult mice belonging to the four genotypes (n=14) 3-4 mice per genotype were used: 4 Gba mutant mice (192, 193, 185, and 201), 3 SNCA tg mice (729, 754, 740), 3 Gba-SNCA double mutant mice (187, 191, 184) and 4 WT (normal control) mice of the B6 strain. We chose to perform this analysis on 12-month-old mice, as Gba-SNCA mice show enhanced behavioral deficits and α-synuclein pathology, while lacking gross neuronal loss or degeneration in the cortex, allowing us to investigate disease relevant mechanisms. Nuclei isolation from cerebral cortex: Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications. All procedures were carried out on ice or at 4 degrees C. Cortical snRNA expression was analysed in mice with a pathogenic mutation - i.e., Gba mutant mice, SNCA tg mice, and Gba-SNCA double mutant mice - and compared, respectively, with WT mice cortical snRNA expression.

first: David

last: Bäckström

first: Vidyadhara

last: Devarunda Jaganath

first: Risha

last: Chakraborty

first: Jiapeng

last: Ruan

first: Jae-Min

last: Park

first: Pramod

middle: K

last: Mistry


title: Single-cell temporal characterization of RSV infection

city: San Francisco

first: Sara

last: Sunshine

address: 1700 4th Street

institute: University of California, San Francisco

summary: Respiratory syncytial virus (RSV) is a prevalent pathogen globally, can cause severe disease in older adults, and remains the leading cause of bronchiolitis and pneumonia in the United States for children during their first year of life. Despite its prevalence worldwide, RSV specific pharmacologic interventions remain unavailable for most infected patients. Although vaccines are available for a subset of adults, further investigation of the molecular interactions between RSV and the host remains essential to understanding this prolific pathogen. To aid our understanding of the host response in both RSV infected cells, and uninfected bystanders, we utilized single-cell RNA sequencing.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We infected A549 cells with Respiratory Syncytial Virus (MOI 0.3) and performed single-cell RNA sequencing at 0, 4, 8 and 12 hours post-infection.

first: Joseph

middle: L

last: DeRisi


title: Tracheal aspirate single cell RNA sequencing from patients with ARDS [scRNA-seq]

status: Public on Apr 14 2025

first: Aartik

last: Sarma

state: CA

address: 513 Parnassus Ave

summary: Trachel aspirates samples were collected from an observational cohort of mechanically ventilated patients to compare respiratory tract gene expression in previous-descried ARDS molecular phenotypes. Patient charts were reviewed by two physicians and patients with ARDS were identified using the Berlin Definition. ARDS molecular phenotypes were defined using a previously-described 3-variable classifier (Sinha 2020)

overall_design:
Tracheal aspirates were collected from mechnically ventilated patients admitted to the intensive care units.
***Please note that the UCSF IRB has restricted sharing the raw data because some of the samples were collected under a waiver of consent and could in theory be identifiable. Therefore, raw data is not provided***

first: Charles

last: Langelier

first: Carolyn

last: Calfee


title: Tracheal aspirate bulk RNA sequencing from patients with ARDS [bulk RNA-seq]

summary: Trachel aspirates samples were collected from an observational cohort of mechanically ventilated patients to compare respiratory tract gene expression in previous-descried ARDS molecular phenotypes. Patient charts were reviewed by two physicians and patients with ARDS were identified using the Berlin Definition. Control subjects were mechanically ventilated for neurologic indications, were not immunosuppressed, and had no evidence of pulmonary disease. ARDS molecular phenotypes were defined using a previously-described 3-variable classifier (Sinha 2020)


title: UVA-induced DNA damage and mutations in melanocytes and melanoma mutations

city: Grand Rapids

first: Gerd

last: Pfeifer

address: 333 Bostwick Ave. NE., 5352W/Phase2

department: Center for Epigenetics

institute: Van Andel Research Institute

summary: Melanomas carry characteristic mutational signatures associated with solar UVB radiation-induced cyclobutane pyrimidine dimers (CPDs) that contain deaminated cytosines. However, there are several other mutation signatures, including those found in melanomas from non-sun-exposed body sites, that have unknown origins. To test if these signatures are linked to UVA radiation from the sun, we exposed human melanocytes to UVA and to UVB for comparison. We mapped DNA damage in the form of CPDs or 8-oxoguanine (8-oxoG) genome-wide at base resolution. We then determined mutational patterns in single melanocyte cell clones by whole genome sequencing. UVA-induced CPDs occurred overwhelmingly at TT sequences resembling melanoma signature SBS7d. We did not observe rising CPD levels after cessation of radiation (dark CPDs). However, the UVA-induced TT-CPDs did not score as mutagenic in the mutation analysis. 8-oxoG was present in melanocytes but was not substantially increased after UVA. G/C to T/A mutations were prominent in melanocyte single cell clones with no major shift after UVA radiation. These mutations matched SBS18, a signature present in melanomas. Our data suggest that melanocytes carry an endogenous but UVA-independent load of oxidative base lesions and their associated mutations that may be associated with a subset of melanoma mutations.

