title: Single cell RNA sequencing of the progeny of PD1hi vs PD1low TCF-1+ P14 precursor cells on day 15 after secondary host infection with LCMV Armstrong [scRNA-Seq BD Rhapsody]

city: Freising

first: Gustavo

middle: P.

last: de Almeida

state: Bavaria

address: Liesel-Beckmann-Str. 1

department: Division of Animal Physiology and Immunology

institute: Technical University of Munich

summary: T-cell exhaustion limits effector T-cell function in chronic infection and tumors. The development of these hypofunctional T-cells and of their precursors was considered to require stimulatory conditions met only upon persisting exposure to antigen and inflammation. In sharp contrast, we found similar T-cell populations in the early phase of acute infections. At that stage early developing TCF1+ precursor population shows an unexpected diversity, which includes precursors of normal memory T-cells but also cells with a phenotype, gene-expression, and epigenetic profile that resembles precursors of exhausted T-cells found in chronic infections. We demonstrate that high ligand affinity promotes, and PD-1 signaling restricts the development of these precursors. While these exhausted precursors are initially frequently found, they decline without being completely lost in infections the immune system resolves. We therefore concluded that precursor T-cells with at least two distinct phenotypes are preemptively generated irrespectively of the outcome of the infection. Here, using adoptively transferred P14 cells, these subsets were isolated early during infection, re-transfered into new hosts that were subsequently infected as well. The entire progeny of the re-transfered cells was analyzed on day 15 pi.

overall_design: CD45.1+ TCR-transgenic P14 T cells co-expressing a dual GFP/mCherry reporter contruct under the control of the Tcf7-promoter were isolated using magentic beads and adoptively transfered into host mice carrying the same reporter construct. On day 1 post transfer host mice were infected with 2x10e5 PFU of LCMV Armstrong intra-peritoneously. On day 4.5 pi P14 cells were re-isolated from these host, stained with flurorescent antibodies against PD-1 and 2x10e3 Tcf7+PD-1hi or Tcf7+PD-1low P14 cells were re-transfered into new host mice. On day 15 pi, total P14 cells from the the spleens of the secondary hosts were isolated and subjected to the BD Rhapsody scRNA-Seq pipeline.

first: Carl-Philipp

last: Hackstein

first: Dietmar

last: Zehn


title: Single cell RNA sequencing of TCF-1+ P14 precursor cells sorted 3.25 days after infection with LCMV Armstrong [scRNA-Seq BD Rhapsody]

status: Public on Feb 21 2025

country: Germany

type: Expression profiling by high throughput sequencing

summary: T-cell exhaustion limits effector T-cell function in chronic infection and tumors. The development of these hypofunctional T-cells and of their precursors was considered to require stimulatory conditions met only upon persisting exposure to antigen and inflammation. In sharp contrast, we found similar T-cell populations in the early phase of acute infections. At that stage early developing TCF1+ precursor population shows an unexpected diversity, which includes precursors of normal memory T-cells but also cells with a phenotype, gene-expression, and epigenetic profile that resembles precursors of exhausted T-cells found in chronic infections. We demonstrate that high ligand affinity promotes, and PD-1 signaling restricts the development of these precursors. While these exhausted precursors are initially frequently found, they decline without being completely lost in infections the immune system resolves. We therefore concluded that precursor T-cells with at least two distinct phenotypes are preemptively generated irrespectively of the outcome of the infection. In this experiment, cells from day 3.25 pi were analyzed to determine if the different subsets could be detected.

overall_design: Using magnetic beads, CD45.1+ 2x10e5 P14 T cells were isolated and adoptively transfered into wildtype B6 mice intravenously. One day after transfer, mice were infected with 2x10e5 PFU of LCMV Armstrong i.p. On day 3.25 after infection, the spleens of the animals were harvested, single cells suspensions were prepared, P14 cells were sorted as CD45.1+ cells and subjected to the BD Rhapsody library prep pipeline.

middle: P


title: Impact of the (p)ppGpp synthesis and maintenance of GTP homeostasis during stationary phase starvation on the transcriptome

city: Tübingen

first: Christiane

last: Wolz

address: Elfriede-Aulhorn-Straße 6

department: Interfaculty Institute for Medical Microbiology and Infection Medicine

institute: University of Tübingen

summary: This work investigates the molecular mechanisms that determine the requirement of (p)ppGpp-mediated GTP homeostasis for viability during prolonged nutritional stress. Initially, we observed that the absence of (p)ppGpp in S. aureus resulted in reduced culturability and elevated levels of guanosine nucleotides (GMP, GDP, and GTP) when cells experienced prolonged starvation during stationary phase. Analysis of metabolic activity and cell membrane function revealed, that (p)ppGpp-deficiency does not immediately  lead to cell death but rather to a VBNC state where cell become division-incompetent and display reduced metabolic activity. The cell membrane stayed intact, however (p)ppGpp-deficient cells displayed reduced membrane potential and increased membrane fluidity. Since missing translation inhibition and elevated oxidative stress levels could not be identified as the cause for the VBNC state of the (p)ppGpp-deficient cells, we conducted transcriptomic analysis on S. aureus wildtype and a (p)ppGpp0 mutant, as well as isogenic guaBA-deficient strains, to gain a more thorough understanding of the genetic basis through which (p)ppGpp maintains cell homeostasis during nutritional stress in the stationary phase and the importance of cellular GTP homeostasis to ensure viability. RNAseq analysis revealed that the TCA cycle and electron transport chain, particularly complex IV/the terminal oxidase qoxABCD, were strongly downregulated in the (p)ppGpp-deficient starved cells. By mutating the initiation nucleotide (TSS +1) of the qoxABCD operon, we were able to increase qoxA expression and membrane potential in a (p)ppGpp0 strain during stationary phase starvation. This resulted in increased culturability during prolonged nutrient starvation, demonstrating the necessity of PMF maintenance. Furthermore , we could show that the decreased membrane potential in starved (p)ppGpp-deficient cells contributes to decreased antibiotic tolerance towards oxacillin and  ciprofloxacin. In summary, our data suggests, that (p)ppGpp-dependent regulation of cellular GTP homeostasis during nutritional stress is crucial for maintenance of culturability and antibiotic tolerance.

overall_design: Samples of S. aureus HG001 wildtype, a (p)ppGpp0 mutant, ΔguaBA mutant and a (p)ppGpp0 ΔguaBA mutant were grown under aerobic conditions (37°C, 200 rpm) to late stationary growth phase (24h)in chemically-defined medium. The final optical densitiy of the cultures was app 4.6 - 5.0. Each strain and condition was performed in biological triplicates.

first: Andrea

last: Salzer

first: Jennifer

last: Müller


title: Transcriptomic analysis of flies with Yki gut tumors

city: Boston

first: Yanhui

last: Hu

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

country: USA

institute: Harvard Medical School

summary:
Purpose: Flies with Yki gut tumors is a widely used Drosophila model of cancer cachexia. Since cancer cachexia is a multi-organ syndrome, its investigation requires understanding how tumors induce metabolic dysfunction in peripheral organs. To address this, we performed a body-wide single-cell transcriptome analysis of Yki tumor model flies.
Methods: snRNA-seq analysis of whole-body flies (without heads) with and without Yki gut tumors.
Results: The data provides information of transcriptome alternations related to tumor-induced cachexia, including expression of metabolic genes and tumor-host organ communications.
Conclusions: Cachexia phenotypes in Yki tumor model flies originated from metabolic dysregulation in peripheral organs that induced by tumor secreted factors.

overall_design: The following genotypes were used: i) control: esg-GAL4, tub-GAL80TS > UAS-GFP. ii) Yki flies: esg-GAL4, tub-GAL80TS > UAS-GFP, UAS-yki3SA. In total, 122,898 nuclei were profiled (25,146 from control and 42,375 from Yki flies at Day 5; 19,050 from control and 36,327 from Yki flies at Day 8).

first: Liu

last: Ying

first: Hu

last: Yanhui

first: Chen

last: Weihang

first: Perrimon

last: Norbert


title: Precursors of exhausted T-cells are preemptively formed in acute infection

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

overall_design: Refer to individual Series


title: Tracing functional (epi)genomic imprints and their evolutionary origins in human defense antiviral cellular response (STARR-transcripts-Seq)

status: Public on Feb 24 2025

city: Athens

first: Marios

last: Agelopoulos

state: Attica

address: 4 Soranou Ephessiou Str

department: Center of Basic Research

country: Greece

institute: Biomedical Research Foundation Academy of Athens

type: Genome binding/occupancy profiling by high throughput sequencing

summary: An integral part of human cellular homeostasis substantially relies on defense transcriptional responses tailored to fight microbial pathogens, including Viruses. However, a definitive anatomy of the “virus-responsive” fates of the non-coding genome was largely elusive. Here, we exhaustively assayed the human transcriptome and epigenome under naïve and antiviral cellular states and defined remarkable reprogramming to mark the exchange of cellular fates, involving previously unspecified, unsupervised, or overlooked non-coding entities endowed with thousands of novel virus-responsive enhancers, Super-enhancers (SEs), and Repetitive DNA enhancers. These functional determinants demonstrate superior chromatin architecture, stimulus-specificity, and transcriptional fitness, and neighbor, reside proximal, or entirely coincide with hundreds of the virus-stimulated genes, while a multitude of those is bound by the master antimicrobial TFs, IRF3 or/and NFκB, upon cell infection. A plethora of these DNA elements is traced within the repetitive fate of the human genome including Simple Tandem Repeats (STRs), Dispersed Repeats (DRs) such as retrotransposons and DNA transposons, and chimeras of those, enriched in HCTFBSs recognized by IRF3 or/and NFκB and exhibits pervasive imprints in the genomes of evolutionary recent, old and ancient species, including viruses. These findings emphasize the role of the architectural and functional compartmentalization of the human epigenome in naïve and infected cells on the perplexing natural conflicts and mechanistic dependencies that impose the frontage of defense gene expression in humans.

overall_design: STARR-transcripts-Seq

first: Marianna

middle: A

last: Koutsi

first: Marialena

last: Pouliou

first: Giannis

last: Vatsellas

first: Konstantinos

last: Zagkas

first: Marili

last: Vasilogianni

first: Lydia

last: Champezou

first: Dimitris

last: Chatzopoulos

first: Alexandra

last: Kouroukli


title: Bulk RNA sequencing of PD1hi vs PD1low TCF-1+ P14 precursor cells sorted 7 days after infection with LCMV Armstrong [bulk RNA-seq]

first: Gustavo

last: de Almeida

summary: T-cell exhaustion limits effector T-cell function in chronic infection and tumors. The development of these hypofunctional T-cells was considered to require stimulatory conditions met only upon persisting exposure to antigen and inflammation. In sharp contrast, we found strong diversity among precursor T-cells formed early in acute infections. This includes precursors of normal memory T-cells and cells with phenotypes, gene-expression, and epigenetic profiles that resemble precursors of exhausted T-cells found in chronic infections. We demonstrate that high ligand affinity promotes, and PD-1 signaling restricts the development of these precursors. While these exhausted precursors are initially frequently found, they decline without being completely lost in infections the immune system resolves. We therefore concluded that T-cells are preemptively generated irrespectively of the outcome of the infection.

