title: In Vivo and in Vitro Assessment of Residual DNA Impurity-Derived Transcriptions [I]

city: Woburn

first: Hsin-I

last: Jen

state: Massachusetts

address: 19 presidential way

department: Analytical Development

institute: Ultragenyx

summary: Gene therapy products, such as rAAV, are typically produced by DNA plasmid transfected to mammalian cell lines. Host cell DNA and plasmid DNA can be inadvertently packaged inside the rAAV capsids during production. It is important to characterize these residual DNA impurities in gene therapy products due to the theoretical risk of immunogenicity, infectivity, and oncogenicity. Previous studies showed the level of residual DNA impurity is around 1-2% of the expected rAAV genome. However, it remains unclear whether these DNAs undergo transcription and translation. To address this question, RNA was isolated from mouse liver various days after rAAV transduction, followed by reverse transcription for cDNA synthesis and library preparation. RNA-seq and dPCR were used to quantify the level of the gene of interest and the impurity genes. Results showed a low but detectable level of AAVhu37 Cap, AAV2 Rep, and KanR transcripts. The result from these studies enables targeted risk assessment and better understanding of the potential adverse effects associated with AAV gene therapy. It also points to the importance of improving vector design to reduce the level of DNA impurities.

overall_design: To understand the genome composition of the rAAV37-EGFP, PacBio sequencing was performed. Circular consensus sequencing (CCS) reads were generated from AAVhu37-EGFP DNA. We also performed RNA-seq on the livers of mice injected with AAVhu37-EGFP to assess if AAV containing residual DNA can successfully enter mammalian cells and initiate transcription.


title: In Vivo and in Vitro Assessment of Residual DNA Impurity-Derived Transcriptions [II]

status: Public on May 09 2025

country: USA

type: Expression profiling by high throughput sequencing


title: Hypoxia is responsible for the altered response of ovarian cancer cells to the mitomycin C-drug

status: Public on May 13 2025

city: Warsaw

first: Aleksandra

last: Gawrylak

email: aklemba@gmail.com, agawrylak@wim.mil.pl

address: Szaserów 128

country: Poland

institute: Military Institute of Medicine – National Research Institute

summary: Using HTA 2.0 microarrays, we demonstrate transcriptome changes in ovarian cancer SKOV3 cells induced by hypoxia, mitomycin C and their combined effect with particular emphasis on the effect of oxygen tension modification on mitomycin c activity. Examining differentially expressed genes (DEGs) in these groups.

overall_design: Total RNA of SKOV3 cells untreated/treated with mitomycin C (MMC) in normoxia or hypoxia (4 experimental groups in total- with 4 biological replicates for each group: normoxia control -without treatment = N-C, normoxia with MMC treatment = N-MMC, hypoxia control - without treatment = H-C, hypoxia with MMC treatment = H-MMC)  was extracted and amplified 100 ng of RNA per sample were then hybridized on GeneChip Human Transcriptome Array 2.0 (HTA 2.0) (Affymetrix, Thermofischer scientific). Differentially expressed genes (DEGs) in these groups were examined.

first: Klaudia

middle: K

last: Brodaczewska

first: Roksana

last: Iwanicka-Nowicka

first: Marta

last: Koblowska

first: Agnieszka

last: Synowiec

first: Lubomir

last: Bodnar

first: Cezary

last: Szczylik

first: Bogdan

last: Lesyng

first: Rafał

last: Stec

first: Claudine

last: Kieda


title: NF1 Loss Promotes EGFR Activation and Confers Sensitivity to EGFR Inhibition in NF1 Mutant Melanoma

city: New York

first: Milad

last: Ibrahim

state: NY

address: 550 1st Avenue

department: Dermatology

institute: NYU Langone

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series

first: Markus

last: Schober

first: Iman

last: Osman


summary: The Neurofibromin 1 (NF1) tumor suppressor gene is mutated in 15-27% of melanoma patients. The overall prognosis of these patients is worse than that of patients with other genetic melanoma subtypes due to a paucity in targeted therapy options for this melanoma subtype, and its limited response to immunotherapy. Here, we compare NF1 mutant to NF1 wild melanoma using a combined multi-omics approaches of patient-derived short-term cultures (STCs) to identify potential therapeutic targets

overall_design: NF1 mutant  and NF1 wild type melanoma short term cultures H3K4Me3 modifications were compared by Cut and Run to identify gene promoter activities differences


overall_design: NF1 mutant  and NF1 wild type melanoma short term cultures were compared by RNA-Seq to identify transcriptional differences


overall_design: NF1 mutant  and NF1 wild type melanoma short term cultures H3K27ac modifications were compared by Cut and Run to identify gene promoter activities differences


title: Novel perspectives on TRM signature and biology

city: Charlestown

first: Neal

middle: Patrick

last: Smith

state: MA

address: 149 13th Street

institute: Massachusetts General Hospital

summary: The goal of this study was to better understand the development of resident memory T cells (Trm) and central memory T cells (Tcm). To do this, we performed single-cell RNAseq on antigen-activated OT-1 T cells at serial timepoints collection from both skin and lymph node across 2 months post-vaccination.

overall_design: CD90.1 OT-1 T cells were adoptively transferred to a CD90.2 mouse, which was then infected with VACV-OVA. Skin and lymph node samples were then collected and digested at different timepoints. OT-1 T cells were sorted from these timepoints and used for single-cell RNAseq

middle: P

first: Yu

last: Yan

first: Alexandra-Chloe

last: Villani

first: Thomas

last: Kupper


title: BMAL1-HIF2α heterodimers contribute to ccRCC [RNA-seq]

status: Public on May 08 2025

city: SAN DIEGO

first: Rebecca

last: Mello

state: CA

address: 11093 CLAIREMONT MESA BLVD

institute: The Scripps Research Institute

summary: Circadian disruption enhances cancer risk, and many tumors exhibit disordered circadian gene expression. We show rhythmic gene expression is unexpectedly robust in clear cell renal cell carcinoma (ccRCC). Furthermore, the clock gene BMAL1 is higher in ccRCC than in healthy kidneys, unlike in other tumor types. BMAL1 is closely related to ARNT and we show that BMAL1-HIF2α regulates a subset of HIF2α target genes in ccRCC cells. Depletion of BMAL1 reprograms HIF2α chromatin association and target gene expression and reduces ccRCC growth in culture and in xenografts. Analysis of pre-existing data reveals higher BMAL1 in patient-derived xenografts that are sensitive to growth suppression by HIF2α antagonists. We show that increasing BMAL1 sensitizes ccRCC-derived A498 cells to growth inhibition by PT2399. Together, these findings indicate that an alternate HIF2α heterodimer containing the circadian partner BMAL1 contributes to HIF2α activity, growth, and sensitivity to HIF2α antagonist drugs in ccRCC cells.

overall_design: To gain insight into mechanisms by which zeitgeber time (ZT)  influences the impact of PT2399 on xenograft tumor growth, we sequenced RNA prepared from xenograft tumors collected from mice treated with vehicle or PT2399 at ZT0 or ZT12.

first: Mello

last: Rebecca

first: Lamia

last: Katja


overall_design: H3K4Me3 modifications with (shNF1) and without (shScramble) NF1 knockdown were compared by Cut and Run to identify gene promoter activities differences


title: Mitochondrial dynamics regulates iron homeostasis and nuclear genome stability [RNA-seq]

city: Boston

first: Kaifu

last: Chen

address: 300 Longwood Ave

department: Cardiology

institute: Boston Children's Hospital

summary: Mitochondrial membrane dynamics control the shape, number, and distribution of mitochondria and regulate energy production and cell health. Defective mitochondrial dynamics in humans are related to optic atrophy, neuropathies, cardiomyopathies, or dementia. In a screen for yeast mutants with increased levels of templated insertions (TINS) in the nuclear genome, we identified mitochondrial fusion deficient mutants (mgm1, ugo1, fzo1). We found that fusion mutants activate the iron regulon, have decreased iron-sulfur clusters (ISC) and increased DNA damage, suggesting a role of iron homeostasis in preventing TINS. Consistently, a secondary screen found many iron homeostasis mutants to exhibit high TINS. We propose that iron dysregulation leading to oxidative DNA damage coupled with compromised DNA repair drives TINS. Poor growth, iron dyshomeostasis, and genome instability can be suppressed in fusion mutants by increasing mitochondrial membrane potential, suggesting a new therapeutic approach. These studies link mitochondrial dynamics to iron homeostasis deficiency and genome stability

overall_design: Cells were grown to 2x10^7 cells/mL as described in YEP-Raffinose and 500 µL were pelleted and stored at -80°C. RNA was extracted using the miRNeasy Mini Kit (Qiagen, #217004) according to manufacturer instructions. Briefly, cells were lysed in a bead miller with acid-washed glass beads and Qiagen Buffer RLT. One volume of 70% ethanol was added to the homogenized lysate and the sample was purified using the RNeasy spin column and eluted in RNAse-free water. The cDNA library preparation and sequencing were conducted by Novogene using a paired-end 150 bp sequencing strategy on the Illumina NovaSeq 6000 platform.

first: Jordan

last: Fox

first: Yang

last: Yu

first: Xin

last: Wang

first: Grzegorz

last: Ira


overall_design: This study was perforemd to compare EGFR knockdown vs Control in NF1 mutant melanoma cell line isolated from a patient


title: Mitochondrial dynamics regulates iron homeostasis and nuclear genome stability

overall_design: To study insertion at DSBs in yeast, we used a high-throughput amplicon sequencing based method called Break-Ins (Break Insertions) which allows screening of hundreds of thousands of NHEJ products simultaneously. We used yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus. This DSB can't be repaired by homologous recombination; only the cells that repaired the break imprecisely, altering the HO recognition site, can survive continuous HO induction and form colonies. Yeast cells were grown overnight in YPD (1% yeast extract, 2% peptone, 2% dextrose), washed twice with YP-raffinose (1% yeast extract, 2% peptone, 2% raffinose) media, inoculated into 10 mL YP-raffinose media, and incubated at 30 °C overnight. When the cell density was about 2x107/mL, 500 µL cells were spread onto YP-galactose (1% yeast extract, 2% peptone, 2% galactose, 2.5% agar) plates to induce HO expression and the DSB at MATa locus, and incubated at 30 °C for 5 days. Each sample was spread on 5-7 150x15 mm YP-galactose plates. The number of colonies was counted. All colonies on YP-galactose plates were collected, combined, and mixed vigorously. Approximately 80 μL cells were spun down for isolating genomic DNA. Standard glass beads-phenol/chloroform/isoamyl alcohol (25:24:1) method. The DNA was dissolved in water and adjusted to a concentration of 10 ng/μL. The construction of the amplicon sequencing library was adapted from Illumina’s protocol #15044223 Rev. B. Briefly, the sequencing libraries were constructed with two rounds of PCR using KAPA HiFi HotStart ReadyMix polymerase (Roche, 7958927001). For the first round of PCR, 3.2 μL genomic DNA and 0.5 μL 10 μM primers were used for a total volume of 25 μL. The forward and reverse primers targeting the MATa locus are located 11 bp upstream or 18 bp downstream of the HO cleavage site respectively, containing Illumina adapter sequence and 3 bases unique home index as described (7). The thermocycling conditions were: 95 °C for 5 min; 22 cycles of 98 °C for 20 s, 65 °C for 30 s, 72 °C for 3 min; 72 °C for 10 min. After the first round of PCR, 18μL PCR product was purified with an equal volume of AMPure XP beads (Beckman Coulter, A63880). The DNA was eluted with 52.5 μL of 10 mM Tris (pH 8.5) and used as the templates for the second round of PCR. For the second round of PCR, 5 μl template DNA, 5 μL index primer N7xx and 5 μL index primer S5xx from Nextera XT V2 Index kit (Illumina, FC-131-2001) were used for the total volume of 50 μL. The following conditions were used for the second round of PCR: 95 °C for 5 min; 8 cycles of 95 °C for 30 s, 55 °C for 30 s, 72 °C for 3 min; 72 °C for 10 min. Then, the PCR product was purified with 1.2x volume of AMPure XP beads and eluted with 10 mM Tris pH 8.5. The average size of each sample was measured with TapeStation and the DNA concentration was measured with Qubit dsDNA BR Assay Kit (ThermoFisher, Q32850). Then, the DNA was diluted to a concentration of 4 nM. An equal volume of DNA from ~20 samples was pooled into the library. The 0.2 M NaOH was used to denature the pooled library and PhiX library (Illumina, FC‐110‐3001). After diluting the libraries with pre-chilled HT1 to 12 pM, pooled library and PhiX library were mixed with the ratio 9:1, further denatured by incubating at 96 °C for 2 min and immediately put in an ice-water bath for 5 min. The MiSeq and Reagent Kit v3 (600 cycles) (Illumina, MS-102-3003) were used for sequencing. The cluster density for all libraries was ~1100 K/mm2.


