title: Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish

city: Charlottesville

first: Delai

last: Huang

state: VA

address: University of Virginia

institute: UVA

summary: The often-prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes, and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish, a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells, “melanoleucophores.” To identify mechanisms underlying this conversion we used ultrastrustructural, transcriptomic, mutational and other approaches.

overall_design: Zerbrafish dorsal fins were collected from different developmental stages, different fin positions, or after different pharmacological treatments. Cells were isolated and sorted for the presence or absence of tyrp1b:palmmcherry, and analyzed by 10x scRNA seq.

first: David

last: Parichy


title: The phenylalanine-and-glycine repeats of NUP98 oncofusions form condensates that selectively partition transcriptional coactivators

status: Public on Jan 30 2025

city: Durham

first: Yiran

last: Guo

state: North Carolina

address: 3 Genome Ct

country: USA

institute: Duke University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Recurrent cancer-causing fusions of NUP98 produce higher-order assemblies known as condensates. How NUP98 oncofusion-driven condensates activate oncogenes remainspoorly understood. Here, we investigate NUP98-PHF23, a leukemogenic chimera of the FG-repeat region of NUP98 and the H3K4me3-binding PHD finger of PHF23. Our integrated analyses using mutagenesis, proteomics, genomics, and condensate reconstitution demonstrate that the PHD finger targets condensates to H3K4me3-demarcated developmental genes and the FG repeats determine condensate composition and gene activation. The FG repeats are necessary to form condensates that partition a specific set of transcriptional regulators, notably the MLL family of H3K4 methylation-writing enzymes and BRD4. The FG repeats are sufficient, when tethered to the genome, to partition these transcriptional regulators and activate genes. NUP98-PHF23 assembles chromatin-bound condensates that partition multiple positive regulators, initiating a feed-forward loop of reading-and-writing active histone modifications. This network of interactions enforces an open chromatin landscape at proto-oncogenes, thereby driving cancerous transcriptional programs.

overall_design: 748T cells, which were derived from V5-tagged NUP98-PHF23 (NP23)-induced primary murine T-cell leukemias, were subject to treatment with a WDR5-specific PROTAC degrader (MS67), in comparison to DMSO, to remove WDR5, followed by CUT&Tag for V5-NP23, as well as the associated cofactors and chromatin modifications. Spikein controls were added to all samples for normalization before CUT&Tag.

first: Greg

last: Wang


title: Analysis of The Senescence Secretome During Zebrafish Retina Regeneration

city: Nashville

first: Gregory

last: Konar

state: TN

address: 1161 21st Ave S

department: Biological Sciences

institute: Vanderbilt University

type: Expression profiling by high throughput sequencing

summary: Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently, we discovered that this process is aided by a population of damage-induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype (SASP), senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However, the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here, we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors after retina injury, including two distinct acute damage regimens, as well as a chronic, genetic model of retina degeneration. We discovered a 31 factor “Regeneration-associated Senescence Signature” (RASS) that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated after damage. Among these, we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration after both acute and chronic retinal damage.

overall_design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT-263 senolytic agents. Whole retinas were collected at 3, 12, and 20 days post injury and samples were collected using Trizol based RNA extraction techniques.

middle: J

first: Kyle

middle: T

last: Vallone

first: Tu

middle: D

last: Nguyen

first: James

middle: G

last: Patton


title: ATOH8 confers the vulnerability of tumor cells to ferroptosis by repressing SCD expression [RNA-Seq]

city: shanghai

first: Huixiang

last: Xiao

state: shanghai

address: pujian road 160

country: China

institute: shanghai jiaotong university

summary: Ferroptosis, a non-apoptotic programmed cell death triggered by excessive iron-dependent lipid peroxidation, plays a pivotal role in tumor progression. Significant progress has been made in elucidating the role of transcription factors in the regulation of ferroptosis. Nevertheless, the identification of the key transcription factor responsible for inducing ferroptosis remains elusive. In this study, we discovered that ATOH8 is upregulated in prostate cancer cells treated with the ferroptosis inducer. Overexpression of ATOH8 increased the vulnerability of prostate cancer to ferroptosis, while ATOH8 deletion promotes ferroptosis evasion. Mechanistically, ATOH8 suppresses the transcription of SCD, reducing the synthesis of monounsaturated fatty acids that confer resistance to ferroptosis. Additionally, ATOH8 works in conjunction with the E protein E47 to form a transcriptional repression complex that inhibits SCD transcription. Furthermore, we discovered that EZH2 epigenetically suppresses the expression of ATOH8 through DNA methylation and H3K27 methylation. Interestingly, EZH2 was found to be downregulated in ferroptosis, resulting in an upregulation of ATOH8. Pharmacological inhibition of EZH2 combined with ferroptosis inducer significantly suppresses prostate cancer growth in vitro and in vivo. Together, our findings unveil that EZH2-mediated ATOH8 downregulation promotes ferroptosis evasion and suggest that pharmacological manipulation of EZH2 and ATOH8 is a promising therapeutic strategy for prostate cancer.

overall_design: To screen new ferroptosis regulator, we treated DU145 cells with RSL3 for 24 hours. Morever, we overexpressed ATOH8 in DU145 cells. We then performed gene expression profiling analyzing data obtained from RNA-seq of DU145_DMSO, DU145_RSL3, DU145-oeCTRL and DU145_oeATOH8 cells. We also performed ChIP-seq to explore the potential target gene of ATOH8 and TCF3 in DU145_oeATOH8 and DU145_oeTCF3 cells, respectivelly.

first: Huan

last: Hou

first: Xinxing

last: Du

first: Wenyun


title: Angiogenic and Immune Predictors of Neoadjuvant Axitinib Response in Renal Cell Carcinoma with Venous Tumour Thrombus

city: Cambridge

middle: O

last: Jones

state: Cambridgeshire

address: Robinson Way

country: United Kingdom

institute: University of Cambridge

summary: Venous tumour thrombus (VTT), where the primary tumour invades the renal vein and inferior vena cava, affects 10-15% of renal cell carcinoma (RCC) patients. Curative surgery for VTT is high-risk, but neoadjuvant therapy may improve outcomes. The NAXIVA trial demonstrated a 35% VTT response rate after 8 weeks of neoadjuvant axitinib, a VEGFR-directed therapy. However, understanding non-response is critical for better treatment. We conducted a multiparametric investigation of samples collected during NAXIVA using digital pathology, flow cytometry, plasma cytokine profiling and RNA sequencing. Responders had higher baseline microvessel density and increased induction of VEGF-A and PlGF during treatment. A multi-modal machine learning model integrating features predicted response with an AUC of 0.868, improving to 0.945 when using features from week 3. Key predictive features included plasma CCL17 and IL-12. These findings may guide future treatment strategies for VTT, improving the clinical management of this challenging scenario.

overall_design: Sequencing data from the 16 of the patients in the NAXIVA clinical trial (NCT03494816) was used to find RNA biomarkers before treatment started to predict response to neoadjuvant axitinib.

first: Johanna

last: Barbieri

first: Abigail

middle: R

last: Edwards

first: Rebecca

last: Wray


title: Hoxblinc lncRNA reprograms CTCF-independent TADs to drive leukemic transcription and HSC dysregulation in NUP98 fusion transformed leukemia [ChIP-Seq]

status: Public on Jan 31 2025

city: Hershey

first: Suming

state: PA

address: 500 University Dr.

department: Pediatrics

institute: Penn State College of Medicine

summary: We found NUP98 fusions activate Hoxb-associated lncRNA, HoxBlinc that occupies homeotic/oncogenic topologically associated domain (TAD) boundaries in malignant hematopoiesis. Aberration of HoxBlinc led to recruitment of MLL1 complex and reorganization of homeotic/oncogenicTADs that enhanced chromatin accessibilities and aberrantly activated homeotic/hematopoietic oncogenes defined by Hoxblinc chromatin occupancies in NUP98-PHF23 related murine leukemia cells. Eliminated HoxBlinc in NUP98 fusion-driven leukemic cells resulted in loss of Hoxblinc binding, TAD integrity, recruitment of MLL complex, and MLL driven H3K4me3 and chromatin accessibility within the HoxBlinc defined domain in a CTCF independent manner, leading to inhibiting homeotic/leukemic oncogenes and mitigating NUP98 fusion-driven leukemia in xenografted mouse models. Moreover, overexpression of HoxBlinc in mouse bone marrow hematopoietic compartment developed multiple leukemia resembling NUP98-PHF23 knock-in mice via enhancing HoxBlinc binding and TAD formation to transcriptionally expanding HS/PC and myeloid/lymphoid subpopulations leading to leukemogenesis. Our studies reveal a CTCF independent role of HoxBlinc in leukemic TAD organization and oncogenic gene regulatory networks in NUP98-fusion related leukemia.

overall_design: We have finished the RNA-seq, ATAC-seq, ChIP-seq, ChIRP-seq, HiC-seq for WT and HoxBlinc KO in NUP98-PHF23 related leukemia cell lines and HoxBlinc Transgenic mice bone marrow cells to investigate HoxBlinc function in leukemogenesis. LK cells (Lin- Kit+) and LSK cells (Lin- Sca1+ Kit+) were sorted by FACS from the bone marrow of WT and HoxBlinc transgenic mice for single cell-RNA seq. We also used primary AML patient samples harboring NUP98-HOXA9 fusion for bulk RNA-seq.

first: Karina

last: Hamamoto


title: B-ALL GPR65 expression influences susceptibility to CAR-T therapy through a VEGF and macrophage-dependent mechanism [enrichement scRNA-Seq]

city: Memphis

first: Yogesh

last: Dhungana

address: 262 Danny Thomas Place

department: Department of Computational Biology

institute: St. Jude Children's Research Hospital

summary: Chimeric antigen receptor (CAR)-T cell therapy has shown promise in treating CD19+ hematological tumors, but some patients fail to respond. Here we used an immune-competent mouse model of B cell acute lymphoblastic leukemia (B-ALL) to assess clonal tumor populations with distinct responses to CAR-T cell therapy. We identified GPR65 as a determinant of tumor responsiveness to CAR-T cell therapy, with high GPR65 expression associated with a complete response. GPR65 KO tumors were resistant to CAR-T treatment in vivo. This was associated with increased tumor VEGFA expression driven by FOXO1 activation and expanded host macrophages. Either depletion of host macrophages or deletion of VEGFA from GPR65 KO tumors restored responsiveness to CAR-T cell treatment. Anti-VEGFa therapy, in combination with CD19-CAR-T, prolongs the survival of GPR65-KO tumor-bearing mice in pre-clinical models. Our results indicate that GPR65 may be a useful biomarker for tumor responsiveness to CAR-T cell therapy and further suggest VEGFA or host macrophages as therapeutic targets to improve CAR-T efficacy.