overall_design: UVA-induced DNA damage was mapped in genome-wide using CD-seq in human melanocyte cells.

first: Seung-Gi

last: Jin

middle: P


title: Succinate drives gut inflammation by promoting FoxP3 degradation through a molecular switch

status: Public on Apr 11 2025

first: Hai

last: Wang

address: 303E Chicago Avenue

department: Department of Pathology

institute: Northwestern University

summary: Succinate levels are elevated in inflammatory bowel disease (IBD), but its role in disease pathogenicity remains unknown. This study shows that succinate promotes colitis in mice by reducing FoxP3 expression in regulatory T cells (Tregs) and increasing IL-17. Succinate selectively reduced the expression of 2-oxoglutarate dehydrogenase complex (OGDHc), the enzyme for succinyl-CoA synthesis, which in turn reduced FoxP3 succinylation and made FoxP3 lysine residues available for ubiquitination and Foxp3 protein degradation. Genetic deletion of Dlst, a member of OGDHc, in Tregs led to reduced FoxP3, impaired Treg function, and severe gut inflammation. Restoring FoxP3 fully rescued Dlst-deficient Treg immune suppressive functions. In IBD patients, FoxP3 and OGDHc levels were reduced in Tregs and negatively correlated with succinate levels and inflammation severity. This study identifies succinate as a pathogenic factor in IBD, uncovering a succinate-driven molecular switch that regulates FoxP3 stability and Treg function during inflammation.

overall_design: Splenic CD4+ T cells from iWT (WT) and Dlst-Treg iKO (KO) mice were cultured in Treg polarization condition for 2 days in the presence of 4-hydroxytamoxifen. Sorted iTregs (CD4+FoxP3-GFP+tdTomato-RFP+) were subjected to RNA sequencing.

first: Deyu

last: Fang


title: DFFB suppresses interferon to enable cancer persister cell regrowth

status: Public on Apr 10 2025

city: La Jolla

first: August

last: Williams

address: 9500 Gilman Dr.

department: Dermatology

institute: UC San Diego

summary: Oncogene targeted cancer therapies can provide deep responses but frequently suffer from acquired resistance. Therapeutic approaches to treat tumours which have acquired drug resistance are complicated by continual tumour evolution and multiple co-occurring resistance mechanisms. Rather than treating resistance after it emerges, it may possible to prevent it by inhibiting the adaptive processes which initiate resistance but these are poorly understood. Here we report that residual cancer persister cells that survive oncogene targeted therapy are growth arrested by drug stress-induced intrinsic Type I interferon (IFN) signaling. To escape growth arrest, persister cells leverage apoptotic machinery to transcriptionally suppress interferon-stimulated genes (ISGs). Mechanistically, persister cells sublethally engage apoptotic caspases to activate DNA endonuclease DNA Fragmentation Factor B (DFFB, also known as Caspase-Activated DNase (CAD)) which induces DNA damage, mutagenesis, and stress response factor Activating Transcription Factor 3 (ATF3). ATF3 limits Activator Protein-1 (AP1)-mediated ISG expression sufficiently to allow persister cell regrowth. Persister cells deficient in DFFB or ATF3 exhibit high ISG expression and are consequently unable to regrow. Therefore, sublethal apoptotic stress paradoxically promotes regrowth of residual cancer cells that survive drug treatment.