overall_design: PD-1 expression levels can be used to distinguish Tpex-like and classic memory precursor CD8 T cells during acute infection . To investigate differences between PD-1lo vs PD-1hi precursors, we used a P14 Tcf7yfp(bright)mCherry reporter mouse that were adoptively transferred into Vb5 TCR transgenic host mice. Host mice were then infected with LCMV-Armstrong. CD8 T cells were isolated on day 7 pi and sorted as KLRG1- Tc7-reporter+ PD-1lo vs PD-1hi and submitted for RNA-sequencing.

first: Carl-Philipp

last: Hackstein

first: Dietmar

last: Zehn


title: Single cell RNA sequencing of TCF-1+  precursor cells reacting to LCMV gp33 vs np396 multimers sorted 30 days after infection with LCMV Armstrong [scRNA-Seq + TCR 10x]

summary: T-cell exhaustion limits effector T-cell function in chronic infection and tumors. The development of these hypofunctional T-cells and of their precursors was considered to require stimulatory conditions met only upon persisting exposure to antigen and inflammation. In sharp contrast, we found similar T-cell populations in the early phase of acute infections. At that stage early developing TCF1+ precursor population shows an unexpected diversity, which includes precursors of normal memory T-cells but also cells with a phenotype, gene-expression, and epigenetic profile that resembles precursors of exhausted T-cells found in chronic infections. We demonstrate that high ligand affinity promotes, and PD-1 signaling restricts the development of these precursors. While these exhausted precursors are initially frequently found, they decline without being completely lost in infections the immune system resolves. We therefore concluded that precursor T-cells with at least two distinct phenotypes are preemptively generated irrespectively of the outcome of the infection. In this experiment, the transcriptome and TCR-sequences of endogenous gp33 or np396 specific CD8 T-cells were analyzed on day 30 post infection to assess the role of TCR-affinity and antigen-specificity in the formation of the different CD8 T-cell precursors.

overall_design: Tcf7-reporter mice were infected with 2x10e5 PFU of LCMV Armstrong intra-peritoneally. On day 30 pi the spleens of the animals were harvested and reporter-positive cells reacting to gp33 or np396 multimers were isolated, sorted and subjected to the 10x library pipeline.


title: De novo transcriptome assembly and annotation of the semi-wild Gayal (Bos frontalis)

status: Public on Feb 19 2025

city: kunming

first: Zhendong

last: Gao

state: -- Please Select --

address: No. 452 Fengyuan Road, Panlong District

country: China

institute: Yunnan Agricultural University

summary: The Gayal (Bos frontalis) is a rare semi-wild Bovine species that inhabits the harsh environments of Indo-China. Although the origins of the Gayal remain largely enigmatic, addressing the lack of comprehensive transcriptomic data is critical for understanding its genetic and molecular characteristics, which are essential for formulating effective conservation and management plans. In this study, an integrated PacBio Iso-seq and RNA-seq analysis was conducted on samples from 10 different organs and tissues of the Gayal, with each being sequenced in triplicate. The samples analyzed included the heart, liver, spleen, lung, kidney, rumen, abomasum, duodenum, ileum, and rectum. This comprehensive analysis resulted in the identification of 30,760 full-length transcripts ranging from 363 bp to 7,157 bp, with transcript information matched to seven commonly used databases. Gene family clustering and phylogenetic analyses encompassed a comprehensive dataset of 9 Bovine species, including the Gayal. Additionally, long non-coding RNAs (lncRNAs) were identified across all sampled tissues, and comprehensive gene expression profiles and differential expression gene analyses were performed. These findings provide a rich repository of genetic information, laying the foundation for comprehensive functional genomics studies and paving the way for deeper insights into the molecular mechanisms of the Gayal, thereby advancing our understanding of its transcriptome architecture and offering crucial data for conservation efforts and practical applications.

overall_design: A 3-year-old male Gayal was sacrificed for tissue sampling, RNA was extracted using TRIzol reagent, treated with DNase I, and evaluated for quality using Nanodrop 2000, agarose gel electrophoresis, and Agilent 2100 platform.

first: Bo

last: Wang

first: Ying

last: Lu

first: Yuqing

last: Chong

first: Mengfei

last: Li

first: Jieyun

last: Hong

first: Jiao

last: Wu

first: Dongmei

last: Xi

first: Weidong

last: Deng


title: HIF Regulates Multiple Translated Endogenous Retroviruses: Implications for Cancer Immunotherapy [Polysome-Seq]

status: Public on Feb 20 2025

first: Qinqin

last: Jiang

state: Ma

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Clear cell renal cell carcinoma (ccRCC), despite having a low mutational burden, is considered immunogenic because it occasionally undergoes spontaneous regressions and often responds to immunotherapies. The signature lesion in ccRCC is inactivation of the VHL tumor suppressor gene and consequent upregulation of the HIF transcription factor. An earlier case report described a ccRCC patient who was cured by an allogeneic stem cell transplant and later found to have donor-derived T cells that recognized a ccRCC-specific peptide encoded by a HIF-responsive endogenous retrovirus (ERVE-4). We report that ERVE-4 is one of many ERVs that are induced by HIF, translated into HLA-bound peptides in ccRCCs, and capable of generating antigen-specific T cell responses. Moreover, ERV expression can be induced in non-ccRCC tumors with clinical-grade HIF stabilizers. These findings have implications for leveraging ERVs for cancer immunotherapy.

overall_design: We aim to systematically identify translated pVHL-responsive ERVs by Polysome-Seq in 786-O and A-498 cells. We generated an isogenic comparison where cells were stably infected with a virus encoding pVHL (VHL) or the empty vector (EV). We then performed Polysome-Seq experiments to quantify ERV amount for each condition in triplicates.

first: David

last: Braun

first: Nicholas

middle: J

last: Karmer

first: Cleo

last: Forman

first: Zachary

middle: T

last: Herbert

first: Sachet

last: Shukla

first: L

middle: S

last: Churchman

first: Catherine

first: William

middle: G

last: Kaelin Jr


title: Estrogen Receptor alpha CUT&RUN analysis of estrogen receptor positive breast cancer cell lines MCF7 and UCD12 with 1h hormone E2 treatment

city: Aurora

first: Kiran

last: Vinod Paul

institute: University of Colorado-Anschutz medical campus

summary: MCF7 and UCD12 cells treated with estradiol 1hr

overall_design: Triplicates of ETOH (vehicle), 0.001nM E2, 0.1nM E2, 10nM E2

first: Amy

last: Han

middle: V

last: Paul

first: Peter

last: Kabos

first: Srinivas

last: Ramachandran


title: Long-range enhancer-controlled genes are hyper-sensitive to regulatory factor perturbations [High-throughput bulk RNA-seq].

city: Utrecht

last: Krijger

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Cell-type-specific gene activation is regulated by enhancers, sometimes located at large genomic distances from target gene promoters. Whether distal enhancers require specific factors to orchestrate gene regulation remains unclear. Here, we used enhancer distance-controlled reporter screens to find candidate factors. We depleted them and employed activity-by-contact predictions to genome-wide classify genes based on enhancer distance. Predicted distal enhancers typically control tissue-restricted genes and often are strong enhancers. We find cohesin, but also mediator, most specifically required for long-range activation, with cohesin repressing short-range gene activation and prioritizing distal over proximal HBB genes competing for shared enhancers. Long-range controlled genes are also most sensitive to perturbations of other regulatory proteins and to BET inhibitor JQ1, this being more a consequence of their distinct enhancer features than distance. Our work predicts that lengthening of intervening sequences can help limit the expression of target genes to specialized cells with optimal trans-factor environments.

overall_design: High-throughput RNA-seq of EC50 K562 reporter cells after depletion of various factors using CRISPRi.

first: Sjoerd

last: Tjalsma

first: Niels

last: Rinzema

first: Marjon

last: Verstegen

first: Michelle

last: Robers

first: Andrea

last: Nieto-Aliseda

first: Richard

last: Gremmen

first: Amin

last: Allahyar

first: Mauro

last: Muraro

first: Wouter

last: de Laat


title: Long-range enhancer-controlled genes are hyper-sensitive to regulatory factor perturbations [BrU-Seq].

overall_design: Nascent RNA-sequencing (BrU-seq) of EC100 K562 reporter cells upon rapid depletion of  RAD21, MED23 and LDB1.


title: Long-range enhancer-controlled genes are hyper-sensitive to regulatory factor perturbations [4C-seq EC100-GFP].

overall_design: 4C-seq profiles of EC100-GFP reporter cells, with or without depletion of RAD21.


title: Supinoxin Blocks Small Cell Lung Cancer Progression by Inhibiting Mitochondrial Respiration through DDX5

city: West Lafayette

first: Elizabeth

last: Tran

state: IN

address: 175 S. University Street

department: Biochemistry

institute: Purdue University

summary: DDX5 is a DEAD-box RNA helicase that is overexpressed and implicated in the progression of several cancers, including small cell lung cancer (SCLC).  Our laboratory has demonstrated that DDX5 is essential for the invasive growth of SCLC and mitochondrial respiration.  SCLC is an extremely lethal, recalcitrant tumor, and currently lacking effective treatments. Supinoxin (RX 5902), a compound having anti-cancer activity, is a known target of phosphor-DDX5.  We now report that Supinoxin inhibits the proliferation of chemo-sensitive and chemo-resistant SCLC lines, H69 and H69AR respectively.  Additionally, Supinoxin mitigates both the growth of H69AR xenograft tumors and SCLC PDX tumors in vivo.    Finally, we find that Supinoxin inhibits expression of mitochondrial genes and effectively blocks respiration.  These studies suggest that Supinoxin functions in anti-tumor progression by reducing cellular energy levels through DDX5.

overall_design: To investigate the molecular pathway through which Supinoxin works on SCLC, we conducted differential gene expression in H69AR chemoresistant SCLC cells with or without 70 nM of Supinoxin.

first: Subhadeep

last: Das

first: Maria

last: Zea

first: Matthew

last: Russon

first: Zheng

last: Xing

first: Sandra

last: Torregrosa-Allen

first: Heidi

middle: E

last: Cervantes

first: Haley

last: Harper

first: Bennett

middle: D

last: Elzey


title: Long-range enhancer-controlled genes are hyper-sensitive to regulatory factor perturbations [CRISPRi screen].

first: Peter

last: Krijger

overall_design: A CRISPRi screen in E0, E50, E100, EC100 K562 reporter cell lines with a custom-made guide RNA (sgRNA) library composed of ∼18 thousand sgRNAs targeting 3200 nuclear protein-encoding genes (5 sgRNAs per TSS, plus 624 non-targeting sgRNAs). After library transduction, we isolated the top and bottom 10% GFP expressing cells and calculated the enrichment of sgRNAs in the low versus high GFP populations, to analyze per cell line the impact of each factor on reporter gene expression.

first: Sjoerd

last: Tjalsma

first: Niels

last: Rinzema


title: Targeting CAFs-Mediated Stromal Signaling in a Patient-Derived Organotypic Colorectal Tumor Model

city: ann arbor

first: gary

last: luker

state: MI

address: 109 zina pitcher place

department: radiology

institute: university of michigan

summary: The goal of this experiment is to understand why co-culturing colon cancer cells with carcinoma associated fibroblasts (CAFs) causes the colon cancer cells to develop chemo-resistance. We cultured a patient-derived colon cancer cell model derived from conditional reprogramming with or without carcinoma-associated fibroblasts. Before sequencing, the co-cultured cells were purified using EpCAM immuno-magnetic beads to isolate cancer cells.

