title: The molecular basis of lamin- chromatin interactions [ChIP-Seq]

city: Milan

first: Chiara

last: Lanzuolo

address: Via Francesco Sforza 35

institute: CNR and Istituto Nazionale Genetica Molecolare

summary: Lamins are the main constituents of the nuclear lamina, a fibrillar layer underlyingthe inner nuclear membrane. The nuclear lamina governs chromatinorganization through lamina-associated domainswithin the densely packed heterochromatin regions. Employing cryo-focused ion beam (cryo-FIB) milling in conjunction withcryo-electron tomography (cryo-ET), we mappedthe concentration of nucleosomesat the lamin-chromatin interface. Depletion of lamin A/C induces nanometer-scale chromatin decompaction, macroscopic-scale alterations in gene expression and chromatin-wide alterations of chromatin properties, revealed by 4f-genome-wide analysis. Cryo-electron microscopy (cryo-EM) structural analysis revealed a specific interaction between nucleosomes and the tail domain of lamin A. A unique motif of lamin A that distinguishes it from other lamin isoforms. These findings illuminatethe dynamic interplay between specific lamins and chromatin, shaping chromatin architecture and epigenetic regulation.

overall_design: To investigate the role of lamin proteins in chromatin organization, we carried out a comprehensive analysis including 4fSAMMY-seq, RNA-seq, and ChIP-seq for H3K9me3 across wildtype (WT), Lmna-/- (LmnaKO), and Lmnb1-/-+Lmnb2-/- (LBDKO) mouse embryonic fibroblasts (MEFs).Additionally we perfomed ChIP-seq for euchromatin-associated H3K27ac and H3K4me3 histone modifications on WT.

first: Baihui

last: Wang

first: Rafael

last: Kronenberg-Tenga

first: Valentina

last: Rosti

first: Emanuele

last: Di Patrizio Soldateschi

first: Qiang

last: Luo

first: Louise

last: Pinet

first: Matthias

last: Eibauer

first: Rajaa

last: Boujemaa-Paterski

first: Benjamin

last: Schuler

first: Ohad

last: Medalia


title: Early IKKb-dependent anabolic and fibrotic signatures govern vascular smooth muscle cells fate and abdominal aortic aneurysm development

status: Public on May 28 2025

city: Montreal

first: Simon-Pierre

last: Gravel

state: QC

address: 2940 ch. de la polytechnique

department: Faculty of pharmacy

country: Canada

institute: University of Montreal

type: Expression profiling by high throughput sequencing

summary: Aims Abdominal aortic aneurysm (AAA) is a complex aortic disease define by a dilatation of the infrarenal aorta and the most common form of aneurysm in humans. Whereas inflammation contribute to AAA development, quenching vascular inflammation using classical pharmacological approaches or inhibiting the immune system does not influence the progression of AAA in humans indicating the lack of a complete picture on the molecular events that drive this aortopathy. This study was designed to comprehend the earliest molecular indicators, aiming to pinpoint a biological target associated with the latter. Methods and results Using ApoE-deficient mice fed with a standard diet and infused with Angiotensin II (Ang II), we conducted bulk RNA-sequencing analysis on suprarenal (SRA) regions obtained from both unchallenged and challenged WT mice, specifically examining responses 24 hours after Ang II infusion to capture the initial phases of aortic stress response. We further created a unique model of hyperlipidemic mice in which the expression of IKK can be conditionally (via tamoxifen injection) suppressed in vascular SMCs (CreERT2 under the control of the Acta2 promoter). The development of AAA was evaluated using in situ examination and quantified using RT-qPCR, immunohistochemistry and fluorescence microscopy. Cultured  vascular SMC were exposed to the selective IKK inhibitor MLN120b and the expression levels of phenotypic markers KLF4, -Catenin and CTGF were addressed using cellular extracts and immunoblot analysis.  Results RNASeq data support the presence of early anabolic events in SRA regions detailing activation of the mTORC1 pathway, which paralleled cellular processes including mitochondria, ribosome and sterol biosynthesis and the Unfolded Protein Response (UPR). Conditional deletion of the Ikbkb gene in vascular SMCs significantly reduces the incidence of SRA lesions as well as the rate of aneurysm ruptures in animals exposed to Ang II. In situ analysis further demonstrated that the protection conferred by the lack of IKK expression in vascular SMC is associated with reduced inflammatory response, the preservation of the contractile over the degradative vascular SMC phenotypes and the absence of anabolic and fibrotic signatures.  Conclusion Our data not only reinforce the major roles play by vascular SMC in the rapid adaptation leading to the deleterious remodeling of the vascular wall and aortic lesions but also support a paradigm aiming at repositioning the efforts focusing on anabolic rather than inflammatory events.

overall_design: We used a transgenic homozygous mouse model referred to as SMA-CreERT2IkkbFlox/FloxApoE-/- in which IKKb expression can be temporally and selectively prevented in ApoE-/- vascular SMCs on a C57BL6 background (referred as KO). Wild-type and KO mice were treated with saline or angiotensin II (Ang II) (500 to 1000 ng/min/kg) s.c. with constant infusion using osmotic pumps for 24 h. Total RNA from the suprarenal aorta was extracted using the RNeasy Mini Kit (No. 74106, Qiagen).

first: Priscilla

last: Doyon

first: Ozge

last: Kizilay Mancini

first: Florence

last: Dô

first: David

middle: H

last: Huynh

first: Gaétan

last: Mayer

first: Huy

last: Ong

first: Maëlle

last: Batardière

first: Vincent

middle: Q

last: Trinh

first: Sylvie

last: Marleau

first: Pierre

last: Chambon

first: Marc

middle: J

last: Servant


title: RNA sequencing facilitates quantitative analysis of PDAC CFPAC-1 cells (including CFPAC-1 NC, CFPAC-1 CGN siRNA) transcriptomes

city: Guangzhou

first: Yuling

last: Su

state: State...

address: Guangzhou University City, Panyu District, Guangzhou City

country: China

institute: South China univerisity of technology

summary: Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest malignancies for its difficult early diagnosis and poor prognosis. The molecular determinants dictating pancreatic cancer initiation and progression remain to be defined and are essential to its effective early detection and successful treatment. Little is known on the cingulin (CGN) expression and function in carcinogenesis. In this study, we demonstrate the critical oncogenic role of CGN in PDAC pathogenesis. Increased expression of CGN promoted pancreatic acinar-to-ductal metaplasia (ADM) and CGN is progressively upregulated during pancreatic cancer initiation and progression. CGN was required for pancreatic cancer cell proliferation, gemcitabine resistance, tumorigenesis and invasion and its overexpression predicted a poor patient prognosis. Mechanistically, CGN enhanced EGFR/AXL/ERK signaling pathway through increasing the mRNA stabilization and the protein expression of nuclear-cytoplasmic transport protein, importin-7 (IPO7) and the nuclear translocation of pERK, thus promoting the malignant behaviors of PDAC cells. Therefore, our study has demonstrated that CGN forms a novel oncogenic signaling axis, which could be an effective therapeutic target for PDAC treatment.

overall_design: To investigate the function of CGN knockdown in the regulation of neoplastic features, we established CGN knockdown PDAC cell lines.        We then performed gene expression profiling analysis using data obtained from RNA-seq of CFAPC-1 (CFPAC-1 NC, CFPAC-1 CGN siRNA).

first: Jie

last: He

first: Keping

last: Xie


title: The molecular basis of lamin- chromatin interactions [RNA-Seq]

first: Chiara

last: Lanzuolo

country: Italy

first: Baihui

last: Wang

first: Rafael

last: Kronenberg-Tenga

first: Valentina

last: Rosti

first: Emanuele

last: Di Patrizio Soldateschi

first: Qiang

last: Luo

first: Louise

last: Pinet

first: Matthias

last: Eibauer

first: Rajaa

last: Boujemaa-Paterski

first: Benjamin

last: Schuler


title: The effects of B cell lymphoma on young and aged T and NK cells (scRNA-Seq)

city: Tampa

first: Rebecca

last: Hesterberg

address: 12902 Magnolia Dr.