overall_design: B6 mice were injected with CR or GPR65 KO tumor cells (i.v.) followed by treatment 7 days later with 10 million activated CAR-T cells or mock PBS injection (retro-orbital). Spleens were harvested from untreated mice at day 7 and from CAR-T treated mice at day 11 after tumor engraftment. Processed spleens were stained and sorted to isolate CR or GPR65 KO tumor cells (RFP+), and the host immune cell compartment (RFP–Thy1.1–CD45.2+). Tumor and host cells from untreated mice were mixed at a 1:1 ratio. Tumor and host cells from treated mice were run independently. Each sample contained a total of 200,000 cells. Sorted cells were counted using AO/PI stain on the Luna following dual fluorescence cell sorter and mixed in a 1:1 proportion for 5’ single cell RNA seq processing. 6000 cells were targeted from each sample using the 10X Chromium Next GEM Single Cell 5’ Reagent kits v2 (Dual Index). Cells were partitioned into droplets and barcoded using the Chromium Controller using Chip K. Reverse transcription, cDNA amplification, TCR amplification, fragmentation, adapter and sample index ligation were all done following the 10X CG000331 Rev C protocol. cDNA and libraries were quantified using the High Sense DNA chip on the Agilent Bioanalyzer. Libraries were pooled and sequenced on the NovaSeq 6000 using paired end reads as recommended by 10X genomics

first: Jayadev

last: Mavuluri

first: Terrence

middle: L

last: Geiger

first: Jiyang

last: Yu


title: B-ALL GPR65 expression influences susceptibility to CAR-T therapy through a VEGF and macrophage-dependent mechanism [RNA-Seq]


title: Helicase Ded1 fine-tunes the reprogramming of gene expression conferred by inhibition of TORC1 by rapamycin.

city: Bethesda

first: Alan

last: Hinnebusch

state: Maryland

address: Building 6, 6 Center Drive, Room  233

department: SNCGE

institute: NICHD

summary: The role of Ded1 helicase is pivotal in reducing ribosomal biogenesis and inducing autophagy under TORC1 inhibition. Incorporating mutations in Ded1 rescues these effects, leading to rapamycin resistance.

overall_design: This study includes a total of 36 samples: 18 for ribosome profiling and 18 for RNA-Seq, derived from triplicates of WT Ded1, ded1-ΔN, and ded1-ΔC untreated and rapamycin-treated cells. All strains were grown in YPD at 30ºC until the OD600 reached approximately 0.4. They were then grown further for 2 hr with or without rapamycin (200ng).

first: Priyanka

last: Singh

first: Hongen

last: Zhang


title: B-ALL GPR65 expression influences susceptibility to CAR-T therapy through a VEGF and macrophage-dependent mechanism [bulk RNA-Seq]


title: RUNX1-PDGFBB-AKT pathway mediated CDK4/6 inhibitor resistance in HR+/HER2- breast cancer

city: WASHINGTON

first: Wenge

last: Zhu

state: DC

address: 800 22ND ST NW, Room 8480, Science & Engineering Hall

department: Biochemistry and Molecular Medicine

institute: George Washington University

summary: Cyclin-dependent kinases 4 and 6 (CDK4/6) are essential drivers of the cell cycle and are also critical for the initiation and progression of diverse malignancies. Pharmacological inhibitors targeting CDK4/6 have demonstrated significant activity against various tumor types such as breast cancer. However, resistance to  CDK4/6 inhibitors (CDK4/6i) (such as palbociclib) remain an immense obstacle in clinical and the underlying mechanisms have not been fully understood.  Using Conditional medium co-culture, quantitative high-throughput combinational screen (qHTCS), and genomic sequencing, we report that the RUNX1-PDGFBB-AKt pathway was significantly elevated in palbociclib-resistance cells. Inhibition of this axis can enhance the therapeutic efficacy of Palbociclib and surmount Palbociclib resistance both in vitro and in vivo. Mechanistically, we found that O-GlcNAc transferase (OGT) modifies RUNX1 with O-GlcNAcylation at Serine 252 (Ser252), thereby stabilizing RUNX1 protein expression, which is crucial in regulating PDGFBB expression. Significantly, clinical studies also confirm that RUNX1-PDGFBB-Akt pahtway was elevated in palbociclib-resistance patients. Collectively, these results reveal a previously unrecognized mechanism by which RUNX1-PDGFBB mediated palbociclib resistance, and provide valuable insights for the development of innovative therapeutic strategies in future clinical contexts.

overall_design:
To investigate the mechanism of Palbociclib resistance in breast cancer cell lines, we first generated Palbociclib-resistant (PR) cell line MCF-7 PR.
Then we compare different genes expression between MCF-7-PR cells and MCF-7 PR-siPDGFB cells by RNA seq.

first: Shuyan

last: Zhou


first: Yiran

last: Guo

summary: Cancer-associated genetic aberrations, such as the nucleoporin 98 (NUP98) gene rearrangement detected in human leukemias, often produce condensates, a type of membrane-less biomolecular assemblies. How exactly the cancer-related condensation contributes to oncogenesis remains far from clear. Here, we investigate NUP98-PHF23, a leukemia-causing chimeric protein that fuses NUP98’s sequence enriched in phenylalanine-and-glycine repeats (FG repeats, also known as intrinsically disordered region [IDR]) in-frame with PHF23’s PHD finger, a domain that specifically ‘reads’ and binds H3K4 trimethylation (H3K4me3). Our integrated analyses using protein module mutagenesis, cell imaging, genomic profiling and condensation reconstitution collectively demonstrate a multifaced role for NUP98’s FG repeats in driving fusion condensation while recruiting and co-mixing with a set of histone modifiers and chromatin remodelers, notably the MLL family of H3K4 methylation-‘writing’ enzymes. The H3K4me3-‘reading’ PHD finger and NUP98’s IDR are cooperative in mediating efficient targeting of NUP98-PHF23 and its coactivators onto leukemic genes, leading to active transcription. Together, we show that NUP98-PHF23 coordinates a set of homotypic and heterotypic interactions (IDR:IDR, IDR:coactivator and PHD:histone) to organize formation of the chromatin-bound multi-component condensates, wherein a feedforward loop involving the ‘reading’ and ‘writing’ of H3K4 methylation acts to enforce an open chromatin landscape at leukemogenic loci, thereby driving oncogenic transformation.

overall_design: In order to dissect requirement of NUP98-PHF23’s protein modules for its biological functions, we generated two function-disruptive mutants — one containing the substitution of Phe in NUP98’s FG repeats with Ala (the “FA” mutant), which was known to disrupt FG repeats-mediated LLPS, and the other containing a W362A mutation at PHF23’s PHD finger, which was reported to abolish the H3K4me3 binding and suppresses leukemogenic transformation. Next, we generated HEK293FT cells with stable expression of NUP98-PHF23 (GFP-FLAG tagged), either wild-type (WT) or mutant. Total RNAs were purified using RNeasy Plus kit (Qiagen, 74136). For RNA-seq, the RNA samples were processed using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490) and NEBNext Ultra II RNA library Prep kit (NEB, E7770) as per the manufacturer’s instructions.

first: JeongHyun

last: Ahn

first: Greg

last: Wang


title: Pre-symptomatic qPCR blood test based on Parkinson’s disease-specific angiogenin-derived transfer RNA fragments

city: Jerusalem

first: Nimrod

last: Madrer

address: The Edmond J. Safra Campus, Guvat Ram

country: Israel

institute: The Hebrew University of Jerusalem

type: Non-coding RNA profiling by high throughput sequencing

summary: Rapid, simple and reliable blood tests for Parkinson’s disease (PD) may enable pre-symptomatic diagnosis and facilitate disease-changing treatments. Here, we report escalated elevated levels of angiogenin-cleaved a disease specific group of nuclear genome-originated tRNA fragments (hereafter, PD-tRFs) carrying a unique seven-nucleotide motif in substantia nigra, cerebrospinal fluid and blood of PD patients. A blood test using RNA isolated from whole blood and dual multiplexl qPCR primers for PD-tRFs and mitochondrial-originated tRFs (MT-tRFs) successfully distinguished pre-symptomatic PD patients from controls, outperforming traditional clinical scoring (ROC-AUC of 0.86 vs. 0.73). Indicating relevance to disease symptoms, PD patients carrying GBA, SNCA or LRRK2 mutations presented elevated blood PD/MT-tRF ratios compared to mutations-carrying non-symptomatic individuals which indicates relevance to disease symptoms. Furthermore, PD-tRFs’ potential for ribosomal association predicted translational inhibition. Intriguingly, PD-tRFs levels declined both in patients’ blood following deep brain stimulation andas well as in in depolarized neuroblastoma cells where PD-tRFs presented transientlydepolirization impaired impacted ribosomal associations. Our findings facilitate a sensitive and accurate blood test for early PD.

overall_design: 37 blood samples of Parkinson's disease (PD) and controls, as well as 8 substantia nigra samples of PD patients were used to exteact short RNA. PD patients had various disease durations and Lewy bodies scores.

first: Shani

last: Vaknine

first: Alon

last: Simchovitz

first: Estelle

last: Bennett

first: Hermona

last: Soreq


title: The phenylalanine-and-glycine repeats of NUP98 oncofusion form condensates that selectively partition transcriptional coactivators

overall_design: In order to dissect requirement of NUP98-PHF23’s protein modules for its biological functions, we generated two function-disruptive mutants — one containing the substitution of Phe in NUP98’s FG repeats with Ala (the “FA” mutant), which was known to disrupt FG repeats-mediated LLPS, and the other containing a W362A mutation at PHF23’s PHD finger, which was reported to abolish the H3K4me3 binding and suppresses leukemogenic transformation. Next, we generated HEK293FT cells with stable expression of NUP98-PHF23 (GFP-FLAG tagged), either wild-type (WT) or mutant. Cells were fixed in 1% formaldehyde (Thermo Scientific, 28908) for 10min, followed by quenching with 125mM glycine for 5min. Cells were then washed twice with cold PBS added with protease inhibitors (Sigma-Aldrich, 4693132001), and then subjected to resuspension and incubation in LB1 buffer (50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100). The cell nuclei were collected for sonication using Bioruptor sonicator (Diagenode, B01020001; at high-energy setting for 45 cycles with 30s on and 30s off). Supernatant was collected after centrifugation (20,000g for 10min at 4 °C) for incubation with the dynabeads (Invitrogen, 11204D) that are pre-bound with antibodies for 8h at 4 °C. After a series of wash with LB1 buffer, LB2 buffer (10 mM Tris-HCl pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA), and LB3 buffer (10 mM Tris-HCl pH 8.0, 100mM NaCl, 1 mM EDTA, 0.5mM  EGTA, 0.1% sodium deoxycholate, 0.5% N-lauroylsarcosine), the chromatin–protein complexes bound to beads were eluted, subject to reverse crosslink overnight at 65 °C, and treated with RNase (Roche, 11119915001; 1 h at 37 °C) and then protease K (Roche, 03115828001; 2h at 55 °C). The final DNA sample, as well as 1% of input chromatin, was recovered using PCR purification kit (Qiagen, 28106). The ChIP–seq library was prepared using NEBNext Ultra II kit (NEB, E7645L) following the manufacturer’s instructions. ChIP–seq libraries were sequenced on the Nextseq 550 system using Nextseq 550 High Output Kit v2.5 (Illumina, 20024906). Drosophila spike-in chromatin for normalization was used for NUP98-PHF23 ChIP-seq as previously described(Active Motif spike-in ChIP–seq reagents, 53083 and 61686).

first: Jeong


title: B-ALL GPR65 expression influences susceptibility to CAR-T therapy through a VEGF and macrophage-dependent mechanism [scRNA-Seq]

first: Yogesh

last: Dhungana

first: Jayadev


title: Gene expression in different root types in pearl millet (Pennisetum glaucum (L.) R. Br)

status: Public on Jan 29 2025

city: Montpellier

first: Laurent

last: Laplaze

address: 911 avenue Agropolis

department: DIADE

country: France

institute: IRD

summary: Pearl millet (Pennisetum glaucum) is a cereal crop well-adapted to arid and high-temperature environments. Its root system exhibits a high degree of complexity, comprising distinct root types with specific anatomical and functional characteristics. These include the primary root, which is established during embryogenesis; crown roots, which develop at the base of the stem post-embryonically; and lateral roots, which emerge from both the primary and crown roots. In this study, we conducted a comparative analysis of gene expression profiles across these distinct root types to better understand their functional specialization.

