title: Ribo-lite, a method defining paired transcriptome (RNA-seq) and translatome (Ribo-seq) at low input on AML cells from mice treated with 5+3 or vehicle and fed standard amino acids (AA) or branched chain amino acid (BCAA) free diets.

status: Public on Jul 21 2025

first: Christina

last: Mayerhofer

state: MA

address: 185 Cambridge St.

department: Center for Regenerative Medicine

institute: MGH, Simches building

summary: Acute Myeloid Leukemia (AML) commonly relapses after initial chemotherapy response. We assessed metabolic adaptations in chemoresistant cells in vivo before overt relapse, identifying altered branched-chain amino acid (BCAA) levels in patient-derived xenografts (PDX) and immunophenotypically identified leukemia stem cells from AML patients. Notably, this was associated with increased BCAA transporter expression with low BCAA catabolism. Restricting of BCAAs further reduced chemoresistant AML cells but relapse still occurred. Among the persisting cells we found an unexpected increase in protein production. This was accompanied by elevated translation of 2-oxoglutarate-and-iron-dependent oxygenase 1 (OGFOD1), a known ribosomal dioxygenase that adjusts the fidelity of tRNA anticodon pairing with coding mRNA1–3 and upregulates protein synthesis in AML driving disease aggressiveness. Inhibiting OGFOD1 impaired translation processing, decreased protein synthesis and improved animal survival even with chemoresistant AML through regulation of protein synthesis. Leukemic cells can therefore persist despite the stress of chemotherapy and nutrient deprivation through adaptive control of translation while sparing normal hematopoiesis. Targeting OGFOD1 may offer a distinctive, translation modifying means of reducing the chemopersisting cells that drive relapse.

overall_design: Mice were fed branched chain amino acid (BCAA) free or standard amino acid (AA) diet to determine effects in gene expression and translated mRNAs using Riboseq, following 5+3 (cytarabine and doxorubicin) chemotherapy

first: Ernst


title: Cell Type Differences in Human Cytomegalovirus Transcription and Epigenetic Regulation with Insights into Major Immediate-Early Enhancer-Promoter Control [RNA-seq]

status: Public on Jul 22 2025

city: Iowa City

first: Jeffery

middle: L

last: Meier

state: IA

address: SW34 GH, Department of Internal Medicine, University of Iowa. 200 Hawkins Drive

department: Departments of Internal Medicine and Epidemiology

country: USA

institute: University of Iowa and Iowa City Veterans Affairs Health Care System

type: Expression profiling by high throughput sequencing

summary: Cell type differences in the human cytomegalovirus (HCMV) transcriptome may result from variations in transcription and/or post-transcription. Here we report unexpected differences in transcription and epigenetic control in late-stage HCMV infection of human differentiated NTera2 cells (D-NT2) compared to fibroblasts, using integrated functional genomic approaches (PRO-Seq, RNA-Seq, DFF ChIP-Seq, rapid viral protein degradation, and promoter mutation and function assays). In D-NT2, but not fibroblasts, RNA polymerase II initiation and elongation at several viral promoters requires viral DNA synthesis and are independent of host P-TEFb, viral IE2, or viral UL87 late transcription factor (LTF). This includes transcription from the enhancer for the major immediate early (MIE) promoter where GC-box sequence mutations increase transcription and mutations in CREB and NF-kB response elements decrease transcription. The GC-box sequence mutations also alter infected cell morphology and gene expression program, whereas mutations in CREB and NF-kB response elements do not. In D-NT2, LTF-driven promoters constitute a smaller proportion of the viral late promoter population and are generally less active. Additionally, viral genomes have more nucleosomes, potentially restricting LTF access. A TBP-IE2-nucleosome complex, with more nucleosome than in fibroblasts, covers the MIE promoter transcription start site, potentially contributing to epigenetically silence of the promoter.

overall_design: RNA-Seq library preparation is carefully detailed in the manuscript. Total RNA was isolated from biological duplicates of D-NT2, either uninfected or infected in parallel with HCMV Towne WT, N1, NB, and CK viruses for 96 h. Total RNA-Seq libraries were prepared using the Illumina TruSeq-Stranded Total RNA Prep kit with Ribo-Zero for Human/Mouse/Rat (Illumina, 200020596), according to manufacturer’s instructions. Library quality was assessed on the Agilent Bioanalyzer 2100 system, after diluting 1 μL of each DNA library to 2.5 ng/μL. Once deemed acceptable, all samples were diluted to 3 ng/μL and pooled in equimolar amounts. Sequencing was performed at the Iowa Institute of Human Genetics on the Illumina NovaSeq 6000 System using SP flow cells, generating 50-bp paired-end reads.

first: Qiaolin

last: Hu

first: Ming

last: Li

first: Mrutyunjaya

last: Parida

first: Benjamin

middle: M

last: Spector

first: Juan

middle: F

last: Santana

first: Arya

last: Zandvakili

first: David

middle: H

last: Price


title: Effect of BCAA free diet plus 5+3 chemotherapy compared to 5+3 chemotherapy alone on gene expression in mouse MLL-AF9 AML cells in vivo

city: Boston

overall_design: Mice were fed branched chain amino acid (BCAA) free or standard amino acid (AA) diet to determine effects in gene expression following 5+3 (cytarabine and doxorubicin) chemotherapy


title: Mechano-osmotic signals control chromatin state and fate transitions in pluripotent stem cells [TT-seq]

city: Münster

first: Sara

middle: A

last: Wickström

address: Röntgenstraße 20

department: Cell & Tissue Dynamics

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

summary: Acquisition of specific cell shapes and morphologies is a central component of cell fate transitions. Although the signaling circuits and gene regulatory networks regulating pluripotent stem cell differentiation have been intensely studied, how these networks are integrated in space and time with morphological transitions and mechanical deformations that occur during state transitions remains a fundamental open question. Here, we discover that stem cell fate transitions are gated by two critical signals - nuclear envelope fluctuations and osmotic stress - that emanate from growth factor signaling-controlled changes in nuclear volume and nucleoplasm viscosity/density to subsequently trigger changes in nuclear architecture and transcription. We observe that fate transitions in the early human embryo and in an in vitro pluripotency exit model are guided by rapid changes in nuclear volume and nuclear envelope mechanics. These changes alter nuclear mechanosensitivity and trigger changes in nucleoplasmic viscosity and nuclear condensates that together prime chromatin for a cell fate transition. However, while this mechanical priming accelerates fate transitions, sustained biochemical signals are required for robust induction of differentiation. Our findings uncover a critical mechanochemical feedback mechanism that integrates nuclear mechanics, shape and volume with biochemical signaling and chromatin state to control cell fate transition dynamics.

overall_design: Transient Transcriptome sequencing (TT-seq) after 30min of treatment with Hypertonic shock or Compression to investigate the role of mechano-osmotic regulation of induced pluripotent stem cell transitions

first: Yekaterina

last: Miroshnikova

first: Kaitlin

last: McCreery

first: Kai

last: Kruse


title: Beneficial infections of the enterovirus genus in patients with liver cancer

city: Bethesda

first: Farid

last: Rashidi Mehrabadi

address: Building 37, Room 3044A

institute: NCI

summary: Hepatocellular carcinoma (HCC) is a significant global cancer burden, with raising incidence and lacks a unified prevention strategy due to complex etiologies. By profiling pan-viral serological antibody repertoires using a microbial phage library among 2,647 study subjects, we have identified a unique set of viral antigens with a significantly reduced serological response in HCC patients compared to healthy individuals. Additionally, a higher serological response to these viral antigens links to better clinical outcomes of patients with chronic liver diseases and HCC. These findings are consistent across different populations across sex, ethnicity, and etiology. We have identified a common epitope (CE1) shared among reactive viral antigens from the highly prevalent rhinovirus and enterovirus families. We demonstrate that CE1 induces T-cell activation and HCC cell killing. Our results suggest that past exposures to members of the Enterovirus genus may be advantageous for cancer patients, highlighting the potential for a viral peptide-based HCC vaccine.

overall_design: Single cell RNA-sequencing and TCR sequencing” was performed on non-treated peripheral blood mononuclear cells (PBMCs) and CE1-treated PBMCs

first: Xin Wei

last: Wang

first: Lichun

last: Ma

first: Man Hsin

last: Hung


title: Mechano-osmotic signals control chromatin state and fate transitions in pluripotent stem cells [CUT&Tag]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Bulk H3K27ac CUT&Tag after 30min of treatment with Hypertonic shock or Compression to investigate the role of mechano-osmotic regulation of induced pluripotent stem cell transitions


title: Mechano-osmotic signals control chromatin state and fate transitions in pluripotent stem cells [bulk RNA-seq]

overall_design: Total RNA sequencing was performed on iPS cells 24 h post recovery from 30 min compression, either in pluripotency maintenance conditions or in basal medium, comparing these scenarios to hypertonic shock in both media conditions.


title: Mechano-osmotic signals control chromatin state and fate transitions in pluripotent stem cells [scMultiome]

overall_design: iPS cells were compressed for 5 or 30 minutes, or pulsed with 30min compression followed by 24hr recovery. Subsequently, single nuclei were harvested. Two independent biological replicates were prepared for each condition, analyzed seperately to ensure reproducibility, and subsequently pooled and analyzed together, treating each cell in the total pool as a biological replicate. Single nuclei were isolated and libraries were prepared for simultaneous ATAC and RNA sequencing on the same single cell.


title: Soluble Nucleoporin, sPOM121, promotes prostate cancer progression and immune evasion through direct promoter regulation at active transcriptional hubs [RNA-seq]

city: Minneapolis

first: Shijia

last: Zhu

state: Minnesota

address: 1200 Washington Avenue S Suite #175

department: Department of Laboratory Medicine and Pathology

institute: University of Minnesota Medical School

summary: The role of nucleoplasmic residing nucleoporins (NUPs) in solid tumors, including prostate cancer, remain unknown. Here we uncover the clinical relevance and mechanistic role of the off-pore NUP soluble POM121 (sPOM121) as a critical transcriptional regulator enhancing lethal prostate cancer aggressiveness. Mechanistically we found that sPOM121, through its C-terminal domain associates with the chromatin remodeler SMARCA5 at nuclear condensates facilitating transcriptional activation at promoter sites. Indeed, sPOM121 through this mechanism regulates a discrete oncogenic gene network, including B-catenin, leading to tumor progression and immune evasion in prostate cancer. Notably, targeting the sPOM121-B-catenin axis in patient derived pre-clinical and syngeneic mouse models halts prostate cancer aggressiveness and enhances anti-tumor immunity. Together, our findings reveal previously unknown actionable transcriptional rewiring functions of the nucleoplasmic residing NUP, sPOM121, in solid tumors, promoting lethal prostate cancer.

overall_design: RNA-sequencing experiments were conducted for sPOM121 knock-down and control in 22Rv1 and DU145 cell lines.

first: Josep

last: Domingo-Domenech

first: Veronica

last: Rodriguez-Bravo


title: Mechano-osmotic signals control chromatin state and fate transitions in pluripotent stem cells