overall_design: There are duplicate samples of colon cancer cultured alone or with colon cancer cells isolated after co-culture with fibroblasts.

first: Hossein

last: Tavana

first: Gary

last: Luker

first: Astha

last: Lamichhane


title: Spatial mapping of transcriptomic and lineage plasticity in metastatic pancreatic cancer [CosMx]

city: New York

first: Anirban

last: Maitra

state: NY

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

institute: New York University Grossman School of Medicine

summary: Patients with treatment-refractory pancreatic cancer often succumb to widespread systemic metastases; however, the transcriptomic heterogeneity that underlies recalcitrance to therapy remains understudied, particularly in the spatial context. We constructed high-resolution spatial maps of transcriptional heterogeneity, clonal architecture and lineage plasticity using spatially resolved transcriptomics (SRT) from 13 primary cancers and 36 corresponding liver, lung, and peritoneal metastases, collected via a rapid (“warm”) autopsy program. To validate findings from our SRT dataset at single-cell resolution, we performed CosMX SMI profiling (Nanostring) on 7 samples from 3 patients, including primary and/or liver metastasis.

overall_design: CosMx SMI profiling (Nanostring) was performed using a 1000-plex gene panel on fresh frozen tissues. A total of 90 Fields of View (FOVs, each 0.51 x 0.51 mm) from the tumour bed, juxtalesional region, and distant area were selected across seven tissue samples, guided by H&E-stained images obtained from a serial section. Four markers, DAPI, CD298/B2M, PanCK, and CD45, were used for cell segmentation.

first: Guangsheng

last: Pei

first: Jimin

last: Min

first: Kimal

middle: I

last: Rajapakshe

first: Paola

last: Guerrero

first: Linghua

last: Wang


title: A combinatorial ubiquitin code degrades substrates protected by deubiquitylation

city: Shinagawa-ku

first: Fumiaki

last: Ohtake

state: Tokyo

country: Japan

institute: Hoshi University

summary: Reversibility of protein ubiquitylation play essential roles in cellular protein homeostasis. How substrates stabilized by deubiquitylation are directed for degradation remains largely elusive. Here, we show that the branched ubiquitin chains promote the degradation of the deubiquitylase (DUB) OTUD5. OTUD5 is sequentially modified by TRIP12 and UBR5, E3s specific for the K29 and K48 linkages, respectively, resulting in the conjugation of K29/K48 branched ubiquitin chains. The TRIP12-OTUD5 antagonism regulates TNF--induced NF-B signaling. Mechanistically, while OTUD5 readily cleaves K48-linkages, K29-linkages are resistant against OTUD5 activity. Consequently, K29-linkages overcome OTUD5 DUB activity to facilitate UBR5-dependent K48-linked chain branching. Regarding generality, this mechanism adopts to other TRIP12 substrates associated with OTUD5. These results uncover a cellular unique strategy in which the sequential addition of DUB-resistant and proteasome-targeting ubiquitin linkages efficiently promote degradation of substrates protected by deubiquitylation, underscoring the role of branched ubiquitin chains in the quality control of hard-to-degrade substrates.

overall_design: HT1080 cells were transfected with the siRNAs (scrambled, siTRIP12, siOTUD5, and siTRIP12+siOTUD5 (double KD), and total RNAs were isolated.

first: Mai

last: Morita


title: Long-range enhancer-controlled genes are hyper-sensitive to regulatory factor perturbations [RNA-seq].

overall_design: To study the effect of factor knock down on genome-wide epression regulation via enhancers, we knocked down target factors in K562 using CRISPRi. We performed RNA-sequencing in cells with a specific knock down to a non-targeting control sgRNA.

first: Marjon

last: Verstegen

first: Michelle

last: Robers

first: Andrea

last: Nieto-Aliseda

first: Richard

last: Gremmen

first: Amin

last: Allahyar

first: Mauro

last: Muraro

first: Wouter

last: de Laat


title: Effect of TRIP12, UBR5, or HOIP in gene expression

summary: The protein ubiquitylation is under the equilibrium between ubiquitin conjugation and deconjugation. How substrates stabilized by deubiquitylation are directed for degradation remains unclear. Branched ubiquitin chains promote substrate degradation through the proteasome, but the underlying mechanisms are not fully understood. TRIP12 and UBR5 are HECT-type E3s specific for the K29 and K48 linkages, respectively. Here, we show that the deubiquitylase (DUB) OTUD5 is cooperatively modified by TRIP12 and UBR5, resulting in the conjugation of K29/K48 branched ubiquitin chains and accelerated proteasomal degradation. The TRIP12–OTUD5 antagonism regulates TNF-–induced NF-B signaling. Mechanistically, although OTUD5 readily cleaves K48 linkages, K29 linkages are resistant against OTUD5 activity. Consequently, K29 linkages overcome OTUD5 DUB activity to facilitate UBR5-dependent K48-linked chain branching. This mechanism is applicable to other TRIP12 substrates associated with OTUD5. These results reveal a unique cellular strategy in which the combination of DUB-resistant and proteasome-targeting ubiquitin linkages efficiently promotes the degradation of substrates protected by deubiquitylation, underscoring the role of branched ubiquitin chains in shifting the ubiquitin conjugation/deconjugation equilibrium.

overall_design: HT1080 cells were transfected with the siRNAs for TRIP12, UBR5, or HOIP. The cells were lysed 72h after the transfection, and total RNA was isolated.


title: Comparative analysis of the cardiomyocyte between 16 day and 140 days after differentiation

status: Public on Feb 18 2025

city: Birmingham

first: Thanh

middle: Minh

last: Nguyen

state: AL

address: 1670 University Blvd, Volker Hall G094

department: Department of Biomedical Engineering

institute: University of Alabama at Birmingham

summary: We generate Bulk-RNA sequencing data from two human-induced pluripotent stem cell-derived cardiomyocyte (hiPSC-CM) cell lines. The first cell line was harvested 16 days after differentiation (hiPSC-CM-D16); this cell line still actively proliferated. The second cell line was harvested 140 days after differentiation (hiPSC-CM-D140); this cell line ceased proliferation. Comparing the Bulk-RNA sequencing data between these two cell lines may reveal regulators promoting hiPSC-CM proliferation.

overall_design: Two human-induced pluripotent stem cell-derived cardiomyocyte (hiPSC-CM) cell lines were generated: The first cell line was harvested 16 days after differentiation (hiPSC-CM-D16); this cell line still actively proliferated. The second cell line was harvested 140 days after differentiation (hiPSC-CM-D140); this cell line did not proliferate

first: Hao

last: Kaili

first: Nakada

last: Yuji

first: Gugarin

last: Bijay

first: Yao

last: Peng

first: Jianyi

last: Zhang


title: Dependence of gene regulation by prostaglandin A1  on a zinc finger protein

city: Hannover

first: Maximilian

last: Fuchs

address: Carl-Neuberg-Str. 1

department: IMTTS

institute: Hanover Medical School

summary:
A zinc finger protein (At3g62900)  was identified as a putative signalling factor mediating gene regulation to reactive electrophilic oxylipin.
We used microarrays to investigate the effect of a defect in the zinc finger on gene expression.

overall_design: Arabidopsis seedlings of Col-0 and mutants were treated with prostaglandin A1 or mock for 4 h.

first: Susanne

last: Berger

first: Martin

last: Mueller


title: A PanOmics approach towards identification and characterization of treatment resistance in B-cell lymphomas

city: Berlin

first: Clemens

last: Schmitt

address: Augustenberger Platz 1

department: Hematology, Oncology and Tumor Immunology

institute: Charité Universitätsmedizin

summary: We performed a large scale Cyclophosphamide (CTX; R-CHOP componenet) treatment based clinical trial reminiscent in vivo study to charaterize Emu-myc mouse B-cell lymphomas for their potential to relapse. Based on the findings of the experiment, the tumors which relapsed within 100 days of the observation period post-CTX were considered relapse prone (RP) and the remaining as never relapsing  (NR). The primary lymphomas were then isolated from the lymph nodes of the RP or NR lymphoma bearing mice, and  purified to enrich CD-19 positive cells. Using multiple OMICS-platforms,these samples were molecularly and metabolically scrutinized to account for the observed differences in drug response phenotypes i.e., NR and RP.

overall_design: To categorize the Never relapsing (NR) and the Relapse prone (RP) status,  individual lymphomas were propagated in up to two strain-matched, non-transgenic (i.e., genetically non-engineered wild-type), fully immuno-competent 6–8-week-old mice each via tail vein injection of 10^6 viable cells . Recipient mice were treated with a single intraperitoneal dose of cyclophosphamide (CTX, Sigma, 300 mg/kg body weight) at the time well-palpable LN enlargements (i.e., about 8–10 mm in diameter) had formed. Treatment responses were monitored during regular visits (at least twice a week; for a maximum of a 100-day observation period), which always included a general inspection of the mice and palpation of the typically affected LN regions (i.e. cervical, pre-scapular/axillar and inguinal) as time-to-relapse (TTR), i.e., progression-free survival (PFS), or reflect the time between treatment and unexpected death of the animal or a preterminal disease stage, collectively measured as overall survival (OS). After CO2 euthanasia, LN, and in some experiments also the spleen or BM, were isolated to generate tissue sections or single-cell suspensions. Lymphomas exhbiting relapse before the observation period of 100 days was considered RP and the rest as NR. These hence categorized lamphoamas were  exclusively expanded in strain-matched, non-transgenic C57BL6 mice and the tumor bearing Lymph nodes were used to isolate primary lymphomas. These lymphomas were then selected for CD19-positivity using mouse B-cell isolation kit (130-090-862; Miltenyi) These cells were then used to isolate total RNA and and perform RNA-seq.

first: Animesh

last: Bhattacharya

first: Paulina

last: Richter-Pechanska

first: Kolja

last: Schleich


title: Social stress in fathers affects sperm small RNA and offspring transcriptome profiles

city: Norwich

first: Alice

last: Godden

state: Not applicable

address: School of Biological Sciences, University of East Anglia, Norwich Research Park

country: United Kingdom

institute: University of East Anglia

type: Non-coding RNA profiling by high throughput sequencing

summary: Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male-male competition induces a physiological stress response and affects male hormone levels, ejaculate traits and development in their offspring. Here we investigated the role of sperm-mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male-male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split-clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements (TE)s at this key developmental stage. We sequenced micro- (mi) and Piwi-interacting (pi)RNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi- and piRNAs, with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs.

overall_design: This data deposit includes the small RNA-seq data for this research. Male zebrafish were subject to high and low social stress environments, with sperm samples collected, RNA extracted and sent for small RNA sequencing.

middle: M

first: Willian

last: Silva

first: Berrit

last: Kiehl

first: Cecile

last: Jolly

first: Leighton

last: Folkes

first: Ghazal

last: Alavioon

first: Simone

last: Immler


title: Long-range enhancer-controlled genes are hyper-sensitive to regulatory factor perturbations [4C-seq MYC, LMO2 and MS4A3].

first: Peter

last: Krijger

overall_design: 4C-seq profiles of EC100-GFP reporter cells, with or without depletion of RAD21 or LDB1.