overall_design: Pearl millet plants of the Tift23DB genotype were grown for 15 days in rhizotrons as described (Passot et al., 2018). Different root types (primary root, crown and lateral roots) were then sampled and used for RNA extraction and sequencing.

first: Alexandre

last: Grondin

first: Carla

last: de la Fuente Canto

first: Charlotte

last: Morgado


title: B-ALL GPR65 expression influences susceptibility to CAR-T therapy through a VEGF and macrophage-dependent mechanism

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

overall_design: Refer to individual Series


title: Extensive folding variability between homologous chromosomes in mammalian cells [RNA-seq]

city: Berlin

first: Alexander

last: Kukalev

address: Hannoversche Str., 28

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max-Delbrueck Center for Molecular Medicine

summary: Genetic variation and  3D chromatin structure have major roles in gene regulation. Structural differences between genotypically different chromosomes and their effects on gene expression remain ill understood, due to challenges in mapping 3D genome structure with allele-specific resolution. Here, we applied Genome Architecture Mapping (GAM) to a hybrid mouse embryonic stem cell (ESC) line with high SNP density. Given its high efficiency of haplotype phasing, GAM resolves allele-specific 3D genome structures with high sensitivity. We discovered extensive genotype-specific folding of chromosomes in compartments, topologically associating domains (TADs), long-range enhancer-promoter contacts and CTCF loops, often coinciding with allele-specific gene expression in association with Polycomb repression. We show that histone genes are expressed with allelic imbalance and involved in allele-specific chromatin contacts marked by H3K27me3. Functional analysis through conditional Ezh2- or Ring1b-knockdown shows a role for Polycomb repression in tuning histone protein levels. Our work reveals that the homologous chromosomes have highly distinct 3D folding structures, and their intricate relationships with gene-specific mechanisms of allelic expression imbalance.

overall_design: Mouse embryonic stem cells (mESC),  F123 cell line, were grown in two biological replicates. RNA was extracted and gene expression profiled by paired-end total RNA-seq.

first: Irastorza-Azcarate

last: Ibai

first: Kukalev

last: Alexander

first: Kempfer

last: Rieke

first: Bing

last: Ren

first: Pombo

last: Ana


title: QRICH1 Mediates an Intracellular Checkpoint for CD8+ T Cell Activation via the CARD11 Signalosome

status: Public on Jan 28 2025

city: Baltimore

first: Joel

middle: L.

last: Pomerantz

state: MD

address: 733 N Broadway, Room 623

department: Department of Biological Chemistry and Institute for Cell Engineering

institute: Johns Hopkins University School of Medicine

summary: Antigen receptor signaling pathways that control lymphocyte activation depend upon signaling hubs and negative regulatory proteins to fine-tune signaling output to ensure host defense and avoid potentially pathogenic hyperresponses. CARD11 is a critical signaling scaffold that translates T Cell Receptor triggering into the activation of branching NF-kB, JNK, mTOR and Akt pathways. Here we identify QRICH1 as a regulator of CARD11 signaling that mediates a previously undiscovered intracellular checkpoint for CD8+ T cell activation. QRICH1 inducibly associates with CARD11 following TCR engagement and negatively regulates CARD11 signaling to the IKK complex and NF-kB. QRICH1 binding to CARD11 occurs after TCR-induced CARD11 opening and is controlled by an autoregulatory intramolecular interaction between QRICH1 protein domains of previously uncharacterized function. Using mice deficient in QRICH1 in the T cell lineage, we show that QRICH1 controls the antigen-induced activation, proliferation, and effector status of CD8+ T cells by regulating numerous gene targets critical for CD8+ T cell function.  Our results define a previously unappreciated component of antigen receptor signaling circuitry that fine-tunes effector output in response to antigen recognition.

overall_design: To analyze differentially expressed genes between QRICH1-KO and control CD8+ T cells in response to antigen-specific stimulation, OT-1 CD8+ T cells were harvested from spleens of QRICH1-KO (QRICH1-fl/fl, OT-1/CD4-Cre) or control (QRICH1-fl/fl, OT-1/+) mice and stimulated under the following conditions: unstim; 1nM MHC Class I N4 Ova tetramer (4hrs); 1nM MHC Class I N4 Ova tetramer + 2µg/mL anti-mouse CD28 (4hrs); 1nM MHC Class I N4 Ova tetramer (24hrs) or 1nM MHC Class I N4 Ova tetramer + 2µg/mL anti-mouse CD28 (24hrs). Three replicates per stimulation condition per genotype were included.

first: Nicole

middle: M

last: Carter

first: Wihib

last: Hankore

first: Yong-Kang

last: Yang

first: Chao

first: Shelby

last: Hutcherson

first: Wyatt

last: Fales

first: Anushka

last: Ghosh

first: Piyusha

last: Mongia

first: Sophie

last: Mackinnon

first: Anna

last: Brennan

first: Robert

last: Leone


title: RNA-seq of rats in the Sham, ICH (Intracerebral hemorrhage), and EDB (Edaravone dexborneol) groups

status: Public on Jan 27 2025

city: Xinxiang

first: Han

last: Li

address: 601 Jinsui Road, Hongqi District, Xinxiang City, Henan Province

institute: Xinxiang Medical University

summary: Edaravone dexborneol (EDB) is widely recognized for its anti-inflammatory and antioxidant properties and is clinically applied in the treatment of acute cerebral infarction. Ferroptosis is a critical process in the pathophysiology of brain injury following intracerebral hemorrhage (ICH). However, it remains unclear whether EDB can ameliorate ICH through the modulation of ferroptosis. This study aimed to evaluate the function and mechanism of EDB in treatment of ICH. With a rat ICH model, animal behavior tests, histopathological staining, magnetic resonance imaging and evans blue staining were used to evaluate the neural protective function of EDB on ICH rats. The potential molecular mechanism was investigated using RNA sequencing. With the administration of Fer-1, a range of ferroptosis-related biomarkers, including Fe2+, 4-hydroxynonenal, malondialdehyde, etc., were analyzed to to ascertain whether EDB confers neuroprotective effects through the modulation of P53/GPX4 pathways to inhibit ferroptosis. Finally, the findings were further corroborated using an in vitro ICH model with a P53 inhibitor. EDB has the potential to markedly enhance nerve and motor function, mitigate pathological damage, facilitate hematoma clearance, and repair BBB injury in ICH rats. KEGG  analysis revealed that the differentially expressed genes were associated with signaling pathways, including P53 and ferroptosis. Both EDB and Fer-1 substantially reduced the concentrations of Fe2+, 4-hydroxynonenal, malondialdehyde, increased the amount of anti-oxidants, decreased the expression of P53, and concurrently upregulated the expression of GPX4. Besides, the P53 inhibitor PFT-α was observed to significantly reduce the levels of 4-HNE and lipid peroxides, while concurrently increasing the expression of GPX4. This investigation has shed light on the crucial neuroprotective role of EDB by regulating ferroptosis in ICH disease, which provided a theoretical basis for the clinical application of EDB in the treatment of ICH.

overall_design: High-throughput mRNA sequencing was utilized to analyze the mRNA expression profiles of striatal tissue samples from rats in the Sham, ICH, and EDB groups.

first: Xiang

first: Jinghui

last: Wei

first: Juntang

last: Lin


title: Cardiac differentiation roadmap for analysis of plasticity and balanced lineage commitment

city: Nijmegen

first: Rebecca

middle: Regina

last: Snabel

state: Gelderland

address: Geert Grooteplein 26-28

department: Molecular Developmental Biology

country: Netherlands

institute: RIMLS

summary: Stem cell-based models of human heart tissue and cardiac differentiation employ monolayer and 3D organoid cultures with different properties, cell type composition, and maturity. Here we show how cardiac monolayer, embryoid body, and engineered heart tissue trajectories compare in a single-cell roadmap of atrial and ventricular differentiation conditions. Using a multiomic approach and gene-regulatory network inference, we identified regulators of the epicardial, atrial and ventricular cardiomyocyte lineages. We identified ZNF711 as a regulatory switch and safeguard for cardiomyocyte commitment. We show that ZNF711 ablation prevents cardiomyocyte differentiation in the absence of retinoic acid, causing progenitors to be diverted more prominently to epicardial and other lineages. Retinoic acid rescues this shift in lineage commitment and promotes atrial cardiomyocyte differentiation by regulation of shared and complementary target genes, showing an interplay between ZNF711 and retinoic acid in cardiac lineage commitment.

overall_design:
Multiome (scRNA-seq and scATAC-seq) experiments used to build an integrated scRoadmap of in vitro cardiac differentiation.
Embryoid Body (EB) cardiomyocyte differentiation cultures.

first: Carla

last: Cofiño-Fabrés

first: Marijke

last: Baltissen

first: Verena

last: Schwach

last: Passier

first: Gert-Jan

middle: C

last: Veenstra


overall_design: scRNA-seq experiments used to build an integrated scRoadmap of in vitro cardiac differentiation.

first: GertJan


title: scRNA-seq analyses of HTO-tagged human peripheral blood mononuclear cells collected at the ART timepoint during HIV-1 disease

city: Silver Spring

first: Rasmi

last: Thomas

address: 503 Robert Grant Avenue

department: MHRP

institute: Walter Reed Army Institute of Research

summary: We investigated if differences in host gene expression modulate the size of the total HIV-1 PBMC reservoir during suppressive ART. Individuals treated with ART during acute infection who demonstrated effective viral suppression but varying frequencies of HIV-1 DNA+ cells were characterized by single-cell RNA sequencing (scRNA-seq). Differentially expressed genes and enriched pathways demonstrated increased monocyte activity in participants with undetectable HIV-1 reservoirs. This was validated in an independent study cohort comprised of 38 participants with different genetic backgrounds and HIV-1 subtype infections.

overall_design: Thawed unstimulated PBMC from 38 human participants at the ART timepoint were stained with HTO antibodies and subsequently pooled into 4 unique batches before single-cell RNA sequencing. Individual participant total HIV DNA and integrated HIV DNA measurements in PBMC were used to categorize participants into HIV reservoir groups.

first: Aviva

last: Geretz

first: Philip

middle: K

last: Ehrenberg


title: Acute Resistance Exercise Modifies Extracellular Vesicle miRNAs Targeting Anabolic Gene Pathways: A Prospective Cohort Study

city: University Place

first: WILLIAM

last: CONKRIGHT

state: WA

address: 2938 73rd Avenue Ct W

institute: US Army

summary: BACKGROUND:  Resistance training confers numerous health benefits that are mediated in part by circulating factors. Towards an enhanced molecular understanding, there is growing interest in a class of signaling biomarkers called extracellular vesicles (EVs). Extracellular vesicles support physiological adaptations to exercise by transporting their cargo (e.g., microRNA [miRNA]) to target cells. Previous studies of changes in EV cargo have focused on aerobic exercise, with limited data examining the effects of resistance exercise. We examined the effect of acute resistance exercise on circulating EV miRNAs and their predicted target pathways. METHODS:  Ten participants (5 men; age: 26.9±5.5 y, height: 1.7±0.1 m, body mass: 74.0±11.1 kg, body fat: 25.7±11.6 %) completed an acute heavy resistance exercise test (AHRET) consisting of six sets of 10 repetitions of back squats using 75% one-repetition maximum. Pre-/post-AHRET, EVs were isolated from plasma using size exclusion chromatography, and RNA sequencing was performed. Differentially expressed (DE) miRNAs between pre- and post-AHRET EVs were analyzed using Ingenuity Pathway Analysis to predict target messenger RNAs and their target biological pathways. RESULTS:  Overall, 34 miRNAs were altered by AHRET (p<0.05), targeting 4,895 mRNAs, with enrichment of 175 canonical pathways (p<0.01), including 12 related to growth/metabolism (p53, IGF-I, STAT3, PPAR, JAK/STAT, growth hormone, WNT/β-catenin, ERK/MAPK, AMPK, mTOR, and PI3K/AKT) and eight to inflammation signaling (TGF-β, IL-8, IL-7, IL-3, IL-6, IL-2, IL-17, IL-10). CONCLUSION:  Acute resistance exercise alters EV miRNAs targeting pathways involved in growth, metabolism, and immune function. Circulating EVs may serve as significant adaptive signaling molecules influenced by exercise training.