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

overall_design: Refer to individual Series


title: Genome-wide alterations of DNA methylation and hydroxymethylation in uroepithelial cells revealed potential carcinogenicity of halobenzoquinone disinfection byproducts [Bisulfite-Seq]

status: Public on Jul 20 2025

city: Hangzhou

first: Xinran

last: Zhao

address: Yuhangtang Road

country: China

institute: Zhejiang University

type: Methylation profiling by high throughput sequencing

summary: Halobenzoquinones (HBQs), a class of emerging disinfection byproducts ubiquitously existed in drinking water, were predicted to be bladder carcinogens. HBQs exhibited a unique capacity to promote the conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). Thus, we propose that a varied epigenetic landscape may serve as an essential initial molecular event in cancer development under HBQs stress. We revealed genome-wide alteration of 5mC, 5hmC and transcription induced by HBQs in human bladder epithelial cells SV-HUC-1. HBQ exposure resulted in more hypo-methylated (39,365) and hyper-hydroxymethylated (26,053) sites, with 7,441 overlapping sites, suggesting the conversion of 5mC to 5hmC. The genes associated with hypo-differentially methylated regions (hypo-DMRs) and hyper-differentially hydroxymethylated regions (hyper-DhMRs) were enriched in cancer-related pathways, such as the Hippo signaling pathway, PI3K-AKT signaling pathway and Wnt signaling pathway. In particular, three bladder cancer-related genes associated with hypo-DMRs or hyper-DhMRs exhibited significantly differential expression. This study revealed epigenetic changes induced by HBQs and a potential association with the risk of bladder cancer.

overall_design: SV-HUC-1 cells were treated with 2,6-Dichloro-1,4-benzoquinone (DCBQ) or blank solution for 3 days. Transcriptome data was obtained from RNA-seq. Genome-wide DNA methylation was obtained from Reduced representation bisulfite sequencing (RRBS). Genome-wide DNA hydroxymethylation was obtained from oxidative reduced representation bisulfite sequencing (oxRRBS).

first: Wei


title: SATB1 is a key regulator of quiescence in stem-like CD8+ T cells

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

summary: Cytotoxic T-cell immunity in response to chronic infection and cancer is sustained by a self-renewing population known as the progenitor CD8+ T (TPRO) cells. These TPRO cells exhibit stem-like characteristics, including quiescence, multipotency, and self-renewal, which are the cardinal features of memory T cells. However, the mechanisms that sustain their stem-like properties under chronic antigen stimulation remain unclear. In this study, we identified SATB1 as a shared feature that is specifically enriched in both TPRO and memory CD8+ T cells. While the roles of SATB1 in stem-like CD8+ T cells remain unknown, its function as an epigenetic regulator in promoting quiescence in hematopoietic stem cells led us to hypothesize that SATB1 plays a pivotal role in regulating the stemness of TPRO and memory CD8+ T cells. To test this hypothesis, we employed CRISPR-mediated gene editing to delete the Satb1 gene specifically in CD8+ T cells. During chronic LCMV infection, we found that SATB1-deficient CD8+ T cells failed to maintain the TPRO subset and instead showed an enhanced transition toward terminally differentiated cells. Similarly, SATB1 deficiency during acute viral infection impaired the formation of memory CD8+ T cells. Mechanistically, our multi-omic assays revealed that SATB1 regulates the chromatin accessibility, transcriptional activities, and genomic architecture of stemness-associated genes, such as Tcf7, Bach2, and Myb. Overall, our results underscore the critical role of SATB1 in maintaining the transcriptional and epigenetic features of stem-like CD8+ T cells, shedding light on the previously unappreciated regulatory mechanisms that sustain the stemness of antigen-specific CD8+ T cells.

overall_design: Hi-C libraries were prepared using a modified three-enzyme Hi-C (3e Hi-C) protocol103. Wild-type (WT) and CD8CreSatb1fl/fl (KO) mice were infected with LCMV Clone 13 and sacrificed at day 21 post-infection. Antigen-specific CD8⁺ T cells were sorted, and 300,000 to 500,000 cells per sample were collected for Hi-C. Cells were crosslinked with 1% formaldehyde for 10 minutes at 25 °C and quenched with 2.5 M glycine. Fixed cells were lysed in 10 mL of ice-cold lysis buffer (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.2% NP-40) supplemented with protease inhibitors and incubated at 4 °C for 1 hour. Nuclei were pelleted and permeabilized in 0.1% SDS in CutSmart buffer (NEB) at 65 °C for 10 minutes, followed by quenching with Triton X-100 to a final concentration of 1%. Chromatin was digested with the restriction enzymes FatI, CviQI, and BfaI (New England Biolabs) at 37 °C for 20 minutes. Digestion was stopped by two washes with buffer containing 10 mM NaCl, 1 mM EDTA, and 0.1% Triton X-100. DNA ends were filled in using Klenow enzyme in the presence of dCTP, dGTP, dTTP, and biotin-14-dATP to label ligation junctions. Proximity ligation was performed using T4 DNA ligase under dilute conditions to promote intranuclear ligation. After reverse crosslinking, DNA was sheared to 200–700 bp fragments using a Diagenode Bioruptor. Fragmented DNA was end-repaired, and biotinylated ligation products were purified using Dynabeads MyOne Streptavidin C1 beads (Invitrogen). Sequencing libraries were constructed by ligating Illumina-compatible paired-end adapters and performing PCR amplification. Size selection (200–700 bp) was performed using E-gel electrophoresis, and libraries were sequenced on an Illumina NovaSeq 6000 platform with 50 bp paired-end reads.

first: Siying

last: Lin

first: Kexin

last: Gai

first: Ryan

last: Brown

first: Ziyang

last: Xu


title: Mechano-osmotic signals control chromatin state and fate transitions in pluripotent stem cells [CUT&Run]

first: Sara

last: Wickström

overall_design: Cells were compressed from 30 min in basal or pluripotency medium followed by 24h recovery in the same media condition. Uncompressed cells in the respective media were used as controls (2 biological replicates/condition). Cbx2 cut&run was performed on 5million cells per condition.

first: Yekaterina


title: Early-life ketone body signaling promotes beige fat biogenesis through changes in histone acetylome and β-hydroxybutyrylome [bulk RNA-seq]

city: Taipei

first: Chung-Lin

last: Jiang

address: 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan

department: Institute of Cellular and Organismic Biology

country: Taiwan

institute: Academia Sinica

summary: Infants experience distinct ketogenesis during the preweaning period, but its physiological significance remains unclear. Here, we show that preweaning ketosis enhances beige fat biogenesis and improves metabolic health in adulthood. To elucidate the underlying mechanisms, we performed multi-omics analyses of inguinal white adipose tissue (iWAT) and its stromal vascular fraction (SVF). Bulk RNA-seq of iWAT was conducted in 8-week-old Hmgcs2 knockout (KO) and control mice housed at room temperature (23 °C) or exposed to cold (4 °C). To further examine the effects of elevated ketosis, we administered oral 1,3-butanediol (1,3BD) or water to pups from postnatal day 2 to 21, and analyzed the iWAT SVF using bulk RNA-seq, single-cell RNA-seq, and ChIP-seq targeting H3K9ac, H3K14ac, and H3K9bhb. These integrative analyses reveal how early-life ketosis programs adipose progenitors to promote beige adipocyte development.

overall_design:
This dataset comprises two experiments.
(1) To assess the impact of ketogenesis loss and cold exposure on the iWAT transcriptome, RNA was isolated from iWAT depots of 8-week-old Hmgcs2 KO and control mice housed at room temperature (23 °C) or exposed to cold (4 °C), followed by bulk RNA sequencing.
(2) To examine the effect of enhanced ketogenesis on the gene expression profile of adipose progenitors, RNA was isolated from the SVF of iWAT in P21 water and 1,3BD-supplemented (1,3BD) male mice and subjected to bulk RNA sequencing.

first: Fu

middle: J

first: Chung


title: Impact of parental obesity on adipose progenitor programming

address: Department of Biochemical Science and Technology, National Taiwan University, No.1, Sec.4, Roosevelt Rd., Taipei, 10617, Taiwan

summary: Parental obesity (PO) increases the risk of obesity and metabolic syndromes in offspring. To investigate how PO influences adipose progenitors, we generated offspring from lean (Ln-F1) or obese (Ob-F1) parents and isolated the stromal vascular fraction (SVF) from inguinal white adipose tissue (iWAT) depots at postnatal day 21 (P21). Bulk RNA sequencing of the SVF was performed to uncover the molecular mechanisms by which PO programs adipose progenitors.

overall_design: To assess the effects of PO on the gene expression profile of adipose progenitors, RNA was isolated from the SVF of iWAT in P21 Ln-F1 and Ob-F1 male mice and subjected to bulk RNA sequencing.

first: Fu-Jung


title: Integration of spatial protein imaging and transcriptomics in the human kidney tracks the regenerative potential of proximal tubules

city: Indianapolis

first: Tarek

last: Ashkar

state: IN

address: 950 W Walnut St.

department: Nephrology

institute: Indiana University

summary: The organizational principles of nephronal segments are based on anatomical and physiological attributes that are linked to the homeostatic functions of the kidney. Recent molecular approaches have uncovered layers of deeper signatures and states in tubular cells that arise at various timepoints on the disease trajectory. Here, we introduce an analytical pipeline of multiplexed spatial protein imaging integrated with RNA expression to characterize proximal tubular subpopulations and neighborhoods in human kidney tissue. We demonstrate that, in reference tissue, a large proportion of S1 proximal tubular epithelial cells express THY1, a mesenchymal stromal and stem cell marker that regulates differentiation. Kidney disease is associated with loss of THY1 and transition towards expression of PROM1, another stem cell marker recently linked to failed repair. Our data support a model in which the interplay between THY1 and PROM1 expression in proximal tubules associates with their regenerative potential and marks the timeline of disease progression.

overall_design:
The preparation and imaging of tissues were done using Visium Spatial Gene Expression protocol for polyA capture in fresh frozen tissue (10x Genomics, CG000240 protocol, Visium Tissue Preparation Guide). Using a Keyence BZ-X810 microscope equipped with a Nikon 10x CFI Plan Fluor objective, hematoxylin and eosin (H&E) stained brightfield mosaics were collected and stitched prior to mRNA capture. mRNA was extracted from tissue after 12 minutes of tissue permeabilization. Isolated mRNA was captured by oligonucleotides in the fiducial capture areas and reverse transcribed. Libraries were prepared based on the Visium 1.0 protocol (10X genomics CG000239 protocol) which included, second-strand synthesis, denaturation, cDNA amplification, and cleanup using SPRIselect (Beckman Coulter).  Multiplexed sequencing was performed on a NovaSeq6000 (Illiumina). Sequencing data was demultiplexed and mapped to the reference genome GRCh38 3.0.0, and counted in Space Ranger (10X Genomics, v1.0.0).  Data processing was performed in Seurat (v.4.4).  The sample in this series is integrated with the samples GSM6047778 and GSM6047779 from GSE183456 (For GSM6047778 and GSM6047779, there  has been no separate reanalysis or additional processing performed).