first: Sjoerd

last: Tjalsma

first: Niels

last: Rinzema

first: Marjon

last: Verstegen

first: Michelle

last: Robers

first: Andrea

last: Nieto-Aliseda

first: Richard

last: Gremmen

first: Amin

last: Allahyar

first: Mauro

last: Muraro

first: Wouter

last: de Laat


title: Systemic IL-23 blockade downregulates IL-23 receptor-expressing Type 17 T-cell subsets and upregulates regulatory gene expression in myeloid cells in human psoriasis skin

city: Sacramento

first: JAEHWAN

last: KIM

state: CA

address: 10535 Hospital Way

department: Dermatology

institute: University of California, Davis

summary: Recent single-cell studies indicated that IL-17-producing T-cells (T17) have diverse subsets expressing IL-17A, IL-17F, or a combination of them in human psoriasis skin. However, it is unknown how T17 subsets are differently regulated by IL-23 versus IL-17A blockades. Here, we studied 93 human psoriasis or control skin single-cell libraries from 42 subjects to understand how IL-23 versus IL-17A systemic blockades differently modify single-cell transcriptome of T17 cell subsets, dendritic cells/myeloid cells, and keratinocytes. Our study shows that IL-23 inhibition down-regulates IL-23 receptor-expressing pathogenic T17 subsets. In contrast, T17 cells expressing both IL-17A and IL-17F did not express the IL-23 receptor, and the percentage of this potentially non-pathogenic T17 subset increased after IL-23 inhibition. We also found out that the expression of the IL-17 negative regulation genes, such as TNFAIP3, increased in myeloid cells more after IL-23 inhibition than after IL-17A inhibition. These findings explain why the risk of candidiasis is not increased after IL-23 inhibition, unlike IL-17 inhibition, and the higher efficacy of IL-23 blockades for inducing psoriasis remission in the long term or suppressing relapses after stopping the injections compared to IL-17A blockades.

overall_design: In the anti-IL-23 monoclonal antibody (risankizumab) clinical trial (NCT04630652), psoriasis patients received risankizuamb 150 mg injections at baseline, month 1, and month 4 (3 injections). Pretreatment (PreTx) lesional (LS) and non-lesional (NL) skin biopsy tissues were harvested at baseline, and posttreatment (PostTx) LS biopsy tissue was harvested at month 7. Skin immune cells were isolated from the harvested skin tissues and analyzed by single-cell RNA sequencing (scRNA-seq) in integration with our previous single-cell libraries (GSE183047 and GSE151177) of control skin from healthy volunteers, psoriasis PreTx LS and NL, psoriasis PostTx LS (after) IL-17A inhibition. PostTx LS IL-17A inhibition single-cell libraries were generated from skin biopsy tissues harvested at month 3, after anti-IL-17A monoclonal antibody (secukinumab) 300 mg injections at baseline, week 1, week 2, week 3, week 4, and week 8 (6 injections). In total, we analyzed 93 human skin single-cell libraries (42 psoriasis PreTx LS, 25 psoriasis PreTx NL, 12 psoriasis IL-23 inhibition PostTx LS, 4 psoriasis IL-17A inhibition PostTx LS, and 10 control skin from healthy volunteers) from 42 subjects

first: Jaehwan

last: Kim

first: James

last: Krueger


title: Long-range enhancer-controlled genes are hyper-sensitive to regulatory factor perturbations

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

overall_design: Refer to individual Series


title: AML senescence capacity is a unifying outcome predictor and plastic APL classifier

status: Public on Feb 17 2025

first: Clemens

last: Schmitt

address: Augustenburger Platz 1

department: Hematology, Oncology, Tumorimmunology

institute: Charite

summary: BACKGROUND Acute myeloid leukemia (AML) is a highly heterogeneous disease. The predictive role of therapy-induced senescence (TIS) in cancer treatment in general and newly diagnosed (nd) AML patients in particular is undetermined. METHODS We established a flow cytometry-based senescence assay to detectsenescence in primary patient blasts to ex vivo chemotherapy (daunorubicin or cytarabine) in patients with newly diagnosed (nd) non-M3 AML. Bulk and single-cell analyses assessed gene expression and recurrent AML mutations. TIS-related gene signatures were interrogated in additional AML patient cohorts. Computational analyses, chromatin immunoprecipitation sequencing and other functional assays characterized TIS-related leukemia biology. RESULTS Ex vivo-determined TIS capacity predicted superior disease-free and overall survival in three independent cohorts comprising 92 patients with nd non-M3 AML across diverse (cyto-)genetic subgroups. Subsequent treatment with Bcl2 inhibitors venetoclax or navitoclax demonstrated their senescence-preferential killing. By interrogating 977 nd all-subtype AML patients from three additional independent cohorts, a TIS-derived gene classifier unexpectedly identified M3-AML/acute promyelocytic leukemia cases with very high accuracy in a PML-RARA-agnostic fashion. We found the polycomb-repressive complex 2 component Suz12 to regulate this classifier. Non-M3-AML cell lines in TIS differentiated upon all-trans retinoic acid (ATRA), or died in response to the Suz12-targeting histone deacetylase (HDAC) inhibitor panobinostat. CONCLUSIONS TIS predicts superior long-term outcome in nd AML and confers unifying plasticity across molecularly highly diverse AML subtypes towards an M3-like state, which enables consolidative senolysis by Bcl2 family or HDAC inhibition, or senodifferentiation by ATRA as novel plasticity-based treatment concepts.

overall_design: To characterize molecular changes occurring in response to AML chemotherapy, we obtained gene expression profiles (GEP) by RNA sequencing (RNA-seq) of 11 paired samples of ex vivo-DNR-exposed vs. UT non-M3 AML blasts.

first: Martin

last: Schönlein

first: Timon

last: Hick

first: Paulina

last: Richter-Pechanska


title: Copy number normalization distinguishes differential signals driven by copy number differences in ATAC-seq and ChIP-seq

first: Yingguang Frank

last: Chan

address: Max Planck Ring 9

department: Chan group

institute: Friedrich Miescher Laboratory of the Max Planck Society

summary: A common objective across ATAC-seq and ChIP-seq analyses is to identify differential signals across contrasted conditions. However, in differential analyses, the impact of copy number variation is often overlooked. Here, we demonstrated copy number differences among samples could drive, if not dominate, differential signals. To address this, we propose a pipeline featuring copy number normalization. By comparing the averaged signal per gene copy, it effectively segregates differential signals driven by copy number differences from other factors. Further applying it to Down syndrome, we unveiled distinct dosage-dependent and -independent changes on chromosome 21. Thus, we recommend normalization as a general approach.

overall_design: We profiled chromatin accessibility in fibroblast cell lines derived from age- and sex-matched healthy and Bloom Syndrome individuals. During the process of characterizing the differential signals, we noticed that copy number differences at local regions between the samples skew the differential analysis towards the sample with a higher copy number. We explored the impacts of copy number variation on the differential analysis and solutions to segregate the differential signals driven by copy number variation.

first: Dingwen

last: Su


title: Impact of BRCA mutations, age, and hormone status on the molecular phenotype of the human Fallopian tube

city: Grand Rapids

first: Ian

last: Beddows

address: 333 Bostwick

institute: Van Andel Institute

summary: The human Fallopian tube (FT) is an important organ in the female reproductive system and has been implicated as a site of origin for pelvic serous cancers, including high-grade serous ovarian cancer (HGSOC). We have generated comprehensive whole-genome bisulfite sequencing, RNA-seq, and proteomic data of over 100 human FTs, with detailed clinical covariate annotations. Our results challenge existing paradigms that extensive epigenetic, transcriptomic and proteomic alterations exist in the FTs from women carrying BRCA1/2 mutations. We find minimal differences between BRCA1/2 carriers and non-carriers prior to loss of heterozygosity, shedding new light into the prevention and/or early detection of tumorigenesis in these women. Covariates such as surgical indications can confound BRCA1/2-related differences reported in the literature.We systematically document and highlight the degree of variations across normal human FT, defining five FT groups capturing major cellular and molecular changes across various reproductive stages and associate these with various clinical covariates but not heterozygous BRCA1/2 mutation status.

overall_design: Benign Fallopian tubes for germline heterozygous carriers of BRCA1 and BRCA2 as well as control Non-BRCA mutated FTs.

first: Hui

last: Shen

first: Ronny

last: Drapkin

first: Charles

last: Drescher


overall_design: To characterize the endogenously formed G-quadruplex structures in wildtype and BLM-/-  cells, we performed G4 ChIPseq with a specific antibody against the secondary DNA structures. During the process of characterizing the differential G-quadruplex forming sites, we noticed that copy number differences at local regions between the samples skew the differential analysis towards the sample with a higher copy number. We explored the impacts of copy number variation on the differential analysis and solutions to segregate the differential signals driven by copy number variation.


title: CTCF N-terminal Domain Regulates Clustered Protocadherin Gene Expression by Enhancing Cohesin Processivity [ChIP-seq]

status: Public on Feb 15 2025

city: Shanghai

first: Yijun

last: Zhang

address: 800 Dongchuan Rd

institute: Shanghai Jiao Tong University

summary: CTCF structures 3D genome folding by anchoring or forestalling cohesin loop extrusion, but the exact mechanism remains obscure. Here, using clustered protocadherins (cPcdh) as model genes, we report that CTCF stabilizes or facilitates cohesin loop extrusion by enhancing its processivity. Specifically, we show that, compared with the Pcdh alpha and gamma clusters, the Pcdh beta cluster is greatly affected upon CTCFY226A/F228A mutation in the N-terminal domain. Given the long-range distance of the Pcdh beta cluster from the distal enhancer, this finding has interesting implications in CTCF regulation of cohesin processivity along the linear chromatin during DNA loop extrusion. In particular, the effect on cohesin processivity upon CTCFY226A/F228A mutation is conspicuously similar to that of WAPL overexpression, demonstrating that, contrary to the general view of blocking or forestalling cohesin, CTCF actually enhances or facilitates cohesin loop extrusion.

overall_design:
Here, through CRISPR editing of the YDF motif - the key cohesin interacting moiety - of the CTCF N-terminal domain (NTD) in N2a cells in vitro and in mice in vivo, in conjunction with RNA-seq, ChIP-seq, 4C, and Hi-C analyses, we found that members of the Pcdh beta cluster are highly susceptible to the perturbed cohesin processivity owing to their distal genomic arrangement relative to the downstream super-enhancer region. Our data broaden the molecular logic that generates Pcdh isoform diversity required for neural circuit assembly via a unique 3D genome organization.
Please note that each processed data generated from both replicates is linked to the corresponding rep1 sample records.

first: Qiang

last: Wu


title: CCCTC-binding Factor N-terminal Domain Regulates Clustered Protocadherin Gene Expression by Enhancing Cohesin Processivity

summary: CTCF (CCCTC-binding factor) instructs 3D genome folding by anchoring or forestalling cohesin loop extrusion, but the exact mechanism remains obscure. Here, using clustered protocadherins (cPcdh) as model genes, we report that CTCF assists or facilitates cohesin loop extrusion by enhancing its processivity. Specifically, we show that, compared with the Pcdh alpha and gamma clusters, the Pcdh beta cluster is greatly affected upon CTCF Y226A/F228A mutation in the N-terminal domain. Given the long-range distance of the Pcdh beta cluster from the distal enhancer, this finding has interesting implications in CTCF regulation of cohesin processivity along the linear chromatin during DNA loop extrusion. In particular, the effect on cohesin processivity upon CTCF Y226A/F228A mutation is conspicuously similar to that of WAPL overexpression, suggesting that, in addition to the general view of blocking or forestalling cohesin, CTCF may also enhances or facilitates cohesin loop extrusion.