country: USA

institute: Moffitt Cancer Center

summary: While lymphomas affect mostly older patients, there are cases of lymphoma across the aging spectrum. However, the effects of these cancers on young versus old immune cells is largely unknown.  Using a transplantable B cell lymphoma mouse model, we generated single cell RNA-seq of isolated T cells and NK cells to define phenotypic and population changes modulated by age and lymphoma. Further, to investigate age-dependent epigenetic changes driven by lymphomas, we used an assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) on isolated CD4 T cells from young and aged mice with lymphomas. These studies demonstrate that lymphoma alters the immune system in an age-dependent manner.

overall_design: Young (<12 weeks) and aged (>78 weeks) C57Bl6 mice were transplanted with Em-Myc lymphoma cells via tail vein injection. Twelve days after tumor transplant, T and NK cells were isolated from the spleens of lympoma-bearing or non-tumor-bearing control mice. Further, CD4 T cells were isolated for ATAC-seq from these same mice. Both sequencing datasets are n = 3 biological replicates.

first: John

last: Cleveland


title: The effects of B cell lymphoma on young and aged T and NK cells

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: RIP-SEQ analysis of CGN binding mRNA in PANC-1 cells stably expressing CGN

overall_design: To investigate the function of CGN in PDAC progression, we established PANC-1-CGN cell lines with CGN overexpressed. Then we analysis of CGN binding mRNA in human PANC-1-CGN cell lines from RIP-SEQ (input, IP)


title: RNA polymerase II binding profile in WT and MED23-KD 293T cells

city: Shanghai

first: Lu

last: CHENGJIANG

state: China, Mainland

address: Yueyang Road 320

institute: Shanghai Institute of Biochemistry and Cell Biology

summary: MED23-KD 293T cells in which MED23 was mostly knockouted were generated by CRISPR-Cas9. We performed CUT&Tag experiments in WT and MED23-KD cells to characterize the change of Pol II binding.

overall_design: CUT&Tag experiments were performed as the commercial kit discribed (Vazyme, #TD901-01) instruments.

first: Chengjiang

last: Lu

first: Xue

last: Bai

first: Hanqing

last: Zhang


title: Transcription profiles of MED23-KD and wildtype 293T cells

summary: To characterize the function of MED23 on transcription, we generated two MED23-KD 293T cell lines in which MED23 was about 75% knockouted by CRISPR-Cas9. Then we performed RNA-seq to analyze the change of transcript levels around termination sites.

overall_design: Gene expression profiling analysis of RNA-seq data for wildtype, MED23-KD1 and MED23-KD2 293T cells.


title: Genomic occupation profile of Mediator MED23 in 293T cells

summary: We performed CUT&Tag experiments in MED23-HA and WT 293T cells to analyze the genomic occupation profiles for the Mediator MED23.

overall_design: HA DNA sequence was inserted into the C-terminus of MED23 to generated MED23-HA 293T cell lines. Commercial CUT&Tag kit (Vazyme, #TD901-01) was used.


title: RNA binding profile of MED23 in 293T cells

summary: To delineate the repertoire of RNA binding of MED23, we performed a denatured CLIP-seq experiment coupled with high-salt wash in MED23-HA 293T cells and wildtype 293T cells as a control.

overall_design: The wildtype and MED23-HA cells were crosslinked with UVC (254 nm, 600 mJ/cm2) and then harvested for denaturation by 1% SDS. The denatured cell lysates were diluted by six fold to capture MED23-RNA complex with HA antibody-conjugated beads. The beads were washed with high-stringent buffer and treated with RNase T1 to partially digest RNAs. The RNA fragments were subjected to small RNA library preparations.


title: A single-cell multiomics atlas of rice

city: Beijing

first: Xiaofeng

last: Gu

address: Zhongguancun south street

institute: Chinese Academy of Agricultrual Sciences

summary: Cell functions across eucaryotes are driven by specific gene expression programs that are dependent on chromatin structure. Here, we report a single-cell multiomics atlas of rice, one of the world’s major crop plants. By simultaneously profiling chromatin accessibility and RNA expression in 116,564 cells from eight organs we were able to identify cell-type specific gene regulatory networks and describe novel cell states, such as the “transition status” in floral meristems during panicle development. Based on our network analyses we uncovered the function of cell type-specific regulatory hubs RSR1, F3H and LTPL120 for rice development. Importantly, our analysis revealed a correlation between cell type and agronomic traits, and conserved and divergent cell type functions during evolution. In summary, this study not only offers a valuable single-cell multiomics resource for a major crop, but also enriches our understanding of the intricate roles and molecular underpinnings of individual cell types in rice.

overall_design: We generated Crispr mutant materials and collected one-month-old hydroponically grown seedling roots and leaves for RNA-seq sequencing.

first: Xiangyu

first: Zhe

last: Liang


title: A single-cell multiomics atlas of rice organs

overall_design: Single-cell RNA-seq and ATAC of developmental stages of panicle

last: Wang


title: The molecular basis of lamin- chromatin interactions [SAMMY-Seq]

first: Chiara

last: Lanzuolo

summary: Lamins are the main constituents of the nuclear lamina, a fibrillar layer underlying the inner nuclear membrane. The nuclear lamina governs chromatinorganization through lamina-associated domainswithin the densely packed heterochromatin regions. Employing cryo-focused ion beam (cryo-FIB) milling in conjunction withcryo-electron tomography (cryo-ET), we mappedthe concentration of nucleosomesat the lamin-chromatin interface. Depletion of lamin A/C induces nanometer-scale chromatin decompaction, macroscopic-scale alterations in gene expression and chromatin-wide alterations of chromatin properties, revealed by 4f-genome-wide analysis. Cryo-electron microscopy (cryo-EM) structural analysis revealed a specific interaction between nucleosomes and the tail domain of lamin A. A unique motif of lamin A that distinguishes it from other lamin isoforms. These findings illuminatethe dynamic interplay between specific lamins and chromatin, shaping chromatin architecture and epigenetic regulation.

overall_design:
To investigate the role of lamin proteins in chromatin organization, we carried out a comprehensive analysis including 4fSAMMY-seq, RNA-seq, and ChIP-seq for H3K9me3 across wildtype (WT), Lmna-/- (LmnaKO), and Lmnb1-/-+Lmnb2-/- (LBDKO) mouse embryonic fibroblasts (MEFs).Additionally we perfomed ChIP-seq for euchromatin-associated H3K27ac and H3K4me3 histone modifications on WT.
To investigate the role of Lamin A in chromatin 3D organization, we compared SAMMY-seq data from the transfection of full-length Lamin A (LA 1-646) and truncated Lamin A lacking the C-tail (LA 1-429) in WT MEFs.

first: Baihui

first: Rafael

last: Kronenberg-Tenga

first: Ohad

last: Medalia


title: The occupied profile of FIP1 in WT and MED23-KD 293T cells

summary: MED23-KD 293T cells in which MED23 was mostly knockouted were generated by CRISPR-Cas9. We performed ChIP experiments in WT and MED23-KD cells to profile the genomic occupation profiles of FIP1, which is one of the components of pre-mRNA 3' end processing complex.

overall_design: RNA-binding-proteins ChIP-seq experiments were performed for FIP1 with validated antibody.


title: Single dose of CD137-Antibody Drug Conjugate protects non-human primate allogeneic HCT recipients against acute GVHD

status: Public on May 27 2025

city: Boston

first: Alal

last: Eran

address: 300 Longwood Ave

institute: Boston Children's Hospital

summary: Rapid CD137 upregulation on alloreactive T-cells upon allogeneic stimulation suggests that their selective elimination could prevent acute graft-versus-host disease (aGVHD) after allogeneic hematopoietic stem cell transplantation (HCT). Here, we developed a novel aGVHD prophylactic regimen consisting of a single dose of an anti-CD137 antibody-drug conjugate (CD137-ADC) administered on the day of transplant without additional immunosuppression. The CD137-ADC depleted both human and non-human primate (NHP) activated T-cells and proved highly effective in preventing xenogeneic aGVHD in mice receiving human hematopoietic stem cell grafts, as well as in NHP undergoing MHC-haploidentical HCT. Flow cytometry analysis of NHP T-cells indicated specific depletion of activated PD-1+ CD4 and CD8 T-cells, while sparing naïve and PD-1-OX40+ memory T-cell subsets. CD137-ADC-treated NHP recipients demonstrated robust hematopoietic and immune reconstitution. Hallmarks of T-cell recovery after CD137-ADC, which were associated with long-term aGVHD-free survival, included reconstitution of CD4 memory T-cells expressing TRAIL, terminally-differentiated CD8 T-cells expressing CX3CR1, and CD4 FoxP3+ Tregs – cell types not expected to be involved in aGVHD pathogenesis. CD137-ADC-treated recipients demonstrated a higher risk of reactivation of rhLCV (the rhesus macaque EBV analogue), which was associated with reconstitution of follicular helper T-cells, interferon signaling-associated memory, and gamma-delta T-cell subsets. This reactivation was controllable with rituximab administration. These results document effective depletion of alloreactive T-cells and prevention of aGVHD following a single dose of CD137-ADC, suggesting that clinical translation should be carefully explored.