title: Reduction of neuronal activity mediated by blood-vessel regression in the adult brain

city: Beijing

first: Xing-jun

address: Bldg.3, NO.9, YIKE Rd, Zhongguancun Life Science Park, Changping District

country: China

institute: Chinese Institute for Brain Research, Beijing(CIBR)

summary: To explore the role of brain vascular TAK1 and its functional mechanism , we performed RNA-seq between Cdh5-CreER::Tak1fl/fl mice and their littermate control mice at the age of 12–14 weeks to identify the expression of some unique genes and possible pathway related to the function of brain vascular TAK1. We confirmed the role of brain vascular TAK1 contributed to Glutamate neuronal survival and activity.

overall_design: Differential expression analysis and Gene Set Enrichment Analysis of RNA seq data. We performed differential expression analysis of RNA seq data obtained from Cdh5-CreER::Tak1fl/fl mice and their littermate control mice at the age of 12–14 weeks and Gene Set Enrichment Analysis

first: Xiaofei

last: Gao

first: Meng

last: Ye

first: Jun-Liszt

last: Li

first: Tianyue

last: Ming

first: Nannan

last: Lu

first: Woo-ping

last: Ge


title: Evaluation of Peromyscus leucopus Bone Marrow-Derived Macrophage Responses to Borrelia burgdorferi and Lipopolysaccharide

first: Jeffrey

last: Bourgeois

address: 136 Harrison Ave

institute: Tufts University

summary: Currently, most tools utilized in host-pathogen interaction studies depend on the use of human or mouse (Mus musculus) cells and tissues. While these species have led to countless breakthroughs in our understanding of infectious disease, there are undoubtably important biological processes that are missed by limiting studies to these two vertebrate species. For instance, it is well-established that the most common North American rodent, the Peromyscus leucopus deermouse, has unique interactions with microbes, which likely shape its ability to serve as a critical reservoir for at numerous zoonotic pathogens—including a Lyme disease spirochete, Borrelia burgdorferi. In this work, we expand the immunological toolkit to study P. leucopus biology by performing the first differentiation of deermouse bone marrow to macrophages using P. leucopus M-CSF producing HEK293T cells.

sample_organism:
Peromyscus leucopus
Mus musculus

platform_organism:
Peromyscus leucopus
Mus musculus

overall_design: P. leucopus and C57BL/6J bone marrow-derived macrophages (BMDMs) were assayed by RNA sequencing for their response to B. burgdorferi B31 (MOI100, 10 hours) or lipopolysaccharide (100ng/mL, S. enterica serovar Minnesota, 10 hours). Samples are compared to mock treated ("media") controls

first: Christopher

middle: C

last: Wells

first: Tanja

last: Petnicki-Ocwieja

first: Shumin

last: Tan

first: Stephen

last: Bunnell

first: Sam

middle: R

last: Telford

first: Linden

middle: T

last: Hu

middle: S


first: Milad

last: Ibrahim

overall_design: NF1 mutant  and NF1 wild type melanoma short term cultures were compared by ATAC-Seq to identify transcriptional differences

first: Markus

last: Schober

first: Iman

last: Osman


title: Isoform characterization of m6A in single cells identifies its role in RNA surveillance [Direct RNA-seq for UPF1 knockdown]

city: GuangZhou

first: Zhijun

last: Ren

address: Sun Yat-sen University

institute: Sun Yat-sen University

summary: The distribution of m6A across various RNA isoforms and its heterogeneity within single cells are still not well understood. Here, we develop m6A-isoSC-seq, which employs both Oxford Nanopore long-read and Illumina short-read sequencing on the same 10x Genomics single-cell cDNA library with APOBEC1-YTH induced C-to-U mutations near m6A sites. Through m6A-isoSC-seq on a pooled sample of three cell line origins, we unveil a profound degree of m6A heterogeneity at both the isoform and single-cell levels. Through comparisons across single cells, we identify widespread specific m6A methylation on certain RNA isoforms, usually those mis-processed RNA isoforms. Compared to the coding isoforms of the same genes, the expression of highly methylated misprocessed RNA isoforms is more sensitive to METTL3 depletion. These mis-processed RNAs tend to have excessive m6A sites in coding regions, which are targets of CDS-m6A decay (CMD). This study offers undocumented insights into the role of m6A on RNA surveillance.

overall_design: To demonstrate m6A mediated degradation of mis-spliced RNAs was independent of UPF1, we knocked down UPF1 by siRNA, followed by ONT DRS sequencing.

first: Xiang

last: Huang

first: Jinkai

last: Wang


title: RNA-Seq of U2OS-MYC-KO-MYC-Tet-On cells with exogenous wild-type and mutant MYC expression

city: Pittsburgh

first: Da

last: Yang

state: PA

address: 3501 Terrace

department: School of Pharmacy

institute: University of Pittsburgh

summary: Transcription factor (TF) MYC binds to thousands of gene regulatory elements in the genome such as promoters and enhancers and exerts an amplification effect on the expression of most genes, regardless of the E-box motif existence. In this study, we discovered that MYC is an RNA-binding protein with a high affinity to guanosine-rich RNAs. RNAs that bind to MYC increase MYC’s chromatin occupancy, which helps with MYC-mediated regulation of gene expression. Mechanistically, two highly conserved sequences, amino acids 355-357 and 364-367, in the basic region of MYC are essential for RNA binding. Notably, alanine substitution of Lys355, Arg356, and Arg357 of MYC abolishes its RNA binding function but does not influence its complex formation ability, and E-box binding capacity of MYC:MAX dimer in vitro. However, loss of RNA binding function alone decreases MYC recruitment at gene regulatory elements in vivo, followed by a decreased MYC:MAX chromatin binding at these regions. This process further attenuates MYC-mediated gene expression. Therefore, RNA-binding-deficient MYC is compromised in promoting cancer cell proliferation. By demonstrating the mechanism of MYC-RNA interaction and the fundamental role of RNA binding activity in MYC-centric functions, our study reveals a new paradigm to MYC function and highlights an essential and probably general role of RNA binding capacity of TFs for their gene regulatory function.

overall_design: RNA-Seq of U2OS-MYC-KO-MYC-Tet-On cells treated 24 h with 1 µg/ml doxycycline (Dox) for wild-type and mutant MYC expression and cells without Dox treatment used as controls.

first: Sihan

last: Li

first: Zehua


title: Distinct cellular and spatial niches within the inflamed synovium of childhood arthritis [xenium]

status: Public on May 11 2025

city: Birmingham

first: Adam

last: Croft

state: Please Select

address: Birmingham

country: United Kingdom

institute: University of Birmingham

summary:
Precision use of targeted therapies is urgently needed to improve long-term clinical outcomes for children affected by inflammatory arthritis, known as Juvenile Idiopathic Arthritis. Progress has been obstructed by a lack of understanding of the cellular basis of joint inflammation in children, given the difficulties in obtaining and studying synovial tissue itself. To this end, we combine single-cell RNA-sequencing, multiplexed immunofluorescence imaging and spatial transcriptomics to define the cellular and transcriptomic landscape of the synovium in children with Juvenile Idiopathic Arthritis. We identify spatial niches of resident and infiltrating cell populations that correlate with the degree of inflammation, and gene programs associated with arthritis severity. Combined with analyses of synovial fluid and peripheral blood from the same children, we distinguish differences in cellular composition, signalling pathways and transcriptional programs across anatomical compartments. Whilst we identify several pathogenic populations shared with adult-onset arthritis, our analyses highlight increased vascularity of the inflamed developing joint and TGFb-driven stromal subsets that upregulate expression of disease risk-associated genes. Overall, these findings illustrate the need for treatment algorithms informed by a tissue-based classification of arthritis.
Slides were prepared, processed, imaged and underwent post-run staining according to Xenium (10X Genomics) protocols: “CG000580 Rev C”, “CG000582 Rev D”, “CG000584 Rev B” and “CG000613 Rev A”, according to manufacturer’s instructions. For gene detection, slides hybridized with probes from the predesigned Xenium Human Multi-Tissue and Cancer Gene Expression and hMulti_v1 design (chemistry v1: 10x Genomics), consisting of 377 genes was used.

overall_design: Chris Mahony


title: ChIP-Seq with reference exogenous genome (ChIP-Rx) of MAX in U2OS-MYC-KO-MYC-Tet-On cells with exogenous wild-type and mutant MYC expression

overall_design: Chromatin immunoprecipitation assays followed by sequencing (ChIP-Seq) with reference exogenous genome (ChIP-Rx) of MAX in U2OS-MYC-KO-MYC-Tet-On cells treated 24 h with 1 µg/ml doxycycline (Dox) for wild-type and mutant MYC expression and cells without Dox treatment included. NIH3T3 cells (mouse) were used as the reference exogenous genome. Two biological replicates were sequenced for each cell.


title: BMAL1-HIF2α heterodimers contribute to ccRCC [RNA-seq_FigS6]

first: Rebecca

last: Mello

overall_design: To measure the contributions of endogenous ARNT and BMAL1 to HIF2α-driven gene expression in ccRCC cells, we sequenced RNA prepared from A498 cells in which either ARNT or BMAL1 was depleted by shRNA. We used DESeq2 to identify transcripts that were significantly altered. We gene set enrichment analysis (GSEA) to examined the expression of 200 transcripts in the Hallmark HYPOXIA gene set.

first: Katja

last: Lamia


title: BMAL1-HIF2α heterodimers contribute to ccRCC [RNA-seq_Fig2]

summary: Circadian disruption enhances cancer risk, and many tumors exhibit disordered circadian gene expression. We show rhythmic gene expression is unexpectedly robust in clear cell renal cell carcinoma (ccRCC). Furthermore, the clock gene BMAL1 is higher in ccRCC than in healthy kidneys, unlike in other tumor types. BMAL1 is closely related to ARNT and we show that BMAL1-HIF2α regulates a subset of HIF2α target genes in ccRCC cells. Depletion of BMAL1 reprograms HIF2α chromatin association and target gene expression and reduces ccRCC growth in culture and in xenografts. Analysis of pre-existing data reveals higher BMAL1 in patient-derived xenografts that are sensitive to growth suppression by HIF2α antagonists. We show that increasing BMAL1 sensitizes ccRCC-derived 786O cells to growth inhibition by PT2399. Together, these findings indicate that an alternate HIF2α heterodimer containing the circadian partner BMAL1 contributes to HIF2α activity, growth, and sensitivity to HIF2α antagonist drugs in ccRCC cells.