***************************************************************
The table below lists GEO accessions reused for this study.
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first: Mahla

last: Asghari

first: Ricardo

last: Melo Ferreira

first: Ying-Hua

last: Cheng

first: Michael

middle: T

last: Eadon


title: T cell cholesterol transport links intestinal immune responses to dietary lipid absorption

city: Los Angeles

first: Yajing

last: Gao

state: CA

address: 675 Charles E Young Dr S

department: Pathology and Laboratory Medicine

institute: University of California, Los Angeles

summary: The intrinsic pathways that control membrane organization in immune cells and the impact of such pathways on cellular functions are not well defined.  Here we show that the nonvesicular cholesterol transporter Aster-A links plasma membrane (PM) cholesterol availability in T cells to immune signaling and systemic metabolism.  Aster-A is recruited to the PM during T-cell receptor (TCR) activation, where it facilitates the removal of newly generated “accessible” cholesterol.  Loss of Aster-A leads to excess PM cholesterol accumulation, resulting in enhanced TCR nano-clustering and signaling, and in Th17 cytokine production.  Furthermore, Aster-A associates with STIM1 and negatively regulates STIM1-dependent calcium flux during activation of mouse and human T cells.  Finally, mucosal Th17 response towards commensals is restrained by PM cholesterol remodeling.  Ablation of Aster-A in T cells stimulates IL-22 production, which reduces intestinal fatty acid absorption, and confers resistance to diet-induced obesity.  These findings delineate a multi-tiered regulatory scheme linking immune cell lipid flux to nutrient absorption and systemic physiology.

overall_design: To investigate how Aster-A deficiency regulates T cell function related to intestinal absorption, we fasted Aster-A F/F (WT) or CD4-Cre; Aster-A F/F (AdCD4) mice for 16 h to synchronize metabolic status, and then gavaged with 200 ul olive oil. 2 h later, we isolated CD4 T cells from small intestinal lamina propria and performed mRNA-sequencing. We performed differential gene expression analysis using  data obtained from RNA-seq of 3 (WT) and 4 (AdCD4) biological replicates.

first: Peter

last: Tontonoz


title: Oxaloacetate sensing promotes innate immune antiviral defence against influenza virus infection

status: Public on Jul 19 2025

city: Guangzhou, Guangdong

first: Shouheng

last: Jin

address: School of Life Sciences, Sun Yat-sen University, No.135, Xingang West Road

department: School of Life Sciences

institute: Sun Yat-sen University

summary: Metabolic pathways instructing the cellular fate and function, however, the exact roles of metabolites in host immune responses remain undefined. Using unbiased metabolomics and pharmacological inhibition analysis, we report natural metabolic intermediate, oxaloacetate (OAA) primes effective broad-spectrum innate immunity against viral infection. OAA serves as an immune signal, rather than alters the metabolic flux to prompt antiviral immunity. Malate dehydrogenase 1 (MDH1) senses OAA to undergo dimerization, thus functions as a scaffold to recruit transcription factor ETS2 for phosphorylation by kinase TAOK1 at serine 313. Phosphorylated ETS2 is involved in the transcriptional regulation of TANK-binding kinase 1 (TBK1). OAA deficiency caused by genetic ablation and enzymatic inhibition of the ATP-citrate lyase (ACLY) decreases the antiviral immune responses through MDH1-TAOK1-ETS2-TBK1 pathway in vivo, and makes mice more susceptible to lethal viral infection. Taken together, our findings delineate an OAA-initiated immunometabolic circuit that links metabolic pathway and antiviral immune responses.

overall_design: To explore the function of OAA in chromatin accessibility, we carried out transposase-accessible chromatin with high throughput sequencing (ATAC-seq) assay in PBMCs with or without OAA supplementation.

first: Xing

last: He


title: Compendium of Disease-Linked Regulatory DNA Variants and Homeostatic Transcription Factors in Epidermis

city: Stanford

first: Douglas

last: Porter

address: 269 Campus Drive

department: Dermatology

institute: Stanford


title: Nonvesicular sterol transport is a metabolic immune checkpoint that guards dietary lipid uptake (scRNA-Seq)

overall_design: Mice were fasted for 16 h and gavaged with olive oil for 2 h. Small intestine lamina propria mononuclear cells were isolated using the method described in the bulk mRNA sequencing section. Single Live EPCAM- Ter119- CD31- CD45+ cells were sorted from 10- to 12-week-old female littermates (n = 3 /genotype) on a BD Aria FACS sorter. 100,000 cells were sorted from each mouse and pooled together.


title: Distinct maternal DNA methylation associations with gestational age at early and late-mid term pregnancy in a low- and middle-income country: Evaluation of biological, genetic, and psychosocial contributors

city: Vancouver

middle: S.

last: Kobor

state: BC

address: 117-2194 Health Sciences Mall

department: Faculty of Medicine

country: Canada

institute: University of British Columbia

type: Methylation profiling by genome tiling array

summary: Mothers undergo physiological and molecular changes over the course of gestation. These modifications “get under the skin” and may be reflected in the maternal epigenome through processes such as DNA methylation. Such an epigenetic mark may offer insights into maternal responses to prenatal influences and biological cues from the developing fetus, thereby functioning as an indirect indicator of the conditions the fetus experiences in utero. We measured whole blood DNA methylation in 22 pregnant women from Pakistan, a low- and middle-income country (LMIC), at two timepoints during their term pregnancies (early: 10-19 weeks and late-mid: 22-29 weeks). We used DNA methylation profiles to predict immune cell proportions and tested differences in these proportions and DNA methylation patterns between the two timepoints. Further, we evaluated DNA methylation associations with gestational age at each timepoint and examined the contribution of genetic, psychosocial, and biological factors. Our analyses documented changes in immune cell proportions and DNA methylation profiles over the course of gestation, albeit in a small percentage of the measured DNA methylome. We also observed timepoint-specific DNA methylation associations with gestational age, predominantly at early pregnancy, with predicted interleukin-6 level and socioeconomic status contributing to a few of these associations. On comparing to three external cohorts from different sociocultural contexts, we also noted these signatures to be unique to LMIC settings. Overall, these changes measured in term pregnancies may be used to assess both fluctuations in pregnancy and birth outcomes, particular in women from LMIC settings.

overall_design:
Bisulphite converted DNA from 52 whole blood samples (26 mothers sampled at two pregnancy timepoints) were hybridized to the Illumina Infinium HumanMethylationEPIC version 1.0 microarray to evaluate: i) Differences in maternal blood DNA methylation profiles between early and late-mid pregnancy timepoints, and ii) Associations between maternal blood DNA methylation at the two pregnancy timepoints and gestational age at birth.
[contributor] Maternal-infant Global Health Team (MiGHT) – Collaborators in Research

first: Marcia

last: Smiti Jude

first: Chaini

last: Konwar

first: Robyn

last: McQuaid

first: Farooq

last: Ghani

first: Nazneen

last: Islam

first: Sharifa

last: Lalani

first: Sarah

last: Merrill

first: Fizza

last: Fatima

first: Julia

last: MacIsaac

first: Ntonghanwah

last: Forcheh

first: Calen

middle: P

last: Ryan

first: Nanette

middle: R

last: Lee

first: Christopher

middle: W

last: Kuzawa

middle: S

first: Shahirose

last: Sadrudin Premji


title: Hyperactive PDGFRβ signaling induces cataractogenesis via TGFβ and STAT5-IGF1

status: Public on Jul 18 2025

city: Columbus

first: Jesse

middle: James

last: Reardon

state: Ohio

address: 420 W 12th Avenue

department: Radiation Oncology

institute: The Ohio State University

summary: Introduction: Cataracts are the world’s leading cause of reversible blindness. Although cataract formation is commonly initiated by lens fiber cell defects, cataractogenesis can be characterized by aberrant proliferation and migration of lens epithelial cells, particularly in posterior capsule opacification. Subsequent overproduction of extracellular matrix components such as fibronectin and collagen by epithelial cells is associated with fibrosis of the lens. Little is known about the role of platelet-derived growth factor receptor β (PDGFRβ) in lens fibrosis. Here, we investigated mice with a conditional knock-in driving mesenchymal-specific PDGFRβ hyperactivation (Fsp1-cre;Pdgfrb+/D849V), which consistently develop cataracts at a young age.  Methods: Lenses from Fsp1-cre;Pdgfrb+/D849V mice and age-matched controls were dissected and visualized via microscopy from 9-15 weeks. Early transcriptional changes were investigated between 10-12 day old Fsp1-cre;Pdgfrb+/D849V and control mice via RNA sequencing followed by gene set enrichment analysis. Confirmation of RNA sequencing results and mechanistic investigation of PDGFRβ-induced cataractogenesis were determined in lenses isolated from 15-week-old Fsp1-cre;Pdgfrb+/D849V and control mice. Results: Gross examination of cataractous lenses from Fsp1-cre;Pdgfrb+/D849V mice revealed complete opacification by 15 weeks of age compared to no opacification in age-matched controls. Structural changes in the anterior, equatorial, and posterior lens were observed in histology. RNA sequencing revealed significant enrichment of gene sets related to extracellular matrix deposition and reorganization. Mechanistic investigation revealed major roles for TGFβ, SOCS2, and STAT5-IGF1 signaling axes in PDGFRβ-induced cataract formation.  Conclusion: PDGFRβ promoted cataractogenesis by modulating pro-fibrotic extracellular matrix changes, likely through TGFβ, SOCS2, and the STAT5-IGF1 pathways. Future experiments will delineate the precise role of the STAT5-IGF1 signaling pathway in PDGFRβ-mediated fibrosis and the interplay between PDGFRβ and TGFβ in the lens and whether this signaling is targetable to modulate cataractogenesis.

overall_design: Lenses were isolated from Fsp1-cre;Pdgfrb+/D849V and control mice and sent to Novogene for RNA-sequencing.

first: Yixuan

last: Ma

first: Nathaniel

last: Grabinski

first: Yalini

last: Ramamoorthy

first: Rebecca

last: Packard

first: Johnathon

middle: G

last: Schiebel

first: Heather

last: Chandler

first: Gina

last: Sizemore


title: Itaconate alleviates cholesterol burden via ABCA1 stabilization and cholesterol efflux

city: Cleveland

first: Andrei

last: Maiseyeu

state: OH

address: 2103 Cornell Rd

department: Medicine

institute: Case Western Reserve University

summary: Background and aims: Itaconate (ITA) is a metabolite produced from the tricarboxylic acid cycle (TCA) that has been shown to regulate atherosclerotic plaque growth and induce stability via immunomodulation. However, lipid metabolism regulation by ITA is currently underexplored in atherosclerosis. Here, we take advantage of plaque-targeting ITA-conjugated nanoparticles (ITA-LNPs) to investigate the effects of ITA on regulating lipid metabolism in foam cells/macrophages in atherosclerosis via ABCA1 stabilization and increased triglyceride metabolism.  Methods: Apoe−/− mice were fed a high-cholesterol/high-fat diet (HCHFD) for 12 weeks and injected once weekly with 50 mg/kg ITA-LNP or Ctrl-LNP. Aortas were tested for ITA-LNP biodistribution, followed by quantification of atherosclerotic plaque burden. Bone marrow-derived macrophages (BMDMs) or Raw 264.7 cells were treated with ITA-LNP or Ctrl-LNP in the presence of oxLDL, acLDL, or free cholesterol to investigate ITA’s actions on lipid metabolism and ABCA1 expression under a variety of conditions, including stable gene knockdown.  Results: ABCA1 was significantly upregulated with ITA-LNP treatment compared to Ctrl-LNP both in vivo and in vitro at the protein level, but not at the transcriptional level. ITA-LNPs were shown to prevent ABCA1 decay via the HO-1-calpain axis, resulting in significantly increased cholesterol efflux in macrophages. This was further confirmed in Raw 264.7 cells with a stable HO-1 knockdown. Additionally, ITA decreased lipid burden in conjunction with increased expression of Slc25a1 in ITA-LNP-treated BMDMs, suggesting enhanced fatty acid-derived citrate shuttling and increased fatty acid metabolism.  Conclusions: ITA-LNPs regulate lipid metabolism in atherosclerosis by inducing triglyceride catabolism and cholesterol efflux.