overall_design: This series extends the dataset in GSE157280 by adding 68 CD4+ samples and two CD8+ samples

first: Victor

last: Tkachev


title: Functional relevance of circRNA aberrant expression in pediatric acute leukemia with MLL/AF4 fusion

city: Padova

first: Stefania

last: Bortoluzzi

address: via G. Colombo 3

department: Department of Molecular Medicine

institute: University of Padova

type: Non-coding RNA profiling by high throughput sequencing

summary: Acute lymphoblastic leukemia (ALL) is the most common malignancy observed in pediatric patients and the MLL-AF4 rearranged is the most frequent and most aggressive subtype of BCP-ALL observed in infant patients that usually shows poor prognosis. Despite many efforts to identify molecular mechanisms sustaining leukemogenesis and to recapitulate disease pathogenesis in models, this subtype of leukemia remains aggressive and difficult to comprehend. The emerging world of circRNAs was never taken into account for this hostile leukemia subtype. CircRNAs are covalently closed RNA molecules produced by a process called backsplicing that gives rise to molecules with unique backsplicing sites, sequences not present in normal transcripts, already described to have different functions and involved in many pathological pathways. In this study, we described for the first time the circRNA landscape of MLL-AF4 BCP-ALL translocated infant patients. Moreover, by high-impact screening, designing siRNA molecules targeting the backsplicing site of deregulated and prioritized molecules, we identified putative oncogenic roles for four circRNAs in MLL-AF4 cell lines. Interestingly, by bioinformatic predictions of circRNAs’ functions we identified putative regulatory axes related to the MLL-AF4 chimera hypothesizing a co-occurring mechanism in the leukemogenesis process between circRNAs and the fusion transcript.

overall_design: CircRNA expression profiling analysis of RNA-seq data for patients (MLLre), patient-derived xenografts (PDX) and cell line (RS4_11) with MLL::AF4 (KMT2A::AFF1) rearrangements, compared to hematopoietic stem cells (CD34).

first: Caterina

last: Tretti Parenzan

first: Anna

last: Dal Molin

first: Giorgia

last: Longo

first: Enrico

last: Gaffo

first: Alessia

last: Buratin

first: Alice

last: Cani

first: Lueder

last: Meyer

first: Paola

last: Guglielmelli

first: Alessandro

middle: M

last: Vannucchi

first: Geertruij

last: Te Kronnie

first: Silvia

last: Bresolin


title: TGF-beta and IL-12 conversely orchestrate formation of CD103+ CD8 tumor-resident memory T cells to regulate response to therapeutic cancer vaccine [RNA-Seq]

city: VILLEJUIF

first: AZIZA

last: CAIDI

address: 114 RUE EDUARD VAILLANT

country: France

institute: GUSTAVE ROUSSY

summary: Using mouse model, we show that CD8 tumor-infiltrating T lymphocytes (TIL) include two major resident T cells subpopulations expressing either CD49a or CD103 integrin, with a subset co-expressing CD103 and Tcf-1 transcription factor. Tumor vaccination induces a decrease in the percentage of Tcf-1+CD103+ TRM-like cells and an expansion of CD49a+ TRM displaying an effector/exhausted profile. Tcf-1+CD103+ TRM-cell density increases in tumors from vaccinated transgenic mice constitutively expressing active TGF-beta-type-2-receptor and wild-type mice challenged with neutralizing anti-IL-12 antibodies. Stimulation of mouse and human CD8 T cells with recombinant (r)TGF-beta combined with anti-CD3 antibodies results in increase in the proportion of CD103+ and Tcf-1+CD103+ CD8 T cells, whereas rIL-12 induces decrease in CD103 expression on CD8 T cells.

overall_design: RNAseq was performed using Illumina Hiseq 200 on sorted CD103+, CD49a+ and CD103negCD49aneg CD8  TIL populations of 4 pools from 3x B16 melanoma tumors

first: Stéphanie

last: Corgnac

first: Fathia

last: Mami-Chouaib

first: Aziza

last: Caidi


title: Macrophage Accumulation and Cyst Expansion in Pkd2, Ift88, and Double Mutant Mouse Models

city: Birmingham

first: Bradley

last: Yoder

address: 1900 University Blvd

department: Cell, Developmental and Integrative Biology

institute: University of Alabama at Birmingham

summary: Kidney cyst formation occurs due to loss of cilia localized polycystin proteins (e.g., Pkd1 or Pkd2) or ciliary structure (e.g., Ift88 or Kif3a). However, cyst progression is more rapid in polycystin mutant mice compared to cilia mutant mice, and loss of cilia in the polycystin mutant background (e.g., Pkd2 and Kif3a mutation) greatly attenuates cyst development. This led to the proposal that the polycystins function to repress a cyst promoting pathway that is dependent on an intact cilium. Renal macrophages are also involved in regulating cyst progression, and the macrophage accumulation paralles with cyst expansion. but it is unknown whether this occurs through a cilia-dependent pathway or the consequence of cyst expansion. To address this question, we compared macrophage accumulation level and phenotypes in cystic kidneys from Pc2 mutant and Ift88; Pkd2 double mutant mice by prefromed 10x Genomics scRNAseq techniques. And to avoid the varying cyst severity in these mouse from different mutations, the cystic kidneys from Pc2 mutant and Ift88; Pkd2 double mutant mice were collected by adjusting for cystic indices rather than age.

overall_design: The experinment was conducted on Pkd2fl/fl ("PC2";Strain #:017292) and CAGG-CreER;Pkd2fl/fl;Ift88fl/fl ("double") mice (C57BL/6J background) mutant kidneys at 16 and 26 weeks post-tamoxifen induction, respectively. Kidneys (n=3 per mutant group, n=1 per each control group, all females; 8 total mice). The libraries were generated with the Chromium Single Cell 3' GEM, Library & Gel Bead Kit v3, following manufacturer's protocols. scRNA-seq analysis was preformed to comparing gene expression and pathway between resident and infiltraing macrophages from kidneys with simlar cyst index from PC2 and double mutant mice.

first: Zhang

last: Li

first: Timothy

middle: C

last: Howton

middle: K

first: Brittany

middle: N

last: Lasseigne


title: Specific and redundant roles for Gli2 and Gli3 in establishing cell fate during hair follicle development

city: Ann Arbor

first: Michigan

middle: CDB

last: Bioinformatics

state: MI

address: 109 Zina Pitcher Pl

department: Cell & Developmental Biology

institute: University of Michigan

summary: Ectodermal appendage formation requires hedgehog (HH) signal reception, its conduction through the primary cilium and activation of Gli transcription factors (TF). How HH signalling induces cell-type-specific responses through Gli TF in stem cells (SCs) and their ciliadependence remain open questions. Here, we use conditional mouse mutants to genetically dissect the roles of Gli and cilia HH mediators in the skin epithelium. Upon Gli2 depletion, hair follicle (HF) morphogenesis is delayed whereas sebaceous gland (SG) formation is enhanced, suggesting a dual role for Gli2 during appendage formation. By controlling proliferation of SG SCs, Gli2 impacts on the number and size of individual SG lobes. Whereas ablation of Gli3 shows no detectable phenotypes, HF cell fate is blocked in Gli2/3 double knockouts. In addition, loss of cilia phenocopies the loss of Gli2 but not the Gli2/3 mutants. Our study reveals that Gli3 exerts activator and cilia-independent functions in the absence of Gli2.