overall_design: To measure the contributions of endogenous ARNT and BMAL1 to HIF2α-driven gene expression in ccRCC cells, we sequenced RNA prepared from 786O cells in which either ARNT or BMAL1 was depleted by shRNA. We used DESeq2 to identify transcripts that were significantly altered. We gene set enrichment analysis (GSEA) to examined the expression of 200 transcripts in the Hallmark HYPOXIA gene set.


title: Widespread impact of nucleosome remodelers on transcription at cis-regulatory elements [ATAC-seq]

first: Sarah

middle: J

last: Hainer

address: 4249 Fifth Ave

department: Department of Biological Sciecnes

summary: Nucleosome remodeling complexes and other regulatory factors work in concert to build a chromatin environment that directs the expression of a distinct set of genes in each cell using cis-regulatory elements (CREs) such as promoters and enhancers which drive transcription of both mRNAs and CRE-associated non-coding RNAs (ncRNAs). Two classes of CRE-associated ncRNAs include upstream antisense RNAs (uaRNAs), which are transcribed divergently from a shared mRNA promoter element, and enhancer RNAs (eRNAs), which are transcribed bidirectionally from active enhancers. The complicated network of CRE regulation by nucleosome remodelers remains only partially explored, with a focus on a select, limited number of remodelers. We endeavored to elucidate a remodeler-based regulatory network governing CRE-associated transcription (mRNA, eRNA, and uaRNA) in murine embryonic stem (ES) cells to test the hypothesis that many SNF2-family nucleosome remodelers collaborate to regulate the coding and non-coding transcriptome. Using depletion followed by transient transcriptome sequencing (TT-seq), we identified thousands of misregulated mRNAs and CRE-associated ncRNAs across the remodelers examined, identifying novel contributions by understudied remodelers in the regulation of coding and non-coding transcription. Our findings suggest that transcription of paired mRNAs and eRNAs are coordinately co-regulated, while mRNAs and uaRNAs sharing a promoter are independently regulated by remodelers. Our mechanistic studies suggest that while SRCAP and CHD8 modulate transcription through classical mechanisms such as transcription factors and histone variants, a broad set of remodelers including SMARCAL1 indirectly contribute to transcription regulation through maintenance of genomic stability and accurate Integrator complex activity. This study systematically examines the contribution of SNF2-remodelers to the CRE-associated transcriptome, identifying at least two classes for remodeler action.

overall_design: ATAC-seq samples from murine embryonic stem cells treated with an RNAi agent for 48 hours. 4 different targets in biological duplicate (Control, Srcap, Chd8, Smarcal1).

first: Benjamin

last: Patty

first: Rinku

last: Dhungana


title: Widespread impact of nucleosome remodelers on transcription at cis-regulatory elements [RNA-seq]

overall_design: rRNA depleted total RNA-seq samples. Wildtype murine embryonic stem cells transfected with an RNAi agent for 48 hours. Twenty nine targets profiled in biological duplicate, and seventeen control samples (Atrx, Btaf1, Chd1, Chd1l, Chd2, Chd3, Chd4, Chd5, Chd7, Chd8, Chd9, Ep400, Ercc6, Ercc6l, Hells, Hltf, Ino80, Radb54b, Radb54l, Rad54l2, Shprh, Smarca2, Smarca4, Smarca5, Smarcad1, Smarcal1, Srcap, Ttf2, Zranb3).


overall_design: This study was performed to compare xenografts of NF1 mutant melanoma treated with Cetuximab or IgG control


title: Widespread impact of nucleosome remodelers on transcription at cis-regulatory elements [TT-seq]

overall_design:
rRNA depleted Nascent RNA-seq (TT-seq) samples. Wildtype murine embryonic stem cells transfected with an RNAi agent for 48 hours. Twenty nine targets profiled in biological duplicate, and control samples (Atrx, Btaf1, Chd1, Chd1l, Chd2, Chd3, Chd4, Chd5, Chd7, Chd8, Chd9, Ep400, Ercc6, Ercc6l, Hells, Hltf, Ino80, Radb54b, Radb54l, Rad54l2, Shprh, Smarca2, Smarca4, Smarca5, Smarcad1, Smarcal1, Srcap, Ttf2, Zranb3).
Also included are TT-seq for DMSO or dTAG treated (3 hr) for Chd4-dTAG, Chd8-dTAG, or Hltf-dTAG endogenously tagged ES cells.


title: Widespread impact of nucleosome remodelers on transcription at cis-regulatory elements

overall_design: Refer to individual Series


title: BMAL1-HIF2α heterodimers contribute to ccRCC [RNA-seq_FigS4]

overall_design: We sequenced RNA prepared from 786O cells or 786O cells expressing wildtype VHL (WT8 cells)  in which BMAL1 was depleted by shRNA.


title: RNA-binding activity plays an important role in MYC function


title: Widespread impact of nucleosome remodelers on transcription at cis-regulatory elements [CUT&RUN]

overall_design: CUT&RUN assays for select targets in either wildtype murine ES cells or cells treated with an RNAi reagent for different targets for 48 hours prior to experiments. Conditions (Targets) done in biological triplicate: Wildtype ES cells (SRCAP, SMARCAL1, IgG). Conditions (Targets) done in biological duplicate: ControlKD (INTS5, H2A.Z, NFYA, H3K27ac, IgG), SrcapKD (H2A.Z, H3K27ac, IgG), Chd8KD (NFYA, H3K27ac, IgG), and Smarcal1KD (INTS5, H3K27ac, IgG).


title: ChIP-Seq with reference exogenous genome (ChIP-Rx) of wild-type MYC and mutant MYC in U2OS-MYC-KO cells

summary: MYC binds to thousands of gene regulatory elements in the genome such as promoters and enhancers and exerts an amplification effect on the expression of most genes, regardless of the E-box motif existence. In this study, we discovered that MYC is an RNA-binding protein with a high affinity to guanosine-rich RNAs. RNAs binding to MYC enhance its chromatin occupancy. This process helps on MYC-mediated regulation of gene expression. Mechanistically, Lys355, Arg356, and Arg357 in the basic region of MYC are essential for RNA binding. Alanine mutation of these three amino acids abolishes MYC RNA-binding function but causes minimal damage to MYC/MAX DNA-binding capacity. Only loss of MYC RNA-binding function, while maintaining DNA-binding function, significantly decreases MYC chromatin occupancy in vivo. Our study reveals a new dimension to MYC-mediated gene regulation by demonstrating that RNA-binding activity plays an important role in MYC’s function.

overall_design: Chromatin immunoprecipitation assays followed by sequencing (ChIP-Seq) with reference exogenous genome (ChIP-Rx) of doxycycline (Dox) inducible FLAG-tagged wild type MYC and mutant MYC in U2OS-MYC-KO cells. NIH3T3 cells (mouse) were used as the reference exogenous genome. Two biological replicates were sequenced for each lysate.


title: Enhanced CLIP-Seq (eCLIP-Seq) of FLAG-tagged wild-type and mutant MYC in U2OS-MYC-KO-MYC-Tet-On cells

overall_design: Enhanced crosslinking and immunoprecipitation followed by sequencing (eCLIP-Seq) of FLAG-tagged wild-type and mutant MYC in U2OS-MYC-KO-MYC-Tet-On cells treated 24 h with 1 µg/ml doxycycline (Dox) and cells without Dox treatment included. Two biological replicates were sequenced for each sample.


title: RNA-dependent ChIP-Seq (rChIP-Seq) of MYC and TBP in MCF-7 cells

overall_design: RNA-dependent chromatin immunoprecipitation assays followed by sequencing (ChIP-Seq, rChIP-Seq) of MYC and TBP in MCF-7 cells treated with or without RNase A. Two biological replicates of the pulldown were sequenced on each lysate.


title: RNA-dependent CUT&RUN (rCUT&RUN) of MYC and TBP in MCF-7 cells

overall_design: RNA-dependent Cleavage Under Targets and Release Using Nuclease (CUT&RUN, rCUT&RUN) of MYC and TBP in MCF-7 cells with RNase A treatment or without RNase A treatment. Two biological replicates were sequenced.


title: Gene expression profile at single cell level of  CD45+ cells from the mouse melanoma after treatment with M1 or M1-mutIL-18

status: Public on May 07 2025

city: guangzhou

first: Fan

last: Zhen

address: No. 74, Zhongshan Er Road, Guangzhou, Guangdong, P. R. China

summary: CD45+ immune cells play an important role in immunotherapy.To investigate the effect of CD45+ immune cells on the efficacy of oncolytic viruses M1 and M1-mutIL-18, We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of CD45+ immune cells in B16F10 tumors of mice after M1 and M1-mutIL-18 treatment.

overall_design: B16F10 cells were injected subcutaneously into the right abdomen of C57BL/6J mice and treated with M1 (1.5 × 107 PFU) or M1-mutIL-18 (1.5 × 107 PFU) when the tumour volume was approximately 200 mm3 . M1 or M1-mutIL-18 was injected through the tail vein for 5 consecutive days. Mice were euthanised on the third day after the last dose and CD45+ immune cells in tumors were isolated by immunomagnetic beads (130-110-618, Miltenyi Biotec). Biological replicates from n = 3 pooled mice were processed for each experimental condition and analyzed by scRNAseq and scTCR-seq.

first: Zhen

last: Fan

first: Jifu

last: Zhang

first: Jiankai

last: Liang


title: SEL1L is Dispensable for ER Homeostasis and Function in Spermatogenic Cells

status: Public on May 06 2025

city: Charlottesville

first: Anwaruddin

last: Mohammad

state: VA

address: Pinn Hall

department: Bioinformatics Core

institute: University of Virginia

summary: The SEL1L-HRD1 complex is a critical component of the endoplasmic reticulum (ER)-associated protein degradation (ERAD) pathway, essential for maintaining ER homeostasis and cellular function. While the importance of SEL1L and HRD1 in various physiological processes have been reported in mice and humans, their specific functions in male germ cells remain unexplored. This study aims to investigate the role of SEL1L-HRD1 ERAD in spermatogenesis process. To achieve this, we conducted whole genome RNA sequencing to identify genes differentially regulated in testes from male germ cell specific SEL1L-deficient mice.

overall_design: Transcriptomic analysis of testes from 7-week-old male germ cell-specific SEL1L knockout (Sel1Lflox/∆;Stra8-Cre, i.e. KOStra8) mice and heterozygous (Sel1Lflox/∆, i.e. HETStra8) littermates by unbiased whole genome RNA sequencing.

first: Nusrat

last: Tushi

first: Zhibing

first: Shengyi

last: Sun


title: Macrophages foster anti-tumor immunity by ZEB1-dependent cytotoxic T cell chemoattraction

city: Erlangen

first: Harald

last: Schuhwerk

address: Glückstrasse 6

country: Germany

summary: Tumor-associated macrophages (TAMs) dynamically influence anti-tumor immunity. Understanding TAM function and plasticity is therefore critical to design immunotherapies. By combining syngeneic models of colorectal and pancreatic cancer with cell type-specific deletion of Zeb1, a key driver of epithelial-to-mesenchymal transition that is expressed in subsets of TAMs, we discovered that ZEB1 is an intrinsic regulator of TAM-controlled T cell trafficking. ZEB1 supports secretion of a subset of chemokines via the constitutive pathway, including CCL2 and CCL22, by promoting their biosynthesis, vesicular transport and release. This elevates CCL2 and CCL22-driven cytotoxic T cell (CTL) recruitment in vitro and fosters immunosurveillance by CTLs in tumors and metastases as well in an organotypic model for adoptive cell transfer. Our study identifies ZEB1 in TAMs as a facilitator of anti-tumor immunity, suggests a window of opportunity for cytokine-guided CTL tropism and reinforces the importance of onco-immunological context, particularly in the design of macrophage-/ cytokine-depleting strategies.