overall_design: Here, through CRISPR editing of the YDF motif—the key cohesin interacting moiety—of the CTCF N-terminal domain (NTD) in N2a cells in vitro and in mice in vivo, in conjunction with RNA-seq, ChIP-seq, 4C, and Hi-C analyses, we found that members of the Pcdh beta cluster are highly susceptible to the perturbed cohesin processivity owing to their distal genomic arrangement relative to the downstream super-enhancer region. Our data broaden the molecular logic that generates Pcdh isoform diversity required for neural circuit assembly via a unique 3D genome organization.


title: Swi4-dependent SWI4 transcription couples cell size to cell cycle commitment

status: Public on Feb 14 2025

city: Toronto

first: Micheal

last: Tyers

state: Ontario

address: 555 University Avenue

country: Canada

institute: The Hospital for Sick Children

summary: Growth-dependent accumulation of the limiting SBF transcription factor, composed of Swi4 and Swi6, occurs in G1 phase in budding yeast and is limiting for commitment to division, termed Start. Here we measure size-dependence of Swi4 protein copy number under different genetic contexts using a quantitative scanning number and brightness technique. Mutation of SBF binding sites in the SWI4 promoter or disruption of SBF activation resulted in ~33-50% decrease in Swi4 accumulation rate and concordantly increased cell size at Start. Ectopic inducible expression of Swi4 in G1 phase cells increased production of Swi4 from the endogenous promoter, upregulated transcription of the G1/S regulon, and accelerated Start. Despite the potential for Swi4 positive feedback, G1 phase Swi4 accumulation was linear unless the Whi5 transcriptional repressor was inactivated. A threshold model in which Swi4 titrates SBF binding sites in G1/S promoters predicted the effects of nutrients, ploidy, and G1/S regulatory mutations on cell size. These results exemplify how transcription factor auto-production can refine a cell state transition.

overall_design: RNA-seq analysis of estradiol-induced SWI4 overexpression in S. cerevisiae along with pre-induction and mock induced (ethanol treated) controls.

first: Pooja

last: Goswami

first: Abhishek

last: Ghimire

first: Carleton

last: Coffin

first: Jing

last: Cheng

first: Jasmin

last: Coulombe-Huntington

first: Ghada

last: Ghazal

first: Yogitha

last: Thattikota

first: María

middle: F

last: Guerra

first: Mike

first: Sylvain

last: Tollis

first: Catherine

last: Royer


title: RNA G-quadruplex dynamics steers the crosstalk between protein synthesis and energy metabolism

city: Trento

first: Erik

last: Dassi

state: TN

address: Via Sommarive, 9

department: CIBIO

country: Italy

institute: University of Trento

summary: Cancer cells rely on mitochondria for their bioenergetic machinery and macromolecule synthesis. The regulation of mitochondrial protein synthesis is central to mitochondrial function. This process primarily depends on the cytoplasmic translation of nuclear-encoded mitochondrial mRNAs whose protein products are imported into mitochondria. Despite the growing evidence that mitochondrial protein synthesis contributes to the onset and progression of cancer, and offers new opportunities for cancer therapy, knowledge of the underlying molecular mechanisms remains limited. Here, we show that RNA G-quadruplexes (RG4s) are localized to mitochondria and regulate mitochondrial function by modulating cytoplasmic mRNA translation of nuclear-encoded mitochondrial proteins . Our data support a model whereby RG4 stabilization induced by small molecule ligands or by depleting RG4-binding proteins alters nuclear-encoded mitochondrial mRNAs protein synthesis. Ultimately, this impairs mitochondrial functions, affecting energy metabolism and consequently cancer cell proliferation.

overall_design: Total and polysomal profiling of 3 biological replicates of wild-type and HNRNPU-silenced HCT116 cells

first: Stefania

last: Millevoi

first: Anne

last: Cammas


title: CCCTC-binding Factor N-terminal Domain Regulates Clustered Protocadherin Gene Expression by Enhancing Cohesin Processivity [RNA-Seq]

first: Yijun


title: Myeloid C3 causes neuronal injury prior to synapse loss

city: Baltimore

first: Matthew

last: Smith

state: MD

address: 600 N Wolfe Street

department: Neurology

institute: Johns Hopkins University


title: scRNAseq of C3 producing myeloid and astrocytic cells from EAE inflamed murine CNS [scRTL]

summary: Complement component C3 mediates pathology in several CNS neurodegenerative diseases, but the cellular and molecular mechanisms leading to neuronal injury remain unclear. Herein, we examined how C3 deletion affects glial profiles and anterior visual pathway pathology in an animal model of neuroinflammation.  scRNA-seq from mouse brain and optic nerve revealed that C3 expression defined disease-associated glial subtypes which were characterized by increased mTOR activation, cell metabolism, and translation. Deletion of C3 restored these glia towards homeostatic profiles.  Myeloid-derived C3 mediated injury in optic nerve axons and retinal ganglion cells (RGCs) at the peak of EAE.  To elucidate the timing of pathology we examined retinas prior to symptom onset and found reductions in Brn3a, an RGC transcription factor involved in dendritic arborization and protection from apoptosis.  Our study supports a direct role for C3 in activating the mTOR-ribosomal biogenesis axis in glia which subsequently mediate early neuro-axonal stress and later synapse loss.

overall_design: From C3 reporter mice at peak of EAE, CNS (brain and spinal cord) were collected from 3 biological replicates, each consisting of 2 animals, and were sorted into 3 populations - Myeloid C3+, Myeloid C3-, and Astrocyte C3+ and C3-. 3 biological replicates, 3 populations per replicate for total of 9 samples

first: Thomas

last: Garton

first: Peter

last: Calabresi


title: DGCR8 haploinsufficiency leads to primate-specific RNA dysregulation and pluripotency defects

city: Castellón de la Plana

first: Guillermo

last: Peris

state: CAstellón

address: Av. Vicent Sos Baynat, s/n

department: Llenguatges i Sistemes Informàtics

country: Spain

institute: Universitat Jaume I


title: Effect of DGCR8 heterozygosity on steady state RNA levels in embryonic teratocarcinoma PA-1 cells

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

institute: Centre for Immunity, Infection and Evolution

summary: In this dataset we use total RNA-seq to study the effect of DGCR8 heterozygosity on steady state RNA levels

overall_design: Comparison between RNA samples from wildtype and DGCR8 heterozygous PA-1 cells

first: Lisanne

last: Knol

first: Sara

last: Macias


title: Myeloid C3 causes neuronal injury prior to synapse loss [snMulti-ome-seq]

overall_design: Optic nerves from 4 pools of mice (2 C3 WT, 2 C3 KO, each pool containing optic nerves from 5 pooled mice) at peak of EAE were flash frozen then subjected to paired snRNAseq and snATACseq analyses via 10X Multi-Ome technology


title: Effect of DGCR8 heterozygosity on steady state miRNA levels in embryonic teratocarcinoma PA-1 cells

summary: In this dataset we use small RNA-seq to study the effect of DGCR8 heterozygosity on steady state miRNA levels

overall_design: Comparison between small RNA samples from wildtype and DGCR8 heterozygous PA-1 cells


title: CCCTC-binding Factor N-terminal Domain Regulates Clustered Protocadherin Gene Expression by Enhancing Cohesin Processivity [4C-Seq]

last: Zhang

first: Qiang

last: Wu


title: Enhanced TLR7-dependent production of type I interferon by pDCs underlies pandemic chilblains

status: Public on Feb 13 2025

city: Lausanne

first: JEREMY

last: DI DOMIZIO

state: Vaud

address: Av Boveresses 155, 1066 Epalinges

country: Switzerland

institute: CHUV

summary: we profiled the inflammatory transcriptome of chilblain skin lesions from patients during the COVID pandemic

overall_design: Inflammation-oriented transcriptomics was performed on RNA extracted from skin biopsies using NanoString technologies

first: Jeremy

last: Di Domizio


title: Dynamic synthesis and transport of phenazine-1-carboxylic acid to boost extracellular electron transfer rate

city: Shenyang

first: Zhang

last: Baocai

address: Shenyang

department: College of Life and Health Sciences

institute: Northeastern University

summary: We employed RNA-sequencing (RNA-seq) and transcriptomic analysis to analyze cell metabolism and electrophysiology, enabling systematically elucidate the mechanisms underlying phenazine-1-carboxylic acid (PCA)-boosted EET. As a result, the PCA-induced transcriptional response of the EET-related genes could be categorized into three groups: (i) lactate catabolism; (ii) c-Cyts biosynthesis; and (iii) biofilm formation.

overall_design: RNA-seq profiling and Transcriptome analyses of engineered S. oneidensis MR-1 (SDV3) and the wild-type strain (WT).

first: Feng

last: Li

first: Baocai

first: Hao

last: Song


summary: The 22q11.2 deletion syndrome (22qDS) is caused by a microdeletion in one of the chromosomes 22, comprising around 40 genes and including DGCR8, an essential gene for miRNA biogenesis and transposable elements control. Most of the clinical manifestations of 22qDS have their origin during embryonic development, but the contribution of human DGCR8 hemizygosity to the disease is unknown. To clarify the overall effect of DGCR8 in the context of 22qDS, we have generated two human embryonic models of DGCR8 +/-.In this dataset we use total RNA-seq to study the effect of DGCR8 heterozygosity on steady state RNA levels in human embryonic stem cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT H9 cells  and two different DGCR8 heterozygous clones generated by CRISPR/Cas9 nickase system.

first: Ana

last: Colomer

middle: R

last: Heras


title: Enhancer RNA transcriptomics-wide association study reveals an atlas of pan-cancer susceptibility eRNAs

city: Shenzhen

first: Wenyan

last: Chen

address: Yutang Street

institute: Shenzhen Bay Laboratory

summary: Increasing evidence has demonstrated that enhancer RNAs (eRNAs) play essential roles in human diseases. However, the complete identification of disease-related subsets of eRNAs remains a major challenge. Here, we construct an atlas of common and rare genetic variants influencing the expression of enhancer RNAs across 49 human tissues. We identify 11,757 eRNA quantitative trait loci (eRNA-QTLs) associated with the expression of 89.75% annotated eRNAs. Mechanically, eRNA-QTLs frequently altered the binding motifs of transcription factors and were further experimentally validated by CRISPR-based base editing. We also observed that 28.48% of cancer signals were co-localized with eRNA-QTLs. Utilizing our newly developed eRNA transcriptome-wide association study (eRNA-TWAS) model, we have effectively identified 259 cancer susceptibility eRNAs spanning 23 distinct cancer types. Notably, among the identified eRNAs, these eRNA-linked cancer susceptibility genes exhibit significant dependence across various cancer cell lines. Interestingly, cancer risk can be significantly influenced by rare functional variants that are linked to eRNAs with transcriptomic outliers. Additionally, we develop a comprehensive and flexible data portal for exploring the genetic underpinnings of eRNAs. Overall, this study reveals a systematic landscape of genetic dependencies on eRNAs across pan-cancers and significantly expands the pool of disease-associated eRNAs.

overall_design: Total RNA extracted from HEK293T cells was subjected to strand-specific RNA sequencing using the Illumina nova seq 6000 platform at Berry Genomics Co, Ltd (Beijing, China). Briefly, strand-specific RNA-Seq libraries were prepared by combining the Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI, USA) and the dUTP method to ensure strand specificity.

first: Jianxiang

last: Lin

first: Lei

first: Yunbo

last: Qiao


title: Clonal lineage tracing and transcriptomics of cortical progenitor populations reveal maintenance of differentiation potential.