overall_design: RNA-seq was performed on whole abdominal aortas isolated from Apoe−/− male mice after 12 weeks of high fat diet and once weekly injection with Ctrl- or ITA-LNPs.

first: Maiseyeu

last: Andrei


title: Circadian clocks and periodic anticipated fasting prevent fasting-associated hepatic steatosis in calorie restriction

first: Roman

last: Kondratov

state: OHIO

address: 2121 euclid ave, bh 411

department: Biological, Geological, and Environmental Sciences (BGES)

institute: Cleveland State University

summary: Calorie restriction (CR) improves health and longevity. CR induces a periodic fasting cycle in mammals; our study compares CR with unanticipated fasting (F), when the food is unexpectedly withheld. F induces hepatic steatosis, while CR reduces it; surprisingly, the difference is not due to hepatic β-oxidation. Liver transcriptome analysis identifies fatty acid transporters (Slc27a1 and Slc27a2), TAG synthesis (Gpat4), and lipid storage (Plin2 and Cidec) genes to be upregulated only in F in agreement with hepatic steatosis. The circadian clock and anticipated fasting contribute to preventing fasting-associate hepatic steatosis in CR. Mechanistically, Slc27a1, Plin2 and Cidec genes are upregulated, and liver TAGs accumulate in circadian clock mutant mice on CR or if wild type CR mice miss their anticipated meal. The results highlight similarities and differences between unanticipated fasting and CR, suggesting that circadian clock dependent gating of transcriptional response to fasting controls lipid homeostasis and prevents hepatic steatosis.

overall_design: Total RNA was isolated from 30 mg of female mouse liver tissue using mini spin column QIAGEN RNeasy Mini Kit according to the manufacturer’s protocol. Sample purity was checked on Nano Drop (Thermo Fisher Scientific, Waltham, MA, USA) with 260/280 and 260/230 ratios ≥ 2.0. The RNA sequencing was performed by Novogene Corporation Inc (Sacramento, CA, USA). After sample quality control, non-directional – polyA enrichment library was prepared using NEBNext Ultra™ II RNA Library Prep Kit for Illumina (New England BioLabs), and 50M reads (150bp, paired end) per sample were generated on Illumina NovaSeq 6000 platform. RNA-seq reads were mapped to the mouse protein coding genes (Ensembl: Mus_musculus; GRCm38) using Bowtie allowing up to 2-mismatches. The gene expected read counts and Transcripts Per Million (TPM) were estimated by RSEM (v1.2.3). The TPMs were further normalized by EBSeq R package to correct potential batch effect.

first: Oghogho

last: Ebeigbe

first: Volha

last: Mezhnina

first: Artem

last: Astafev

first: Nikkhil

last: Velingkaar

first: Jillian

last: Kodger

first: Allan

last: Poe

first: Jonathan

last: Fritz

first: Kadaia

last: Williams

first: Evelina

last: Trokhimenko

first: Josefa-Marie

last: Rom

first: Yana

last: Sandlers


title: Epigenetic reprogramming via EZH2 inhibition rescues fibroadipose pathogenesis in secondary lymphedema through activating PPARγ signaling

city: Shenzhen

first: Ziyu

last: Chen

state: Guangdong

address: 1120 Lianhua Rd

institute: Peking University Shenzhen Hospital

summary: Secondary lymphedema, a progressive disorder characterized by pathological fibroadipose tissue accumulation, is a common problem after cancer treatment and orthopedic surgery. It remains a therapeutic enigma due to its self-perpetuating fibrotic cascade and lack of disease-modifying therapies.Human skin tissue was collected from lymphedema patients and normal controls. Histological/immunofluorescence staining and RNA sequencing were performed. Fibrous tissue was observed in lymphedema samples. RNA sequencing and gene set enrichment analysis (GSEA) revealed significant downregulation of the peroxisome proliferator-activated receptor (PPAR) signaling in lymphedema tissue.

overall_design: Human subcutaneous tissue from ISL stage III lymphedema patients (n = 5) and from normal controls (n = 3) were collected for RNA-seq.

first: Zhi

last: Yao

first: Mengfan

last: Wu

first: Yuluan

first: Jianlin

last: Zhang

first: Lixiang

last: Xue

first: Deli

last: Wang


title: CAIS molecular pathways unveil Testosterone/Estradiol ratio to germ cell tumor risk in non-obstructive azoospermia

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

country: Italy

institute: OSR - San Raffaele Scientific Institute

summary: Context. Non-obstructive azoospermia (NOA) is the most severe form of male infertility affecting 1% of all men, with a clinical picture characterized by no sperm production, hyalinization of the basal membrane of the seminiferous tubules, primary hypogonadism and earlier onset of age-related comorbidities compared with fertile men. NOA is also characterized by etiologic heterogeneity and the non-genetic form has higher incidence of testicular germ cell cancer (TGCC) compared to the forms with genetic abnormalities. Objective. We aimed to establish molecular pathways in the testicular somatic cells that are either shared or specific for non-genetic and genetic forms of NOA, as Complete Androgen Insensitivity Syndrome (CAIS) and Klinefelter Syndrome (KS). Methods. Single cell RNAseq of the testis somatic cells of an individual with CAIS, and data integration with published scRNA-seq datasets of testis with normal spermatogenesis, NOA, KS and germinal testicular cancer. Detailed clinical data of the CAIS patient, Testosterone and Estradiol levels in age-matched men (120 fertile, 155 infertile, 116 NOA, 18 KS, and 343 with TGCC). Results. In all conditions, Leydig cells are immature and senescent, but those of NOA associated with primary hypogonadism depict the highest expression of transcripts associated with the seminoma microenvironment, including estrogen-responsive genes. An oncological transcriptional signature in the Leydig cells has been confirmed at the systemic levels by showing a prognostic role of the decreasing Testosterone/Estradiol ratio for TGCC in men with non-genetic NOA. Conclusion. This study offers molecular insights into the prediction of TGCC in persons with NOA and eligibility for the use of aromatase inhibitors.

overall_design:
Single cell RNAseq of the testicular somatic cells of an individual with CAIS was obtained. This sample was integrated with published scRNA-seq datasets of testis with normal spermatogenesis, NOA, KS and germinal testicular cancer. We re-analyzed count matrices for 3 men with NOA (Alfano et al. 2021 - GSE154535 = GSM4673006, GSM4673007, GSM4673008 ), 2 men with KS (Mahyari et al. 2021 - GSE169062 = GSM5175967, GSM5175968, GSM5175972, GSM5175973), and 9 healthy men (3 from Guo et al. 2018 - GSE112013 = GSM3052917-GSM3052918, GSM3052919-GSM3052920, GSM3052921-GSM3052922) , 2 from Sohni et al. 2019 - GSE124263 = GSM3526588, GSM3526590 , and 4 young adults from Guo et al. 2022 - GSE182786  = GSM5536958, GSM5536959, GSM5536960, GSM5536961) using R scripts. All gene annotations were updated to GENCODE v31 using Ensembl IDs for consistency across versions. All these samples were integrated with our CAIS samples using the standard Seurat v4 workflow. To identify cell populations, the Seurat v4 graph-based clustering approach (using the FindNeighbours and FindClusters functions) was applied with a resolution of 0.2, and cell identities were assigned as previously described in our previous work (Alfano M, Tascini AS, Pederzoli F, Locatelli I et al. Aging, inflammation and DNA damage in the somatic testicular niche with idiopathic germ cell aplasia. Nat Commun 2021 Sep 1;12(1):5205. PMID: 34471128)

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The table below lists GEO accessions reused/reanalyzed for this study.
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first: Massimo

last: Alfano

first: Anna Sofia

last: Tascini

first: Jose M


title: Pulmonary tolerance to ozone is associated with changes in the alveolar macrophage transcriptome

first: Jeremy

last: Simon

address: 450 Brookline Ave

department: Department of Data Science

institute: Dana-Farber Cancer Institute

summary: Tolerance to the air pollutant ozone refers to the phenomenon by which pre-exposure to a relatively low concentration confers protection against from lung injury and inflammation caused by a subsequent challenge with high concentration ozone. We investigated whether alveolar macrophages play a central role in this process. First, we established a model of ozone tolerance in which inbred C57BL/6NJ mice were pre-exposed to 0.8 ppm ozone for 4 days then challenged with 2 ppm ozone on day 7, followed by sacrifice and phenotyping on Day 8. As expected, pre-exposure significantly reduced ozone-induced airway injury and inflammation on day 8. To investigate the role of alveolar macrophages, we treated mice with clodronate on day 5, which reduced macrophage number by ~5-fold. Following ozone challenge on day 7, clodronate treated mice exhibited increased injury compared to vehicle treated controls. Cytokines involved in neutrophil chemotaxis such as IL-6, MIP-1b, and KC, were also significantly elevated in clodronate treated mice. Collectively, these data indicate an important role of AMs in this model of tolerance. To identify differences in the phenotype of AMs caused by pre-exposure to ozone, we isolated AMs from ozone pre-exposed mice vs. filtered air controls using flow sorting and performed RNA-seq analysis of these samples. We found that a number of genes and pathways were altered by ozone pre-exposure, most importantly downregulation of pathways involved in toll-like receptor cell signaling, proinflammatory gene expression, and NF-kB mediated gene regulation.

overall_design: RNA-seq of alveolar macrophages isolated from female C57BL6/NJ mouse lungs after exposure to Filtered Air or 0.8ppm Ozone, with 6 biological replicates

first: Samir

middle: N

last: Kelada


title: Genome-wide alterations of DNA methylation and hydroxymethylation in uroepithelial cells revealed potential carcinogenicity of halobenzoquinone disinfection byproducts [RNA-Seq]

first: Xinran

last: Zhao

first: Wei


title: Apolipoprotein A-I Influences The Transcriptional Profile Of Fatty Liver In Apolipoprotein E Knockout Mice

city: Milano

first: Stefano

last: Manzini

state: Lombardia

address: via Balzaretti, n. 9

department: DISFEB

institute: Università degli Studi di Milano

summary: Fatty liver disease is a condition characterized by lipid accumulation in the hepatocytes and it is generally accompanied by a dyslipidemic condition characterized by low HDL levels. Being the interrelation between fatty liver disease and low HDL not clearly understood, in the present study, the impact of different apoA-I/HDL levels on the transcriptome of diet-induced fatty liver was investigated. Eight-week-old mice lacking apoA-I/HDL (DKO) and mice with physiological levels of apoA-I/HDL (DKO/hA-I) were fed either a standard rodent diet (SRD) or a Western diet (WD) for 22 weeks. Steatosis was quantified, and the hepatic transcriptome was analyzed by RNAseq. Following WD, both genotypes showed marked lipid accumulation in the liver, without relevant histological differences. The transcriptome analysis showed an upregulated expression of immune/inflammatory genes and a reduced activation of the retinoid metabolism in both WD-fed genotypes. Strong divergences in genes involved in metabolic pathways were observed only in the presence of apoA-I/HDL, where the results suggested reduced endogenous biosynthesis of cholesterol and other sterols, glutathione metabolism together with increased glucose metabolism. In conclusion, although not histologically overt, apoA-I/HDL seems to exert a substantial impact on hepatic metabolism during steatosis, that goes beyond cholesterol metabolism.