overall_design: Each 3 BMDM lines (=BMDMs bone marrow derived macrophages) of the mouse strains ZEB1LysMCtrl (ZEB1 competent) and ZEB1LysMDel (ZEB1 incompetent) were generated. These were either treated with LPS, Il-4 or left unstimulated (M0) for 24h. Bulk RNA-Seq was performed to detect differences in polarization capacity between the two genotypes.


title: Comprehensive Genomic Profiling of Renal Cancer Cases

city: Suita City

first: Yohei

last: Okuda

state: Osaka

address: Yamadaoka 2-2,

country: Japan

institute: The University of Osaka

summary: Comprehensive Genomic Profiling (CGP) is a technique that comprehensively examines a wide range of cancer-related genetic alterations—such as mutations, copy number variations, and gene fusions—from a single specimen. In the field of renal cancer (primarily renal cell carcinoma), where treatment options like molecularly targeted therapies and immune checkpoint inhibitors continue to expand, there is growing interest in understanding each patient’s mutational profile to enable more personalized treatment strategies.

overall_design: At our hospital, we collected both tumor and normal tissue samples from the nephrectomy specimens of patients who had been diagnosed with renal cancer and underwent surgery for treatment. DNA and RNA were then extracted from these samples, and a genomic analysis was performed using next-generation sequencing.

first: Taigo

last: Kato

first: Yoko

last: Koh

first: Gaku

last: Yamamichi

first: Akihiro

last: Yoshimura

first: Atsuki

last: Matsukawa


title: Enhanced CLIP-Seq (eCLIP-Seq) of endogenous MYC in different cell lines

first: Da

last: Yang

overall_design: Enhanced crosslinking and immunoprecipitation followed by sequencing (CLIP-Seq, eCLIP-Seq) of MYC in different cell lines. Two biological replicates were sequenced for each cell line.

first: Sihan

last: Li

first: Zehua

last: Wang


title: Analysis of changes in inter-cellular communications during Alzheimer's Disease pathogenesis reveals conserved changes in glutamatergic transmission in mice and humans

status: Public on May 05 2025

city: Irvine

first: Kevin

last: Beier

address: 825 Health Sciences Road Med Sci D320

department: Physiology and Biophysics

institute: UCI

summary: Analysis of system-wide cellular communication changes in Alzheimer’s disease (AD) has recently been enabled by single nucleus RNA sequencing (snRNA-seq) and new computational methods. Here, we combined these to analyze data from postmortem human tissue from the entorhinal cortex of people with AD and compared our findings to those from multiomic data from the 5xFAD amyloidogenic mouse model at two different time points. Using the cellular communication inference tool CellChat we found that disease-related changes were largely related to neuronal excitability as well as synaptic communication, with specific signaling pathways including BMP, EGF, and EPHA, and relatively poor conservation of glial-related changes during disease. Further analysis using the neuron-specific NeuronChat revealed  changes relating to metabotropic glutamate receptors as well as neuronal adhesion molecules including neurexins and neuroligins. Our results that cellular processes relating to excitotoxicity are the best conserved between 5xFAD mice and AD suggest that excitotoxicity is the main common feature between pathogenesis in 5xFAD mice and people with AD.

overall_design: Multiome-seq: the entorhinal cortex region was extracted from the brains of WT and 5xFAD mice at 2 months and 8 months of age. Single nuclei were isolated and snRNA-seq and snATAC-seq libraries were prepared using the 10x Multiome kit

first: Katrina

last: Bartas

first: Megan

last: Nguyen

first: May

last: Hui

first: Wei

last: Zhao

first: Qing

last: Nie


title: Reduced JAG1 expression through miR-200 overexpression or Crispr-Cas mediated knockout impairs TNBC growth and metastasis.

city: Guelph

first: Roger

last: Moorehead

address: 50 Stone Rd E

department: Biomedical Sciences

country: Canada

institute: University of Guelph

summary: Studies from our lab and others demonstrated that increasing miR-200 expression in TNBC cell lines reduced proliferation and invasion in vitro and tumor growth and metastasis in vivo. However, the mechanisms through which miR-200s suppress TNBC growth and metastasis remains incompletely characterized. In this study, we found that overexpression of miR-200s in MDA-MB-231 and MDA-MB-436 cells significantly reduced the expression of several Notched-Jagged genes including JAG1. To further investigate the importance of JAG1, JAG1 was knocked out using Crispr-Cas in MDA-MB-231 cells which express high endogenous JAG1. Loss of JAG1 in MDA-MB-231 cells significantly reduced proliferation and invasion as well as increasing apoptosis in vitro. Moreover, loss of JAG1 delayed mammary tumor onset, mammary tumor growth rate and metastatic dissemination in vivo. RNA sequencing of control and MDA-231JAG1KO tumors revealed that knocking out JAG1 altered the expression of genes associated with the extracellular matrix, angiogenesis, and epithelial to mesenchymal transition. These results imply that miR-200s may mediate some of their anti-tumor actions through reducing JAG1 expression. In addition, the loss of JAG1 dramatically suppressed TNBC growth and metastasis thus suggesting that agents targeting JAG1 should be further evaluated as a therapeutic strategy for TNBC.

overall_design: RNA was extracted from mammary tumors induced by MDA-MB-231 cells expressing a control vector (MDA-231EV) or MDA-MB-231 where JAG1 had been knocked out (MDA-231JAG1KO)

first: Moorehead

last: Roger


title: ATAC-seq profiling of MORC2 overexpression in wild-type HEK293T cells

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: We report an in vitro reconstitution of full-length MORC2, the most commonly mutated MORC member, linked to various cancers and neurological disorders. MORC2 possesses multiple DNA binding sites that undergo structural rearrangement upon DNA binding. MORC2 locks onto the DNA using its C-terminal domain (CTD) and acts as a sliding clamp. A conserved phosphate-interacting motif within the CTD was found to regulate ATP hydrolysis and cooperative DNA binding. Importantly, MORC2 mediates chromatin remodelling via ATP hydrolysis-dependent DNA compaction, regulated by the phosphorylation state of its CTD.

overall_design: We performed assays for transposase-accessible chromatin with sequencing (ATAC-seq) to determine the effects in chromatin accessibility by overexpressing MORC2 in the HEK293T cell line. Sequencing experiments were run in duplicate on wild-type HEK293T cell lines for lipofectamine-only (control) and transfected MORC2 (overexpression).

first: Pedro

middle: L

last: Baldoni


title: A cohort of mRNAs undergo high-stoichiometry NSUN6-mediated site-specific m5C modification

city: shanghai

first: Li

last: Cai-tao

state: shanghai

address: 393 Middle Huaxia Road, Pudong New Area, Shanghai

institute: Shanghaitech University

type: Methylation profiling by high throughput sequencing

summary: mRNA modifications are vital in regulating cellular processes. Beyond N6-methyladenosine (m6A), most other internal mRNA modifications lack dedicated catalytic machinery and are typically introduced by tRNA-modifying enzymes. The distribution and stoichiometry of these modifications on mRNAs remain debated and require further validation. Furthermore, their precise function remains controversial due to the challenges of excluding the intricate combinational effects of tRNA modifications. Here, we biochemically validate that NSUN6, a tRNA structure-dependent methyltransferase, independently catalyzes 5-methylcytidine (m5C) formation with robust activity on mRNA by recognizing the CUCCA motif in a certain stem-loop structure. NSUN6 employs different strategies to recognize tRNA and mRNA substrates. By introducing mutations, we further separate its catalytic capabilities toward mRNA and tRNA revealing that NSUN6 promotes breast cancer cell migration depending on mRNA m5C modification. Mechanistically, a cohort of mRNAs involved in cell migration carries high levels of NSUN6-mediated site-specific m5C modification, thus being stabilized by the preferential binding of m5C readers YBX1 and YBX3. Moreover, introducing a single-site high-level m5C can significantly increase the stability of therapeutic mRNAs in cells. Our findings underscore the pivotal role of m5C-modified mRNAs in promoting breast cancer metastasis and their potential for therapeutic applications.

overall_design: RNA-seq were performed on MDA-MB-231 breast cancer cell line for both control and NUN6 knockout to identify NSUN6 downstream target genes.

first: Yuan-Yuan

last: Zhang

first: Cai-Tao

first: You-Jia

last: Zhou

first: Hao

first: Jing

first: Qing-Ping

last: Xiong

first: Wenze

last: Huang

first: Qiangfeng Cliff

first: Yangfei

last: Xiang

first: En-Duo

first: Beisi

last: Xu

first: Ru-Juan

last: Liu


title: Gene expression profile at single cell level of endometrial cells at postimplantation stage both in vivo and ex vivo.

city: Suita

first: Takehiro

last: Hiraoka

address: 3-1 Yamadaoka

institute: Osaka University

summary: We have newly established a novel ex vivo implantation system. To verify the ex vivo endometrial gene expression profile in comparison with in vivo, we performed single cell RNA-sequencing (scRNA-seq).

overall_design: The endometria at dpc 4.5 in vivo and at 24h ex vivo were fixed 10% neutralized formalin. Then, implantation sites (ISs) and inter-implantation sites (I-ISs) were surgically dissected under a microscope. 10x genomics flex technology was applied.

first: Shizu

last: Aikawa

first: Daisuke

last: Mashiko

first: Masahito

last: Ikawa


title: Gene expression profile at single cell level of embryonic cells at postimplantation stage both in vivo and ex vivo.

summary: We have newly established a novel ex vivo implantation system. To verify the ex vivo postimplantation embyonic gene expression profile in comparison with in vivo, we performed single cell RNA-sequencing (scRNA-seq).

overall_design: The embryos at E4.5 in vivo and at 24h ex vivo were isolated with a glass capillary.Then, the dissociated cells were processed for scRNA-seq and the gene expression prollifes were compared.


title: ATAC-seq profiling of MORC2 knock-out HEK293T cells

first: Gordon

overall_design: We performed assays for transposase-accessible chromatin with sequencing (ATAC-seq) to determine if MORC2 was binding to open chromatin in the HEK293T cell line. Sequencing experiments were run in duplicate on wild-type and MORC2-knock-out HEK293T cell lines.

first: Pedro


title: H3K9me3 and MORC2 ChIP-seq profiling of wild-type and MORC2-knock-out HEK293T cells

overall_design: To identify the preferred genomic regions of MORC2 binding, we performed chromatin immunoprecipitation sequencing (ChIP-seq) on the HEK293T cell line utilising antibodies specific for MORC2 and H3K9me3, a mark of constitutive heterochromatin. Negative control IgG ChIP-seq experiments were performed. All sequencing experiments were run in duplicate on wild-type and MORC2-knock-out HEK293T cell lines.


title: wild-type and MORC2 knock-out HEK293T cells

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

overall_design: Refer to individual Series


title: RNA-seq profiling of MORC2 knock-out HEK293T cells

overall_design: To investigate how MORC2 regulates gene expression, we performed RNA-seq analysis using the HEK293T cell line. Sequencing experiments were run in duplicates with wild-type and MORC2-knock-out HEK293T cell lines.


title: Effect of CMA inhibitor on gene expression in A549 non-small cell lung cancer cells

status: Public on May 04 2025

city: Bronx

first: Mericka

last: McCabe

address: 1300 Morris Park Avenue

institute: Albert Einstein College of Medicine

summary: Transcriptomics of A549 cells treated with CIM7 in the presence of WT or AHT RARa to evaluate gene expression changes.

overall_design: Messenger RNA was extracted from total RNA purified from A549 cells transfected with WT or AHT RARa and treated with DMSO or CIM7.