overall_design: Bulk and single cell RNA sequencing data. Bulk RNA sequencing with Illumina Stranded mRNA. A375 WT, DFFB KO, and ATF3 KO cells in triplicate were untreated (parental), treated for 14 days with 250 nM dabrafenib and 25 nM trametinib (persister), or persisters were co-treated with 20 uM AP-1 inhibitor T-5224 for the duration of persister formation. Single cell RNA sequencing of PC9 and A375 cells with 10X Genomics. For single cell RNA sequencing, PC9 WT lung cancer cells were untreated (parental) or treated with 2.5 µM erlotinib for 14 days (persister cells). A375 WT or DFFB KO cells were untreated (parental) or treated with 250 nM dabrafenib and 25 nM trametinib in combination for 14 days (persister cells). A375 WT and DFFB KO drug tolerant expanded persister cells (DTEPs) were treated with 250 nM dabrafenib and 25 nM trametinib for 9 weeks.

first: Matthew

last: Hangauer


title: Single-cell transcriptomics reveals cellular evolution underlying pleomorphic adenoma recurrence and malignant transformation

city: Chengdu

first: Chunjie

last: Li

state: Sichuan

address: No.14, Section 3rd, Renmin Nan Road

institute: West China Hospital of Stomatology, Sichuan University

summary: Pleomorphic adenoma (PA), the most common benign salivary gland tumor, presents unpredictable risks of recurrence and malignant transformation into carcinoma ex pleomorphic adenoma (CXPA), posing significant clinical challenges. To better delineate the tumor progression trajectory, we performed single-cell RNA sequencing on normal salivary glands, primary PA, recurrent PA (rPA), and CXPA, integrating cell trajectory reconstruction, differential gene expression analysis, and key gene network exploration to uncover molecular transitions and intercellular crosstalk underlying PA recurrence and malignant transformation. Our findings revealed GALNT13⁺ myoepithelial cells as CXPA-specific malignant progenitors, marking early malignant conversion, while MIF⁺ myoepithelial cells exhibited enhanced tissue-destructive capabilities. Fibroblasts played dual roles, enforcing fibrotic restraint in primary PA and promoting extracellular matrix degradation in CXPA. The tumor microenvironment demonstrated stage-specific adaptations, with CXPA favoring pro-inflammatory MIF–CD74/CD44 signaling, whereas rPA adopted immunosuppressive characteristics. Together, stromal reprogramming and immune-editing dynamics orchestrated microenvironmental adaptation, linking cellular heterogeneity to clinical aggressiveness. This study presents the first comprehensive molecular atlas of PA progression, highlighting the malignant specialization of myoepithelial subpopulations, fibroblast-mediated stromal remodeling, and immune-driven microenvironmental evolution, offering a valuable framework for precision stratification of malignant potential and future microenvironment-targeted therapeutic strategies.

overall_design: Fresh tumor tissues from human normal salivary gland, primary pleomorphic adenoma (PA), recurrent PA (rPA), and carcinoma ex pleomorphic adenoma (CXPA) were collected during surgery.  Single-cell suspensions were generated by enzymatic digestion and processed using the 10x Genomics Chromium Single Cell 3' platform.  scRNA-seq libraries were constructed and sequenced for all samples.  The data were analyzed to investigate cellular heterogeneity, infer tumor progression trajectories, and characterize changes in the tumor microenvironment during recurrence and malignant transformation.

first: Yike

first: Zhixuan

first: Guile

last: Zhao

first: Qi

last: Han

first: Zhangfan

last: Ding

first: Cheng


title: Expanded chromatin accessibility mapping explains genetic variation associated with complex traits in liver

city: Philadelphia

first: Brandon

last: Wenz

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

summary: Genome-wide association studies (GWAS) have identified thousands of genomic loci associated with a variety of common, complex human traits. The contribution of genetic variants to gene expression regulation has been well studied, supporting the idea that gene expression plays a causal role at some complex trait-associated loci. However, many current studies have not comprehensively investigated the impact of genetic variation on chromatin accessibility at a large scale within a single tissue. Genetic variants associated with differences in chromatin accessibility, known as chromatin accessibility quantitative trait loci (caQTLs), are major contributors to gene expression differences and GWAS signals. We assessed chromatin accessibility in 189 human liver tissue samples using ATAC-seq and identified over two million accessible chromatin regions enriched for gene regulatory characteristics. We integrated chromatin accessibility and genotype data from 175 samples and identified 14,076 caQTLs. Using publicly available blood lipid GWAS data, we found 157 loci where the colocalization of caQTLs, expression quantitative trait loci (eQTLs), and GWAS signals generated specific molecular hypotheses about causal regulatory elements, affected genes, and, in some cases, transcription factors, resolving these associations to single-nucleotide resolution. We performed a comprehensive analysis of the GWAS signals that remain without a proposed mechanism beyond liver caQTLs and eQTLs. After incorporating additional potential regulatory mechanism data, we found that approximately 26% of blood lipid GWAS signals remain without a proposed mechanism. Overall, our results demonstrate the benefits of integrating multiple datasets to improve our understanding of GWAS signals while emphasizing the need for additional experiments to fully characterize them.