overall_design: RNA-seq performed in mouse liver from double apolipoprotein E and apolipoprotein A-I knockout mice (DKO), or double apolipoprotein E and apolipoprotein A-I knockout mice expressing the human APOA1 gene (DKO/hA1),  n=2, 3 or 4 per experimental group, using the Illumina Genome Analyzer IIx. Two diets (chow, Western), one time point (22 weeks).

first: Elsa

last: Franchi

first: Alice

last: Colombo

first: Marco

last: Busnelli

first: Giulia

last: Chiesa


title: Gene expression analysis in canine peripheral blood mononuclear cells (PBMCs) from dogs with diffuse large B cell lymphoma (DLBCL)

status: Public on Jul 17 2025

city: North Grafton

first: Jillian

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine

summary: We performed a veterinary clinical oncology trial in client-owned dogs to determine if immune modulating drugs could be combined in rational approaches to treat spontaneous canine diffuse large B cell lymphoma (DLBCL).

overall_design: Gene expression in peripheral blood mononuclear cells (PBMCs) at Day 0, Day 7, Day 21/28 and relapse from dogs enrolled in three different treatment arms was analyzed using the NanoString canine IO panel Sprint platform.

first: Cheryl

last: London

first: Heather

last: Gardner


title: CRISPR activation for SCN2A-related neurodevelopmental disorders

city: San Francisco

first: Nadav

last: Ahituv

address: 1550 4th Street

institute: UCSF

summary: Here, we are measuring mRNA expression of CRISPRa targeting the promoter of mouse Scn2a in Neuro2a cells and in Mice.

overall_design: plasmid CRISPRa transfection in mouse Neuroblastoma-2a cells. Injections of CRISPRa into mice and mRNA sequencing of brain samples sorted for neurons.

first: Vladyslav

last: Barskyi

first: Coline

last: Arnould

first: Beniamin

last: Krupkin


title: OTTR-seq of FXTAS brain reveals tRNA ligase dysfunction

city: Boston

first: Raghu

last: Chivukula

address: 185 Cambridge Street

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: Protein aggregates are a hallmark of neurodegenerative disease proposed to promote neurotoxicity through a diverse and growing set of mechanisms. Aggregation of polyglycine is specifically implicated in the pathogenesis of an emerging group of neurodegenerative GGC repeat expansion diseases. Here, we find that polyglycine aggregates incorporate endogenous proteins harboring glycine-rich sequences, including FAM98B, a conserved component of the vertebrate tRNA ligase complex. Through sequestration and accelerated proteosome-dependent turnover mediated by the FAM98B glycine-rich intrinsically disordered region (IDR), polyglycine depletes the ligase complex and disrupts tRNA processing. Accordingly, brains of affected patients reveal aggregate-associated sequestration and depletion of the tRNA-LC as well as accumulation of aberrant tRNA species.

overall_design: Total RNA from 4 control human cerebellum samples and 4 FXTAS individuals was isolated using TRIzol reagent. Total RNA from clonal FAM98B-knockout HEK293T cells lentivirally complemented with a doxycycline (DOX) suppressible full-length (FAM98B_FL) allele was isolated using TRIzol reagent. Libraries were generated for sequencing using ordered two-template relay (OTTR) sequencing.

first: Jason

last: Yang


title: MYB and HIF1α crosstalk drives hypoxia-induced transcriptional reprogramming and adaptive signaling alterations in pancreatic cancer [ChIP-seq]

city: Jackson

first: Shashi

last: Anand

state: MS

address: 2500 N State St

department: Cell and Molecular Biology

institute: University of Mississippi Medical Center

summary: Pancreatic cancer is an aggressive malignancy, characterized by extensive desmoplasia and a hypoxic tumor microenvironment that contributes to therapy resistance. MYB, a proto-oncogene encoding a transcription factor, plays a crucial role in pancreatic tumor growth, metastasis, and desmoplasia. Recently, we also revealed a role of MYB in hypoxic survival of pancreatic cancer by promoting metabolic reprogramming through interaction with HIF1α, modulating its expression and influencing its binding to glycolytic gene promoters. In this study, we examined the impact of hypoxia on the genome-wide occupancy of MYB by performing chromatin immunoprecipitation sequencing (ChIP-seq) analysis. We also used HIF1A knockout cells to investigate the role of HIF1α in altered genomic occupancy of MYB. In addition, we examined the genomic distribution of HIF1α in presence and absence of MYB and the impact of their crosstalk on transcriptional reprogramming and associated signaling alterations by RNA-seq and pathway analyses. Our findings show that hypoxia induces significant changes in MYB’s genomic distribution, partially dependent on HIF1α, and that MYB facilitates HIF1α binding to specific gene promoters. We also identify a subset of hypoxia-induced genes co-regulated by MYB and HIF1α, involved in oncogenic signaling pathways critical for hypoxic adaptation. These results highlight the reciprocal crosstalk between MYB and HIF1α, providing novel mechanistic insights into pancreatic cancer adaptation under hypoxia and suggesting MYB as a potential therapeutic target.

overall_design:
ChIP-seq of MYB in MiaPaCa-2 control cells cultured under normoxia (20% O2) and their respective Input Controls.
ChIP-seq of MYB in MiaPaCa-2 control cells cultured under hypoxia (1% O2) and their respective Input Controls.
ChIP-seq of MYB in MiaPaCa HIF1α knockout (HIF1α KO) cells cultured under hypoxia (1% O2) conditions and their respective Input controls.
ChIP-seq of HIF1α in MiaPaCa-2 control cells cultured under hypoxia conditions.
ChIP-seq of HIF1α in MYB knockout (MYB KO)-HIF1α overexpressing cells cultured under hypoxia and their respective Input Controls.

first: Kunwar Somesh

last: Vikramdeo

first: Mohammad Aslam

last: Khan

first: Seema

last: Singh

first: Ajay Pratap


title: RNA Sequencing of HEK293T cells expressing 15xGly or 99xGly

summary: Protein aggregates are a hallmark of neurodegenerative disease proposed to promote neurotoxicity through a diverse and growing set of mechanisms. Aggregation of polyglycine is specifically implicated in the pathogenesis of an emerging group of neurodegenerative GGC repeat expansion diseases. Here, we find that polyglycine aggregates incorporate endogenous proteins harboring glycine-rich sequences, including FAM98B, a conserved component of the vertebrate tRNA ligase complex. Through sequestration and accelerated proteosome-dependent turnover mediated by the FAM98B glycine-rich intrinsically disordered region (IDR), polyglycine depletes the ligase complex and disrupts tRNA processing.

overall_design: HEK293T cells were infected with lentiviruses encoding doxycycline (DOX)-repressible fusion protein constructs encoding either 15xGly-eGFP-3xHA or 99xGly-eGFP-3xHA. After selection in blasticidin, single cell clones were grown and expanded. Clonal transduced cell lines were either maintained in growth media containing DOX (for suppression of transgene expression) or in DOX-lacking media (for induction of transgene expression) for 14 days before isolation of RNA for sequencing.


title: DNA language models reveal the architecture of nucleotide dependencies in genomes

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

summary:
While the genome is composed of individual nucleotides, functional elements such as cis-regulatory elements and structural interactions are formed from sets of interdependent nucleotides. In principle, these dependencies are reflected in coevolutionary relationships. However, classical comparative genomics approaches struggle to detect these dependencies beyond alignable highly conserved sequences such as within coding regions.
DNA language models (LMs), which are trained by predicting nucleotides given their sequence context, have recently been proposed as foundational models for sequence-based prediction problems. DNA LMs implicitly capture functional elements from genomic sequences alone. However, which dependencies DNA LMs learn and whether they reflect known or even novel biology remains an open question.
Here we introduce nucleotide dependency maps to systematically study nucleotide dependencies captured by DNA LMs in a purely unsupervised setup.
We compute these maps genome-wide and show that they reveal and clearly delineate known functional genomic features such as transcription factor binding motifs, functional interactions between splice sites, RNA tertiary structures, and coding sequences. This allowed to uncover novel experimentally validated RNA structures.
We furthermore investigate dependency maps from in silico manipulated sequences, revealing the ability of DNA LMs to capture operations such as copying and reverse complementarity without memorization.
Lastly, we compare dependency maps from openly available DNA LMs, showcasing the drawbacks and advantages of different models. We find stark differences in the ability of models to accurately learn conserved but infrequent features.
Altogether, by leveraging the flexibility of DNA language models, nucleotide dependency mapping emerges as a general methodology to discover and study functional interactions in genomes.

overall_design: RNA structure analysis of Escherichia coli by DMS chemical probing and mutational profiling (DMS-MaPseq)

first: Pedro

last: Tomaz da Silva

first: Alexander

last: Karollus

first: Johannes

last: Hingerl

first: Gihanna

last: Galindez

first: Nils

last: Wagner

first: Xavier

last: Hernandez-Alias

first: Julien

last: Gagneur


title: Molecular Subtypes of Human Skeletal Muscle in Cancer Cachexia

city: Edmonton

first: Sambasivarao

last: Damaraju

state: Alberta

address: 11560 University Avenue

department: Laboratory Medicine and Pathology

institute: University of Alberta

summary: Cancer-associated muscle wasting associates with poor clinical outcomes1, but its underlying biology is largely uncharted in humans2. Unbiased RNAome analysis (coding and non-coding RNAs) with unsupervised clustering using Integrative Non-negative Matrix Factorization (intNMF)3 provides an avenue to identify distinct molecular subtypes, here applied to muscle of patients with colorectal or pancreatic cancer. Rectus abdominis biopsies from 84 patients was profiled using high-throughput next generation sequencing. Here we show that intNMF with stringent quality metrics of clustering identifies 2 highly coherent molecular subtypes within muscle of patients with cancer. Patients in Subtype 1 (vs Subtype 2) showed clinical manifestations of cachexia: high-grade weight loss, low muscle mass, atrophy of Type IIA and Type IIX muscle fibres and reduced survival. Based on differential expression between the subtypes, our results indicate biological processes that may contribute to cancer-associated loss of muscle mass and function, including altered post-transcriptional regulation, and perturbation of neuronal systems, cytokine storm/cellular immune response, extracellular matrix, and metabolic abnormalities spanning xenobiotic metabolism, hemostasis, signal transduction, embryonic/pluripotent stem cells, and amino acid metabolism. Differential expression between subtypes indicates involvement of multiple, intertwined higher-order gene regulatory networks, suggesting potential for interacting (hub)lncRNA-miRNA-mRNA interaction networks as targets for future research.

overall_design: RNA sequencing was performed from muscle of rats bearing tumor, those treated with chemotherapy and healthy controls

first: Bhumi

last: Bhatt

first: Vera

last: Mazurak


title: Cardiac Enrichment of Mutant Calmodulin Protein in a Murine Model of a Human Calmodulinopathy

status: Public on Jul 16 2025

city: Taipei

first: Kai-Chien

address: No.1, Sec. 1, Jen-Ai Rd, 1150R

department: Graduate Institute and Department of Pharmacology

institute: National Taiwan University

summary: Heterozygosity for missense mutations in one of 3 seemingly redundant calmodulin (CaM)-encoding genes can cause life-threatening ventricular arrhythmias, suggesting that small fractions of mutant CaM protein suffice to cause a severe phenotype. However, the exact molar ratios of wildtype to mutant CaM protein in calmodulinopathy hearts remain unknown. The aim of the present study was to directly quantitate mutant versus wildtype CaM transcript and protein levels in hearts of knock-in mice harboring the p.N98S mutation in the Calm1 gene. We found that the transcripts from the mutant Calm1 allele were the least abundantly expressed Calm transcripts in both hetero- and homozygous mutant hearts, while mutant hearts accumulate high levels of N98S-CaM protein in a Calm1N98S allele dosage-dependent manner, exceeding those of wildtype CaM protein. We further show that the severity of the electrophysiological phenotype incrementally increases with the graded increase in the mutant-to-wildtype CaM protein expression ratio seen in homozygous versus heterozygous mutant mice. We finally show a decrease in N98S-CaM protein degradation, suggesting that mutant CaM stabilization contributed to its enrichment in the heart. Our results support a novel mechanism by which a mutation in a single Calm gene can give rise to a severe phenotype.