first: Ana Maria

last: Cuervo

first: Evripidis

last: Gavathiotis


title: Chromatin interaction maps of human arterioles reveal new mechanisms for the genetic regulation of blood pressure [RRBS]

city: Tucson

first: Yong

state: AZ

address: The University of Arizona

department: Physiology

institute: University of Arizona

summary: Arterioles are small blood vessels located just upstream of capillaries in nearly all tissues. The constriction and dilation of arterioles regulate tissue perfusion and are primary determinants of systemic blood pressure (BP). Abnormalities in arterioles are central to the development of major diseases such as hypertension, stroke, and microvascular complications of diabetes. Despite the broad and essential role of arterioles in physiology and disease, current knowledge of the functional genomics of arterioles is largely absent, partly because it is challenging to obtain and analyze human arteriole samples. Here, we report extensive maps of chromatin interactions, single-cell expression, and other molecular features in human arterioles and uncover new mechanisms linking human genetic variants to gene expression in vascular cells and the development of hypertension. Compared to large arteries, arterioles exhibited a higher proportion of pericytes which were strongly associated with BP traits. BP-associated single nucleotide polymorphisms (SNPs) were enriched in chromatin interaction regions in arterioles, particularly through enhancer SNP-promoter interactions, which were further linked to gene expression specificity across tissue components and cell types. Using genomic editing in animal models and human induced pluripotent stem cells, we discovered novel mechanisms linking BP-associated noncoding SNP rs1882961 to gene expression through long-range chromatin contacts and revealed remarkable effects of a 4-bp noncoding genomic segment on hypertension in vivo. We anticipate that our rich data and findings will advance the study of the numerous diseases involving arterioles. Moreover, our approach of integrating chromatin interaction mapping in trait-relevant tissues with SNP analysis and in vivo and in vitro genome editing can be applied broadly to bridge the critical gap between genetic discoveries and physiological understanding.

overall_design: DNA methylation for human arterioles or tissue components of human arterioles.

first: Rajan

last: Pandey

first: Qiongzi

last: Qiu

first: Pengyuan

first: Hong

last: Xue

first: Jingli

last: Wang

first: Bhavika

last: Therani

first: Rong

last: Ying

first: Kristie

last: Usa

first: Michael

last: Grzybowski

first: Chun

last: Yang

first: Manoj

last: Mishra

first: Andrew

last: Greene

first: Allen

middle: W

last: Cowley Jr

first: Sridhar

last: Rao

first: Aron

middle: M

last: Geurts

middle: E

last: Widlansky

first: Mingyu

last: Liang


title: Chromatin interaction maps of human arterioles reveal new mechanisms for the genetic regulation of blood pressure [pan_promoter_Micro-C]

first: Yong

last: Liu

overall_design: We generated data for promoter-focused chromatin conformation of human arterioles or tissue components of human arterioles.


title: Nucleosome positioning dynamics during the cold-induced silencing of the Arabidopsis FLC gene using targeted MNase-seq

city: Norwich

first: Miguel

last: Montez

address: Norwich Research Park, Colney Ln

department: Department of Cell and Developmental Biology

institute: John Innes Centre

summary: Micrococcal nuclease (MNase) has been extensively used to map nucleosomes genome wide. Here, we used a targeted MNase-seq approach to map nucleosomes at high resolution at the FLC locus during the cold-induced silencing. This strategy uncovered that the +1 nucleosome at FLC is repositioned closer to the promoter in response to cold. The nucleosome repositioning alters the chromatin structure locally at the 5’ end of FLC and is linked to the silencing of the gene. Moreover, this is in part modulated by VRN1, a non-sequence-specific DNA binding protein that associates with FLC promoter and is required for its silencing.

overall_design: Arabidopsis Col-0 with an active FRIGIDA allele (WT FRI), and vrn1-4 FRI seedlings were grown at ambient temperature and subject to 1 week of cold. Seedlings before and after cold were used for MNase-seq.


title: Identification of a novel intracellular function of the secreted ribonuclease RNASE1 in inhibiting gene expression

city: Bethesda

first: Ashish

last: Lal

state: MD

address: 37 Convent Drive, Bldg 3, Room 6134

department: Genetics Branch

institute: NCI, NIH

summary: RNASE1 is a ribonuclease secreted by cells and degrades extracellular RNAs. Here, we unexpectedly found that endogenous RNASE1, in addition to being secreted, is predominantly localized to the nucleus and primarily functions to inhibit gene expression in human colorectal cancer (CRC) cells. In CRC cells, RNASE1 expression is highly cell type-specific and is restricted to well-differentiated cells where its transcription is activated by the pioneer transcription factor FOXA1. Using CRISPR interference (CRISPRi) utilizing three independent sgRNAs targeting the RNASE1 locus followed by RNA-seq, we found that upon depletion of RNASE1, most of the differentially expressed RNAs are modestly but significantly upregulated suggesting that RNASE1 may predominantly function to inhibit gene expression. In CRC patients, RNASE1 is significantly downregulated and high RNASE1 expression is associated with better patient survival indicating a potential tumor suppressive function. Consistent with this, RNASE1 depletion results in increased proliferation and clonogenicity indicating that RNASE1 inhibits the growth of CRC cells. Finally, a promising RNASE1 target amongst the most significantly upregulated mRNAs upon RNASE1 depletion is DKK1 (Dickkopf inhibitor 1) which is upregulated in CRC and negatively regulated by RNASE1. Collectively, these data uncover an intracellular function of RNASE1 in inhibiting gene expression and CRC cell proliferation.

overall_design: mRNAseq profile of established RNASE1 CRISPRi cell lines

first: Xinyu

last: Wen


title: Insights into Human Melanocyte Development and Characteristics through Pluripotent Stem Cells Combined with Single-Cell Sequencing

city: Zhenjiang

first: Jie

state: Jiangsu

address: 301 Xuefu Road

institute: Jiangsu University

summary: Many human pigment-related diseases are closely linked to melanocytes. However, our understanding of human melanocyte development has primarily relied on studies conducted on animal models which cannot fully simulate the biological characteristics and disease manifestations of humans. The utilization of pluripotent stem cells (PSCs) has shown immense potential in exploring human developmental biology. In this study, combination of human PSCs differentiation model and single-cell sequencing analysis was conducted to uncover the cellular heterogeneity and dynamic changes in biological characteristics, differentiation trajectory, and signaling interactions during melanocyte development. By integrating single-cell data from normal human melanocytes, we confirmed that induced melanocytes derived from PSCs encompassed all stages of human melanocyte development. Compared to mouse melanocytes, induced melanocytes better mimic the characteristics of human melanocytes, particularly at early stage of development. Exploration of cell-cell communication revealed the interactions among sub-populaiton of induced melanocytes involved pathways including BMP, WNT, TGF-beta, etc. Additionally, surface markers of melanocyte stem cells were screened and PDGFRB was identified as a potential marker. Collectively, these findings demonstrate that the PSCs can effectively stimulate human melanocyte development, providing a valuable tool for further investigation of melanocyte-related diseases.

overall_design: In this study, induced pluripotent stem cells (iPSCs) and WA09 (H9) human embryonic stem cells were used. Melanocytes differentiated from iPSCs were collected at Day 23, Day 32, and Day 44, and then subjected to scRNA-seq analysis.

first: Zihan

last: Wang

first: Hang

last: Zhou

first: Yuyun

last: Xiong

first: Yumei

last: Li

first: Yunwen

last: Zheng

first: Liping


title: A lysosomal surveillance response to stress extends healthspan [Exp3]

status: Public on May 03 2025

city: Lausanne

first: Terytty Yang

address: EPFL SV IBI-SV LISP AI 1145

country: Switzerland

institute: EPFL

summary: Lysosomes are cytoplasmic organelles central for the degradation of macromolecules to maintain cellular homeostasis and health. However, how lysosomal activity can be boosted to counteract aging and aging-related diseases remains elusive. Here, we reveal that silencing specific vacuolar H+-ATPase subunits (e.g. vha-6), that are essential for intestinal lumen acidification in Caenorhabditis elegans, extends lifespan by ~60%. This longevity phenotype can be explained by an adaptive transcriptional response typified by induction of a set of transcripts involved in lysosomal function and proteolysis, which we termed the lysosomal surveillance response (LySR). LySR activation is characterized by boosted lysosomal activity, enhanced clearance of protein aggregates in worm models of Alzheimer's disease, Huntington’s disease and amyotrophic lateral sclerosis, thereby improving fitness. The GATA transcription factor ELT-2 governs the LySR program and its associated beneficial effects. Activating the LySR pathway may therefore represent an attractive mechanism to reduce proteotoxicity and, as such, potentially extend healthspan.

overall_design: Wild-type C. elegans treated with dietary restrition

first: Terytty

middle: Y

first: Arwen

last: Gao

first: Xiaoxu

first: Lin

last: Chen

first: Johan

last: Auwerx


title: Exercise alters the single-nuclei and spatial transcriptional profiles of mouse aging brain

city: Shanghai

first: Kai

last: Zhang

address: No. 600 Yishan Road

institute: Shanghai Jiao Tong University

summary: Aging drives a progressive decline in cognition that may be delayed by exercise (Ex). Whether and how Ex induces changes in molecular and spatial signatures of aging across the brain remains little known. Herein, we assessed the effects of Ex against cognitive aging, and characterized the molecular and spatial changes by aging and upon Ex across the brain at the single-nuclei resolution. Overall, Ex demonstrated cognitive benefits in old mice and largely protected the brain cells against aging, especially the neurons. Ex regulated the inhibitory neuron-specific aging-associated genes Alcam, Cacna2d3, and Foxp2, and reorganized the spatial distribution of cells across the aging brain, which may collectively contribute to the rejuvenation of cognitive function in aged mice. This study provides invaluable insights into Ex-induced benefits against brain aging.

overall_design: To explore the effects of Ex on brain aging, and to investigate whether and how Ex induces changes in molecular and spatial signatures of aging across the brain.

first: Xue

last: Xie

first: Hongyu

last: Yan

first: Wenying

last: Xu

first: Fahuan

last: Song

first: Liwen

first: Lixian

last: Jiang

first: Yuxuan

last: Qian

first: Xiaolei

last: Yi

first: Wei

first: Xiaojun

last: Cai

first: Yuanyi


title: Condensin Accelerates Long-Range Intra-Chromosomal Interactions

city: State College

first: Yi

address: 406 SOUTH FREAR, UNIVERSITY PARK

institute: Penn State University

summary: The 3D genome organization plays a key role in regulating interactions among chromosomal loci. While Chromosome Conformation Capture (3C)-based methods have provided static snapshots of chromatin architecture, the kinetics of chromosomal encounters in live cells remain poorly characterized. In this study, we employ Chemically Induced Chromosomal Interaction (CICI) to measure encounter times between multiple loci pairs in G1-arrested budding yeast. Our results show that chromosome motion closely follows the Rouse polymer model, with similar diffusion parameters at all tested loci. Surprisingly, we find that long-range intra-chromosomal encounters occur significantly faster than inter-chromosomal encounters at similar 3D distances. Using targeted depletion experiments, we identify condensin, but not cohesin, as the complex responsible for these rapid intra-chromosomal interactions. This is further supported by Hi-C analysis, which reveals that condensin promotes long-distance intra-chromosomal interactions in G1 yeast. Through polymer simulations, we estimate that condensin extrudes chromatin at ~2 kb/s with a density of one complex per 1-2 Mb and a processivity of 120-220 kb. These findings uncover a novel role for condensin in shaping the interphase genome organization and provide new insights into chromosomal search dynamics in vivo.

overall_design: Hi-C experiments are performed on G1-arrested, WT yeast strain and SMC4-AID strains with/without auxin (IAA).

first: Fan

last: Zou

first: Timothy

last: Földes

first: Henrik

middle: D

last: Pinholt

first: Courtney

last: Smith

first: Leonid

last: Mirny

first: Lu

last: Bai


title: A cohort of mRNAs undergo high-stoichiometry NSUN6-mediated site-specific m5C modification to promote breast cancer metastasis

city: Memphis

first: Beisi

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

overall_design: RNA-seq were performed on MDA-MB-231 breast cancer cell line for both control and NUN6 knockdown to identify NSUN6 downstream target genes.