overall_design: Epidermal whole mounts were isolated from the back skin of P2 wild-type and Gli2 epidermal knockout mice using Collagenase/DNase digestion. These epidermal whole mounts were processed into single-cell suspensions, which were subsequently used for single-cell RNA sequencing (scRNA-seq) analysis.

first: Catherin

last: Niemann

first: Lakshit

last: Sharma

first: Craig

last: Johnson

first: hisham

last: Bazzi


title: Arabidopsis PRMT5 Buffers Pre-mRNA Splicing and Development Against Genetic Variation in Donor Splice Sites

city: Buenos Aires

first: Ariel

last: Chernomoretz

address: Av Patricias Argentinas 435

country: Argentina

institute: Fundacion Instituto Leloir

summary: Genetic variation at splice site signals significantly influences alternative splicing, leading to transcriptomic and proteomic diversity that enhances phenotypic plasticity and adaptation. However, novel splice variants can negatively impact gene expression and developmental stability. Canalization—the ability of an organism to maintain a consistent phenotype despite genetic or environmental variations—helps balance the effects of genetic variation on development and evolution. Protein arginine methyltransferase 5 (PRMT5) is a key splicing regulator in plants and animals. Most splicing changes in prmt5 mutants are linked to weak donor splice sites, suggesting that PRMT5 may buffer splicing against genetic variation. We examined PRMT5's effects on splicing and development in two genetically divergent Arabidopsis thaliana accessions with different single nucleotide polymorphisms (SNPs) affecting donor splice sites. We found that PRMT5 inactivation significantly increased splicing and phenotypic differences between the accessions. Our findings suggest that PRMT5 contributes to canalization, mitigating the impact of splice site polymorphisms and facilitating the evolution of adaptive splicing patterns.

overall_design: RNA-seq profiling of wild-type and prmt5-5 Arabidopsis thaliana plants belonging to Columbia and Landsberg accessions. RNA-seq profiling of wild-type and prmt5-5 F1 reciprocal hybrids of theses accessiones.

first: Maximiliano

middle: S

last: Beckel

first: Abril

last: San Martín

first: Sabrina

middle: E

last: Sánchez

first: Danelle

last: Seymour

first: María

last: de Leone

first: Daniel

last: Careno

first: Santiago

last: Mora-García

first: Detlef

last: Weigel

first: Marcelo

last: Yanovsky


title: RNAseq profiling of back dermis from epidermal-specific SPRY1-deficient (Spry1 cKO) mice and control mice

city: hangzhou

first: Fan

last: Xu

state: zhejiang

address: 88 Jiefang Road,Shangcheng District Hangzhou,China

institute: Zhejiang university

summary: Spry1 cKO mice were found spontaneously developed psoriasis-like skin inflammation and arthritis.To further investigate the gene expression differences between the back dermis of Spry1 cKO mice and control mice, RNAseq was performed.

overall_design: The back skin of Spry1 cKO mice and control mice were harvested after tamoxifen administration, and the dermis was separated after digestion with 5% dispase overnight at 4°C. Then RNA-seq was performed on total RNA from the back dermis.

first: Ying-Zhe

last: Cui

first: Xiao-Yong

last: Man


title: Structure of the TXNL1-bound proteasome

first: Zachary

last: Mirman

state: MA

address: 5 Lester Pl

department: Genetics

institute: Brigham and Womens

summary: Proteasomes degrade diverse proteins in different cellular contexts through incompletely defined regulatory mechanisms. Here, we report the cryo-EM structure of thioredoxin-like protein 1 (TXNL1) bound to the 19S regulatory particle of proteasomes via interactions with PSMD1/Rpn2, PSMD4/Rpn10, and PSMD14/Rpn11. Proteasome binding is necessary for the ubiquitin-independent degradation of TXNL1 upon cellular exposure to metal- or metalloid-containing oxidative agents, thereby establishing a structural requirement for the stress-induced degradation of TXNL1.

overall_design: RNA sequencing from the indicated cells lines treated with vehicle, arsenite, or hydrogen peroxide

first: Jingjing

last: Gao

first: Christopher

last: Nardone

first: Matthew

last: Yip

first: Haruka

last: China

first: Xin

last: Gu

first: Michael

last: Rale

first: Joao

middle: A

last: Paulo

first: Stephen

last: Elledge

first: Sichen

last: Shao


title: B cell deficiency induces cytotoxic memory CD8+ T cells during influenza-associated bacterial pneumonia

city: PITTSBURGH

first: Leigh

last: Miller

state: PA

address: 4401 Penn Ave

department: Pediatrics

institute: University of Pittsburgh

summary: This study explores the role B cells play in protection against super-infection with previous heterotypic influenza memory. B cell deficiency results in increased inflammatory lung environment and lung tissue injury during super-infection. Loss of B cells increased populations of memory CD8+ T cells in the lung and these CD8+ T cells were transcriptionally and functionally distinct from WT mice. RNA-seq: WT (C57BL6) and uMT mice were challenged with influenza (X31) at D0, challenged with influenza (PR8) at day 54, challenged with MRSA USA300 or PBS vehicle at day 60 followed by lung tissue harvest at day 61. RNA was extracted from CD8 T cells sorted from harvested lungs.

overall_design: WT FF (n=4) WT FFS (n=4) uMT FF (n=3) uMT FFS (n=3) Comparisons were made between mouse genotype and infection type (FF vs. FFS)

first: John

middle: F

last: Alcorn


title: Respiratory viral infection promotes the awakening and outgrowth of dormant metastatic breast cancer cells in lungs [RNA-seq]

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

summary: Breast cancer is the second most common cancer globally, with most deaths caused by metastatic disease, often following long periods of clinical dormancy1. Understanding the mechanisms that disrupt the quiescence of dormant disseminated cancer cells (DCC) is crucial for addressing metastatic progression. Respiratory viruses infections such as influenza or SARS-CoV-2, trigger both local and systemic inflammation2,3. Here we demonstrate that influenza virus and SARS-CoV-2 infections lead to loss of the pro-dormancy phenotype in breast DCC in the lung, causing DCC proliferation within days of infection, and a massive expansion of carcinoma cells into metastatic lesions within two weeks. This phenotypic transition and expansion are interleukin-6 (IL-6)-dependent. We show that CD4+ T cells sustain pulmonary metastatic burden post-influenza infection by suppressing CD8+ T cell responses. Additionally, DCCs impair lung T-cell activation and tumor cell killing in infected mice. Critically, these experimental findings align with human observational data. Analyses of cancer survivors from the UK Biobank and Flatiron Health databases reveal that SARS-CoV-2 infection substantially increases the risk of lung metastasis and cancer-related mortality compared to uninfected cancer survivors. Notably, the heightened risk is most pronounced in the months following infection, paralleling experimental observations of accelerated DCC proliferation and metastatic progression shortly after viral infection. These discoveries underscore the significant impact of respiratory viral infections on metastatic cancer resurgence, offering novel insights into the interconnection between infectious diseases and cancer metastasis.

overall_design: MMTV-Her2 mice were given PBS or influenza A virus through intranasal administration. Lungs were harvested 9dpi, single cell suspsension were generated, Her2+ cells were FACS-sorted.