overall_design: To assess the effect of hetero- and homozygosity for the Calm1N98S allele on CaM gene expression, we performed RNA-sequencing (RNA-seq) to quantify expression levels of Calm1, Calm2, and Calm3 transcripts in male hearts (left ventricles) of Calm1+/+, Calm1N98S/+ and Calm1N98S/N98S littermate mice at 2 to 4 months of age.

first: Wen-Chin

last: Tsai


title: Single-cell multi-omics characterize colorectal tumors, adjacent healthy tissue and matched organoids identifying CRC-unique features

city: Utrecht

first: Hendrik

last: Stunnenberg

state: Utrecht

address: Heidelberglaan 25

department: Research Department

institute: Princess Maxima Center for Pediatric Oncology

summary: Colorectal cancer (CRC) arises in the colorectal tissue driven by genetic disorder or the accumulation of somatic mutations, leading to abnormal epithelial cell growth. In this study, we employed single-nucleus multi-omics analysis, including single-nucleus RNA-seq and single-nucleus ATAC-seq, on over 100,000 high-quality nuclei to investigate the molecular landscape of both primary tissue and patient-derived organoids (PDOs). Our analysis showed that normal PDOs (N-PDOs) derived from tissue adjacent to tumors replicate the cellular composition and differentiation trajectory of colorectal crypts. In contrast, tumor PDOs (T-PDOs) showed patient-specific transcriptomic and epigenomic heterogeneity yet consistently maintained a stem cell-like state. T-PDOs retained the somatic mutation profile of the primary tumor while also exhibiting de novo mutations not detected in either the primary tumor or N-PDOs. Notably, inferred cell-cell interaction analysis highlighted the activin signaling pathway as a potential unique feature of fibroblast-epithelial interactions within tumor microenvironment. This study provides a comprehensive view of the transition from normal to malignant colorectal epithelium and underscores the utility of PDOs as faithful model for capturing both conserved and patient-specific features of colorectal cancer.

overall_design:
Multiome-seq: single-nuclei were isolated from primary colorectal normal and tumor tissues, their derived normal and tumor organoids. Joint snRNA and snATAC libraries were constructed from 10x Genomics Multiome kit.

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Raw files for human/patient samples are being made available in EGA (https://www.ebi.ac.uk/ega/) for controlled access to the personally identifiable sequence data. The  accession numbers are EGAS00001008067 and EGAS00001008110.
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first: Zhijun

last: Yu

first: Merel

last: Derksen

first: Brigit

last: te Pas

first: Sabrina

last: Ladstatter

first: Rene

last: Overmeer

first: Peter

last: Brazda

first: Marc

last: van de Wetering

first: Farzin

last: Pourfarzad

first: Robert

last: J Vries

first: Wout

last: Megchelenbrink

first: Christoph

last: Bock

first: Lucia

last: Altucci


title: Circadian rhythmicity and biopsychosocial characteristics influence opioid use in chronic low back pain

city: Kingston

first: Amanda

last: Zacharias

state: Ontario

address: 99 University Avenue

institute: Queen's University

summary: Background. Inter- and intra-individual fluctuations in pain intensity pose a major challenge to treatment efficacy, with a majority perceiving their pain relief as inadequate. Recent preclinical studies have identified circadian rhythmicity as a potential contributor to these fluctuations and therapeutic target. Methods. We therefore sought to determine the impact of these rhythms in people with chronic low back pain (CLBP) through a detailed characterization, including questionnaires to evaluate biopsychosocial characteristics, ecological momentary assessment (7-day e-diaries at 8:00/14:00/20:00) to assess pain fluctuations, and intra-day blood transcriptomics (8:00/20:00) to identify genes/pathways of interest. Results. While most individuals displayed constant or variable/mixed pain phenotypes, a distinct subset had daily fluctuations of increasing pain scores (>30% change in intensity over 12-hours in ≥4/7 days). This population had no opioid users, better biopsychosocial profiles, and differentially expressed transcripts relative to other pain phenotypes. The circadian-governed neutrophil degranulation pathway was particularly enriched among arhythmic individuals; the link between neutrophil degranulation and opioid use was further confirmed in a separate CLBP cohort. Conclusion. Our findings identify pain rhythmicity and the circadian expression of neutrophil degranulation pathways as indicators of CLBP outcomes, which may help provide a personalized approach to phenotyping biopsychosocial characteristics and medication use. This highlights the need to better understand the impact of circadian rhythmicity across chronic pain conditions.

overall_design: RNA-sequencing of human peripheral blood cells. Blood samples were collected during the day (7:00-9:00) and night (19:00-21:00) from participants with chronic low back pain.

first: Qingling

last: Duan

first: Nader

last: Ghasemlou


title: Imidazole propionate is a driver and therapeutic target in atherosclerosis [scRNA-seq]

city: Madrid

first: Diego

last: Mañanes

state: Madrid

address: C. de Melchor Fernández Almagro, 3

country: Spain

institute: Spanish National Center for Cardiovascular Research

summary: Atherosclerosis is the main underlying cause of cardiovascular diseases (CVDs). Its prevention is based on traditional cardiovascular risk factor-based scores but often fails to identify individuals at early stages of the disease. Here, we identified microbially produced imidazole propionate (ImP) as an early biomarker of atherosclerosis in mice and in two independent human cohorts. Furthermore, ImP administration induced atherosclerosis without altering lipid metabolism and it was associated with activation of both systemic and local innate and adaptive immunity and inflammation. Here, we used single-cell RNA-seq to characterize the local changes of aorta-derived cells in mice under treatment with ImP for 4 and 8 weeks. Notably, ImP caused atherosclerosis through the Imidazoline-1 receptor (I1R), and the blockade of the ImP/I1R axis inhibited the development of atherosclerosis induced by ImP as well as by high cholesterol diet in mice. Identification of ImP as an early biomarker for atherosclerosis and uncovering the contribution of the ImP/I1R axis in disease progression open new avenues to improve atherosclerosis early diagnosis and therapy.

overall_design: Gene expression profile at the single-cell level of aorta-derived cells from ApoE-/- mice treated (or not) with ImP (400μg/mouse/day) for 4 or 8 weeks in the drinking water and under chow diet. Two biological replicates (each a pool of 3 mice) for each experimental condition were analyzed. Multiplexing was done using CMO tags fpr single-cell RNA-seq protocol from 10x Genomics.

first: Iñaki

last: Robles-Vera

first: Annalaura

last: Mastrangelo

first: David

last: Sancho


title: Imidazole propionate is an early biomarker and therapeutic target for atherosclerosis [bulk RNA-seq]

summary: Atherosclerosis is the main underlying cause of cardiovascular diseases (CVDs). Its prevention is based on traditional cardiovascular risk factor-based scores but often fails to identify individuals at early stages of the disease. Here, we identified microbially produced imidazole propionate (ImP) as an early biomarker of atherosclerosis in mice and in two independent human cohorts. Furthermore, ImP administration induced atherosclerosis without altering lipid metabolism and it was associated with activation of both systemic and local innate and adaptive immunity and inflammation. Notably, ImP caused atherosclerosis through the Imidazoline-1 receptor (I1R), and the blockade of the ImP/I1R axis inhibited the development of atherosclerosis induced by ImP as well as by high cholesterol diet in mice. Here, we profiled three cell lines which represent cell types typically found in aortas (bone marrow-derived macrophages, mouse embryonic fibroblasts and mouse aortic endothelial cells) upon in vitro stimulation with ImP at different time points to better understand the transcriptional regulation of the ImP/I1R axis and its role in the development of the disease. Identification of ImP as an early biomarker for atherosclerosis and uncovering the contribution of the ImP/I1R axis in disease progression open new avenues to improve atherosclerosis early diagnosis and therapy.

overall_design: To investigate the transcriptional pathways upregulated by ImP stimulation in different cell types, we analyzed gene expression profile using bulk RNA-seq of cultutred bone marrow derived macrophages (BMDMs), mouse embryonic fibroblasts (MEFs) and mouse aortic endothelial cells (MAECs) stimulated in vitro with ImP (10µg/mL) for 0, 1 or 2h.


title: Effects of WDFY3 overexpression on the transcriptomic profile of murine bone-marrow derived macrophages.

city: New York

first: Hanrui

last: Zhang

state: United States

address: 630 West 168th Street

institute: Columbia University Irving Medical Center

summary: We determined the transcriptomic profile of bone-marrow derived macrophages (BMDMs) from mice overexpressing human WDFY3 and their wild-type littermate control mice. Specifically, these mice were engineered by knocking a construct consisting of the cDNA sequence encoding a 3x FLAG tag fused to human WDFY3 cDNA, preceded by a STOP cassette flanked by loxP sites, into the Rosa26 locus (Rosa26 loxP-STOP-loxP-3xFLAG-hWDFY3/+), with expression driven by the endogenous Rosa26 promoter. To achieve constitutive overexpression, male mice carrying the floxed allele were crossed with female carriers of the HprtCre strain (Stock No. 004302, The Jackson Laboratory), a Cre-deleter strain with 100% Cre-mediated recombination in oocytes, to generate heritable deletion of the loxP-STOP-loxP cassette (Rosa26 3xFLAG-hWDFY3/+). These Rosa26 3xFLAG-hWDFY3/+ mice were interbred to produce homozygotes (Rosa26 3xFLAG-hWDFY3/3xFLAG-hWDFY3) for knock-in (KI) of 3xFLAG-hWDFY3 (hWDFY3KI/KI) and wild-type littermate controls (Ctrl).

overall_design: RNA-seq of BMDMs from 6-8 week old male mice (n = 5 Ctrl mice, and 5 hWDFY3KI/KI mice).

first: Xun

last: Wu


title: Alternate isoforms of IRF7 Differentially Regulate Interferon Expression

city: Philadelphia

first: Kristen

last: Lynch

state: Pennsylvania

address: 906 Stellar Chance Labs 422 Curie Blvd

department: Biochemistry and Molecular Biophysics

institute: University of Pennsylvania

summary: Interferon Regulatory Factor 7 (IRF7), and its homologue IRF3, are master transcriptional regulators of the innate immune response. IRF7 binds to promoters of interferon beta (IFNb) and several IFNas, as a homodimer or as a heterodimer with IRF3 to drive expression of these type I IFNs, which in turn activate additional signaling pathways to promote expression of anti-viral genes. Here we demonstrate that retention of the first intron within the coding region of IRF7 is highly regulated across immune tissues and in response to viral infection and other immunologic signals. Importantly, retention of this intron generates an alternative translation start site, resulting in a N-terminally extended form of the protein (exIRF7). Using CRISPR gene editing to generate cells that only express exIRF7, or the canonical version of IRF7 (cIRF7), we demonstrate that exIRF7 uniquely activates a program of genes, including IFNb, in response to innate immune triggers. We conclude that alternative splicing of IRF7 is a previously unrecognized mechanisms used by human cells to tune the interferon response to viral infection and other immune challenges.