status: Public on Feb 12 2025

first: Scott

last: Yuzwa

address: 1 King's College Circle, Medical Sciences Building, Rm 6316

department: Laboratory Medicine and Pathobiology

institute: University of Toronto

summary: Postnatal neocortical development is a complex period wherein radial glial progenitors complete excitatory neurogenesis and transition to the production of glia. Here, we take advantage of a multi-layered lineage tracing tool pbacBarcode, to examine the contributions of individual cortical RGPs to the postnatal cortex. We reveal that some individual cortical RGPs are multipotent and give rise to olfactory bulb interneurons, astrocytes, and oligodendrocytes in a ~2:1:1 ratio. We provide evidence that differentiation potential into terminal cell types is maintained as late as P4, suggesting a population decline model, as opposed to cell fate restriction, underlies cortical progression . Moreover, a pool of proliferative intermediary cells which may represent a multipotent postnatal intermediate progenitor cell population may contribute to the production of the three major cell types. Lastly, we examine RGP postnatal contribution to oligodendrocytes and show that oligodendrocyte progenitor founder cell production by cortical RGPs is largely complete by P3.

overall_design: Single-cell RNA-sequencing of mouse neocortex electroporated at E14.5 and collected at P4. Curio Seeker spatial transcriptomics of wild-type P4 and P22 mouse forebrain.

first: Danyon

last: Harkins

first: Shawar

last: Ali

first: Teodora

last: Tockovska

last: Ciganovic

first: Daniela

last: Lozano Casasbuenas

first: Samuel

last: Watanabe

first: Stephanie

last: Ouzikov


first: Guillermo

last: Peris

summary: The 22q11.2 deletion syndrome (22qDS) is caused by a microdeletion in one of the chromosomes 22, comprising around 40 genes and including DGCR8, an essential gene for miRNA biogenesis and transposable elements control. Most of the clinical manifestations of 22qDS have their origin during embryonic development, but the contribution of human DGCR8 hemizygosity to the disease is unknown. To clarify the overall effect of DGCR8 in the context of 22qDS, we have generated two human embryonic models of DGCR8 +/-.In this dataset we use small RNA-seq to study the effect of DGCR8 heterozygosity on steady state miRNA levels in human embryonic stem cells.

overall_design: Comparative gene expression profiling analysis of small RNA-seq data for WT H9 cells  and two different DGCR8 heterozygous clones generated by CRISPR/Cas9 nickase system.

first: Lisanne

last: Knol

first: Sara

last: Macias


title: Myeloid C3 causes neuronal injury prior to synapse loss [scRNA-seq]

first: Matthew

last: Smith

overall_design: Brains from 4  C3-tdTomato reporter mice were collected 16 days post-immunization and were dissociated, pooled, then sorted into two populations - Myeloid C3+ cells and Myeloid C3- cells. Single cell RNA-sequencing was performed using 10X Genomics 3' chemistry

first: Thomas

last: Garton

first: Peter

last: Calabresi


title: Broad rim lesions are a novel pathological / morphological and imaging biomarker for rapid disease progression in Multiple Sclerosis

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster

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

overall_design: Refer to individual Series


title: Full-Body Transcriptome Uncovers Hepatic Gluconeogenesis and PDK3 Upregulation as a Key Driver of Cancer Cachexia

city: New York

first: Ezequiel

middle: Carlos

last: Dantas

state: Y

address: 550E First Street

institute: NYU Langone

summary: Cachexia, a severe wasting syndrome characterized by tumor-induced metabolic dysregulation, is a leading cause of death in cancer patients, yet its underlying mechanisms remain poorly understood. We performed a longitudinal full-body single-nuclei resolution transcriptome analysis in a Drosophila model of cancer cachexia to capture interorgan dysregulations. Our study revealed that the tumor-secreted interleukin-like cytokine Upd3 induces fat body expression of Pepck1 and Pdk, key regulators of gluconeogenesis, disrupting glucose metabolism and contributing to cachexia. Similarly, in mouse cancer cachexia models, we observe regulation of their orthologs Pck1 and Pdk3 by IL-6/JAK-STAT signaling. Elevated expression of these genes in fly, mouse, and patients correlates with poor prognosis, and hepatic expression of Pdk3 emerges as a novel mechanism contributing to metabolic dysfunction in cancer cachexia. This study highlights the conserved nature of tumor-induced metabolic disruptions and identifies new therapeutic targets to mitigate cachexia in cancer patients.

overall_design: Liver transcriptomics of mice with lung cancer, with and without cachexia

first: Marcus

last: Goncalves

middle: C

first: Ying

last: Liu

first: Norbert

last: Perrimon


title: Effect of DGCR8 knockout and heterozygosity pri-miRNA processing in PA-1 cells

first: Alasdair

last: Ivens

summary: In this dataset we extract and sequence chromatin-associated RNA to study the effect of DGCR8 knockout and heterozygosity on pri-miRNA processing

overall_design: Comparison between chromatin-associated RNA samples from wildtype, DGCR8 knockout and DGCR8 heterozygous PA-1 cells


title: The role of DGCR8 in RNA processing in human embryonic teratocarcinoma PA-1 cells.The role of DGCR8 in RNA processing in human embryonic teratocarcinoma PA-1 cells.


title: MCL‑1 is essential for hair growth by preventing BAK‑mediated apoptosis of activated adult hair follicle stem cells

city: Parkville

first: Yunshun

last: Chen

state: VIC

address: 1G Royal Parade

department: ACRF Cancer Biology and Stem Cells

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Hair follicles (HFs) cycle between expansion, regression and quiescence. To investigate the role of MCL-1, a BCL-2 family protein with anti-apoptotic and non-apoptotic functions in this dynamic process, we delete Mcl-1 within the skin epithelium, using both constitutive and inducible systems. Mcl-1 deletion does not impair HF organogenesis but results in gradual hair loss and HF stem cells (HFSC) elimination. Single-cell RNA-seq profiling unveils activated DNA repair and P53 signaling pathways in HFSCs during hair regeneration. Acute Mcl-1 deletion led to the depletion of activated HFSCs. Moreover, the ERBB pathway is found to promote MCL-1 protein expression in HFs. Accordingly, ERBB inhibition depletes activated HFSCs in adult mice. Remarkably, the loss of a single Bak allele rescues Mcl-1 deletion-associated defects in both HFs and mammary glands. These findings emphasize the pivotal role of MCL-1 in inhibiting proliferation stress-induced apoptosis when quiescent stem cells re-enter cell cycling to fuel tissue regeneration.

overall_design: Single-cell RNA-seq profiling on the dynamics of adult hair follicles regeneration at 0-hour, 4-hour, 16-hour, 2-day, 4-day, and 6-day post depilation.

first: Jinming

last: Cheng

first: Gordon

middle: K

last: Smyth

first: Hui

last: Chin

first: Naiyang

last: Fu


title: Two mutations associated with leukemia that change a single tyrosine residue in the STAT5B SH2 domain have opposite effects on the transcriptional programs controlling hematopoiesis [ChIP-seq]

city: Bethesda

first: Hye Kyung

last: Lee

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

summary: Normal hematopoiesis is regulated by various cytokines via the JAK-STAT signaling pathway. Gene deletion studies in mice have demonstrated the crucial role of STAT5B in the proliferation, differentiation, and survival of immune cells. However, the physiological effects of human STAT5B mutations remain poorly understood. Mutations within the SH2 domain of STAT5B have been identified in leukemia patients. In this study, we investigate two specific variants: one that substitutes tyrosine 665 with phenylalanine (STAT5BY665F) and another that substitutes tyrosine 665 with histidine (STAT5BY665H). We introduced these two mutations into the mouse genome and observed distinct and divergent impacts on immune cell function. The STAT5BY665F mutation enhanced STAT5B activity and the establishment of transcriptional enhancers and genetic programs. Conversely, the STAT5BY665H mutation was largely inactive, failing to induce the interleukin-regulated enhancer landscape and gene expression. Both mutations modified immune cell profiles, inducing features characteristic of autoimmune disease. In STAT5BY665F mice, there was an expansion of CD8+ and regulatory CD4+ T cells, whereas STAT5BY665H mice didn’t. Both mutant strains exhibited skin abnormalities; however, only the STAT5BY665F mice developed progressive dermatitis. Introduction of equivalent mutations into STAT5A did not significantly impact hematopoiesis. However, mice carrying mutations in both STAT5A and STAT5B displayed additive effects with highly elevated CD4+ and CD8+ T cells. Our findings demonstrate that different naturally occurring missense mutations identified in leukemia patients, changing a single amino acid within the SH2 domain, can either activate or inactivate STAT5B and thereby impact T cell populations.

overall_design: ChIP-seq for TFs and histone markers using T cells from spleen of wild-type and mutant mice at carrying a point mutation in Stat5b-Y665.

first: Hye


title: Critical functions and key interactions mediated by the RNase E scaffolding domain in Pseudomonas aeruginosa

city: Geneve

first: George

last: Allen

state: Geneve

address: Rue Michel-Servet 1

institute: University of Geneva

summary: The RNA degradosome, a multi-protein complex regulating mRNA levels in bacteria, assembles in Pseudomonadota (Proteobacteria) on the RNase E C-terminal domain (CTD) via short linear motifs (SLiMs) that bind other RNA degradosome components and RNA. The composition of Pseudomonas aeruginosa RNA degradosome remains unknown, and its RNase E CTD shows limited similarity to those in well-studied Proteobacteria models like Escherichia coli or Caulobacter crescentus. Our study identified and characterized the SLiMs in P. aeruginosa RNase E, revealing a large duplicated sequence termed the 'REER-repeats' region. This region, along with AR1 and AR4 SLiMs, mediates RNase E CTD RNA binding and is necessary for the subcellular localization of the RNA degradosome in foci. Pull-down and bacterial two-hybrid assays identified PNPase and RhlB as RNase E-interacting proteins. We confirmed through protein-protein binding assays that PNPase and RhlB directly interact with RNase E, and additionally show that the interactions are mediated by the NDPR and AR1 SLiMs, respectively. Additionally, we confirm that the RhlE2 RNA helicase interacts with RNase E, but this interaction involves RNase E N-terminal domain. Finally, we show that RNase E CTD truncations are impaired in growth on cold and mutations affecting CTD RNA binding impaired twitching motility and virulence in a Galleria mellonella infection model. This study elucidates and highlights the critical role of RNase E CTD-mediated RNA binding and RNA degradosome assembly in the virulence and adaptability of P. aeruginosa.

overall_design: PAO1 wild type and mutants were grown in 50 mL Erlenmeyer flasks (10 mL NYB broth) until OD600nm= 1.0-1.2. RNA was purified  using the Monarch Total RNA Miniprep kit, following manufacturer instruction. The absence of residual gDNA contamination was verified by performing a PCR for 35 cycles using primer pairs targeting rpoD. Ribosomal RNA was depleted with Ribo-Zero rRNA Removal Kit (Illumina). Then, libraries were prepared and sequenced using the Illumina HiSeq 2000, 150 bp double end read at Novogene.