overall_design: Repeated measures study, pre- and immediate-post acute resistance exercise

first: William

last: Conkright

first: Chris

last: Kargl

first: Monica

last: Hubal

first: Dakota

last: Tiede

first: Meaghan

last: Beckner

first: Adam

last: Sterczala

first: Kellen

last: Krajewski

first: Brian

last: Martin

first: Shawn

last: Flanagan

first: Julie

last: Greeves

first: Thomas

last: O'Leary

last: Wardle

first: Amrita

last: Sahu

first: Fabrisia

last: Ambrosio

first: Brad

last: Nindl


title: Extensive folding variability between homologous chromosomes in mammalian cells

first: Alexander

last: Kukalev


title: Altered extracellular matrix structure and elevated stiffness in a brain organoid model for disease

status: Public on Jan 25 2025

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

institute: The Weizmann Institute

summary: Mutations in Lissencephaly 1 (LIS1) result in various human brain developmental diseases, such as changes in brain structure, lissencephaly, and epilepsy. RNA-sequencing data from on-chip organoids derived from human embryonic stem cells (hESCs) revealed significant changes in the expression of extracellular matrix (ECM) – related genes in LIS1+/- samples. This project examined the biomechanical properties of LIS1+/- mutated and healthy hESCs-derived cortical organoids. A rheological test using the pipette aspiration technique revealed that LIS1+/- cortical organoids are stiffer than control organoids. The increased stiffness of the LIS1+/- cortices was proportional to an increased expression of the nuclear mechano-sensing protein, Lamin A, highlighting the adverse cellular and nuclear changes underlying the stiffening of LIS1+/- organoids. To delineate the ECM composition associated with the stiffening effect in LIS1+/-, healthy and mutated hippocampal and cortical organoids were examined at the protein, mRNA, and miRNA levels. Whole RNA sequencing showed altered expression of multiple collagen-related pathways, including the 'collagens containing ECM' and the 'Collagen trimer' pathways. Differential mRNA expression has inversely correlated with the expression of their targeting miRNAs in the LIS1+/- organoids. This inverse miRNA-mRNA expression was most pronounced in genes associated with the ECM-receptor signalling pathway. At the protein level, the mutated hippocampal organoids showed unilateral, substantial increased expression of collagens and proteins involved in collagen synthesis, modification, and remodelling. Following a collagenolytic treatment with the catalytic domain of the MMP9 enzyme, the stiffness levels in the LIS1+/- organoids were reduced to control values. Overall, this work provides new information about the role of LIS1 in controlling collagen expression and the abnormal mechanical properties associated with mutation to the LIS1 gene in the development of the human cortex and hippocampus.

overall_design: Expetiment1-2: RNA-seq (exp.1) and small RNA-seq (exp.2) were used to compare the expression of 105-days-old wild type and LIS1+/- cortical organoids derived from human embryonic stem cells. In another experiment (Exp.3), RNA seq was used to compare the expression of wild-type and LIS1+/- brain organoids derived from human embryonic stem cells, with and without MMP9 catalytic domain treatment. Each biological repeat included 8-10 organoids on day 105 or 8-10 on day 18.

first: Maayan

last: Karlinski

first: Sivan

middle: B

last: Dror

first: Inna

last: Solomonov

first: Jennifer

last: Schwarz

first: Amnon

last: Buxboim

first: Irit

last: Sagi

first: Orly

last: Reiner


title: Rules of engagement for cohesin and condensin complexes during mitotic chromosome formation

city: Worcester

first: Johan

middle: Harmen

last: Gibcus

state: MA

address: 368 Plantation Street, Dekker Lab HHMI, AS5.1015,

department: Department of Systems Biology

institute: UMass Chan Medical School

summary: During mitosis interphase chromatin is rapidly converted into rod-shaped mitotic chromosomes. Using Hi-C, imaging, proteomics, and polymer modeling we determine how the interplay between loop-extruding SMC motors accomplishes this dramatic transition. We find that condensin disassembles interphase chromatin loop organization by evicting or displacing extrusive cohesin. In contrast, condensins bypass cohesive cohesins, thereby maintaining sister chromatid cohesion while separating the sisters. We also estimate a speed of loop extrusion in vivo ~1-3 kb/sec. Our new models of mitotic chromosome conformation reveal that the loop organization by a discontinuous helical condensin II scaffold can vary greatly between chromosomes. We define a small set of rules of engagement for SMC complexes that together explain how cells refold interphase chromatin into mitotic chromosomes.

overall_design:
Synchronized mitotic entry for DT40 cells that were depleted of cohesin and condensin components through auxin induced degradation. Controls include wildtype and uninduced cells.

Grant: Austrian Science Fund (FWF) grant SFB F 8804-B, rewarded to Dr. Anton Goloborodko

last: Harmen Gibcus

first: Kumiko

last: Samejima

first: Sameer

last: Abraham

first: Fernanda

last: Cisneros-Sobrano

first: Anton

last: Goloborodko

first: Job

last: Dekker

first: Leonid

last: Mirny

first: William

last: Earshaw


title: SARS-CoV-2 neurotropism induces anxiety/depression-like behaviors in mice [RNA-seq]

city: Port St. Lucie

first: Shan

last: Zhou

state: FL

address: 9801 Southwest Discovery Way

institute: Cleveland Clinic

summary: The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been linked to a wide range of neurological symptoms. In this study, the impact of SARS-CoV-2 infection on neuropsychiatric disorders in mice was investigated. To elucidate the role of SARS-CoV-2 infection in behavioral changes, we utilized a highly virulent mouse-adapted SARS-CoV-2 strain (SARS2-N501YMA30) to infect young C57BL/6 mice.

overall_design: RNA-seq profiling of whole-brain tissues from mock-infected and SARS-CoV-2-MA30-infected mice at days 0, 4, and 14.

first: Ge

last: Qian

first: Zhou

last: Shan

first: Porras

last: Jose

first: Fu

last: Panfeng

first: Wang

last: Ting

first: Du

last: Jianyang

first: Li

last: Kun


title: Effect PELO knockdown in FOCAD intact vs deleted KP4 pancreatic cancer cells

status: Public on Jan 24 2025

first: Patricia

last: Borck

address: 415 Main St

department: Cancer Program

institute: Broad Institute

summary: To invetigate how sensitive cells respond to PELO suppression we performed a bulk RNA-seq in an isogenic pair of KP4 cell line with or without FOCAD deletion.

overall_design: RNA-seq profiling of KP4 cells with either Ch2 or FOCAD CRISPR knockout alongside dox-inducible PELO knockdown.

first: Edmond

last: Chan

first: Francisca

last: Vazquez


title: Extensive folding variability between homologous chromosomes in mammalian cells [GAM]

first: Alexander

last: Kukalev

overall_design: Genome architecture mapping (GAM) of  mouse embryonic stem cells F123 (a male, hybrid cell line, derived from S129/Jae and Cast). Two biological replicates were collected. '0NP' samples have no nuclear profiles and were collected as negative controls. ‘1NP’ samples that passed quality control were merged into in-silico 3NP samples at the level of sergregation table.

first: Irastorza-Azcarate

last: Ibai

first: Kukalev

last: Alexander

first: Kempfer

last: Rieke

first: Loof

last: Gesa

first: Bing

last: Ren

first: Pombo

last: Ana


title: Transcriptomic Genes Identified in  Familial Eosinophilic Esophagitis

city: Holladay

first: Jeffery

last: Stevens

state: UT

address: 2004 East Lincoln Circ

department: Epidemiology

institute: Univristy of Utah

summary: Background and Aims: Evidence for a genetic contribution to eosinophilic esophagitis (EoE) exists from family and genome-wide association studies. Extensive investigation into rare variants contributing to EoE has not been performed. The Aim is to evaluate families with multiple cases of EoE by genomic and transcriptomic sequencing to identify genes predisposing to EoE.  Methods: We whole exome sequenced (WES) distant relative pairs (e.g., cousins) in extended EoE pedigrees and other affected relatives to identify rare, shared, potentially pathologic variants. Whole-transcriptome sequencing by RNA-Seq was performed in nuclear families with multiple EoE cases. We compared the overlap of genes from DNA and RNA sequencing for relevance to disease manifestations.  Results: WES was performed in 50 familial cases in 21 EoE extended pedigrees. We observed 219 rare, candidate predisposition variants in 210 genes with complete sharing among all affected family members. Transcriptome sequencing was performed for 43 EoE cases in 18 nuclear kindreds, including 6 relatives without EoE. We observed 10,070 total differentially expressed genes compared to controls. We identified three genes (MUC16, ADGRE1, and TENM3) with evidence of rare variant sharing and differential gene expression among all affected family members. We identified 43 other genes with partial sharing of rare variants among affected family members and with differential gene expression. Several genes identified as prominent in EoE were also differentially expressed in unaffected relatives. Conclusions: Multiple genes related to immune response, barrier dysfunction, and cell adhesion were identified in familial EoE cases and unaffected family members supporting a genetic familial predisposition and a possible multi-hit background to disease pathophysiology.

overall_design: We obtained leftover formalin-fixed, paraffin-embedded (FFPE) tissue blocks as the source for RNA; the FFPE tissue blocks were originally obtained for clinical diagnostic purposes.  All included specimens were confirmed to meet diagnostic criteria for eosinophilic esophagitis (> 15 eosinophils/high power field for the esophageal biopsy specimen) as determined by pathologists.  Individuals with a diagnosis of eosinophilic esophagitis (EoE) were selected from multiplex EoE families that included EoE cases who were 2-3 meioses apart (siblings, parent-offspring, and avuncular relationships) and included all known EoE cases in the family with esophageal FFPE specimens available. We also included unaffected family members who had no history of esophageal eosinophilia and had available esophageal biopsies that were devoid of eosinophils. All unaffected relatives were from nuclear families with at least two cases of EoE. Controls for RNA sequencing were obtained from individuals who had undergone esophageal biopsies and confirmed to have normal esophageal histology on pathology. Controls did not have autoimmune or eosinophilic disease and were not on immunosuppressive medications. Controls did not report a family history of eosinophilic disease.