overall_design: RNA-seq profiling of Jurkat T-cells (JSL1) engineered by CRISPR to be deficient in IRF7 or express solely one spliced isoform. Cells were untreated or treated with either IFNa or poly(I:C) for 8 hours

first: Asmita

last: Panthi

first: Max

middle: B

last: Ferretti


first: Sambasivarao

last: Damaraju

overall_design: We performed whole transcriptome profiling from muscle of patients with cancer to decipher complex biological processes contributing to cachexia

first: Bhumi

last: Bhatt

first: Vickie

last: Baracos


title: SATB1 is a key regulator of quiescence in stem-like CD8+ T cells [RNA-seq]

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

summary: Chronic infections and cancers induce CD8+ T cell exhaustion, but within this exhausted CD8+ T cell pool, a self-renewing, stem-like subset known as progenitor CD8+ T (TPRO) cells play a crucial role in maintaining long-term immunity. These TPRO cells exhibit stem-like characteristics, including quiescence, multipotency, and self-renewal, which are the cardinal features of memory T cells. However, the mechanisms that preserve their stem-like properties under chronic antigen stimulation remain unclear. In this study, we identified that SATB1 as a shared feature is highly expressed in both TPRO and memory CD8+ T cells. While the role of SATB1 in stem-like CD8+ T cells remains unknown, its function as epigenetic regulator in promoting quiescence in hematopoietic stem cells led us to hypothesize that SATB1 plays a pivotal role in regulating the stemness of TPRO and memory CD8+ T cells. To test this hypothesis, we employed CRISPR-mediated gene editing to delete Satb1 gene specifically in CD8+ T cells. Upon chronic LCMV infection, we found that SATB1-deficient CD8+ T cells failed to maintain TPRO subset with enhanced transition towards terminally differentiated cells. Similarly, the SATB1 deficiency in acute viral infection impaired the formation of memory CD8+ T cells. Mechanistically, our multi-omic assays revealed that SATB1 regulates the chromatin accessibility and transcriptional activities of stemness-associated genes, such asTcf7, Bach2,andMyb. Overall, our results underscore the critical role of SATB1 in maintaining the transcriptional and epigenetic features of stem-like CD8+ T cells, shedding light on the previously unappreciated regulatory mechanisms that sustain the stemness of antigen-specific CD8+ T cells.

overall_design: Naive P14 CD8 T cells isolated from mouse spleens were transfected with CRISPR ribonucleoprotein (RNP)  to knock out CD19 (sgCtrl) or Satb1 (sgSatb1). 2500 transfected CD45.1+ P14 T cells were transferred to CD45.1- C57BL/6 mice followed by LCMV Clone 13 infection. P14 T cells were FACS-sorted from  spleens on day 21 p.i. and extracted total RNA was used for RNA sequencing.

first: Siying

last: Lin


title: SATB1 is a key regulator of quiescence in stem-like CD8+ T cells [ATAC-seq]

overall_design: Naive P14 CD8 T cells isolated from mouse spleens were transfected with CRISPR ribonucleoprotein (RNP)  to knock out CD19 (sgCtrl) as control or Satb1 (sgSatb1). 2500 transfected CD45.1+ P14 T cells were transferred to CD45.1- C57BL/6 mice followed by LCMV Clone 13 infection. P14 T cells were FACS-sorted from  spleens on day 21 p.i. and extracted nucei were used for ATAC-seq library construction following the Omni-ATAC protocol (Nature Methods, 2017).

last: cui


title: SATB1 is a key regulator of quiescence in stem-like CD8+ T cells [Multiome]

overall_design: scRNA + scATAC


title: Transcriptomics of BMSCs and BMDMs

city: Hangzhou

first: Kaiyu

last: Liang

address: Qingchun East Road

department: Sir Run Run Shaw Hospital

institute: Zhejiang University

summary: The RNA-seq data of BMSCs and BMDMs

overall_design: BMDM and BMSC were treated with NZM after pretreatment with model drugs.

first: Xiangqian

last: Fang

first: Yueqi

last: Zhao

first: Ruikang

last: Tang


title: Bulk RNA Sequencing of Human PDAC: TLS-Positive vs. TLS-Negative

city: St. Petersburg

first: JUNKO

last: SAWADA

address: 600 5th Street South

institute: Johns Hopkins All Children's Hispital

summary: The formation of tertiary lymphoid structures (TLSs) in tumors is significantly correlated with prolonged patient survival, better prognosis, and improved response to immunotherapy. Understanding the tumor microenvironments involved in TLS formation is crucial. This bulk RNA sequencing study utilized archived FFPE samples from PDAC patients to reveal gene expression profiles in tumors with TLS formation.

overall_design: Archived PDAC FFPE tumor samples were categorized as TLS-positive or TLS-negative based on H&E staining

first: Junko

last: Sawada

first: Nobuyoshi

last: Hiraoka

first: Masanobu

last: Komatsu


title: Bulk RNA Sequencing of Mouse Models for TLS Formation in KxPxCx Pancreatic Cancer

summary: The formation of tertiary lymphoid structures (TLSs) in human cancer patients is significantly correlated with prolonged survival, better prognosis, and improved responses to immune checkpoint therapy. We generated mouse models to investigate TLS formation using the KxPxCx pancreatic cancer model

overall_design: Tumor-inoculated mice were treated with an agonistic antibody of LTβR, a STING agonist (ADU-S100), or a combination of these agents. Following treatment, tumor tissues were collected and used for bulk RNA sequencing

first: Ashley

middle: E

last: Fournier-Goss


title: Neutral sphingomyelinase 2 inhibition alters inflammatory gene expression signatures in the brain of mice infected with West Nile virus

first: Miguel A.

last: Martín-Acebes

address: Ctra. de La Coruña, km 7, 5

institute: INIA-CSIC

summary: To investigate the in vivo effects of DPTIP during WNV infection in a mouse model, we compared infected mice with WNV NY99 treated with DPTIP or vehicle and uninfected (mock) mice. DPTIP is a pro-dug that targets mouse nSMASE. We then performed gene expression profiling analysis using data obtained from RNA-seq from infected-vehicle mice, uninfected mice and infected DPTIP-treated mice

overall_design: Comparative gene expression profiling analysis of brain RNA-seq data for infected vehicle-mice, uninfected mice and infected DPTIP-treated mice

first: Patricia

last: Mingo-Casas

first: Ana-Belén

last: Blázquez

first: Miguel


title: Cellular states associated with metastatic organotropism and survival in patients with pancreatic ductal adenocarcinoma

city: NY

first: Morteza

last: Chalabi Hajkarim

state: NY

department: Hemo/Onco

institute: CUIMC

summary: Some patients with localized pancreatic ductal adenocarcinoma (PDAC) undergo resection with curative intent, but most experience disease recurrence and succumb to their disease. Through examination of 743 PDAC patients in a single-center we find that the site of first recurrence is a major predictor of survival. Patients with initial liver-metastatic recurrence (LIV-MR, n = 100) had significantly shorter disease-free and overall survival compared to those with initial recurrence to the lung (LUN-MR, n = 31). We performed single-nucleus RNA-seq (snRNA-seq) and low-pass whole-genome sequencing (lpWGS) on a representative population of this cohort, including 21 primary PDACs with either LIV-MR or LUN-MR, and found that malignant cells adopt transcriptional programs that mimicked that of their ultimate metastatic target organ. We validated the LIV-MR and LUN-MR signatures in multiple data sets, including single-cell RNA-seq of normal human adult and fetal liver and lung tissues, bulk, single-cell, and spatial transcriptomics of PDAC lung and liver metastases, and in vivo data modelling metastatic organotropism in PDAC and other lineages. We reconstructed two different trajectories of malignant transformation in PDAC and find that the LIV-MR and LUN-MR are associated with these, suggesting that subsequent metastatic organotropism may be determined early in tumorigenesis. Furthermore, primary PDAC tumors recurring with LIV-MR compared to LUN-MR were deplete of infiltrating T cells and enriched with M2-like macrophages, highlighting potential contributions to subsequent outcomes. Taken together, this work provides evidence for pre-existing cellular adaptations that determine metastatic organotropism and may be useful for prognostication and development of therapeutic strategies at the time of diagnosis of resectable PDAC.

overall_design: Pool matched lp-WGS was performed in addtion to single-nucleus RNA sequencing of 91,872 nuclei from 21 primary PDAC specimens, including 8 from patients with subsequent liver- and 13 with lung-metastatic recurrence. Out of 21 patients, 4 received neoadjuvant therapy and the rest were treatment-naïve. Together, this data served to improve the identification of the malignant and non-malignant cell compartments.

middle: C

last: Hajkarim

first: Michael

last: May

first: Amit

middle: D

last: Amin

first: Basil

last: Bakir

first: Somnath

last: Tagore

first: Parin

last: Shah

first: Lindsay

last: Caprio

first: Zachary

last: Walsh

first: Sinan

last: Abuzaid

first: Jacob

last: Jamison

first: Alissa

last: Michel

first: Winston

last: Wong

first: Neha

last: Shaikh

first: Priyanka

last: Ramaradj

first: Hanina

last: Hibshoosh

first: Anil

middle: K

last: Rustgi

first: Alexander

last: Raufi

first: Gulam

last: Manji

first: Benjamin

last: Izar


first: Morteza

last: Chalabi Hajkarim

overall_design: Single-nucleus RNA sequencing of 91,872 nuclei from 21 primary PDAC specimens, including 8 from patients with subsequent liver- and 13 with lung-metastatic recurrence. Out of 21 patients, 4 received neoadjuvant therapy and the rest were treatment-naïve.

last: Hajkarim

first: Michael

last: May

first: Amit

last: Amin

middle: A


title: Gene expression profiling of human glioblastoma cells under culture with endothelial cell condition media using Affymetrix arrays

status: Public on Jul 15 2025

city: Nantes

first: Julie

last: Gavard

address: 8 quai Moncousu

country: France

institute: INSERM

summary:
This study investigates the gene expression changes in human glioblastoma cells subjected to endothelial cell condition media. Samples were collected and processed at the GENOMIC platform of Institut Cochin, Paris.
RNA was extracted, labeled, and hybridized onto Affymetrix GeneChips. Data were processed using standard normalization pipelines.

overall_design:
The study includes 4 samples divided into [control and treated groups. Each condition was replicated 2 times. The goal was to identify differentially expressed genes associated with EC coculture
Submitter comment: cel files are missing as data were generated in 2010-12

first: S

last: Rosinka

first: J


title: Bulk RNAseq of in vitro human Rett syndrome neurons with addition of NAD supplementation

city: Oxnard

first: Abril

last: Morales

state: CA

address: 1300 East Pleasant Valley Road, Spc 119

institute: University of California, Los Angeles

summary: Here we employed RNA-seq on neuronal cultures differentiated from human induced pluripotent stem cells (hIPSCs) derived from Rett syndrome patients. The study aims to understand the effects of PARP stimulation through the treatment of nicotinamide adenine dinucleotide (NAD) on gene expression of MECP2 mutant neurons.