first: Sandra

last: Geslain

first: Stéphane

last: Hausmann

first: Johan

last: Geiser

first: Diego

last: Gonzalez

first: Martina

last: Valentini


title: TGF-β1-induced m6A modifications accelerate onset of nuclear cataract in high myopia by influencing the PCP pathway [meRIP-seq]

city: Chengdu

first: Ling

last: Wei

institute: Sichuan provincial peaple's hospital

summary: High myopia is a major cause of blindness worldwide, characterized by early-onset nuclear cataracts, whose underlying mechanisms remains largely unexplained. Here, we identify a conspicuously polarized lens fiber alignment in highly myopic cataracts (HMC) and a simultaneous rise in N6-methyladenosine (m6A) modifications induced by elevated transforming growth factor-β1 (TGF-β1) in lens. Mechanistically, methyltransferase METTL3 and m6A reader insulin-like growth factor 2 mRNA binding protein 3 synergistically enhance planar cell polarity (PCP) signaling through affecting mRNA stability of dishevelled 2. This, in turn, alters proliferation, migration, and polarity formation of lens epithelial cells. Moreover, Mettl3 conditional knockout in mice leads to disrupted lens fiber arrangement and alleviates TGF-β1-induced increase of lens nuclear density. Collectively, these findings highlight the significance of m6A-modified PCP pathway in regulating postnatal lens fiber organization, which may hold great promise as a therapeutic target for HMC.

overall_design: RNA profile from human lens capsule tissues from age-related cataract (ARC) and highly myopic cataract (HMC) patients. Expression profiling by high throughput sequencing. Methylation profiling by high throughput sequencing

first: Yu

last: Du

first: Yi

last: Lu

first: Xiangjia

last: Zhu


title: Two mutations associated with leukemia that change a single tyrosine residue in the STAT5B SH2 domain have opposite effects on the transcriptional programs controlling hematopoiesis [scRNA-seq]

overall_design: scRNA-seq was performed with spleen, lymph node and bone marrow tissue from wild-type and mutant mice at carrying a point mutation in Stat5b-Y665.


title: Nkx2.7 is a Conserved Regulator of Craniofacial Development

city: Trieste

first: UDAY

last: RANGASWAMY

state: Trieste

address: via bonomea 265

department: NEUROSCIENCE

institute: SISSA

summary: Pharyngeal arch cells are comprised of endoderm, mesoderm, and neural crest layers. We used single cell RNA sequencing (scRNA-seq) to analyze the genetic differences in pharyngeal arch cell types between wild-type and nkx2.7-/- samples.

overall_design: Pharyngeal arch cells were obtained through manual dissection of wild-type and nkx2.7-/- embryos at 26 hpf. All embryos were positive for TgBAC(tcf21:mcherry-NTR), which was used as a visual guide for dissection. Cells were FACS sorted to eliminate dead cells from sequencing. 2 wild-type embryos and 2 nkx2.7-/- samples were pooled for submission.

first: Uday

last: Rangaswamy

first: Caitlin

last: Ford

first: Remo

last: Sanges

first: Kimara

last: Targoff


title: Insights into dentatorubral-pallidoluysian atrophy from a new Drosophila model of disease

status: Public on Feb 11 2025

city: Detroit

first: Oluwademilade

last: Nuga

address: 540 E Canfield

department: Pharmacology

institute: Wayne State University School of Medicine

summary: Dentatorubral-pallidoluysian atrophy (DRPLA) is a polyglutamine neurodegenerative disorder caused by CAG expansions in ATN1. To investigate its pathogenesis, we developed and characterized  Drosophila models expressing human ATN1 with normal (Q7) or pathogenic (Q88) repeats.

overall_design: Drosophila mdels expressing human ATN1 with normal (Q7) or pathogenic (Q88) repeats.

first: Matthew

last: Prift

middle: O

first: Ryan

last: Dulay

first: Nikhil

last: Patel

first: Truman

last: Kula

first: Kozeta

last: Libohova

first: Autumn

last: Jackson-Butler

first: Wei-Ling

last: Tsou

first: Kristin

last: Richardson

first: Sokol

last: Todi


title: Effect of NUTF2 overexpression on gene expression in MCF-7 cells

city: Jupiter

first: Jerome

last: Nwachukwu

state: Florida

address: 130 Scripps Way

department: Department of Immunology and Microbiology

institute: The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology

summary: We generated MCF-7 cells stably expressing an exogenous NUTF2 gene or the empty vector

overall_design: We performed gene expression profiling analysis by RNA-seq of the 2 stable cell lines. We also performed CUT&RUN for Estrogen Receptor-alpha and HA-tagged NUTF2 in the stable cell lines after treatment with vehicle, 17beta-estradiol, or 4-hydroxytamoxifen for 1 hour.

first: Robin

last: Russo

first: Kendall

middle: W

last: Nettles


title: Different fibroblast subtypes propel spatially defined ileal inflammation through TNFR1 signalling in murine ileitis

city: Vari

first: George

last: Kollias

state: Attica

address: 34 Fleming Street

department: Institute for Bioinnovation/ Department of Physiology, School of Medicine

institute: BSRC "Alexander Fleming"/ National and Kapodistrian University of Athens

summary: TNFΔΑRE mice represent a model for Crohn's Disease (CD) ileitis. We wanted to examine the cellular and trascriptional heterogeneity of immune and stroma cells (not including the epithelium) in the ileum of wild type and TNFΔΑRE mice.

overall_design: Intestinal samples were digested using a mix of Collagenase XI/ Dnase/ Dispase II after removing epithelial cells. To ensure sufficient representation of all the basic cellular compartments, especially given that stromal cells in TnfΔARE accounted for less than 10% of the total cell population, we sorted myeloid cells (CD45+CD11B/CD11C+), lymphoid cells (CD45+CD11B-CD11C-), and stroma cells (CD45-EPCAM1-), mixed them to an equal ratio.The scRNA-seq libraries were prepared following the 10X Genomics user guide Single Cell 3’ v3.1 reagent kits pooled and sequenced with the DNBSEQ-G400 sequencer (PE100) (BGI Genomics).

first: Lida

last: Iliopoulou

first: Christos

last: Tzaferis

first: Alejandro

last: Prados

first: Fani

last: Roumelioti

first: Vasiliki

last: Koliaraki


title: Spinal cord single-nuclei RNA sequencing of human ALS spinal cords [ALS human snRNAseq]

status: Public on Feb 10 2025

city: Cambridge

first: Timothy

last: Hammond

state: MA

address: 350 Water Street

institute: Sanofi

summary: Transcriptomic analysis of postmortem cervical spinal cord samples from 8 people with ALS (6 sporadic and 2 familial cases) and 4 age-matched non-neurological controls using snRNA-seq

overall_design: Spinal cords were acquired from the NIH brain biobank, nuclei were isolated by FACS, and sequenced using 10x Genomics and Illumina platforms.


title: Transcriptomic analysis of Omicron Pseudovirus(PsV)-infected HSPCs(hematopoietic stem and progenitor cells)

status: Public on Feb 09 2025

city: Seoul

first: Dong hoon

last: Chae

address: Gwanak-ro 1

country: South Korea

institute: Seoul National University

summary: We have developed a SARS-CoV-2 PsV system that expresses the spike protein on the viral surface and carries spike protein genomic sequences, enabling this pseudovirus to activate infection signaling pathways through ACE2 and stimulate intracellular spike protein gene expression. To understand the impact of SARS-CoV-2 on hematopoietic system, we infected heman HSPCs with Omicron PsV and analyzed changes in transcriptome

overall_design: To investigate the effect of SARS-CoV-2 on hematopoietic system, we constructed pseudovirus system that contained spike genome and expressed spike protein on the surface of virus, which could enter through ACE2.

first: Hyunsung

last: Park


title: Bulk RNA-seq of Bone marrow stem cells with or without 50 uM docosatrienoic acid treatment

city: Shanghai

first: Haihan

last: Gao

address: Xuhui District

department: Department of Orthopaedic Surgery

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: In order to investigate the effect of  50 uM docosatrienoic acid on the transcription profile of Bone marrow stem cells

overall_design: RNA-seq profiling of  Bone marrow stem cells with or without 50 uM docosatrienoic acid treatment for 48 hours.


title: Bulk RNA sequencing of human ALS spinal cords

summary: There remains a poor understanding of cell-specific responses in the human ALS spinal cord, including differences in cell type composition, changes in cell state, and contribution of various cell types to neuroinflammation.

overall_design: Transcriptomic analysis of postmortem cervical spinal cord samples from 8 people with ALS (6 sporadic and 2 familial cases) and 4 age-matched non-neurological controls


title: Disrupting bile acid metabolism by suppressing Fxr causes hepatocellular carcinoma induced by YAP activation

city: Boston

first: Yuchen

last: Liu

state: Massachusetts

address: 188 Longwood Avenue, REB 514B

institute: Harvard school of dental medicine

summary: Bile acid (BA) production is a critical metabolic function of the liver, and its disruption leads to various liver diseases including hepatocellular carcinoma (HCC). However, the underlying molecular mechanism remained elusive. Here, we report that BA metabolism is directly controlled by a previously unidentified repressor function of YAP, a transcriptional activator known to promote HCC formation. We show in hepatocytes, activated YAP suppressed Fxr, a BA-sensing nuclear receptor that critically regulates BA production and export. The repressor function of activated YAP induced cholestasis damaged the liver, and altered liver and serum BA concentrations and composition. Specifically, YAP activation inhibited expression of an Fxr target gene, Bsep (Abcb11), impairing BA exportation and injuring hepatocytes. Elevated BA in the blood due to hepatocyte injury further activated hepatic YAP, resulting in a vicious cycle leading to HCC. In both mouse liver and human HCC patient samples, transcriptomic analysis negatively correlated YAP and Fxr activities. Mechanistically, Fxr was found to bind Teads in a DNA-binding-independent manner; and Teads recruited YAP to epigenetically reprogram Fxr by replacing the histone acetyltransferase, P300, with the histone deacetylase, HDAC1. Importantly, alleviating YAP repressor function in BA metabolism by activating Fxr with its agonist GW4064, inhibiting HDAC1 with Entinostat, or overexpressing Bsep, reduced cholestatic phenotypes including hepatic injury, fibrosis, and inflammation, alleviating the HCC caused by YAP activation. Our results identify Yap's transcriptional repressor role as a key driver of Yap-induced HCC and BA metabolism as a potential therapeutic target for HCC.

overall_design:
YAP Overexpression in Mature Hepatocyte Organoids (MHOs): Hepatocytes isolated from the TetO-YAP mice were used for the experiments. The HOs were switched to maturation medium (RGF+T3) for HO maturation, and AAV-TBG-Cre was added at the same time to activate rtTA expression. Three days after maturation started, doxycycline (Dox) was added to the medium for another three days to induce YAP overexpression, paired samples without Dox treatment were used as control. Samples were collected six days after being cultured in the maturation medium (RGF+T3). Yap Knockout in the MHOs: Hepatocytes isolated from Yap fl/fl mice were used for the experiments. The HOs were switched to maturation medium (RGF) for HO maturation, and AAV-TBG-Cre was added at the same time to knockout Yap in the organoids. Samples were collected 12 days  after being cultured in the maturation medium (RGF). Paired control samples for Yap knockout were uploaded perviously(GSM7846237,GSM7846238, GSM7846239). Each sample group has three replicate samples.