first: Kristina

last: Allen-Brady

first: Kathryn

middle: A

last: Peterson

first: Mark

last: Hazel


title: Myeloid-derived suppressor cells exhibit distinct characteristics in bone marrow and blood of individuals with diffuse large B-cell lymphoma

status: Public on Jan 21 2025

city: Heraklion

first: Matthieu

middle: David

last: Lavigne

address: Nikolaou Plastira 100

country: Greece

institute: IMBB-FORTH

summary: Antitumor immune surveillance is the key feature of tumour progression and response to treatment in various malignancies, such as lymphomas. Myeloid derived suppressor cells (MDSCs) are bone marrow (BM)-derived cells with potent suppressive properties, implicated in T cell inhibition and tumour dissemination. In Diffuse Large B-cell Lymphoma (DLBCL), circulating MDSCs constitute the immunosuppressive tumor microenvironment, while the contribution of BM MDSCs in disease pathogenesis remains elusive. In the present study we aimed to evaluate both the frequencies as well as the molecular signatures of MDSCs in blood and BM from newly diagnosed DLBCL patients prior to treatment initiation and from age matched healthy donors. Circulating levels of total, monocytic (M-) and polymorphonuclear (PMN-) MDSCs were found increased in DLBCL compared to healthy control, while in DLBCL patients the BM MDSCs were significantly increased compared to blood. Transcriptomic analysis revealed significantly different molecular fingerprints to characterize circulating and BM M-MDSCs, implying that MDSCs exhibit their function with distinct mechanisms depending on the anatomical compartment. Despite that MDSC frequencies did not demonstrate any significant correlation with disease characteristics and outcome, our findings propose that gene expression profiling should be evaluated for their potential prognostic impact. Overall, the findings presented here, provide new insights in the immunosuppressive networks that operate in DLBCL and importantly propose new molecular mechanisms expressed by BM MDSCs which may be explored therapeutically.

overall_design:
RNA-seq (3′ mRNA-Seq FWD QuantSeq) profiling of Diffuse Large B-cell Lymphoma (DLBCL) monocytic (M-) Myeloid derived suppressor cells (MDSCs) in peripheral blood (PB) and Bone marrow (BM) from newly diagnosed DLBCL patients prior to treatment initiation and from age matched healthy donors. in particular, we compared peripheral M-MDSCs from DLBCL patients (d) and healthy (h) individuals, and M-MDSCs from blood and BM of DLBCL patients.

**Please note that the 'raw_counts_all_samples.txt' and GSM8744469 raw data file have been updated on May 7, 2025**

first: Panagiotis

last: Verginis

first: Electra

last: Tsagliotis

first: Christina

last: Kalpadakis

first: Athina

last: Damianaki


title: Screen of traumatic brain injury-associated genes from lncRNA m6A-modified transcriptomes in the cerebral cortex of mice after repetitive mild traumatic brain injury

status: Public on Jan 22 2025

city: Tianjing

first: Ping

last: Lei

address: No. 154, Anshan Road, Heping District, Tianjin

institute: Tianjin Medical University General Hospital

summary: N6-methyladenosine (m6A), a prevalent post-transcriptional modification in eukaryotic RNA, plays a significant role in regulating sensory experiences, learning, and injury in the mammalian central nervous system. However, the pattern of lncRNA m6A methylation in the mouse cortex following repetitive mild traumatic brain injury (rmTBI) has not been explored. This study conducted a genome-wide analysis of lncRNA m6A methylation in the mouse cortex using methylated RNA immunoprecipitation sequencing (MeRIP-Seq). Our analysis revealed 43,103 peaks were significantly upregulated or downregulated. Notably, the expression of m6A peaks indicated altered methylation and expression levels of 423 lncRNAs after rmTBI. In addition, employing METTL3 inhibitor STM2457 demonstrated that functional METTL3 was essential for repairing neural damage caused by rmTBI and influenced spatial learning and memory in rmTBI-model mice. Thus, the m6A methylation pattern of lncRNA in the mouse cortex after rmTBI identifies METTL3 as a potential intervention target for epigenetic modification following such injuries.

overall_design: This study conducted a genome-wide analysis of lncRNA m6A methylation in the mouse cortex via methylated RNA immunoprecipitation sequencing (MeRIP-Seq). In addition, by using the METTL3 inhibitor STM2457, functional METTL3 was found to be necessary for repairing neural damage caused by rmTBI and to affect spatial learning and memory in rmTBI-model mice.


title: Systems genetics reveals the influence of eQTLs in mouse embryonic stem cells on transcriptional variation later in differentiated neural progenitor cells

city: Bar Harbor

first: Selcan

last: Aydin

state: Maine

address: 600 Main Street

institute: The Jackson Laboratory

summary: Genetic variation leads to phenotypic variability in pluripotent stem cells that presents challenges for regenerative medicine. Although recent studies have investigated the impact of genetic variation on pluripotency maintenance and differentiation capacity, less is known about how genetic variants affecting the pluripotent state influence gene regulation later in development. Here, we characterized expression of 12,000 genes in a large panel of donor-matched Diversity Outbred (DO) mouse embryonic stem cell (mESC) and neural progenitor cell (mNPC) lines. Quantitative trait locus (QTL) mapping identified 4,060 expression QTL (eQTL) in mNPCs, including 2,998 local and 1,062 distant eQTL. In a comparison of mNPC and mESC eQTLs, we found that local eQTLs were more likely than distant eQTL to be detected in both cell types. Distant eQTL were largely unique to one cell type, and we mapped three mNPC-specific eQTL hotspots on Chromosomes (Chrs) 1, 10, and 11. Mediation analysis of the Chr 1 hotspot identified Rnf152 as the best candidate mediator expressed in mNPCs, while cross-cell type mediation using mESC gene expression along with partial correlation analysis strongly implicated genetic variant(s) affecting Pign expression in the mESC state as regulating the mNPC Chr 1 hotspot. These findings highlight that local mNPC eQTL are more likely than distant eQTL to be shared with mESCs; distant mNPC eQTL are numerous but largely unique to that cell type, with many co-localizing to mNPC-specific hotspots; and mediation analysis across cell types suggests that expression of Pign in mESCs shapes the transcriptome of the more specialized mNPC state.

overall_design: RNA-seq data obtained from neural progenitor cells differentiated from embryonic stem cells derived from Diversity Outbred mice

first: Daniel A.

last: Skelly

first: Hannah

last: Dewey

first: Matt

last: Mahoney

first: Ted

last: Choi

first: Laura G.

last: Reinholdt

first: Christopher L.

last: Baker

first: Steven C.

last: Munger


title: Dysregulation of mRNA expression by miR-186 overexpression in arsenic-induced skin carcinogenesis

status: Public on Jan 23 2025

city: Louisville

first: Jae Yeon

last: Hwang

state: Kentucky

address: 505 S. Hancock Street

department: Division of Medical Oncology & Hematology

institute: University of Louisville

summary: Dysregulated miRNA expression contributes to development of arsenic-induced cutaneous squamous cell carcinoma (cSCC). hsa-miR-186 (called “miR-186” henceforth) is overexpressed in arsenical cSCC tissues as well as in preclinical cell line model of arsenical cSCC. Simultaneous miR-186 overexpression and chronic inorganic trivalent arsenite (iAs; 100 nM) exposure transformed human HaCaT cell line preferentially over miR-186 exposure or iAs exposure alone. Both iAs and miR-186 regulate the expression of wide range of mRNA targets. However, how their interaction impact the transcriptome-wide mRNA expression landscape ushering in cancer is unknown. We performed longitudinal RNA-seq analysis in passage-matched HaCaT cells clones (±miR-186 overexpression) with simultaneous chronic iAs exposure (0/100 nM; 29 weeks) at 12 and 29 weeks. We determined the impact of each factor and their interaction towards differential gene expression and pathways dysregulation employing to different statistical approaches (t-statistic and 2-factor ANOVA). We show that a core set of pathways are dysregulated deterministically irrespective of the statistical approach chosen, possibly representing necessary changes for transformation. Our data suggests that each clonal line could take unique routes to dysregulate these core set of pathways necessary for transformation, highlighting the possible role of stochasticity in cancer development. We provide evidence to sift the strengths of weaknesses of each statistical methodology in providing biological understanding of events that play crucial role in carcinogenesis in large datasets with multiple contributing variables.

first: Mayukh

last: Banerjee

first: Angeliki

last: Lykoudi

first: Juw Won

last: Park

first: J Christopher

last: States


title: Interferon gamma-induction of TH1-like regulatory T cells controls anti-viral responses

status: Public on Jan 19 2025

city: Pittsburgh

first: Jian

last: Cui

address: E1002 Biomedical Science Tower,  200 Lothrop Street

department: Department of Immunology

institute: University of Pittsburgh

summary: Abstract: Regulatory T cells (Tregs) are an immunosuppressive population that are required to maintain peripheral tolerance and prevent tissue damage during immunopathology, via anti-inflammatory cytokines, inhibitor receptors and metabolic disruption. We report that Tregs acquire an effector-like state, yet remain stable and functional, when exposed to IFNγ during chronic infection with lymphocytic choriomeningitis (LCMV) and Influenza A virus (IAV). Mechanistically, Treg-restricted-deletion of the IFNγ receptor 1 (IFNGR1), but not the IL12 receptor, prevented TH1-like polarization (decreased expression of T-bet, CXCR3 and IFNγ) and promoted TH2-like polarization (increased expression of GATA-3, CCR4 and IL4). TH1-like Tregs limited CD8+ T cell effector function, proliferation and memory formation during chronic and acute infection. These findings provide fundamental insights into how Tregs sense inflammatory cues from the environment (IFNγ) during viral infection to provide immune guidance to the effector T cell response, to prevent prolonged immunoinflammatory responses and shape the quality of the memory response.

overall_design: Splenic Tregs and Tetramer+ CD8+ T cells were harvested from Foxp3Cre-YFP or Ifngr1L/LFoxp3Cre-YFP mice that remained naïve or were infected with lymphocytic choriomeningitis virus (LCMV) Clone 13 (Cl 13) for 16d

first: Angela

last: Gocher-Demske

first: Dario

last: Vignali


title: Mycoremediation of copper-azole wood preservatives by Phanerochaete chrysosporium with a focus on resistance mechanisms and azole detoxification

status: Public on Jan 17 2025

city: Champenoux

first: Annegret

last: Kohler

address: Centre Grand Est Nancy

institute: INRAE

summary: Copper-azole based formulations were widely used against fungal decay for preservation of wood timbers. While efficient for wood protection, leaching of both copper and azole within the environment has deleterious impact on soils and surface waters. Moreover, no recycling process is currently available for these wood waste. By taking advantage of the fact that certain fungi have the capacity to cope with these active compounds, we propose that some ligninolytic fungi could be good biocatalysts for detoxifying copper-azole formulations. Using the white-rot fungus Phanerochaete chrysosporium as a model, we demonstrated that the main strategies implemented by this fungus to counteract the antifungal effect of the product, in particular azoles, are the modulation of the lipids and sterols content, the maintenance of DNA integrity, detoxification of azoles by extracellular degradation likely through the Fenton chemistry, biosorption at the cell wall, efflux, and intracellular detoxification by the three-step detoxification pathway. By using comparative transcriptomics between a copper-azole formulation and a copper-quaternary ammonium formulation, we manage to identify genes specifically involved in azole resistance and detoxification within this complex system, opening perspectives for both the identification of key molecular players that could be the targets for developing long-term acquired antifungal resistance mechanisms, and the management of azoles residues by mycoremediation processes.

overall_design: Phanerochaete chrysosporium RP78 was cultivated  with or without Tanalith E3474 and Korasit KS2. Fungal mycelium was harvested post 3 days fungal growth. Libraries from total RNA (PolyA) were constructed and 2 × 150 bp Illumina NovaSeq6000 sequencing (RNA-Seq) was performed.Three biological replicates from each treatment were generated.

first: Carla

last: Vandekerkhovea

first: Sylvain

last: Darnet

first: Mélanie

last: Morel-Rouhier


title: In situ detection of PD1–PD-L1 interactions as a functional predictor for response to immune checkpoint inhibition in NSCLC.

city: Huddinge

first: Lars

last: Muhl

address: Blickagången 6

department: MedH

country: Sweden

institute: Karolinska Institutet

summary:
Introduction: Immune checkpoint inhibitors (ICIs) have transformed lung cancer treatment, yet their effectiveness seem restricted to certain patient subsets. Current clinical stratification on the basis of programmed death ligand 1 (PD-L1) expression offers limited predictive value. Given the mechanism of action, directly detecting spatial programmed cell death protein 1 (PD1)–PD-L1 interactions might yield more precise insights into immune responses and treatment outcomes.