first: Yuan-Yuan

first: Cai-Tao

last: Li

first: You-Jia

last: Zhou

first: Hao

first: Jing

first: Qing-Ping

last: Xiong

first: Wenze

last: Huang

first: Qiangfeng

first: Yangfei

last: Xiang

first: En-Duo

last: Wang

first: Ru-Juan

last: Liu


title: ATAC-seq profiling of mutated MORC2 overexpression in MORC2-knocked-out HEK293T cells

first: Gordon

last: Smyth

overall_design: MORC2 knockout cell lines were contructed from the HEK293T cell line using two different sgRNAs. Plasmid were then used to restore MORC2 expression, either of WT MORC2 or of two mutated MORC2 variants. ATAC-seq profiling was conducted in duplicate on knock-out HEK293T cell lines with (i) a plasmid carrying MORC2-GFP (WT), (ii) a plasmid carrying MORC2 phosphodead-GFP (S6A), and (iii) a plasmid carrying MORC2 phosphomimetic-GFP (S6D).

first: Pedro

last: Baldoni


title: Gene expression profile at the single cell level of hematopoietic stem/progenitor cells (HSPCs) derived from iPSC at day 12 of differentiation; and from erythroid cultures derived from HS/PC-iPSC at day 4

status: Public on May 02 2025

city: Birmingham

first: Peter

last: Keane

address: Vincent Drive

department: Institute for Cancer and Genomic Sciences

institute: University of Birmingham


title: Gene expression profile at the single cell level of hematopoietic stem/progenitor cells (HSPCs) derived from iPSC at day 12 of differentiation; and from erythroid cultures derived from HS/PC-iPSC at day 4 (RNA-Seq)

summary: Myelodisplastic syndromes are a oligoclonal disease starting at the level of the stem/progenitor compartment. We use scRNAseq to determine the transcriptome changes and clonal evolution of MDS low and high risk

overall_design: iPSC were differentiated for 12 days towards HSPCs  using StemDiff Hematopietiese media. Erythroid cultures were derived from these HS/PC-iPSC and scRNAseq performed at day 4 of erythroid differentiation (cultured with SCF, IL3 and EPO)

first: Paloma

last: Garcia

first: Carl

last: Ward


title: Chromatin interaction maps of human arterioles reveal new mechanisms for the genetic regulation of blood pressure [snRNA-seq]

first: Yong

overall_design: We generated data for single-nucleus gene expression of human arterioles.

first: Rajan

last: Pandey

first: Qiongzi

last: Qiu

first: Pengyuan

first: Hong

last: Xue

first: Jingli

first: Bhavika

last: Therani

first: Rong

last: Ying

first: Kristie

last: Usa

first: Michael

last: Grzybowski

first: Chun

last: Yang

first: Manoj

last: Mishra

first: Andrew

last: Greene

first: Allen

last: Cowley Jr

first: Sridhar

last: Rao

first: Aron

last: Geurts

last: Widlansky

first: Mingyu

last: Liang


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

city: Boston

first: Johannes

last: Wedel

address: 300 Longwood Ave

institute: Boston Children's Hospital

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

last: Kong

first: David

last: Briscoe


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

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

overall_design: Refer to individual Series


title: Interferon responsive high endothelial venules drive tumor tertiary lymphoid structure formation and predict response to anti-PD-1 immunotherapy in nasopharyngeal carcinoma

city: Guangzhou

first: Shangxin

last: Liu

state: Guangdong

address: No. 651 Dongfeng East Road, Yuexiu District, Guangzhou Province, China

institute: Sun Yat-Sen University Cancer Center

summary: The outcome of immune checkpoint blockade (ICB) therapy largely hinges on the antitumor immune response of tertiary lymphoid structures (TLSs), but the driver factors behind tumor TLS formation remain poorly understood. Through integrated analysis of spatial and pan-cancer single-cell transcriptomics, we reveal the characteristics of TLSs in nasopharyngeal carcinoma (NPC) and identify a subset of interferon responsive high endothelial venules (IFN-HEVs) that is responsible for the emergence of tumor-specific chemokines, especially CXCL9. Functionally, IFN-HEVs facilitate the recruitment of CD4+ T cells into TLSs via the CXCL9-CXCR3 axis. IFN-HEV-related phenotypes are strongly correlated with positive prognostic outcomes and better responses to ICB therapy. Leveraging these phenotypes, we develop a pretreatment CXCL9-TLS Response-predictive scoring system (CTRscore) to forecast the efficacy of ICB therapy and validate its predictive efficiency in three independent NPC cohorts. Our study provides biological and functional insights into the IFN-HEVs in tumor TLSs, highlighting their potential role in the development of biomarkers and predictors for the success of ICB therapy.

overall_design: Twelve FFPE tissue samples including 9 nasopharyngeal carcinoma tumours and 3 chronic nasopharyngitis tissues were analyzed by NanoString GeoMX Digital Spatial Profiling. Samples were stained with morphology markers: CD20, CD45, PanCK and processed through the Nanostring GeoMx Digital Spatial Profiler. Using morphology stains, PanCK-CD45+CD20+ tertiary lymphoid structures were collected as regions of interest (ROIs).

first: Qian

last: Zhong


title: A wave of Thetis cells imparts tolerance to food antigens early in life

status: Public on May 01 2025

city: New York

first: Chrysothemis

last: Brown

address: 417 East 68th Street

department: Immunology Program, Sloan Kettering Institute

institute: Memorial Sloan Kettering Cancer Center

summary: In the intestine, peripherally induced regulatory T (pTreg) cells play an essential role in suppressing inflammatory responses to food proteins. However, the identity of the antigen-presenting cells that instruct food-specific pTreg cells is poorly understood. We found that a subset of Thetis cells, TC IV, is required for food-specific pTreg cell differentiation. TC IV were almost exclusively present within mesenteric lymph nodes, suggesting that their presence underlies the phenomenon of oral tolerance. A wave of TC IV differentiation in the periweaning period was associated with a window of opportunity for enhanced pTreg cell generation in response to food antigens. Our findings indicate that TC IV may represent a therapeutic target for the treatment of food-associated allergic and inflammatory diseases.

overall_design: CITE-seq (gene expression and HTOs) of CD45+Lin–RORgt+CXCR6-MHCII+ cells from lymph nodes of 2-week-old Rorc_Venus-creERT2 pooled from 7 biological replicates.

first: Vanja

last: Cabric

first: Yollanda

last: Parisotto

first: Tyler

last: Park


title: dCas9 level on chromatin to validate the specificity of CRISPRi-sgRNAs

first: Elissa

middle: WP

last: Wong

address: 1275 York Avenue

department: HOPP

summary: dCas9 level on chromatin was studied after CRISPRi

overall_design: Cas9 ChIP-seq was done using 501mel cells after CRISPRi with various sgRNAs

first: Merve

last: Sahin

first: Rui

last: Yang

first: UkJin

last: Lee

first: Rohan

last: Misra

first: Effie

last: Apostolou

first: Deyou

last: Zheng

first: Yu

last: Chen

first: Christina

last: Leslie

first: Ping

last: Chi


title: Chromatin interaction maps of human arterioles reveal new mechanisms for the genetic regulation of blood pressure [Micro_C]

first: Yong

overall_design: We generated data for global chromatin conformation of human arterioles or tissue components of human arterioles.

first: Rajan

last: Pandey

first: Qiongzi

last: Qiu

first: Pengyuan

first: Hong

last: Xue

first: Jingli

last: Wang

first: Bhavika

last: Therani

first: Rong

last: Ying

first: Kristie

last: Usa

first: Michael

last: Grzybowski

first: Chun

first: Manoj

last: Mishra

first: Andrew

last: Greene

first: Allen

last: Cowley Jr

first: Sridhar

last: Rao

first: Aron

last: Geurts

last: Widlansky

first: Mingyu

last: Liang


title: Gene expression analysis on melanoma cell line after NIPBL depletion

first: Elissa

last: Wong

summary: Effects on gene expression was analyzed after knockdown of NIPBL in melanoma cell lines 501mel.

overall_design: RNA-seq was performed on shLuc, shNIPBL_#4, shNIPBL_#5 knockdown cells for 501mel.

first: Merve

last: Sahin

first: Rui

last: Yang

first: UkJin

last: Lee

first: Rohan

last: Misra

first: Effie

last: Apostolou

first: Deyou

last: Zheng

first: Yu

last: Chen

first: Christina

last: Leslie

first: Ping


title: HDL-bound S1P affects the subventricular niche and early neuropathological features of Alzheimer’s disease

city: Daegu

first: Hee Kyung

last: Jin

address: 80 Daehakro, Buk-gu

country: South Korea

institute: Kyungpook National University

summary: Circulating blood factors have an important impact on the homeostasis of the adult ventricular-subventricular (V-SVZ) and subgranular zones (SGZ), which contains neural stem cells (NSCs) crucial for sustained neurogenesis. Circulating sphingosine-1-phosphate (S1P) bound to apolipoprotein M (ApoM), a principal protein component of high-density lipoproteins (HDL), is an important circulating factor involved in various biological processes, but its specific role in neurogenic niches is poorly understood. Herein, we show that deficiency of the blood ApoM-S1P complex results in impairment of the SVZ-NSC pool, neurogenesis, ependymal cell polarity, and cerebrospinal fluid flow, leading to olfactory dysfunction and ventricular enlargement, early neuropathological features of Alzheimer’s disease (AD). Moreover, enhancement of the complex significantly improved these defects by activating S1P1 receptor signaling in NSCs of the V-SVZ. Thus, these data reveal new insights into the pathogenic mechanisms associated with early neuropathological features of AD and suggest the potential of using the blood ApoM-S1P complex as a diagnostic and therapeutic target for early AD.

overall_design: To investigate the mechanism of ApoM-S1P-S1PR1 signaling in SVZ-NSCs, we treated SVZ-NSCs from both control mice and S1PR1-deficient mice with ApoM-HDL or ApoM+HDL

first: Byung

last: Choi

first: Jae-sung

last: Bae

first: Hee


title: The transcription factor IRF-5 is an essential metabolic checkpoint in CD8 T cells during chronic infection

city: Laval

first: Simona

last: Stager

state: Quebec

address: 531 Boul. des Prairies

department: Centre Armand-Frappier

institute: INRS

summary: Numerous transcription factors are involved in promoting an intricate gene expression program that leads to CD8 T cell exhaustion. Here, we found that the transcription factor IRF-5 is involved in limiting functional exhaustion of murine CD8 T cells by regulating the cell cycle and contributing to sustaining the mitochondrial functions and oxidative phosphorylation during the chronic stage of LCMV Cl13 infection. CD8 T cells lacking IRF-5 display reduced survival capacity and show increased signs of functional exhaustion during the chronic stage of infection. IRF-5-deficiency also resulted in a severely defective lipid metabolism, in an increased mitochondrial ROS production, and in the reduced capacity to produce ATP. Additionally, we observed increased lipid peroxidation in CD8 T cells lacking IRF-5, when compared with WT cells. These findings identify IRF-5 as a pivotal metabolic checkpoint in CD8 T cells during the chronic stages of infection and highlight its role in protecting cells from lipid peroxidation.

overall_design: RNA-seq profiling of adoptively transferred wildtype and Irf5-/- p14 CD8 T cells from male and female mice 21 days post-infection with LCMV cl13.