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

last: Yang


title: Gene expression profiling of immune cells at the single-cell level from livers of URI and glutamine synthetase knockout mice

status: Public on Feb 07 2025

city: Madrid

first: Ruth

last: Álvarez-Díaz

address: C/ Melchor Fernández Almagro, 3

department: Molecular Oncology

institute: Spanish National Cancer Research Center (CNIO)

summary: We used single-cell RNA sequencing (sc-RNAseq) to examine the diversity and potential function of CD45+ immune cells from URI and glutamine synthetase knockout mouse livers along with their littermate controls.

overall_design: CD45+ inmmune liver cells isolated by FACSARIA (30M) and processed for scRNA sequencing as described in other protocols

first: Maria del Mar

last: Rigual

last: Alvarez-Diaz

first: Nabil

last: Djouder


title: THE HISTONE CHAPERONE SPN1 PRESERVES SUBNUCLEOSOMAL STRUCTURES AT PROMOTERS AND NUCLEOSOME POSITIONING IN OPEN READING FRAMES

city: Aurora

first: Srinivas

last: Ramachandran

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

summary: Spn1 is a multifunctional histone chaperone essential for life in eukaryotes. While previous work has elucidated regions of the protein important for its many interactions, it is unknown how these domains contribute to the maintenance of chromatin structure. Here, we employ digestion by micrococcal nuclease followed by single-stranded library preparation and sequencing (MNase-SSP) to characterize chromatin structure in yeast expressing wild-type or mutants of Spn1. We mapped nucleosome and subnucleosomal protections genome-wide, and surprisingly, we observed a genome-wide loss of subnucleosomal protection over nucleosome-depleted regions (NDRs) in the Spn1-K192N-containing strain, indicating critical functions of Spn1 in maintaining normal chromatin architecture in promoter regions. Additionally, alterations in nucleosome and hexasome positioning were observed in markedly different mutant Spn1 strains, demonstrating that multiple functions of Spn1 are required to maintain proper chromatin structure in open reading frames. Moreover, the impact of these functions correlated with gene expression and length. Taken together, our results reveal a previously unknown role of Spn1 in the maintenance of NDR architecture and deepen our understanding of Spn1-dependent chromatin maintenance over transcribed regions.

overall_design:
MNase-SSP of following yeast strains: WT, spn1 K192N, aaand spn1 141-305 at 32U and 128U of MNase.
Spike-in normalized RNA-seq of following yeast strains: WT, spn1 K192N, aaand spn1 141-305

first: Andrew

middle: J

last: Tonsager

first: Alexis

last: Zukowski

first: Catherine

middle: A

last: Radebaugh

first: Abigail

last: Weirich

first: Laurie

last: Stargell


title: Development of a potent epigenetic editor targeting human PCSK9 with durable reduction of cholesterol in mice and non-human primates [twist methylome methyseq]

status: Public on Feb 05 2025

first: Frederic

last: Tremblay

address: 201 Brookline Ave, Suite 1101

institute: Chroma Medicine

summary: DNA methylation in gene promoter regions is a conserved, innate epigenetic mechanism to control gene expression. Transient application of epigenetic editors designed to induce DNA methylation has been shown to silence genes in cultured cells and in mice. Here we report the development of a potent, efficacious, and specific human PCSK9-targeting epigenetic editor. A single administration of lipid nanoparticles encapsulating mRNA encoding the epigenetic editor which precisely targets the PCSK9 locus was sufficient to drive near-complete silencing in transgenic mice expressing human PCSK9. Silencing was durable for at least one year and was fully maintained following partial hepatectomy-induced liver regeneration. In addition, we showed reversibility of epigenetic editing in previously silenced mice upon treatment with a targeted epigenetic activator designed to demethylate the PCSK9 locus. Importantly, a single administration of the epigenetic editor robustly, potently, and durably decreased circulating PCSK9 (~90%) in cynomolgus monkeys with concomitant reduction in low-density lipoprotein cholesterol (~70%). These findings support the development of an epigenetic editor targeting PCSK9 for the treatment of hypercholesterolemia and demonstrate the broad therapeutic potential of precise, efficacious, durable, and reversible epigenetic editing in vivo

overall_design: Twist Human Methylome hybrid capture methylation sequencing in PXB primary human hepatocytes treated with epigenetic editor effector without gRNA (Effector Only), and PCSK9-EE at day 15.

first: Qiang

last: Xiong

first: Shrijal

middle: S

last: Shah

first: Chih-Wei

last: Ko

first: Kenneth

last: Kelly

first: Mary

last: Morrison

first: Cristiana

last: Giancarlo

first: Ricardo

middle: N

last: Ramirez

first: Erica

last: Hildebrand

first: Sarah

middle: B

last: Voytek

first: Gabriel

last: El Sebae

first: Shane

middle: H

last: Wright

first: Liam

last: Lofgren

first: Scott

last: Clarkson

first: Samantha

last: Linder

first: Songlei

first: Taesun

last: Eom

first: Shefal

last: Parikh

first: Yuki

last: Weber

first: Salette

last: Martinez

first: Padma

last: Malyala

first: Sahar

last: Abubucker

first: Ari

last: Friedland

first: Morgan

middle: L

last: Maeder

first: Angelo

last: Lombardo

first: Vic

last: Myer

first: Aron

last: Jaffe


title: Development of a potent epigenetic editor targeting human PCSK9 with durable reduction of cholesterol in mice and non-human primates [amplicon methylation]

first: Frederic

last: Tremblay

type: Methylation profiling by high throughput sequencing

overall_design: Amplicon bisulfite sequencing of the PCSK9 TSS region in cynomolgus monkey liver biopsies 24 days after treatment with vehicle or PCSK9-EE-V2 (0.5mpk, 1.0mpk, or 1.5mpk).

first: Qiang

last: Xiong

first: Shrijal

last: Shah

first: Chih-Wei

last: Ko

first: Kenneth

last: Kelly

first: Mary

last: Morrison

first: Cristiana

last: Giancarlo

first: Ricardo

last: Ramirez

first: Erica

last: Hildebrand

first: Sarah

last: Voytek

first: Gabriel

last: Liu

middle: E


title: IGF2BP3 as a Prognostic Biomarker and Regulator of Metastasis in Merkel Cell Carcinoma

city: Solna

first: Yajie

last: Yang

address: BioClinicum J6:20, Karolinska University Hospital Solna, Visionsgatan 4

country: Sweden

institute: Karolinska Institute

summary: Merkel cell carcinoma (MCC) is an aggressive skin cancer with frequent development of metastases, however effective treatment options for advanced disease are often missing. In this study, we investigated the clinical significance and functional impact of the Insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) in MCC. Our results revealed elevated IGF2BP3 expression in metastases as compared to primary tumors. High IGF2BP3 levels in primary MCCs were associated with shorter disease-specific survival. In an MCC xenograft model, lung metastases exhibited increased IGF2BP3 expression. Functional studies showed that IGF2BP3 primarily regulates cell migration and invasion in MCC. We identified 281 direct RNA targets of IGF2BP3 with enriched functions linked to metastasis-related processes and several targets overlapped with genes differentially expressed between MCC primary tumors and metastases, implying that IGF2BP3 and its targets contribute to tumor progression. Inhibition or silencing of bromodomain-containing protein 4 (BRD4) reduced IGF2BP3 expression, suggesting BRD4 as a potential regulator of IGF2BP3. Our study underscores the role of IGF2BP3 in MCC metastasis and its potential as a prognostic biomarker.

overall_design: We conducted RNA immunoprecipitation followed by RNA sequencing (RIP-seq) in WaGa cells,  using IGF2BP3 or IgG (negative control) antibody, with three independant replicates.

first: Jiwei

last: Gao

first: Weng-Onn

last: Lui


title: Potential driver genes involved in the initiation of CRC

status: Public on Feb 08 2025

city: Guangzhou

first: Jinlong

last: Lin

address: Dongfeng dong road

institute: Sun Yat-sen university cancer center

summary: To identify the potential driver gene modulate the metabolism reprogramming during the initiation of CRC, we conducted RNA-seq among CRCs, paired normal tissues, and adenomas.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CRC, paired normal tissues, and adenomas.

first: Fengwei

last: Wang


title: A Chemically Defined Feeder-free System for the Establishment and Maintenance of the Human Naive Pluripotent State

city: HangZhou

first: Zhengyi

last: Li

state: ZheJiang

address: 866 Yuhangtang Rd, Hangzhou

department: Institute of Genetics

institute: Zhejiang University School of Medicine

type: Methylation profiling by genome tiling array

summary: The distinct states of pluripotency in the pre- and post-implantation embryo can be captured in vitro as naive and primed pluripotent stem cell cultures, respectively. The study and application of the naive state remains hampered, particularly in humans, partially due to current culture protocols relying on extraneous undefined factors such as feeders. Here we performed a small-molecule screen to identify compounds that facilitate chemically defined establishment and maintenance of human feeder-independent naive embryonic (FINE) stem cells. The expression profile in genic and repetitive elements of FINE cells resembles the 8-cell-to-morula stage in vivo, and only differs from feeder-dependent naive cells in genes involved in cell-cell/cell-matrix interactions. FINE cells offer several technical advantages, such as increased amenability to transfection and a longer period of genomic stability, compared with feeder-dependent cells. Thus, FINE cells will serve as an accessible and useful system for scientific and translational applications of naïve pluripotent stem cells.

overall_design:
TeSR cultured primed ESCs, 4iL cultured or FINE cultured naïve ESCs were labeled by bisulfide labelling kit and subjected to 850k array to profile for the DNA methylation loci

***Raw data not provided***

first: Hongqing

last: Liang

first: Yun-Shen

last: Chan


title: Two mutations associated with leukemia that change a single tyrosine residue in the STAT5B SH2 domain have opposite effects on the transcriptional programs controlling hematopoiesis [RNA-seq]

first: Hye Kyung

last: Lee

institute: National Institutes of Health (NIH)

summary: Normal hematopoiesis is regulated by various cytokines via the JAK-STAT signaling pathway. Gene deletion studies in mice have demonstrated the crucial role of STAT5B in the proliferation, differentiation, and survival of immune cells. However, the physiological effects of human STAT5B mutations remain poorly understood. Mutations within the SH2 domain of STAT5B have been identified in leukemia patients. In this study, we investigate two specific variants: one that substitutes tyrosine 665 with phenylalanine (STAT5BY665F) and another that substitutes tyrosine 665 with histidine (STAT5BY665H). We introduced these two mutations into the mouse genome and observed distinct and divergent impacts on immune cell function. The STAT5BY665F mutation enhanced STAT5B activity and the establishment of transcriptional enhancers and genetic programs. Conversely, the STAT5BY665H mutation was largely inactive, failing to induce the interleukin-regulated enhancer landscape and gene expression. Both mutations modified immune cell profiles, inducing features characteristic of autoimmune disease. In STAT5BY665F mice, there was an expansion of CD8+ and regulatory CD4+ T cells, whereas STAT5BY665H mice didn’t. Both mutant strains exhibited skin abnormalities; however, only the STAT5BY665F mice developed progressive dermatitis. Introduction of equivalent mutations into STAT5A did not significantly impact hematopoiesis. However, mice carrying mutations in both STAT5A and STAT5B displayed additive effects with highly elevated CD4+ and CD8+ T cells. Our findings demonstrate that different naturally occurring missense mutations identified in leukemia patients, changing a single amino acid within the SH2 domain, can either activate or inactivate STAT5B and thereby impact T cell populations.

overall_design: Total RNA-seq wwas performed with spleen, lymph node and bone marrow tissue from wild-type and mutant mice at carrying a point mutation in Stat5b-Y665.

first: Hye