overall_design: Two isogenic hIPSC-derived patient were differentiated into neurons. R18 corresponds to the control line and R15 corresponds to the MECP2 mutant line. Mutant neurons were also treated with 10 mM of NAD for 48 hours.

first: William

last: Lowry


title: Reduced vaccine-induced germinal center outputs in inflammatory bowel disease patients treated with anti-TNF biologics

city: Toronto

first: Tania

middle: H

last: Watts

address: 1 King's College Circle

department: Immunology

institute: University of Toronto

summary: Tumor necrosis factor (TNF) blocking agents are widely used to treat patients with immune-mediated inflammatory diseases. The complete absence of TNF in mice impairs germinal center responses. Less is known about the impact of anti-TNF therapy on specific immune responses in humans. The widespread vaccination against SARS-CoV-2 offered an unprecedented opportunity to investigate the effects of biological therapies on the response to a specific immunization. Previous work demonstrated that inflammatory bowel disease (IBD) patients treated with anti-TNF agents exhibit decreased Spike (S)-specific antibody responses compared to IBD patients treated with anti-IL-12/23 or healthy controls, even after four doses of mRNA vaccine. Here, we performed immune profiling of S-specific memory B cells (MBCs) isolated from anti-TNF treated- or anti-IL-12/23- treated IBD patients and healthy controls via 5' single cell RNA-sequencing, CITE-sequencing, and BCR-sequencing, to examine the transcriptome of and breadth of memory B cell responses to SARS-CoV-2 mRNA vaccination. This study provided in vivo evidence that anti-TNF, but not anti-IL-12/23, therapy impairs the quantity of and quality of antigen-specific germinal center outputs in humans.

overall_design: CITE-seq and BCR-seq: From the PBMCs of healthy controls (n=3), anti-TNF treated IBD patients (n=5) and anti-IL-12/23 treated IBD patients (n=4) isolated 3-4 months post vaccine dose 2 (Timepoint 4) and vaccine dose 3 (Timepoint 6), we tagged each individual with an unique TotalSeqC hastag antibody (HTOs) and sorted for Spike-specific memory B cells, which were then analyzed using CITE-seq and BCR-seq. Patients were matched between timepoints, with the exception of one anti-TNF treated IBD patient (TotalSeq-C hashtag #12) that was only sampled at Timepoint 4.

first: Michelle

last: Cheung

first: Mark

last: Silverberg


title: Using a female-specific isoform of doublesex to explore male-specific hearing in mosquitoes

city: London

first: Joerg

last: Albert

address: 332 Grays Inn Rd

department: Ear Institute

country: United Kingdom

institute: University College London

summary: Animal reproduction relies on elaborate divisions of labour and multiple dimorphisms between the sexes. Primary dimorphisms affect core elements of reproduction, secondary dimorphisms affect more indirect traits, including complex behaviours. In disease-transmitting mosquitoes, males locate females acoustically prior to copulation (phonotaxis). No comparable acoustic behaviour is known for females. As a result, the males’ ears – and hearing performance - have evolved to become substantially more complex. Sex-specific hearing in mosquitoes is in part controlled by the doublesex (dsx) gene. Intriguingly, dsx forms a linker between primary and secondary dimorphisms: spermatogenesis and ear morphogenesis share considerable molecular overlap and both depend on dsx expression patterns. We have combined transcriptomics with functional-anatomical analyses to dissect dsx-dependent hearing in the malaria mosquito Anopheles gambiae. By cross-linking our auditory findings to the genetic bases of spermatogenesis we advance the molecular understanding of sex-specific hearing mechanisms in insects, highlighting the special roles of ciliary factors therein.

overall_design: RNA-seq profiling of Anopheles gambiae Johnston's organs (JOs), including G3-strain male (dsxF+/+ XY) and female (dsxF+/+ XX) controls, as well as intersex (dsxF-/- XX) samples.

first: Matthew

last: Su

first: Marcos

last: Georgiades

first: Marta

last: Andrés

first: Jason

last: Somers

first: Judit

last: Bagi

first: YuMin

middle: M

last: Loh

first: Yifeng

middle: Y

last: Xu

first: Kyros

last: Kyrou

first: Andrea

last: Crisanti

middle: T


title: Defining the Ovarian Cancer Precancerous Landscape through Modeling Fallopian Tube Epithelium Reprogramming Driven by Extracellular Vesicles

city: Kansas City

first: Andrew

last: Godwin

state: Kansas

address: 3901 Rainbow Blvd

institute: Kansas University Medical Center

summary: Serous tubal intraepithelial carcinomas (STIC lesions) in the human fallopian tube epithelium (hFTE) are theorized to give rise to high grade serous ovarian cancers (HGSOC). Small extracellular vesicles (sEVs) are known to mediate key signaling in both normal and cancerous tissues, but few ex vivo systems exist for studying sEV impact on hFTE tissue. Here, we present a microfluidic tissue culture platform with combined spatial transcriptomic and proteomic readouts that allows us to profile dual responses in tissue exposed to sEV “messages”—capturing both short-term transcriptomic shifts in the tissue and long-term changes in protein cargo of secreted EVs (the “reply”). Using spatial transcriptomics, we show that the short-term 1-day exposure to ovarian cancer-derived sEVs alters expression of 61 transcripts in secretory cells, the progenitor of HGSOC, notably upregulating immune-related mRNA, including CXCL family chemokines, VCAM1, and pro-inflammatory mediators (NFKB1, IL1B, IFNA7/17). Additionally, we observed the long-term 14-day exposure to sEVs alters the expression of 7 transcripts and 25 EV cargo proteins of fallopian tube derived EVs (“secondary release EVs”) following stimulus from cancer EVs. Together, tissue transcriptomics and tissue-derived EV proteomics indicate that ovarian cancer derived sEVs rewire target cell signaling to modify the tubal immune landscape. This study provides insights into the early molecular changes associated with the pathogenesis of ovarian cancer in its tissue of origin, providing a platform to study EV-tissue interactions and identify how sEVs drive cell signaling reprogramming in hFTE.

overall_design: Fallopian tube (FT) tissue explants were cultured on an organ-on-chip tissue culture system. Samples were treated daily with either: 1) PBS (control), 2) FT sEVs (FT240-derived, 1.5x10^9 particles/day), or 3) HGSOC sEVs (OVCAR3-derived, 1.5x10^9 particles/day). To study both short- and long-term consequences of EV insult, we exposed the tissue to sEVs for either 1 day (n = 12 samples) or repeatedly over 14 days (n = 10 samples). At the end of the treatment period, fallopian tissue samples were collected for both 1-day and 14-day conditions and analyzed on the GeoMx Digital Spatial Profiler using the Cancer Transcriptome Atlas (CTA) panel. The GeoMx platform was used to segment the FT epithelium into ciliated and secretory cell types based on staining for PAX8 (secretory cell marker) and FOXJ1 (ciliated cell marker). Final output is transcript expression in ciliated or secretory cells, in each of three treatment conditions (PBS, OVCAR3, FT240), after culture for either 1 day or 14 day.

first: Jared

last: Sipes

first: Didi

last: Zha

first: Sagar

last: Rayamajhi

first: Leonidas

last: Bantis

first: Rashna

last: Madan

first: Amrita

last: Mitra

first: Rajni

middle: V

last: Puri

first: Mohammod Mahmudur

last: Rahman

first: Foyez

last: Ahmmed

first: Harsh

last: Pathak

first: Angela

last: Russo

first: Mihaela

last: Sardiu

first: Brett

last: Isenberg

first: Brian

middle: P

last: Cain

first: Jonathan

last: Coppeta

first: Pamoda

last: Galhenage

first: Shailja

last: Pathania

first: Shannon

last: MacLaughlan David

first: Joanna

last: Burdette


title: A single-cell multiomics roadmap of zebrafish spermatogenesis reveals conserved regulatory principles of male germline formation [scRNA-Seq]

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

institute: CABD/CSIC

summary: Spermatogenesis is a highly complex biological process through which male sperm cells, or spermatozoa, are produced in the testes. Besides enabling the flow of genetic information, spermatogenesis also creates a potential template for inter- and transgenerational inheritance of gene-regulatory states. While extensively studied in mammals, current knowledge of anamniote spermatogenesis remains limited. Here we provide a comprehensive resource consisting of single-cell gene expression and chromatin accessibility data complemented by base-resolution DNA methylome profiling of sorted germ cell populations, obtained from zebrafish (Danio rerio) testes. We identify major germ and somatic cell types implicated in zebrafish spermatogenesis as well as transcriptional drivers associated with each cell type. Moreover, we describe a localised DNA methylome reconfiguration event associated with the spermatocyte stage, and both local and global changes in chromatin accessibility leading to chromatin compaction in spermatids. Finally, we identify loci that escape global chromatin compaction, and which remain accessible thus forming a potential template for the intergenerational transmission of epigenetic states. In summary, our high-resolution cellular atlas of zebrafish spermatogenesis constitutes a major community resource that will enable further studies of germ cell development, evolution, and that will deepen our understanding of diverse molecular mechanisms implicated in genetic and epigenetic inheritance.

overall_design: scRNAseq and scATACseq experiments in zebrafish testes.

first: Ana Maria

last: Burgos-Ruíz

first: Michael

last: Fansuo-Geng

first: Gala

last: Pujol

first: Estefanía

last: Sanabria

first: Thirsa

last: Brethouwer

first: María

last: Almuedo-Castillo

first: Aurora

last: Ruiz-Herrera

middle: J

first: Ozren

last: Bogdanovic


title: ZBTB11 Depletion Targets Metabolic Vulnerabilities in K-Ras Inhibitor Resistant PDAC [CRISPRi RNA-seq]

city: La Jolla

first: Eric

middle: S.

last: Wang

address: 10901 North Torrey Pines Road

department: Cancer Metabolism and Microenvironment Program

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Over 95% of pancreatic ductal adenocarcinomas (PDAC) harbor oncogenic mutations in K-Ras. However, upon treatment with K-Ras inhibitors, PDAC cancer cells undergo rapid metabolic reprogramming towards an oxidative phosphorylation-dependent, drug-resistant state. In this work, we demonstrate that this metabolic shift is associated with upregulation of the transcription factor ZBTB11, and both the metabolic state and the K-Ras inhibitor drug resistance can be attenuated by ZBTB11 depletion. We develop molecular glue degraders of ZBTB11 and demonstrate that they reprogram the aberrant transcriptome, proteome, metabolome, and bioenergetics of K-Ras inhibitor resistant PDAC, resensitizing them to K-Ras inhibition. ZBTB11 degradation leverages cell-type and cell-state specific differences in gene regulatory mechanisms controlling OXPHOS-pathway transcripts to selectively target the K-Ras inhibitor resistant state in PDAC while sparing hiPSC-derived neurons. Together, this work establishes ZBTB11 as a druggable vulnerability in K-Ras inhibitor-resistant PDAC and provides a suite of molecular glue degrader tool compounds to investigate its function.

overall_design: Time-course RNA-seq analysis following dCas9-KRAB induction of ZBTB11 knockdown in the Sotorasib-resistant MiaPaCa-2 cell line to map the impact of ZBTB11 knockdown on the global PDAC transcriptome

middle: S

first: Nathan

middle: L

last: Tran

first: Fleur

last: Ferguson


title: A single-cell multiomics roadmap of zebrafish spermatogenesis reveals conserved regulatory principles of male germline formation [scATAC-Seq]