Methods: We applied a second-generation in situ proximity ligation assay to detect PD1–PD-L1 interactions in diagnostic tissue samples from 16 different cancer types, a tissue microarray with surgically resected early-stage NSCLC, and finally diagnostic biopsies from 140 patients with advanced NSCLC with and without ICI treatment. RNA sequencing analysis was used to identify potential resistance mechanisms.

Results: In the early-stage NSCLC, only approximately half of the cases with detectable PD-L1 and PD1 expression exhibited PD1–PD-L1 interactions, with significantly lower levels in EGFR-mutated tumors. Interaction levels varied across cancer types, aligning with reported ICI response rates. In ICI-treated patients with NSCLC, higher PD1–PD-L1 interactions were linked to complete responses and longer survival, outperforming standard PD-L1 expression assays. Patients who did not respond to ICIs despite high PD1–PD-L1 interactions exhibited additional expression of stromal immune mediators (EOMES, HAVCR1/TIM-1, JAML, FCRL1).

Conclusion: Our study proposes a diagnostic shift from static biomarker quantification to assessing active immune pathways, providing more precise ICI treatment. This functional concept applies to tiny lung biopsies and can be extended to further immune checkpoints. Accordingly, our results indicate concerted ICI resistance mechanisms, highlighting the need for combination diagnostics and therapies.

overall_design: RNA-seq samples from lung cancer patients that received immune checkpoint inhibitor therapy. Samples are grouped accoding to the corresponding PLA-signal for PD1--PD-L1 interaction.

first: Amanda

last: Lindberg

first: Hui

last: Yu

first: Louise

last: Hellberg

first: Rebecca

last: Artursson

first: Jakob

last: Friedrich

first: Max

last: Backman

first: Neda

last: Hekmati

first: Johanna

last: Mattsson

first: Cecilia

last: Lindskog

first: Hans

last: Brunnström

first: Johan

last: Botling

first: Artur

last: Mezheyeuski

first: Erika

last: Broström

first: Miklos

last: Gulyas

first: Klas

last: Kärre

last: Isaksson

first: Patrick

last: Micke

first: Carina

last: Strell


title: Cellular and Immune Landscape of Chronic Liver Diseases: Insights from Immunophenotyping

status: Public on Jan 20 2025

city: Solna

first: Hong

last: Yang

state: Stockholm

address: Tomtebodavägen 23A

department: Systems Biology

institute: KTH Royal Institute of Technology/Science For Life Laboratory

summary: Background: Chronic liver disease due to alcohol-related liver disease and chronic viral hepatitis pose a substantial burden on healthcare systems. Chronic liver disease may predispose to hepatocellular carcinoma, for which therapeutic options are limited. This study aimed to explore the immune cell characteristics of the clinical conditions. Methods: Explant liver samples were collected from 25 patients for bulk RNA sequencing and flow cytometry analysis. Immune cell populations were characterized by flow cytometry from isolated hepatic and peripheral mononuclear cells. Results: Significant differences in immune cell characteristics were observed among patients with three clinical conditions. Viral hepatitis and peri-tumor samples exhibited higher hepatic B cell counts compared to alcohol-related liver disease. Additionally, chronic liver disease patients showed higher levels of CD57+ T cells, suggestive of T cell differentiation. Differential expression analysis identified several genes associated with immune regulation, including downregulation of CD27 and upregulation of granzyme B in ARLD, consistent with a highly differentiated phenotype. LAG3 and PDCD1 were upregulated in peri-tumor samples. The NK cell count was lower in peri-tumor liver specimens compared to ARLD, and an upregulation of TIGIT, an inhibitory marker, was observed in those peri-tumor specimens. Conclusion: This study contributes to the understanding of immune dynamics in chronic liver disease among different etiologies. B lymphocytes are relatively reduced in alcohol-related liver disease compared to other groups, and T cells exhibit a more differentiated subtype. The peritumor microenvironment in HCC suggests a relatively diminished presence of NK cells and a potential tendency toward increased inhibitory characteristics.

first: Shaghayegh

last: Soleimani

first: Ozgur

last: Albayrak

first: Kayra

last: Somay

first: Buket

last: Yigit

first: Burge

last: Ulukan

first: Dila

last: Atak

first: Murat

last: Akyildiz

first: Metehan

last: Gursoy

first: Elif

last: Demirtas

first: Adil

last: Mardinoglu

first: Atay

last: Vural

last: Dayangac

first: Mujdat

last: Zeybel


title: Epiregulon: Inference of single-cell transcription factor activity to dissect mechanisms of lineage plasticity and drug response

city: South San Francisco

first: Tomasz

last: Włodarczyk

state: California

address: 1 DNA Way

institute: Genentech

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

overall_design: Refer to individual Series


title: Transcriptomic profiling performed in bladder carcinomas collected from Neodurvarib clinical trial (NCT03534492)

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

summary: RNASeq profiling of bladder carcinomas from different histologies (urothelial carcinomas or squamous cell carcinomas) which were collected at different moments of the Neodurvarib-related clinical procedure (pretreatment ("SCR") or post-treatment ("Q")).  The main goals of the screening were 1) to define potential predictive/prognostic biomarkers (genes or molecular pathways) through the comparison of diagnostic samples ("SCR") according to the clinical response observed in the patients under study; ii) to evaluate the molecular changes observed in the tumors under study by comparing the profiles of diagnostic samples ("SCR") versus cystectomies ("Q"), which would be a direct consequence of the neoadjuvant therapy used in this clinical trial.

overall_design: Diagnostic samples were collected from TURBT specimens ("SCR"), just before the start of neoadyuvancy treatment with both Olaparib (PARPi, Astra Zeneca) and Durvalumab (PDL1 inhibitor, Astra Zeneca). On the other hand, samples named with "Q" indicated tumoral tissues collected from surgical procedure (cystectomy). Samples analyzed included tissues from 19 different patients, either from the TURBT, cystectomy or both surgical procedures. The arabic numbers included in the sample title indicate the id of the patient under study. No technical or biological replicates from such specimens were included in the RNA sequencing approach.

first: Sergio

last: Ruiz-Llorente

last: Graña-Castro

first: Jesús

last: García-Donas


title: Cross-sectional study of human spermatozoa mRNA from infertility study participants and proven-fertile control participants

status: Public on Jan 16 2025

city: Providence

first: Daniel

middle: James

last: Spade

state: RI

address: Box G-E5

department: Pathology and Laboratory Medicine

institute: Brown University

summary: The goal of this study was to identify mRNAs in spermatozoa that differ between idiopathic infertile men and proven-fertile men. The rationale is that there are many idiopathic infertile or subfertile men, and that semen parameters cannot reliably distinguish idopathic infertile men from fertile men. Spermatozoa contain thousands of RNAs, and the levels of those RNAs may reflect the extent of normal spermatogenesis and sperm maturation. We hypothesized that we could identify differences between two patient populations that would reflect their clinical fertility status.

overall_design: Infertility study participants (n=53) presented to Brown Urology for fertility assessment and provided a semen sample. Proven-fertile control study participants (n=14) were men who had fathered children and were presenting for vasectomy. Proven-fertile patients provided a semen sample prior to undergoing the vasectomy procedure. Sperm were isolated from semen samples, and sperm RNA was prepared using an established procedure. mRNA libraries were sequenced on an Illumina HiSeq 4000 sequencer in 150 bp paired-end format. Three infertility study participants submitted two samples, which were averaged after sequencing. Those samples are identified as "duplicates" in the sample matrix, and the description column contains the column header that was used in the supplementary file, log2_norm_count_collapsed.csv. Analysis by Wilcoxon signed-rank test identified 1,885 differentially abundant transcripts between the two study populations.

first: Xinran

last: Qi

first: Han

last: Ji

first: Enrica

last: Bianchi

first: Susan

last: Hall

first: Gabriella

last: Avellino

first: William

last: Berg

first: Priyanka

last: Bearelly

first: Mark

last: Sigman

first: Xijin

last: Wu


title: Effect of high glucose on trabecular meshwork

status: Public on Jan 15 2025

city: Indianapolis

first: Padmanabhan

middle: P

last: Pattabiraman

state: IN

address: Department of Ophthalmology, Room number 402, 1160 West Michigan Street

department: Ophthalmology

institute: Indiana University Purdue University Indianapolis

summary: The purpose of this study was to understand the effect of high glucose on trabecular meshwork using RNAseq.

overall_design: Gene expression profiling analysis for primary human trabecular meshwork cells subjected to high glucose treatent compared to normal glucose. Biological replicates (n=3) were treated with 30 mM (high glucose) or 5 mM (control/normal glucose) for 7 days and processed further for mRNAseq analysis.

first: Chevy

last: Singh

first: Avinash

last: Soundararajan


title: Effects of astrocytic absence of glucose transporter 1 (GLUT1) on the cortical astrocytic translatome

city: Zürich

first: Lukas

middle: Matthias

last: von Ziegler

address: Winterthurerstrasse 190

department: D-HESZ

country: Switzerland

institute: ETH Zürich

summary: Brain activities rely on a steady supply of blood glucose, which is shuttled into the brain by glucose transporters and used to fuel metabolic pathways and energy demands in all neural cells. Astrocytes express glucose transporter 1 (GLUT1), which is considered the key glucose uptake route for glycolytic astrocytes to ensure their metabolic support functions to neurons and other glial cells in vivo. GLUT1 deficiency causes severe developmental impairments, however, the role of GLUT1 in astroglial glucose metabolism and brain function is poorly understood. Here we examine the effect of astrocytic GLUT1 deletion on the active translatome of astrocytes in the the mouse cortex.

overall_design: GLUT1 knockout animals were compared to control animals under naïve conditions. To assess the astrocytic translatome we employed aTranslating Ribosome Affinity Purification (TRAP) approach.

first: Rebecca

last: Waag

first: Laetitia

last: Thieren

first: Fabienne

last: Rössler

first: Johannes

last: Bohacek

first: Aiman

last: Saab


title: RNA-seq analysis of rat fetal testis following in utero dipentyl phthalate exposure

first: Daniel

last: Spade

summary: RNA-seq analysis was conducted as part of an experiment investigating the effects of the phthalate, dipentyl phthalate (DPeP), on the rat fetal testis. The goal of the study was to test what gene expression responses occurred in a dose-dependent fashion, and which were most sensitive, following exposure to 1, 11, 100, or 300 mg/kg/d DPeP from gestational day (GD) 17-21.

overall_design: Timed pregnant female Sprague Dawley rats were treated with 0 (corn oil vehicle), 1, 11, 100, or 300 mg DPeP/kg/d in a 2.5 mL/kg dosing solution, by oral gavage from GD 17-21. Fetal testes were collected on GD 21. Each biological replicate consists of total RNA extrated from 1 testis or 2 pooled testes from the same litter (pregnant dam).