first: Shi

middle: B

last: Chia

first: Bryan

last: Johnson

first: Junxiao

last: Hu

first: Felipe

last: Valenca-Pereira

first: Marc

last: Chadeau-Hyam

first: Fernando

last: Guntoro

first: Hugh

last: Montgomery

first: Meher

middle: P

last: Boorgula

first: Varsha

last: Sreekanth

first: Bennett

last: Davenport

first: Marco

last: De Dominici

first: Vadym

last: Zaberezhnyy

first: Wolfgang

last: Schleicher

first: Dexiang

first: Andreia

last: Cadar

last: Papanicolaou

first: Afshin

last: Beheshti

last: Baylin

first: Joseph

middle: W

last: Guarnieri

first: Douglas

last: Wallace

first: James

last: Costello

first: Jenna

last: Bartley

first: Thomas

last: Morrison

first: Roel

last: Vermeulen

first: Julio

last: Aguirre-Ghiso

first: Mercedes

last: Rincon

last: DeGregori


title: Wilms’ tumor 1 impairs apoptotic clearance of fibroblasts in distal fibrotic lung lesions

city: Cincinnati

first: Satish K

last: Madala

state: Ohio

address: 3230 Eden Avenue

department: Internal Medicine

institute: University Of Cincinnati

summary: Idiopathic pulmonary fibrosis (IPF) is a fatal fibrotic lung disease characterized by impaired fibroblast clearance, accumulation, and excessive extracellular matrix (ECM) protein production. Wilms' Tumor 1 (WT1), a transcription factor, is selectively upregulated in IPF fibroblasts. However, the mechanisms by which WT1 contributes to fibroblast accumulation and ECM production remain unknown. Here, we investigated the heterogeneity of WT1-expressing fibroblasts using single-nucleus RNA sequencing on the distal lung tissues of IPF patients and healthy controls. WT1 was selectively upregulated in a subset of IPF fibroblasts that co-expressed several pro-survival genes. Both the loss-of-function and gain-of-function studies support the idea that WT1 functions as a positive regulator of multiple pro-survival genes to impair apoptotic clearance and promote ECM production. In support, fibroblast-specific overexpression of WT1 augmented fibroproliferation, myofibroblast accumulation, and ECM production during bleomycin-induced pulmonary fibrosis in both young and old mice. Together, these findings identify WT1 as a potential therapeutic target to attenuate fibroblast expansion, and ECM production in the distal areas of fibrosing lungs.

overall_design: snRNA-Seq was performed on human lung tissue samples retreived to characterize all cell populations for the first time with nuclear RNA. CST method was used to isolate the nuclei from tissue samples from both IPF and healthy lung tissues and were processed according to instructions provided by the instrument manufacturer.

first: Harshavardhana

last: Ediga

first: Chanukya Pavan

last: Vemulapalli

first: Vishwaraj

last: Sontake

first: Hikaru

last: Miyazaki

first: Dimitry

last: Popov

first: Martin

last: Jensen


title: The effects of B cell lymphoma on young and aged T and NK cells (ATAC-Seq)

first: Rebecca

last: Hesterberg

summary: While lymphomas affect mostly older patients, there are cases of lymphoma across the aging spectrum. However, the effects of these cancers on young versus old immune cells is largely unknown.  Using a transplantable B cell lymphoma mouse model, we generated single cell RNA-seq of isolated T cells and NK cells to define phenotypic and population changes modulated by age and lymphoma. Further, to investigate age-dependent epigenetic changes driven by lymphomas, we used an assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) on isolated CD4 T cells from young and aged mice with lymphomas. These studies demonstrate that lymphoma alters the immune system in an age-dependent manner.

overall_design: Young (<12 weeks) and aged (>78 weeks) C57Bl6 mice were transplanted with Em-Myc lymphoma cells via tail vein injection. Twelve days after tumor transplant, T and NK cells were isolated from the spleens of lympoma-bearing or non-tumor-bearing control mice. Further, CD4 T cells were isolated for ATAC-seq from these same mice. Both sequencing datasets are n = 3 biological replicates.

first: John

last: Cleveland


title: Restriction of innate Tgd17 cell plasticity by an AP-1 regulatory axis [multiome]

city: Durham

first: Maria

last: Ciofani

state: NC

address: 207 Research Drive, 128 Jones Building

department: Integrative Immunobiology

institute: Duke University School of Medicine

summary: IL-17-producing gd T (Tgd17) cells are innate-like mediators of intestinal barrier immunity. While Th17 cell and ILC3 plasticity have been extensively studied, the mechanisms governing Tgd17 cell effector flexibility remain undefined. Here, we combined type 3 fate-mapping with single cell ATAC/RNA-seq multiome profiling to define the cellular features and regulatory networks underlying Tgd17 cell plasticity. During homeostasis, Tgd17 cell effector identity was stable across tissues, including for intestinal T-bet+ Tgd17 cells that restrained IFNg production. However, S. typhimurium infection induced intestinal Vg6+ Tgd17 cell conversion into type 1 effectors, with loss of IL-17A production and partial RORgt downregulation. Multiome analysis revealed a trajectory along Vg6+ Tgd17 effector conversion, with TIM-3 marking ex-Tgd17 cells with enhanced type 1 functionality. Lastly, we characterized and validated a critical AP-1 regulatory axis centered around JunB and Fosl2 that controls Vg6+ Tgd17 cell plasticity by stabilizing type 3 identity and restricting type 1 effector conversion.

overall_design: Single cell Multiome (combined ATAC and GEX) was performed on sort purified colon lamina propria total gd T cells and ILCs isolated from mice following 4 days of oral Salmonalla typhimurium infection (STm) or mock infection (naïve).

first: Morgan

last: Parker

first: Tzu-Chieh

last: Liao


title: Pyridine based MYC degraders truncate endogenous MYC proteins and shift the balance of the MYC proteome

city: Houston

first: Hu

last: Chen

state: TX

address: 1250 Moursund St,

institute: Baylor College of Medicine

summary: MYC is a DNA binding transcription factor whose sustained dysregulation promotes the initiation and maintenance for numerous cancers. Small molecules directly binding and blocking the disordered MYC monomer from forming critical protein interactions have supplied numerous probes highlighting the complexities of inhibiting this monumental target and have helped legitimize MYC as a tractable therapeutic target. Unfortunately, most of the inhibitors that have shown promise in pre-clinical settings have not made significant advances towards practical clinical applications. The rise of proximity induced pharmacology has lent new opportunities to understand complex biological pathways and vulnerabilities to help target proteins like MYC where small molecule inhibition has proved challenging. We demonstrate the application of proximity inducing heterobifunctional PROteolysis TArgeting Chimeras (PROTACs) towards regulating concentrations of oncogenic MYC monomers derived from the pyridine scaffold of MYC inhibitor, KJ-Pyr-9. We found MTP3 depletes endogenous full-length MYC proteins and uniquely exacerbates levels of a functional, N-terminally truncated MYC species, tMYC. MTP3 destabilizes the MYC proteome in favor of a tMYC dominant cell state with a distinct regulatory landscape. Our results highlight the complexities of proximity-induced chemistry against highly regulated and dynamic protein targets like MYC and indicate that PROTACs can regulate alternative outcomes beyond target protein degradation.

overall_design: PC3 cells were routinely cultured in RPMI1640 supplemented with 10% FBS at 37oC, 90% RH, and 5% CO2. Cultures were sub-cultured twice a week (at ~80% confluence) and split 1:5. PC3 cells were seeded in 12 well plates to achieve 70% confluence and incubated over-night. The following day, adherent cells were washed with DPBS and supplemented with fresh media containing indicated treatments in 1.2mL final volume (MTP3 is a MYC Targeting PROTAC that truncates MYC proteins at the N-terminus. HO3395 is a MYC-binding small molecule used as a binding control in this study.). After 24 hours, treatment media was aspirated and cells were washed with DPBS. Cells were treated briefly using 0.05% trypsin*EDTA for 3 minutes at RT. Trypsin was neutralized using complete culture media and cells were harvested by scraping. Harvested cells were transferred to 1.5 mL Eppendorf tubes and pelleted for five minutes at 4oC with 125 x rcf. Resulting supernatants were aspirated by pipette and cells were washed using DPBS. PC3 cell pellets were snap frozen using liquid nitrogen and stored at -80oC until processing. Total RNA was extracted and purified from cells using Qiagen RNeasy Plus Mini Kit (Qiagen Cat#74134) and gDNA eliminated using supplied gDNA eliminator columns as instructed by manufacturer. RNA was quantified by DeNovix DS-11 Spectrophotometer. ~2 μg total RNA was provided to Azenta-Genewiz for library production and sequencing reactions prior to analysis

first: Shelton

middle: R

last: Boyd

first: Alexander

last: Trostle

first: Damian

last: Young


title: Tumor-instructed glutamine synthesis in cancer-associated fibroblasts promotes pro-tumor macrophages