first: Linh Thuy

last: Mai

first: Sharada

last: Swaminathan

first: Trieu Hai

last: Nguyen

first: Etienne

last: Collette

first: Tania

last: Charpentier

first: Liseth

last: Carmona-Pérez

first: Hamza

last: Loucif

first: Alain

last: Lamarre

first: Krista

last: M. Heinonen

first: David

last: Langlais

first: Jörg

last: H. Fritz

last: Stäger


title: Augment proteasome inhibitor efficacy activates CD8+ T cell-mediated antitumor immunity in breast cancer

city: Macau

first: Dongyang

last: Tang

address: Keyan Street

institute: University of Macau

summary: Although three proteasome inhibitors have been used for liquid tumor treatment, their effectiveness against solid tumors remains inadequate. To address this issue, we employed a drug combination strategy and discovered that ammonium tetrathiomolybdate (TM) and AMD3100 can sensitize solid cancer cell lines to proteasome inhibitors. Mechanistically, we found that TM and AMD3100 reduce proteasome activity by decreasing the protein level of PSMB5. This reduction occurs through the activation of the AMPK pathway, which inhibits STAT3 phosphorylation. Notably, our in vivo studies revealed that drug combinations retarded tumor growth dependent on CD8+ T cells. The combination of bortezomib with TM or AMD3100 induced cancer cell antigen presentation and the production of CCL5, which together stimulated the recruitment and generation of cytotoxic CD8+ T cells. This study identifies new synergistic lethal pairs that enhance the effectiveness of bortezomib-centered therapy against breast cancer.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: HCC1937 cells treated with vehicle, 10μM TM or 10μM AMD3100 were collected for RNA-Seq. MDA-MB-231 cells treated with 10nM Bortezomib combined with 10μM TM or 10μM AMD3100 were collected for RNA-Seq. 4T1 tumor implanted into Balb/c mice were treated with 1mg/kg bortezomib every 4 days combined with 0.05mg/ml TM in drinking water or 5mg/kg AMD3100 every 2 days and collected for RNA-Seq.

first: Chuxia

last: Deng


title: Pyruvate kinase M2 activation reprograms mitochondria in CD8 T cells, enhancing effector functions and efficacy of anti-PD1 therapy

city: Washington

first: Lu

last: Jin

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University

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


summary: Mitochondria regulate T cell functions and response to cancer immunotherapy. We show that pharmacologically induced PKM2 activation enhances mitochondria-dependent effector functions in mouse and human CD8 T cells and CAR-T cells. Multi-omics analysis and 13C-glucose tracer experiments showed that PKM2 activation alters one-carbon metabolism with decreased levels of methionine leading to hypomethylation of mitochondrial and nuclear DNA and enhanced expression of genes supporting mitochondrial biogenesis and respiratory complex formation in CD8 T cells. Functionally, PKM2 activation increased the recall responses and anti-tumor functions of CD8 T cells after adoptive cell therapy. Using preclinical melanoma and colon cancer models, we found that PKM2-agonist induced CD8 T cell-dependent anti-tumor responses that synergized with PD1 blockade therapy. Immunologically, PKM2 agonists resulted in enhanced activation and decreased exhaustion of effector T cells while reducing the numbers of suppressive FoxP3+ Treg cells in the tumor microenvironment. Anti-PD1 combination further enhanced the frequency and activation of tumor specific CD8 T cells in the tumors. Together, we show that PKM2 agonism modulates mitochondrial structure and function, leading to enhanced effector functions of cytotoxic lymphocytes. Hence, targeting PKM2 via pharmacologically available small molecules can be a clinically viable strategy for the enhancement of therapeutic potential of in-situ immune responses, adoptive cell therapy, and immune checkpoint blockade therapy

overall_design: There are 4 experimental group. Isolated CD8 T cells from OT1 mice supplemented with 30 international units (IU) of IL-2, activated with Ova peptide (0.5 μM) for 24h and 48h, and activated with Ova peptide (0.5 μM) in combination with TEPP46 for 24h and 48h, each experimental group has 4 biological replicates.

first: Seyedeh Sahar

last: Farsani

first: Jignesh

last: Soni

first: Anil

last: Yadav

first: Shivani

last: Bansal

first: Tian

last: Mi

first: Vivek

last: Verma


title: Transcriptomic changes of the aging choroid plexus in wistar rats.

city: Copenhagen

first: Søren

middle: Norge

last: Andreassen

state: Region Hovedstaden

address: Blegdamsvej 3

department: Department of Neuroscience

country: Denmark

institute: University of Copenhagen

summary: Choroid plexus is the main producer of cerebrospinal fluid (CSF). It is speculated that CSF production decreases with aging. We are investigating the transcriptomic changes happening in the aging choroid plexus together with quantative measurements of the CSF production to elucidate the possible molecular mechanisms for these CSF production changes.

overall_design: Differential expression analysis of the aging choroid plexus at 1, 3, 6, 12, 18, 24 months old in wistar rats.

middle: N

first: Nanna

last: MacAulay


overall_design: Genomic DNA was isolated from CD8 T cells after activation in the presence or absence of TEPP46 and treated with bisulfite by the EZ DNA Methylation gold kit (Zymo Research). There are 3 biological replicates per experiment group

middle: K


title: Microtopography-induced changes in cell nucleus morphology enhance bone regeneration by modulating the cellular secretome

city: Evanston

first: Xinlong

last: Wang

address: 2145 Sheridan Road

institute: Northwestern University

summary: To investigate the influence of micropillar implants on bone regeneration, we created two critical size cranial wound repair model using implants with flat and micropillar surface topography

overall_design: We performed spatial transcriptomics using the regenerated tissues with the different treatments

first: Yiming

last: Li

first: Zitong

last: Lin


title: Identification of CD84 as a potent survival factor in acute myeloid leukemia

city: Duarte

first: Mariam

last: Murtadha

address: 1500 E. Duarte Rd

institute: City of Hope

summary: Acute myeloid leukemia (AML) is an aggressive and often deadly malignancy associated with proliferative immature myeloid blasts. Here, we identified CD84 as a critical survival regulator in AML. High levels of CD84 expression provide survival advantage to leukemia cells, whereas CD84 downregulation disrupts their proliferation, clonogenicity and engraftment capabilities in both human cell lines and patient derived xenograft cells. Critically, loss of CD84 also markedly blocks leukemia engraftment and clonogenicity in MLL-AF9 and inv(16) AML mouse models, highlighting its pivotal role as survival factor across species. Mechanistically, CD84 regulates leukemia cells’ energy metabolism and mitochondrial dynamics. Depletion of CD84 alters mitochondrial ultra-structure and function of leukemia cells, and it caused down-modulation of both oxidative phosphorylation and fatty acid oxidation pathways. CD84 knockdown induced a block of Akt phosphorylation and down-modulation of nuclear factor erythroid 2-related factor 2 (NRF2) impairing AML antioxidant defense. Conversely, CD84 over-expression stabilizes NRF2 and promotes its transcriptional activation, thereby supporting redox homeostasis and mitochondrial function in AML. Collectively, our findings indicate that AML cells depend on CD84 to support antioxidant pro-survival pathways, highlighting a previously unexplored therapeutic vulnerability of leukemia cells.

overall_design: AML cell lines (THP1 and HEL) were transduced with shCtrl and shCD84-2 at MOI=5 and cells were collected at 72 hours in Trizol and subjected to RNA-seq. shCD84-2(human) sequence is following: TTATGGCACACTGGGATAAAC Purchased from Millpore Sigma, catalog # is TRCN0000371708


title: Gene expression profile at the single cell level of hematopoietic stem/progenitor cells (HSPCs) derived from iPSC at day 12 of differentiation; and from erythroid cultures derived from HS/PC-iPSC at day 4 (ATAC-Seq)

first: Peter

last: Keane

summary: Myelodisplastic syndromes are a oligoclonal disease starting at the level of the stem/progenitor compartment. We use ATACseq to determine  changes in chromating landscape between MDS low and high risk samples.

overall_design: iPSC were differentiated for 14 days towards HSPCs  using StemDiff Hematopietiese media.  Cells were collected and sorted based on CD34+/CD45+ staining. 50,000 sorted cells were used for ATAC-seq.

first: Paloma

last: Garcia

first: Carl

last: Ward

first: Akermann

last: Ildem


title: THG-1/TSC22D4 promotes inflammatory IL-1/NF-κB pathway.

city: Tsukuba City

first: Yasuhito

last: Okano

state: Ibaraki Prefecture

address: 1-1-1 Tennodai

department: Institute of Medicine

institute: University of Tsukuba

summary: Malignant neoplasms arise within a region of chronic inflammation caused by tissue injuries. Inflammation is a key factor involved in all aspects of tumorigenesis including initiation, proliferation, invasion, angiogenesis, and metastasis. Interleukin-1 (IL-1) plays critical functions in tumor development with influencing the tumor microenvironment and promoting cancer progression. RNA sequencing analysis performed with HaCaT-HRasG12V cells, HaCaT-HRasG12V-THG-1 (WT) cells and HaCaT-HRasG12V THG-1 (S264A mutant) cells revealed that THG-1 overexpression enhances the transcription of NF-κB targets including IL1A, IL1B, TNFA, and IL8.

overall_design: A human keratinocyte HaCaT cell line was used in this study. Oncogenic HRasG12V mutant was first expressed in HaCaT cells (HaCaT-Ras). The HaCaT-Ras cells were further transduced with empty vector (-), THG-1 wild type (WT), and THG-1 (S264A). As a result, HaCaT-Ras (-),  HaCaT-Ras-THG-1 (WT), and THG-1 (S264A) cell lines were generated. Total RNA was extracted from the three cell lines cultured in DMEM containing 10% fetal bovine serum.

first: Hiroyuki

last: Suzuki


title: Mitophagy Mitigates Mitochondrial Fatty Acid β-oxidation Deficient Cardiomyopathy

city: Columbus

first: Gang

last: Xin

state: OH

address: 460 W 12th Ave

department: MI&I

institute: The Ohio State University

summary: Cardiomyocytes rely on mitochondrial fatty acid β-oxidation (FAO) for ATP production in the healthy heart but can exhibit marked metabolic flexibility in response to diverse physiological circumstances. Mutations or deficiencies in FAO enzymes can lead to a spectrum of symptoms, ranging from muscle weakness to severe cardiomyopathy, and, in some instances, culminate in neonatal/infantile mortality. It is generally believed that under FAO deficit, mitochondria encounter stress, potentially triggering the initiation of mitophagy, a process crucial for maintaining mitochondrial quality. We explored the link between FAO deficiency and mitophagy utilizing FAO-deficient mice generated through cardiomyocyte-specific deletion of the Carnitine Palmitoyltransferase 2 (CPT2). Intriguingly, our findings contradicted the prevailing hypothesis, revealing an unexpected decline in mitophagy in FAO-deficient hearts. Employing an integrated approach involving quantitative proteomics, metabolomics, and transcriptomics assays, we identified suppressed a PINK1/Parkin signaling pathway in CPT2-deficient heart tissues. Our study demonstrated that the loss of cardiac FAO impairs the PINK1 pathway by modulating the mitochondrial rhomboid protease PARL (presenilin-associated rhomboid-like protein). Furthermore, inhibiting USP30, a mitochondrial deubiquitinating enzyme antagonizing PINK1/Parkin function, restored cardiac mitophagy, thereby alleviating FAO-associated cardiac dysfunction. Notably, the deletion of USP30 conferred a significant survival advantage to FAO-deficient animals, doubling the median survival and substantially improving the maximum survival rate. The study unveiled a novel connection between FAO and PINK1-dependent mitophagy, presenting a potential therapeutic avenue for addressing FAO-deficient cardiomyopathies.