overall_design: ATAC-seq was performed on biopsies from normal human liver samples and consensus peaks were called across all samples.

middle: M

first: Benjamin

last: Voight


title: IL-10 Targets IRF1/5 to Suppress IFN and Inflammatory Responses by Epigenetic Mechanisms [Cut & Run]

city: New York

first: Bikash

last: Mishra

state: NY

address: 515 E 71st ST

institute: Hospital for Special Surgery

summary: Interleukin-10 (IL-10) is pivotal in suppressing inflammation and innate immune activation, in large part by suppressing induction of genes by potent inflammatory factors such as TLR ligands. Despite decades of research, molecular mechanisms underlying this inhibition have not been resolved. This study utilized an integrated epigenomic analysis of gene transcription, chromatin accessibility, histone modifications and transcription factor binding to investigate IL-10-mediated suppression of LPS and TNF responses in primary human monocytes. Instead of inhibiting core TLR4-activated pathways such as NF-kB, MAPK-AP-1 and TBK1-IRF3 signaling, IL-10 targeted IRF5 an IRF1-mediated amplification loop that is important for IFNB, ISG and inflammatory gene induction in monocytes. This resulted in near-complete suppression of ISGs, and significant inhibition of inflammatory NF-kB target genes, in whose activation IRFs play an amplifying role. Mechanisms of TLR4 and TNFR target gene inhibition included downregulation of chromatin accessibility, de novo enhancer formation, and IRF1-associated H3K27ac activating histone marks. These results describe an underappreciated suppression of IFN responses by IL-10 and provide epigenetic mechanisms by which IL-10 suppresses TLR/TNF-induced gene expression.

overall_design: To investigate regulation of LPS and TNF responses by IL-10 in primary human monocytes. We purified CD14+ monocytes from human buffy coats. Monocytes were cultured overnight at 37°C, 5% CO2 in RPMI-1640 medium supplemented with 10% heat-inactivated defined FBS, penicillin-streptomycin, L-glutamine and 20 ng/ml human M-CSF and treated with indicated stimulation.


title: Tracheal aspirate bulk and single cell RNA sequencing from patients with ARDS

first: Aartik

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

overall_design: Refer to individual Series


title: Aromatic acid metabolism in Methylobacterium extorquens reveals interplay between methylotrophic and heterotrophic pathways

status: Public on Apr 09 2025

city: Berkeley

first: N. Cecilia

last: Martinez-Gomez

address: 421 Koshland Hall

department: Plant and Microbial Biology

institute: UC Berkeley

summary: Efforts towards microbial conversion of lignin to value-added products face many challenges because lignin’s methoxylated aromatic monomers release toxic C1 byproducts such as formaldehyde. The ability to grow on methoxylated aromatic acids (e.g., vanillic acid) has recently been identified in certain clades of methylotrophs, bacteria characterized by their unique ability to tolerate and metabolize high concentrations of formaldehyde. Here, we use a phyllosphere methylotroph isolate, Methylobacterium extorquens SLI 505, as a model to identify the fate of formaldehyde during methylotrophic growth on vanillic acids. M. extorquens SLI 505 displays concentration-dependent growth phenotypes on vanillic acid without concomitant formaldehyde accumulation. We conclude that M. extorquens SLI 505 overcomes potential metabolic bottlenecks from simultaneous assimilation of multicarbon and C1 intermediates by allocating formaldehyde towards dissimilation and assimilating the ring carbons of vanillic acid heterotrophically. We correlate this strategy with maximization of bioenergetic yields and demonstrate that formaldehyde dissimilation for energy generation rather than formaldehyde detoxification is advantageous for growth on aromatic acids. M. extorquens SLI 505 also exhibits catabolite repression during growth on methanol and low concentrations of vanillic acid, but no diauxie during growth on methanol and high concentrations of vanillic acid. Results from this study outline metabolic strategies employed by M. extorquens SLI 505 for growth on a complex single substrate that generates both C1 and multicarbon intermediates and emphasizes the robustness of M. extorquens for biotechnological applications for lignin valorization.