status: Public on May 26 2025

city: Epalinges

first: Ping-Chih

last: Ho

address: Ch. des Boveresses 155

country: Switzerland

institute: Ludwig Cancer Institute, UNIL

summary: In the tumor microenvironment (TME), cancer-associated fibroblasts (CAFs) play a crucial role in promoting tumor progression by creating an immunosuppressive environment through cytokine secretion and antigen presentation. While previous studies have demonstrated that CAFs exhibit distinct metabolic profiles compared to normal fibroblasts, it remains unclear how these metabolic programs influence the immune landscape within tumors and which factors drive metabolic reprogramming in CAFs. Here, we found that glutamine synthesis by CAFs promotes the polarization of pro-tumorigenic tumor-associated macrophages (TAMs), and supports tumor growth by altering TAM composition, highlighting the pivotal role of CAFs in shaping the immunosuppressive TME. Mechanistically, we found that tumor-derived palmitic acid activates a signaling cascade involving Toll-like receptor 4 (TLR4), Syk, and NF-κB in fibroblasts, leading to inflammatory CAF polarization, and IL-6-induced glutamine synthesis. These findings uncover a novel metabolic symbiosis whereby tumor cells manipulate TAM polarization through CAF-mediated glutamine metabolism, presenting potential therapeutic targets for cancer immunotherapy.

overall_design: Primary normal fibroblast treated Yumm1.7 tumor cell conditioned medium or tumor cell conditioned medium depleted with lipid for bulk RNA-seq analysis, 3 replicates are included in each group.

first: Xiaoyun

last: Li

first: Sofie Hedlund

last: Møller

first: Yu-Ming

last: Chuang


title: Enhancer-driven gene regulatory networks reveal transcription factors governing T cell adaptation and differentiation in the tumor microenvironment.

city: Chapel Hill

first: Justin

last: Milner

address: 450 West Drive, Lineberger Comprehensive Cancer Center Rm 11-117

institute: University of North Carolina at Chapel Hill

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

overall_design: Refer to individual Series

first: William

middle: D

last: Green

first: Amber

last: Gomez

first: Alec

middle: L

last: Plotkin

first: Brandon

last: Pratt

first: Emily

last: Merritt

first: Genevieve

last: Mullins

first: Nancy

last: Kren

first: Jennifer

last: Modliszewski

first: Vasyl

last: Zhabotynsky

first: Mark

middle: G

last: Woodcock

first: Jarred

first: Gabrielle

last: Cannon

first: Matthew

last: Pipkin

first: Gianpietro

last: Dotti

first: Yuliya

last: Pylayeva-Gupta

first: Jessica

last: Thaxton

first: Albert

last: Baldwin

last: Morris IV

first: Natalie

last: Stanley


title: Modulation of inflammatory responses in mouse models of pericyte-depletion retinopathy

city: Cologne

first: Urbanus

last: Kinuthia

state: North Rhine Westafalen

address: Kerpener str. 62

department: Ophthalmology

country: Germany

institute: University of Cologne

summary: A major feature of diabetic retinopathy is pericyte loss. Here, we have utilzed a model of pericyte depletion retinopathy that recapitulates key features of human diabetic retinopathy to study the cellular and molecular components of the diease and response to immunomodulation with minocylcine. Pericyte depletion was achieved via injection of a rat anti-mouse PDGFRB mAb at Postnatal day 1 (P1) in C57BL6/J WT mice. Treatment with minocyline begaun at P5, daily until P27, and retinas analysed from P28 mice. Transcriptomic analyses identifies signature pathways in pericyt-depletion retinopathy and response to minoccyline

overall_design: RNAseq-profiling of 4-weeks (p28) old retina transcriptome of WT mice (C56BL6/J) following treatment with IgG or a rat anti-mouse PDGFRB mAb at postnatal day 1 with and withut daily treatment with minocyline (P5-p27) at a dose of 45mg/kg bw

first: Kinuthia

last: Urbanus

first: Moehle

last: Moehle

first: Langmann

last: Thomas


title: Single-cell RNA sequencing profiling of periarticular tissue from epidermal-specific SPRY1-deficient (Spry1 cKO) mice and control mice

first: Fan

last: Xu

summary: Spry1 cKO mice were found spontaneously developed psoriasis-like skin inflammation and arthritis.To further investigate the periarticular immune microenvironment in paws, single-cell RNA sequencing of the periarticular tissue from Spry1 cKO and control mice was performed.

overall_design: The periarticular tissue of Spry1 cKO mice and control mice were harvested after tamoxifen administration, and single-cell suspensions of periarticular tissue were prepared using collagenase IV. To obtain sufficient immune cells for analysis, four mice were pooled as one sample for the control group (12 control mice in total for n=3), and then CD45+ and CD45- cells were sorted and mixed at a ratio of 3:1 in both groups for scRNA-seq analysis.

first: Ying-Zhe

last: Cui

first: Xiao-Yong

last: Man


title: Biparental inheritance of germline-specific chromosomes in the sea lamprey and their roles in oocytes

city: Lexington

first: Jeramiah

middle: James

last: Smith

state: KY

address: 101 Morgan Building

department: Biology

institute: University of Kentucky

summary: Many eukaryotic species undergo programmed elimination of specific chromosomes during embryogenesis, typically retaining these chromosomes only in their germ cells. In some species, programmatic elimination of GRCs, or sex chromosomes, also occurs in a sex-specific manner, with specific chromosomes being transmitted or eliminated by only one sex. As such, these chromosomes provide a unique perspective on the evolution of gene functions that are advantageous to the germline and genetic tradeoffs between somatic vs germline or oocyte vs sperm biology. While GRCs have been extensively characterized in male sea lampreys (Petromyzon marinus), the status of GRCs in females has not yet been resolved, though it has been hypothesized that male-specific expression/transmission of these chromosomes might provide a solution to resolving the long-standing mystery of lamprey sex determining mechanisms. To gain insight into the roles of GRCs in female lampreys, we performed several karyological, transcriptomic, and genomic analyses, which demonstrate that GRCs are present in the female lamprey germline, transmitted by oocytes and somatically eliminated in both sexes. These analyses also show that GRCs play important roles in the maintenance and development of female germline but provide no evidence for sex-specific variation in the elimination and transmission of lamprey GRCs. These findings underscore the diversity of germline functions that are carried out by GRCs in both male and female lampreys and highlight the fact that sex-specific transmission/retention of GRCs likely follows no universal rules across the diverse lineages that have independently evolved to undergo developmentally programmed DNA elimination.

overall_design:
RNA was extracted from two pools of approximately 100 snap frozen oocytes via the standard Trizol extraction protocol, but supplementing the lysis reaction with 10mM dithiothreitol. Library preparation and sequencing was performed by NovoGene using the company’s “Plant and Animal Eukaryotic mRNA” pipeline. Resulting RNAseq reads from this study and a previous studies targeting meiotic teste were aligned to the reference genome using HISAT2 v.2.2.1 and the resulting alignments were used to quantify the expression of annotated genes using Stringtie v.2.2.3. Differential gene expression was assessed using median of ratios normalization in R. For comparisons among paralogs, Orthofinder v2.5.4 was used to compare the complements of somatic vs germline genes and identify groups of paralogous genes that share a common ancestor with groups of one or more somatic gene.
This study includes re-analysis of SRP009181.