overall_design:
To gain insights into the mitophagic regulation underlying impaired FAO in the heart, we generated FAO-deficient mice with cardiomyocyte-specific deletion of the Carnitine Palmitoyltransferase 2 (CPT2) and USP30H-KO mice (Myh6-Cre/USP30fl/fl) lacking cardiac USP30
To study the loss of USP30 in the context of CPT2 deletion we also generated CPT2/USP30H-KO mice
We then conducted RNASeq from the total RNA was isolated from mouse cardiac samples of each genotypes and performed a comprehensive transcriptomic analysis

first: Nuo

last: Sun

first: Hayley

last: Barta

first: Samhita

last: Chaudhuri

first: Kangxuan

last: Chen

first: Jiacheng

last: Jin

first: Hongke

last: Luo

first: Mingchong

last: Yang

first: Judith

last: Krigman

first: Ruohan

last: Zhang

first: Shridhar

last: Sanghvi

first: Shiori

last: Sekine

first: Kedryn

last: Baskin

first: Harpreet

last: Singh

first: Pengyi

first: Toren

last: Finkel


title: Chromatin modification of melanoma cell line after CRISPRi-sgRNAs

first: Elissa

last: Wong

state: NY

summary: Chromatin modification was studied using various histone modification marks after CRISPRi in 501mel

overall_design: CUT&RUN was performed using H3K27ac and H3K9me3 antibodies using 501mel cells with CRISPRi

first: Merve

last: Sahin

first: Rui

first: UkJin

last: Lee

first: Rohan

last: Misra

first: Effie

last: Apostolou

first: Deyou

last: Zheng

first: Yu

first: Christina

last: Leslie

first: Ping

last: Chi


title: The cAMP responsive element modulator (CREM) transcription factor influences susceptibility to undernutrition and infection

city: Charlottesville

first: Audrey

last: Brown

state: Virginia

address: 345 Crispell Dr.

institute: The University of Virginia

summary: We have identified statistically significant SNPs influencing susceptibility to diarrhea due to Entamoeba histolytica infection at the locus encoding the transcription factor CREM (10p11.21; rs58000832, P=6.1x10-9; rs2148483, P=9.6x10-8) using genome wide association studies (GWAS). Considering undernutrition increases susceptibility to enteric infection, we investigated if CREM locus variants were also associated with nutritional status. Genetic analysis on birth cohorts of Bangladeshi children demonstrated that risk alleles of rs58000832 and rs2148483 were associated with lower weight-for-age z-scores at 12 months of age (rs2148483: 0.188 reduction in WAZ, P= 0.014; rs58000832: 0.135 reduction in WAZ, P= 0.001), independent of E. histolytica diarrhea. Small intestinal transcriptome data from children homozygous for the rs2148483 risk allele compared to heterozygotes demonstrated enrichment of mitochondrial function and catabolism among upregulated genes and enrichment of B-cell activation and adaptive immune pathways among downregulated genes, consistent with dual roles of the CREM locus in immunity and metabolism. Full body deletion and/or intestinal epithelial cell (IEC)-specific deletion of CREM in mice produced decreased body weight. Transcriptome analysis of cecal tissue from E. histolytica challenged mice also showed upregulation of metabolic processes in both full body and IEC-specific deletion mice. Processes with downregulated genes in full body deletion mice were enriched for myeloid cell activation and chemotaxis while immune process changes were absent when deletion was limited to IECs. These data suggest that CREM modulates both metabolism and immune function at mucosal sites.

overall_design: To determine the role of CREM mediated transcription in the cecum, we have conducted RNA-seq on both full body (CREM fl/fl CRE-ER) and intestinal epithelium specific (CREM fl/fl Vil-CRE) CREM deletion mouse models. Each tissue deletion model was compared to same sex litter mates without CRE recombinase

first: William

middle: A

last: Petri Jr


title: Microglia innate immune memory is retained after enforced repopulation [ATAC-seq]

city: Groningen

first: Bart

middle: J L

last: Eggen

address: Antonius Deusinglaan 2

country: Netherlands

institute: University Medical Center Groningen

summary: Microglia are crucial for CNS homeostasis and involved in a wide range of neurodegenerative and neuroinflammatory diseases. Systemic inflammation and infections can contribute to neurodegeneration later in life by affecting microglia. Like other innate immune cells, microglia can develop innate immune memory in response to a challenge, altering their response to future stimuli. Innate immune memory can ameliorate or worsen CNS pathology, but its persistence is unclear. Recently, several methods have been developed to stimulate microglia turnover. Here, we investigated whether colony-stimulating factor 1 (CSF1R)-dependent microglia depletion followed by repopulation reversed microglial tolerance to systemic inflammation in mice. Repopulated microglia displayed a reduced expression of homeostatic genes and genes related to mitochondrial respiration and TCA cycle metabolism and an increased expression of immune effector and activation genes. Nonetheless, the blunted inflammatory gene expression induced by the LPS-preconditioning was retained after a depletion-repopulation cycle. Our study highlights the persistence of epigenetic changes underlying microglial tolerance and indicates potential implications of microglia depletion and repopulation therapies on microglia functions.

overall_design: We pre-conditioned mice with intraperitoneal LPS (or PBS), transiently depleted microglia with BLZ945, and, after repopulation, assessed microglia gene expression by bulk RNA-seq and chromatin accessibility by bulk ATAC-seq after a secondary LPS (or PBS) challenge. 10-week-old male mice were challenged with 1 mg/kg intraperitoneal (i.p.) LPS from Escherichia coli O111:B4. For unchallenged (PP, PBP) and naïve (PL, PBL) mice, sham injections consisted of the same volume/body mass of Dulbecco’s phosphate-buffered saline (DPBS). A week after the first challenge, microglia depletion was induced by colony-stimulating factor 1 receptor (CSF1R) inhibition for five days. Microglia depletion was established with daily administration via oral gavage of the CSF1R inhibitor (CSF1Ri) BLZ945 (or Sotuletinib) at a dosage of 169 mg/kg per day. Control (non-depleted) animals were treated with the same volume/body mass of vehicle containing 20% (w/v) 2-hydroxypropyl-beta-cyclodextrin (HPβCD). Five weeks after the initial challenge, mice were similarly re-challenged with 1 mg/kg LPS or PBS (i.p.) and housed in warming cabinets for three hours before brain tissue collection. Microglia were isolated via FACS, and their chromatin accessibility was assessed by bulk ATAC-seq.

first: Bart JL

first: Tiago

last: Medeiros-Furquim


title: Microglia innate immune memory is retained after enforced repopulation [RNA-seq]

overall_design: We pre-conditioned mice with intraperitoneal LPS (or PBS), transiently depleted microglia with BLZ945 and, after repopulation, asssessed microglia gene expression by bulk RNA-seq after a secondary LPS (or PBS) challenge. 10-week-old male mice were challenged with 1 mg/kg intraperitoneal (i.p.) LPS from Escherichia coli O111:B4. For unchallenged (PP, PBP) and naïve (PL, PBL) mice, sham injections consisted of the same volume/body mass of Dulbecco’s phosphate-buffered saline (DPBS). A week after the first challenge, microglia depletion was induced by colony-stimulating factor 1 receptor (CSF1R) inhibition for five days. Microglia depletion was established with daily administration via oral gavage of the CSF1R inhibitor (CSF1Ri) BLZ945 (or Sotuletinib) at a dosage of 169 mg/kg per day. Control (non-depleted) animals were treated with the same volume/body mass of vehicle containing 20% (w/v) 2-hydroxypropyl-beta-cyclodextrin (HPβCD). Five weeks after the initial challenge, mice were similarly re-challenged with 1 mg/kg LPS or DPBS (i.p.) and housed in warming cabinets for three hours before brain tissue collection. Microglia were isolated via FACS and their gene expression were assessed by bulk RNA-seq.


title: Dietary 3-Aminobenzoic Acid Enhances Intestinal Barrier Integrity and Attenuates Experimental Colitis

city: Tokyo

first: Takahiko

last: Toyonaga

address: 3-19-18 Nishishinbashi, Minato-ku

department: Gastroenterology and Hepatology

institute: The Jikei University School of Medicine

summary: Dietary components and their metabolites produced by intestinal bacteria play a crucial role in maintaining intestinal epithelial integrity. Disrupted epithelial integrity can lead to increased permeability and chronic inflammation in the colon, known as ulcerative colitis (UC), in genetically predisposed individuals. Our data identified 3-aminobenzoic acid (3-ABA) as a key metabolite that reduces epithelial permeability and enhances barrier integrity in Caco2 cells by modulating the tight junctional regulatory pathway. Attenuated experimental colitis in mice treated with 3-ABA and decreased fecal 3-ABA in patients with UC implied the potential usefulness of 3-ABA as a novel treatment target for UC.

overall_design: To clarify the mechanism through which 3-ABA reduces epithelial permeability in Caco2 cell monlayers, we conducted a transcriptional analysis on Caco2 cells stimulated with 3-ABA.

first: Miho

last: Tanaka

first: Fumiyuki

last: Nakagawa

first: Takeo

last: Iwamoto

first: Yudai

last: Hasegawa

first: Akira

last: Komatsu

first: Natsuki

last: Sumiyoshi

first: Naoki

last: Shibuya

first: Ayaka

last: Minemura

first: Tadashi

last: Ariyoshi

first: Asami

last: Matsumoto

first: Kentaro

last: Oka

first: Masayuki

last: Shimoda

last: Saruta


title: Exercise alters the single-nuclei and spatial transcriptional profiles of mouse aging brain

city: Shanghai

first: Kai

last: Zhang

address: No. 600 Yishan Road

institute: Shanghai Jiao Tong University

summary: Aging drives a progressive decline in cognition that may be delayed by exercise (Ex). Whether and how Ex induces changes in molecular and spatial signatures of aging across the brain remains little known. Herein, we assessed the effects of Ex against cognitive aging, and characterized the molecular and spatial changes by aging and upon Ex across the brain at the single-nuclei resolution. Overall, Ex demonstrated cognitive benefits in old mice and largely protected the brain cells against aging, especially the neurons. Ex regulated the inhibitory neuron-specific aging-associated genes Alcam, Cacna2d3, and Foxp2, and reorganized the spatial distribution of cells across the aging brain, which may collectively contribute to the rejuvenation of cognitive function in aged mice. This study provides invaluable insights into Ex-induced benefits against brain aging.

overall_design: To explore the effects of Ex on brain aging, particularly cognitive aging, and to investigate whether and how Ex induces changes in molecular and spatial signatures of aging across the brain.

first: Xue

last: Xie

first: Hongyu

last: Yan

first: Wenying

last: Xu

first: Fahuan

last: Song

first: Liwen

last: Li

first: Lixian

last: Jiang

first: Yuxuan

last: Qian

first: Xiaolei

last: Yi

first: Wei

last: Gao

first: Xiaojun

last: Cai

first: Yuanyi

last: Zheng


title: The mechanotransducer Piezo1 coordinates metabolism and inflammation to promote skin regeneration.

city: Baltimore

first: Sam

last: Lee

address: 1550 Orleans Street

institute: Johns Hopkins University School of Medicine

summary: The skin has remarkable ability to grow under constant stretch. We developed a mouse model to imitate human tissue expansion to study the cellular and molecular mechanisms involved in tension-induced skin growth. We examined specific pathway changes within the entire skin at both the spatial and single-cell level. Our analysis has revealed the fractions of basal and suprabasal cells increased after expansion. We observed elevated infiltration of immune cells in the skin, suggesting a tension-induced skin inflammatory response.

overall_design: Expanded skin and nonexpanded skin of mice collected at time point PI-14 were used for analysis. Mice expanded skin with Yoda1 treatment and mice expanded skin without Yoda1 treatment collected at time point PI-7 were used for analysis. Samples from expanded tissue, nonexpanded control tissue, expanded tissue with Yoda1 treatment, and expanded tissue without Yoda1 treatment were analyzed using spatial transcriptomics.

last: Yingchao

first: Garza

last: Luis

first: Reddy

last: Sashank