middle: J

first: Maansi

middle: V

last: Gupta


title: Single-cell RNA sequencing identifies Atf3+ senescent chondrocytes in the aged rat meniscus

status: Public on Jan 14 2025

city: shanghai

first: Yaohui

last: Liu

address: 500 Zhennan Road，Putuo District

department: School of Medicine

institute: Tongji University

summary: we conducted single-cell RNA sequencing (scRNA-seq) analysis using the 10x Chromium platform to uncover the cellular composition and molecular profiles of meniscal cells from different age groups.The meniscus, a fibrocartilaginous structure essential for joint load distribution, is highly susceptible to age-related degeneration. With aging, the meniscus experiences structural and functional deterioration, contributing to the progression of osteoarthritis(OA). This study aims to bridge this gap by profiling the cellular landscape and analyzing age-related changes in the aging meniscus using scRNA-seq.

overall_design:
we conducted single-cell RNA sequencing (scRNA-seq) analysis using the 10x Chromium platform to uncover the cellular composition and molecular profiles of meniscal cells from different age groups
Briefly, tissues were minced into ~1 mm³ pieces, digested with 4 mg/mL protease for 1 hour, followed by 0.25 mg/mL collagenase P for 4-6 hours. After washing with 0.04% bovine serum albumin (BSA) in phosphate-buffered saline (PBS), the cells were resuspended in 0.04% BSA and filtered through a 35 µm cell strainer. Viable cells were visually inspected, sorted via flow cytometry, and collected. Flow cytometry sorting ensured a viability threshold of >85% for single-cell RNA-seq

first: Jingyi

last: Wang

first: Zhangyi

last: Pan

first: Zheng

first: Kun

last: Tao

first: Feng

last: Yin


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

city: Boston

first: The Gene Lay Institute of

last: Immunology and Inflammation

address: 60 Fenwood Road,

institute: Brigham and Women's Hospital


title: Antcin K inhibits chondrosarcoma motility by reducing MMP-7 expression via down-regulating PI3K, Akt, mTOR and NF-κB signaling pathway

status: Public on Jan 18 2025

city: Taichung

first: Chih-Hsin

last: Tang

address: 91 Xueshi

country: Taiwan

institute: China Medical University

summary: Chondrosarcoma is recognized as the second most common form of primary bone cancer originating from cartilage. Antrodia cinnamomea is the source of the triterpenoid Antcin K, renowned for its immunomodulatory and anti-inflammatory properties. However, the therapeutic function of Antcin K on chondrosarcoma remains unclear. Our investigation found that Antcin K reduces migration and invasion in two chondrosarcoma cell lines. Finally, our study provided evidence of Antcin K as a novel candidate for inhibiting chondrosarcoma motility by inhibiting MMP-7 expression through suppressing the PI3K, Akt, mTOR, and NF-κB signaling cascades.

overall_design: To discover differentially expressed mRNAs modulated by Antcin K, JJ012 cells were treated with Antcin K (10 μM) for 24 h in the culture medium, followed by mRNA sequencing.

first: Bao-Tran

last: Nguyen


title: High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion [HiChIP]

first: Martin

last: Aryee

address: 3 Blackfan Circle, 11th Floor

department: Data Science

institute: Dana Farber Cancer Institute

summary: Cohesin-mediated DNA loop extrusion enables gene regulation by distal enhancers through the establishment of chromosome structure and long-range enhancer-promoter interactions. The best characterized cohesin-related structures, such as topologically associating domains (TADs) anchored at convergent CTCF binding sites, represent static conformations. Consequently, loop extrusion dynamics remain poorly understood. To better characterize static and dynamically extruding chromatin loop structures, we use MNase-based 3D genome assays to simultaneously determine CTCF and cohesin localization as well as the 3D contacts they mediate. Here we present CTCF Analyzer (with) Multinomial Estimation (CAMEL), a tool that identifies CTCF footprints at near base-pair resolution in CTCF MNase HiChiP. We also use Region Capture Micro-C to identify a CTCF-adjacent footprint that is attributed to cohesin occupancy. We leverage this substantial advance in resolution to determine that the fully extruded (CTCF-CTCF loop) state is rare genome-wide with locus-specific variation from ~1-10%. We further investigate the impact of chromatin state on loop extrusion dynamics and find that active regulatory elements impede cohesin extrusion. These findings support a model of topological regulation whereby the transient, partially extruded state facilitates enhancer-promoter contacts that can regulate transcription.

overall_design: We employed K562 CTCF MNase HiChIP to footprint CTCF & cohesin and investigate cohesin extrusion dynamics at the fragment level. We additionally re-sequenced the mESC RCMC libraries from Goel et al. Nature Genetics 2023 to 150bp reads (WT, DMSO, and IAA conditions for Fbn2, Klf1, and Ppm1g loci) to verify the cohesin footprint we observed in CTCF HiChIP.

first: Corriene

middle: E

last: Sept


title: High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion [RCMC]


title: ACSS2 mediates an epigenetic pathway to regulate maternal Beta-cell adaptation and progression of gestational diabetes

status: Public on Jan 26 2025

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

institute: Peking University


title: Activation and memory of the heatshock response is mediated by Prion-like domains in Arabidopsis [RNA-seq]

status: Public on Jan 13 2025

city: Grossbeeren

first: Maolin

last: Peng

address: Theodor-Echtermeyer-Weg 1

institute: Leibniz Institute of Vegetable and Ornamental Crops (IGZ) e.V.

summary: The heatshock factors (HSFs) play a crucial role in this process: but the mechanisms by which plants sense heat stress are not well understood. We find that HSFs act in a network: with sensory HSFs having a modular Prion-domain (PrD) structure that confers temperature dependent phase change behaviour.

overall_design:
To investigate the function of prion-like domains (PrDs) of HSFA1a under basal and acquired heat stress: we generated transgenic lines for PrD deletions in the HSFA1a. Plants were grown at 22 ºC and then either shifted to 37 ºC or maintained at 22 ºC.

C: no heat stress day 7 (Control)
R: recovery at 22C after 37C on day 4 for 5 min (Recovery)
T: 37C on day 7 for 5 min (Triger)
PT: 37C for 5 min on day 4 and day 7 (Primes + Triger)
QK: hsfa1abde (QK)

first: Katja

last: Jaeger

first: Yunlong

last: Lu


title: ZFP36-family RNA-binding proteins in regulatory T cells reinforce immune homeostasis [bulk RNA-seq - creERT2]

city: Cambridge

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

institute: The Babraham Institute

summary: RNA binding proteins (RBP) of the ZFP36 family limit the differentiation and effector functions of CD4 and CD8 T cells, but little is known of their expression or function in regulatory T cells (Treg). By Treg-restricted deletion of Zfp36 family members we identify the essential role of Zfp36l1 and Zfp36l2 in Treg to maintain immune homeostasis. Mice with Tregs deficient in these RBP display an inflammatory phenotype with an expansion in the numbers of type-2 conventional dendritic cells, T effector cells, T follicular helper and germinal center B cells and elevated serum cytokines and immunoglobulins. In the absence of Zfp36l1 and Zfp36l2, the pool of cycling CTLA-4 in naïve Treg was reduced, Tregs were less sensitive to IL-2 and IL-7 but were more sensitive to IFNγ. In mice lacking both RBP in Treg, the deletion of a single allele of Ifng is sufficient to ameliorate the pathology. Thus, ZFP36L1 and ZFP36L2 regulate multiple pathways that enable Tregs to enforce immune homeostasis.

overall_design: RNA-seq in tamoxifen-treated naïve and effector Treg and ex-Treg from Zfp36l1/Zfp36l2 conditional inducible KO (Foxp3-eGFP-creERT2) and Foxp3-eGFP-creERT2 controls. A loxP-flanked transcriptional repressor of a tdRFP transgene, introduced into the Rosa26 locus, was used to fate map Treg which had expressed cre, with Treg defined as CD4+RFP+eGFP+ and ex-Treg defined as CD4+ cells that were RFP+ but no longer expressed eGFP. 4-5 replicates were included for each cell type/condition.

first: Beatriz

last: Sáenz-Narciso

first: Sarah

last: Bell

middle: S

first: Ram

last: Venigalla

last: Turner


title: High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion

summary: We employed K562 CTCF MNase HiChIP to footprint CTCF & cohesin and investigate cohesin extrusion dynamics at the fragment level. We additionally re-sequenced the mouse embryonic stem cell (mESC) Region Capture Micro-C libraries from Goel et al. Nature Genetics 2023 to 150bp reads (WT, DMSO, and IAA conditions for Fbn2, Klf1, and Ppm1g loci) to verify the cohesin footprint we observed in CTCF HiChIP.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: K562 CTCF MNase HiChIP and mESC RCMC (Fbn2, Ppm1g, Klf1 loci) in WT, DMSO, and IAA conditions (150bp reads for all experiments).


title: ACSS2 mediates an epigenetic pathway to regulate maternal β-cell adaptation and progression of gestational diabetes (ATAC-seq and CUT&RUN)

summary: Maternal pancreatic β-cell state is adapted to accommodate gestation metabolism. Defects in this process may cause gestational diabetes mellitus (GDM), with risk factors including a high-calorie diet during pregnancy. However, the regulatory mechanism of maternal β-cell adaptation is largely unknown. Using single-cell transcriptome combining genetic analyses, we discovered a precise process of β-cell adaptation in mice which is associated with progression of metabolic stress-related β-cell dysfunction, increased acetyl-CoA biosynthesis, and gene element-specific histone acetylation. STAT3 recruits p300 to promote histone acetylation levels of pregnancy-associated genes, and Acetyl-CoA Synthetase 2 (ACSS2) enhances this process. High-fat feeding causes hyperacetylation of chromatin that is specifically opened during pregnancy, which results in overexpression of genes that impair β-cell functions and, consequently, hyperglycemia. However, these impairments can be rescued by β-cell-specific deletion of Acss2. Therefore, our study reveals a precise adaptation process in β-cells at the single-cell level during pregnancy and a specific epigenetic pathway that regulates this process. We also explain the epigenetic regulatory mechanism by which a high-fat diet can lead to GDM and identify ACSS2 as a potential molecular target for controlling the progression of GDM.

overall_design: ChIP-seq and ATAC-seq of mouse pancreatic islets during gestation and puerperium days.

first: Cheng-Ran

first: Yu

last: Zhang

first: Shuang

last: He

first: Xi

last: Wang

first: Xin

first: Mao-Yang

first: Xin-Xin

last: Yu


title: MYC and HSF1 Cooperate to Drive PLK1 inhibitor Sensitivity in High Grade Serous Ovarian Cancer

city: Bloomington

first: Richard

middle: L

last: Carpenter

department: Biochemistry and Molecular Biology

institute: Indiana University

summary: MYC and HSF1 genes are amplified in approximately 1/3 of ovarin cancer patients. However, their molecular interactions and cooperation to drive ovarian cancer has not been studied nor has their DNA binding patterns been compared in ovarian cancer cells. This project studies the interactions between MYC and HSF1 in ovarian cancer cells, including identifying their binding patterns across the genome for comparison. Ovarian cancer cells with MYC-HSF1 co-amplification (OVCAR8) underwent CUT&RUN for IgG, MYC, and HSF1 followed by sequencing.

overall_design: OVCAR8 cells were subjected to CUT&RUN for IgG, MYC, and HSF1 followed by sequencing.