first: Vladimir

last: Timoshevskiy

first: Nataliya

last: Timoshevskaya

first: Kaan

middle: I

last: Eşkut

first: Kasturi

last: Rajandran

middle: J


title: Decoding Gene Networks Governing Hypothalamic and Prethalamic Neuron Development

city: Baltimore

first: Dong Won

middle: Thomas

last: Kim

state: Maryland

address: 733 N.Broadway, MRB building (Rm 332)

department: Neuroscience

institute: Johns Hopkins University

summary: Purpose: sc/snRNA-Seq and scATAC-Seq were performed to characterize the developing hypothalamus

overall_design: Cell Dissociation for scRNA-Seq: To prepare samples for scRNA-Seq, tissues were dissociated in Hibernate medium (Hibernate-E Minus Calcium (#HECA500, BrainBits) for embryos or Hibernate-A Minus Calcium (#HACA500, BrainBits) for postnatal stages), supplemented with 2 mg/ml papain (#LS003119, Worthington Biochemical) and 0.5 mM Glutamax. The enzyme mixture was pre-incubated for 15 minutes, then added to tissues for 5 - 30 minutes with 0.1 U/μl RNase inhibitor (N2615, Promega). Toward the end of digestion, 100 μg/ml final DNase I (#, 4716728001, Sigma-Aldrich) was added. Cells were subsequently centrifuged, resuspended in HABG buffer, filtered through a 40 μm cell strainer (BAH136800040-50EA, Sigma-Aldrich), and resuspended in HABG buffer containing RNase inhibitor (0.5 U/μl). Cell viability and counts were assessed with Trypan Blue staining (#15250061, Thermo Fisher Scientific) and a hemocytometer /  Nuclei Preparation for scATAC-Seq:Nuclei for scATAC-Seq were extracted following post-cell dissociation and purified following a 10x Genomics protocol. Nuclei count and yield were verified with Trypan Blue staining and a hemocytometer / Nuclei Preparation for snRNA-Seq:For snRNA-Seq, adult mouse brains were rapidly dissected, and 100 um coronal sections were prepared using a mouse brain matrice. Regions spanning the ZI, TRN, and thalamus were microdissected under a dissection microscope. Nuclei were extracted following a 10x Genomics protocol.

first: Seth

last: Blackshaw


title: Enhancer-driven gene regulatory networks reveal transcription factors governing T cell adaptation and differentiation in the tumor microenvironment

first: Justin

last: Milner

summary: Tumor infiltrating lymphocytes (TIL) with a CD8+ T cell tissue-resident memory (Trm) phenotype are associated with improved patient outcomes in solid malignancies. To define programs governing the formation of Trm-like TIL, we performed paired single-cell RNA sequencing and single-cell ATAC sequencing of T cell receptor (TCR)-matched CD8+ T cells in models of infection and cancer. Enhancer-driven regulons assembled from multiomic profiling data revealed epigenetic and transcriptional programs regulating the formation of Trm-like TIL in relation to canonical exhausted and memory T cell states. The transcriptional regulator KLF2 repressed the formation of CD69+CD103+ Trm-like TIL and limited anti-tumor activity. Conversely, sustained expression of the transcription factor BATF enhanced formation of CD69+CD103+ TIL, contingent upon downregulation of KLF2. Transforming growth factor β (TGF-β) signaling and CD103 expression were necessary for Trm-like TIL formation, but BATF overexpression was sufficient to drive formation of CD69+CD103+ TIL in TGFBR2-silenced cells. These findings reveal mechanisms of Trm-like TIL differentiation and provide a framework for considering tissue residency in the context of CD8+ T cell heterogeneity in the tumor microenvironment.

overall_design: Oligo-hashtag barcoded CD45+CD3+CD8+ TIL were single cell sorted from n=3 wild-type female 10wk old C57BL/6J mice bearing orthotopically implanted KPC-4662 pancreatic cancer at day 15 post tumor implant. Cells were sequenced using 10X Genomics 5' GEX+VDJ using a NextSeq2000 P3 flow cell and were processed using standard CellRanger multi and Seurat pipelines.

first: William

last: Green

first: Amber

last: Gomez

first: Alec

last: Plotkin

first: Brandon

middle: M

last: Pratt

first: Emily

last: Merritt

first: Genevieve

middle: N

last: Mullins

first: Nancy

last: Kren

first: Jennifer

last: Modliszewski

first: Vasyl

last: Zhabotynsky

first: Mark

last: Woodcock

first: Jarred

first: Gabrielle

last: Cannon

first: Matthew

last: Pipkin

first: Gianpietro

last: Dotti

first: Yuliya

last: Pylayeva-Gupta

first: Jessica

last: Thaxton

last: Baldwin

first: John


title: TSA-sequencing in untreated (UN), sodium arsenite (SA) and heat shock (HS) stressed HeLa cells

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

summary: Mammalian cells activate diverse defense mechanisms in response to stresses. Nuclear stress bodies (nSBs) are transient membraneless organelles in primates that only form upon severe stresses. Little is known on how their formation contributes to cellular homeostasis or whether nSBs have any pathophysiological roles. We observed that the de novo formation of nSBs accompanies enlarged pericentromeric SatⅢ DNA chromatin loci, prompting us to investigate whether such an acute alteration impacts regional chromatin accessibility and gene expression. To test this, we performed an improved Tyramide Signal Amplification (TSA) mapping to identify genes proximal to newly formed nSBs.

overall_design: We performed TSA-seq in untreated (UN), sodium arsenite (SA) and heat shock (HS) stressed HeLa cells. Two biological independent experiments in each condition were included.

first: Ling-Ling

last: Chen

first: Bao-Qing

last: Gao

first: Xiao-Qi

last: Liu

first: Pan

last: Li


title: RNA sequencing in untreated (UN), sodium arsenite (SA) and heat shock (HS) stressed HeLa,HUVEC and  THP-1 cells

summary: Mammalian cells activate diverse defense mechanisms in response to stresses. Nuclear stress bodies (nSBs) are transient membraneless organelles in primates that only form upon severe stresses. Little is known on how their formation contributes to cellular homeostasis or whether nSBs have any pathophysiological roles. We observed that the de novo formation of nSBs accompanies enlarged pericentromeric SatⅢ DNA chromatin loci, prompting us to investigate whether such an acute alteration impacts regional chromatin accessibility and gene expression.

overall_design: We performed rRNA-depleted (ribo-) RNA-seq in untreated (UN), sodium arsenite (SA) and heat shock (HS) stressed HeLa, HUVEC and THP-1 cells. Two biological independent experiments in each condition were included.


title: Podocyte-specific YAP activation triggers crescentic glomerulonephritis through cross-talk with parietal epithelial cells

city: Paris

first: Pierre

last: Isnard

address: 156-160, rue de Vaugirard

institute: INEM

summary: YAP, a transcriptional co-activator, is known to control programs that are both cell- and context-dependent. We report that the overactivation of YAP (YAP5SA) in podocytes has both cell autonomous and non-cell autonomous consequences. RNA-seq analysis of YAP5SA-expressing compared to control podocytes revealed pathways and candidate genes that could explain both these effects.

overall_design: To decipher the podocyte-specific transcriptional programs driven by YAP5SA, we generated human podocyte-derived cell lines stably expressing either pCW-(FLAG-NLS-)YAP5SA or pCW-eGFP (as a control), where transcription of the gene of interest is tetracycline inducible (Tet-On). This cell line, which was established by Saleem et al., is transformed by a thermolabile large-T antigen (ts SV40LT), so that these cells proliferate at 33 °C (active large-T antigen) but halt proliferation at 37 °C (inactive large-T antigen) and re-differentiate into podocytes over 10-14 days. To selectively overexpress (FLAG-NLS-)YAP5SA or GFP only in differentiated podocytes, cells were cultured at 37 °C for 12 days prior to tetracycline treatment. These differentiated podocytes were then treated with ± doxycyline (Dox) 0.1 µg for 24 hours.

first: Lisa

last: Turinsky

first: Terzi

last: Fabiola


first: Justin

last: Milner

overall_design: Antigen specific P14 CD8 T cells were single cell sorted from 11 conditions spanning: naive, acute infection (LCMV Armstrong) at early and late time points from lymphoid and non-lymphoid tissues, chronic infection (LCMV CL13) from early and late time points in lymphoid tissue, and tumor models (B-ALL, PDAC, melanoma, and TNBC). Single cells were sorted for Viable donor (CD45.1 or CD45.1.2) CD8+Va2+ and processed for the 10X Genomics multiomic single-nuclei RNAseq + ATACseq kit (10x Genomics). Libraries were sequenced using either the Illumnia NovaSeq6000 or NextSeq 2000 and processed using CellRanger-Arc (v2.0.0 for NovaSeq6000 samples; or v2.0.2 for NextSeq2000 samples). Downstream analysis of filtered matrix files followed standard Seurat v5 and Signac multiomic GEX+ATAC Weighted Nearest Neighbors (WNN) pipelines.