overall_design: To understand how Methylobacterium extorquens SLI 505's transcriptome responds to different substrates, RNA-seq was performed on M. extorquens cultures growth in 5 or 10 mM vanillic acid, 50 mM methanol, or 10 mM acetate. Three biological replicates were analyzed for each of the four conditions

first: Alekhya

last: Govindaraju

first: N


title: Modulation of the Pseudomonas aeruginosa quorum sensing cascade by MexT-regulated factors

city: Seattle

first: Andrew

last: Frando

state: WA

address: 1705 NE Pacific Street

department: Pulmonary, Critical Care, and Sleep Medicine

institute: University of Washington

summary: Pseudomonas aeruginosa (Pa) is a ubiquitous bacterium that uses quorum sensing (QS), a cell-cell communication system that enables it to sense cell density and to alter gene expression. Pa has three complete QS circuits controlled by the transcriptional regulators LasR, RhlR, and PqsR (MvfR), that together control hundreds of genes, including virulence factors. In the well-described strain PAO1, QS is organized hierarchically, with PqsR and RhlR activity dependent on LasR. In PAO1, this hierarchy depends on the non-QS transcription factor MexT; by an unknown mechanism, deletion of mexT allows for RhlR activity in the absence of LasR. We aimed to identify how regulators such as MexT modulate the QS architecture in Pa. We compared the transcriptome of PAO1 to that of PAO1ΔmexT and identified 152 differentially expressed genes. MexT does not appear to regulate rhlR or pqsR directly; however, we identified two MexT-regulated operons that may affect the hierarchy in PAO1. These operons encode the drug efflux pump genes mexEF-oprN and the Pseudomonas quinolone signal (PQS) synthesis genes pqsABCDE. We performed genetic experiments to test whether the products of these genes affected the QS hierarchy. As with the mexT knockout mutant, we found that a PAO1 mexEF knockout mutant exhibited RhlR activity earlier, and to a higher magnitude, than wild-type PAO1. MexEF-OprN is known to export the PQS precursor HHQ, and we found that exogenous addition of PQS to PAO1 partially affects RhlR activity, resulting in earlier timing and higher magnitude compared to wild-type PAO1. We further elucidated that this is likely due to positive regulation by PqsE. These data link both the drug efflux pump MexEF-OprN and PQS QS to the regulation of the QS hierarchy in PAO1. We wondered if the same applied to QS architectures in Pa clinical isolates. We discovered that there are alternate QS architectures in clinical isolates, where RhlR activity is not fully dependent on LasR. In these isolates, surprisingly, MexT does not influence the relationship between LasR and RhlR, and this is indicative of a different QS architecture in the clinical isolates. Overall, we further elucidated the regulation of QS architecture in PAO1 and identified unique QS architectures in clinical isolates. Importantly, our work reveals a new suite of factors that regulate QS in Pa, with implications for a variety of Pa behaviors both in the laboratory and clinical settings.

overall_design: Bacteria from wild-type PAO1 and PAO1∆mexT were harvested at mid log and early stationary phase.  RNA was isolated and gene expresion quantified by sequencing.

first: Robert

last: Parsek

first: Jamal

last: Omar

first: Nicole

middle: E

last: Smalley

first: Ajai

last: Dandekar


title: RNA-Seq of mGULL knockdown and hGULL rescue in C57BL6 wild-type mice

city: Bethesda

first: Haiming

last: Cao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

summary: For determined h/mGULL have the function similarities, we employed rescue experiments in mice. We knocked down mGULL in mouse liver using shRNAs delivered by adenovirus, and subsequently co-expressed hGULL to assess its capacity to rescue for the loss of function effect of mGULL. After confirmed the mGULL knockdown or hGULL overexpression efficiency, we isolation the total RNA for RNA seq.

overall_design: Seven-weeks old C57BL/6 male were injected via intravitreal injection with adenovirus expressing Control(Lac+pAdv5 virus), shmGULL (shmGULL+pAdv5)or shmGULL+hGULL (for each group, total active viral particles is 5×108) for 7 days before sacrifice.

first: Zhe

first: Sunmi

last: Seok

first: Chengfei

last: Jiang


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

status: Public on Apr 08 2025

first: Marco

last: Trizzino

state: UK

address: Imperial College Road

department: Life Sciences

institute: Imperial College London

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

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

first: Martina

last: Demurtas

first: Samantha

last: Barnada

first: Zoe

middle: H

last: Mitchell

first: Laura

last: Deelen