title: Honey bee (Apis mellifera) queen quality: Host-microbial transcriptomes exploring the influence of age and hindgut symbiont Commensalibacter melissae

status: Public on Jan 10 2025

city: Tucson

first: Duan

last: Copeland

state: AZ

address: 2000 E. Allen Rd.

institute: USDA-ARS

summary: Understanding the biological mechanisms underlying extreme lifespan variation within species remains a fundamental challenge in aging research. Here, we investigated the role of gut microbiota and age in honey bee (Apis mellifera) queens combining metagenomics and transcriptomics. Analysis of 40 queen hindguts revealed that Commensalibacter melissae (Alpha 2.1) relative abundance was significantly higher in young queens compared to old queens. Using queens with the highest and lowest C. melissae relative abundance, RNA sequencing identified 1,451 differentially expressed genes associated with C. melissae abundance, twice the number associated with age alone (719 genes). Queens with high C. melissae abundance showed distinct transcriptional profiles related to stress response, protein homeostasis, and longevity-regulating pathways, particularly genes involved in oxidative stress response and cellular maintenance. Our analysis revealed complex relationships between age, C. melissae abundance, and gene expression patterns, suggesting that multiple interacting factors contribute to queen quality. These findings contribute to our understanding of host-microbe interactions in honey bee queens and highlight the intricate relationship between gut microbiota composition and host physiology in honey bees.

overall_design: 3.1 Queen Sampling Queens were sourced from two locations: the USDA-ARS Carl Hayden Bee Research Center in Arizona and a commercial beekeeping operation in Illinois. Arizona queens were all established and had survived more than one year in their colonies. Illinois queens represented a mixed-age population, consisting of both newly introduced queens (requeened in spring 2023, April-May) and older queens that had not been requeened that spring, though natural supersedure could not be ruled out.  All queens were sampled in June 2023 from robust double-deep colonies. The selected colonies were highly productive with strong populations, often reaching space limitations for both brood production and honey storage. To ensure sample quality and consistency, we specifically selected queens from thriving colonies and deliberately excluded any colonies showing signs of queen failure or irregular egg-laying patterns. Forty queens in total were collected into sterile 2.0-ml tubes and immediately frozen on dry ice and stored at −80 °C for nucleic acid extraction. 3.2 Dissections, carbonyl protein oxidation assay, and nucleic acid extractions Queens were pinned through the thorax in 70% ethanol to wash and aid in dissection.  Micro-dissection scissors were used to cut through the sides of the abdomen to access the digestive tract.  The entire digestive tract was removed and floated in ethanol to manually separate the gut tissues with dissection tweezers.  C. melissae is most abundant in the hindgut, so we targeted the ileum and rectum together for analysis.  The abdominal fat body was extracted as a single unit for use in gene expression and protein oxidation assays to assess biological aging.  Queen fat body, ileum, and rectum tissues were each bead-beaten separately in 1X TE buffer for 2 min at 30-second intervals and centrifuged at 30 seconds at 3000 rcf to recover the supernatant.  The fat body supernatant fraction was used in a protein oxidation assay to quantify the accumulation of protein carbonyl groups associated with oxidative stress and aging (Reznick and Packer, 1994),  as in Copeland et al., 2022b.   Protein oxidation was expressed as nanomoles of carbonyl groups per mg of protein.  To extract nucleic acids (DNA and RNA simultaneously) we used Qiagen AllPrep PowerViral DNA/RNA Kit (Qiagen, Hilden, Germany) following the manufacturer’s protocol and methodology also reported in Copeland et al., 2022b. 20L of ileum and 20L rectum elution from the extractions were then pooled into hindgut samples for downstream sequencing and analysis. Using purified total DNA, we quantified total bacterial abundance for the hindgut using a quantitative PCR (qPCR) assay of the 16 rRNA gene (Liu et al., 2012). We created a standard curve using a 10-fold serial dilution series of a plasmid standard containing a full-length Escherichia coli 16S rRNA gene sequence.  We amplified a 466 bp fragment in the V3–V4 region of the 16S rRNA gene using universal primer pair (5′-CCTACGGGDGGCWGCA-3′ and 5′-GGACTA CHVGGGTMTCTAATC-3′). PCR reactions were performed in triplicate on a BioRad CFX96 (Biorad, Hercules, California, US) as follows: 12 μl reactions containing 9 μl of iTaq Universal SYBR Green Supermix (BioRad, Hercules, California, US), 0.5 μl forward primer, 0.5 μl reverse primer, and 2 μl of DNA template. The cycling conditions were 95 °C for 3 min followed by 40 cycles of 95 °C for 10 s and 60 °C for 60 s. The qPCR results were expressed as the total number of 16S rRNA gene copies per DNA extraction (200 μl volume elution).  3.3 Sequencing DNA from gut tissues was amplified in a single step procedure to amplify full-length 16S rRNA (V1-V9) using degenerate primers 27F (GCATC/barcode/AGRGTTYGATYMTGGCTCAG) and 1492R (GCATC/barcode/RGYTACCTTGTTACGACTT).  PCR was performed with Q5 2× Hot Start High-Fidelity Master Mix (New England Biolabs) using the following conditions: 98℃ 30s; 98℃ 10s, 55℃ 30s, and 72℃ 2 min for 22 cycles; final extension of 72℃ for 10 min. Reactions (30 µL) were performed following manufacturer recommended master mix concentrations, with primer concentrations of 250 nM. Positive (ZymoBiomics Microbial Community DNA Standard; Zymo Research) and negative, non-template controls were included as process controls. After PCR amplification, target amplicons were purified from residual primers and primer-dimer using an AMPure bead cleanup and DNA concentrations were determined using a Qubit fluorometer (Thermo Fisher). Samples were then pooled (~ 3 ng per sample) and were prepared for sequencing by generating a SMRTbell library with a Pacific Biosciences SMRTbell prep kit 2.0 using manufacturer suggested inputs and procedures. Amplicons were sequenced on a single Pacific Biosciences 8M SMRT Cell on a PacBio Sequel IIe (Pacific Biosciences) at USDA-ARS PBARC (Hilo, HI). After sequencing, circular consensus sequences from the subreads were obtained using the SMRTLink v8.0 software. RNA from extracted samples was processed for sequencing by depleting the rRNA from samples using a RiboFree cDNA Kit (Zymo Research). Samples were pooled in equimolar concentrations and libraries were prepared for sequencing using an Adept Rapid PCR-Plus Kit (Element Biosciences). Libraries were sequenced on an Element Biosciences AVITI sequencer using an AVITI 2×150 Cloudbreak High Output sequencing kit at USDA-ARS PBARC.  One queen sample dropped out of sequencing due to insufficient cDNA yield, leading to a failure in library preparation. Consequently, this sample was excluded from downstream RNA-seq analyses. All paired-end raw reads were filtered and trimmed using Trimmomatic v0.38 (Bolger et al., 2014) with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15  MINLEN:75.  FASTQC was used to ensure quality control (Babraham Bioinformatics - FastQC A Quality Control tool for High Throughput Sequence Data).  Kraken2 was used to map and split reads to the Apis mellifera genome assembly Amel_HAv3.1 (PRJNA471592) and the gut symbiont Commensalibacter melissae (PRJNA495947) (Wood et al., 2019).  A. mellifera  reads were mapped against A. mellifera genome using STAR v2.7.10b (Dobin et al., 2013) and C. melissae reads were mapped to C. melissae genome using Bowtie 2 v2.5.2 (Langmead and Salzberg, 2012).  Gene counts were obtained using Subread v2.0.4 package FeatureCounts (Liao et al., 2013).  Genes with read counts below 4 were removed, and genes with variance less than 15% across samples were filtered out.  Final counts were normalized by employing a log2-counts per million (logCPM) transformation.

first: Copeland

last: Duan

first: Kortenkamp

last: Oliver

first: Mott

last: Brendon

first: Mason

last: Charles

first: Anderson

last: Kirk


title: Activation and memory of the heatshock response is mediated by Prion-like domains  in Arabidopsis [ChIP-seq]

first: Maolin

last: Peng

summary: The heatshock factors (HSFs) play a crucial role in this process, but the mechanisms by which plants sense heat stress are not well understood. We find that HSFs act in a network, with sensory HSFs having a modular Prion-domain (PrD) structure that confers temperature dependent phase change behaviour.

overall_design: To investigate the network of heat shock factors (HSFs) in Arabidopsis and the function of prion-like domains (PrDs) of HSFA1a, we generated transgenic lines for all 21 HSFs with flag tags and transgenic lines with PrD deletions in the HSFA1a. Plants were grown at 22 ºC and then either shifted to 37 ºC or maintained at 22 ºC.

first: Katja

last: Jaeger

first: Yunlong

last: Lu


title: RNA sequencing (RNA-seq) of Streptococcus pyogenes - group A Streptococcus (GAS) S119 strain in the presence or absence of asparagine (Asn) grown in a chemically defined medium (CDM) (van de Rijn, I. & Kessler, R.E. (1980).

status: Public on Jan 09 2025

city: Jerusalem

first: Abhinay

last: Sharma

address: Hadassah Ein Kerem

department: Department of Microbiology and Molecular Genetics

institute: Hebrew University of Jerusalem

summary: The study was conducted to test the global effect of Asn on the transcriptome of the GAS S119 strain. Transcriptome levels in the presence or absence of Asn of cultures harvested at OD600 = 0.7 were compared. We report here that a global differential expression of genes belonging to diverse functional categories, including virulence, metabolism, transporters, regulatory proteins, kinases, hypothetical proteins, and other categories.

overall_design: A total of four biological replicates for each condition were analyzed.

first: Aparna

last: Anand

first: Miriam

last: Ravins

first: Emanuel

last: Hanski


title: A nonenzymatic dependency on inositol-requiring enzyme 1 controls cancer cell cycle progression and tumor growth

status: Public on Jan 07 2025

first: Robert

last: Piskol

state: CA

department: gRED Computational Sciences

institute: Genentech Inc.

summary: Endoplasmic-reticulum resident inositol-requiring enzyme 1a (IRE1) supports protein homeostasis via its cytoplasmic kinase-RNase module. Known cancer dependency on IRE1 entails its enzymatic activation of the transcription factor XBP1s and of regulated RNA decay. We discovered that some cancer cells surprisingly require IRE1 but not its enzymatic activity. IRE1 knockdown but not enzymatic IRE1 inhibition or XBP1 disruption attenuated cell cycle progression and tumor growth. IRE1 silencing led to activation of TP53 and CDKN1A/p21 in conjunction with increased DNA damage and chromosome instability, while decreasing heterochromatin as well as DNA and histone H3K9me3 methylation. Immunoelectron microscopy detected endogenous IRE1 at the nuclear envelope. Thus, cancer cells co-opt IRE1 either enzymatically or nonenzymatically, which has significant implications for IRE1’s biological role and therapeutic targeting.

overall_design: To follow the consequences of IRE1 silencing, we performed an RNA sequencing transcriptomic analysis of AMO1 human multiple myeloma cells subjected to IRE1 vs. XBP1 knockdown. AMO1 shIRE1 cl.1, cl.3 or shXBP1 cl.1, cl.18 cells were harvested in biologic triplicates at 0, 24, 48 and 72 h after treatment with Doxycycline (Dox, 0.2 μg/ml).

first: Iratxe

last: Zuazo-Gaztelu

first: Ximo

last: Pechuan-Jorge

first: Zora

last: Modrusan

first: Avi

last: Ashkenazi