first: William

last: Green

first: Amber

last: Gomez

first: Alec

last: Plotkin

first: Brandon

last: Pratt

first: Emily

last: Merritt

first: Genevieve

last: Mullins

first: Nancy

last: Kren

first: Jennifer

last: Modliszewski

first: Vasyl

first: Albert

middle: S

last: Morris IV

first: Natalie

last: Stanley


title: Transcriptome analysis of the effects of sorafenib and osimertinib in PC9 cells

city: Rennes

first: Cedric

last: Coulouarn

address: CLCC Eugène Marquis, Rue de la Bataille Flandres Dunkerque, Bat D, 1er étage

institute: INSERM

summary:
The aim of the study was to characterize the gene expression profiles of PC9 cells exposed to sorafenib and osimertinib, alone or in combination.
PC9 cells were cultured in presence of sorafenib and osimertinib for 1day, 2 days and 4 days. Genome-wide expression profiling (Agilent microarrays) were used to characterize the transcriptome of PC9 cells and to identify specific gene exptression signatures and functionally relevant gene networks linked to sorafenib and osimertinib treatments.

overall_design: PC9 cells (NSCLC) were obtained from ECACC (distributed by Sigma-Aldrich). PC9 cells were grown in RPMI1640 (2Mm L-Glutamine + 25 mM HEPES) supplemented with 10% FBS. Osimertinib and sorafenib were purchased from LC Laboratories. PC9 cells were treated in triplicate with or without osimertinib (1 µM) and/or sorafenib (5 µM) for 1, 2 or 4 days (for the longest time point, the media was renewed after 2 days), and total RNA was isolated using the miRNeasy kit (Qiagen) following the manufacturer’s instructions.

first: Luca

last: Grumolato


title: Centromeric DNA amplification triggered by viral proteins activates nuclear cGAS

status: Public on May 25 2025

first: Nicolas

last: Manel

address: 12 rue Lhomond

department: INSERM U932

institute: Institut Curie

summary: The cGAS-cGAMP-STING pathway is crucial for antiviral immunity. While cytosolic cGAS detects viral DNA, most DNA viruses shield their genome and invade the nucleus, where chromatin restricts cGAS activation. How viruses may activate nuclear cGAS is not well understood. Here, we show that several herpesvirus proteins trigger nuclear cGAS activation by perturbing centromeres, where cGAS is enriched. The herpes simplex virus type 1 (HSV-1) ubiquitin ligase ICP0, which degrades centromeric proteins, promotes centromeric DNA amplification through the translesion DNA synthesis (TLS) pathway in quiescent monocyte-derived cells, thereby activating nuclear cGAS. During infection, HSV-1 evades this detection by also expressing UL36USP, a suppressor of TLS. Similarly to ICP0, the cytomegalovirus IE1 protein causes centromeric DNA amplification and cGAS activation. We define this mechanism as Viral-Induced Centromeric DNA Amplification and Recognition (VICAR), uncovering a non-mitotic, immune-activating role of centromeres.

overall_design:
CD14+ Human Peripheral Blood Mononuclear cells (PBMCs) were isolated from healthy human donors and selected for using anti-CD14 magnetic beads.
They are then differentiated into Monocyte-derived Dendritic Cells (MDDCs) by treatment with GM-CSF and IL-4 and transduced with either control lentivector or lentivector expressing wild-type ICP0 or mutant ICP0-FxE protein.
After 4 days of differentiation and transduction, cells are collected for chromatin accessibility profiling by ATAC-seq. Details are described in the Methods section of the paper.

first: Xavier

last: Lahaye

first: Ngoc Tran Bich

last: Cao

first: Ouardia

last: Ait-Mohamed


title: ChemPerturb-Seq Screen to Identify Small Molecules Enhancing Human Beta Cell Survival After Subcutaneous Transplantation

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

summary: Although high throughput/content chemical screens have been employed to characterize cellular response to small molecules treatment, traditional chemical screens have only focused on a single assay per screen, making them labor intensive and costly. Here, we combined a chemical screen with scRNA-seq to perform Chemical Perturb-Seq (ChemPerturb-Seq), enabling a systematic analysis of cellular responses and molecular changes of human beta cells upon individual hormone treatments. Furthermore, we developed an AI-powered website, ChemPerturbDB, which provides user friendly open-access analysis of this extensive dataset.  Next, we performed an in vivo barcoded screen and developed a hormone cocktail, including Insulin growth factor-1, Lipotropin, and Prostaglandin E2. Pre-conditioning human beta cells and primary islets with this hormone cocktail significantly enhanced their function and survival when transplanted subcutaneously to female, but not to male mice. Combining scRNA-seq and ChemPerturb-seq, we identified two additional moleculeshormones, serotonin and histamine, that promote the function of human islets when transplanted subcutaneously to male mice. Together, we not only generated a comprehensive ChemPerturb-Seq dataset, which can be utilized to systematically investigate the effects of hormones on human beta cells, but also developed hormone cocktails that enhance the survival of human beta cells following subcutaneous transplantation.  With further validation, this, which could be applied to improve the current FDA-approved islet transplantation procedure.

overall_design: Multiplexed scRNA-seq analysis of human EndoC-betaH1 cells treated with different small molecules from an in-house small molecule screening library

first: J Jeya

last: Vandana

first: Jiajun

last: Zhu

first: Alice

last: Giani


title: LHX2 regulates dendritic morphogenesis in layer II/III of the neocortex via distinct pathways in progenitors and postmitotic neurons

city: Mumbai

first: Shubha

last: Tole

state: Maharashtra

address: B304 TIFR Homi Bhabha road

department: Biological Sciences

country: India

institute: Tata Institute of Fundamental Research

summary: In the mammalian neocortex, excitatory neurons that send projections via the corpus callosum are critical to integrating information across the two brain hemispheres. The molecular mechanisms governing the development of the dendritic arbours and spines of these callosal neurons are poorly understood, yet these features are critical to their physiological properties. LIM Homeodomain 2 (Lhx2), a regulator of fundamental processes in cortical development, is expressed in postmitotic callosal neurons occupying layer II/III of the neocortex and also in their progenitors in the embryonic day (E) 15.5 ventricular zone of the mouse neocortex. We tested whether this factor is essential for dendritic arbour configuration and spine morphogenesis of layer II/III neurons. Here, we report loss of Lhx2 either in postmitotic callosal neurons or their progenitors, resulting in shrunken dendritic arbours and perturbed spine morphology. In postmitotic neurons, we identified that LHX2 regulates dendritic and spine morphogenesis via the canonical Wnt/β Catenin signalling pathway. Constitutive activation of this pathway in postmitotic neurons recapitulates the Lhx2 loss-of-function phenotype. In E15.5 progenitors, we identified that bHLH transcription factor Neurog2 mediates LHX2 function in regulating dendritic and spine morphogenesis. We show that Neurog2 expression increases upon loss of Lhx2 and that shRNA-mediated Neurog2 knockdown rescues the loss of Lhx2 phenotype. Our study uncovers novel LHX2 functions consistent with its temporally dynamic and multifunctional roles in the cortical circuit assembly.

overall_design: To assess the implications of the loss of Lhx2 in the dendritogenesis of Layer II/III neurons, either EGFP (Control) or Cre-EGFP (Progenitor mutant) plasmids were transfected in E15.5 progenitors of the developing cerebral cortex of Lhx2lox/lox mice using in utero electroporation. The brain was isolated once the animal was of age Postnatal Day 5. The labelled layer II/III neurons were microdissected, and their RNA was isolated. For postmitotic deletion similar strategy was used to label layer II/III neurons by in utero electroporating EGFP in Lhx2lox/lox (Control) or NexCre/+; Lhx2lox/lox (Postmitotic mutant) mouse cortices.

first: Mahima

last: Bose

first: Sreenath

last: Ravindran


title: Microglial SHIP1 controls synaptic pruning in the developing hippocampus via the complement system

status: Public on May 23 2025

city: Berlin

first: Andranik

last: Ivanov

address: Chariteplatz 1

department: Core Unit Bioinformatics

institute: Berlin Institute of Health

summary: INPP5D, which encodes the lipid phosphatase SHIP1, is one of the most common genes associated with the risk of Alzheimer’s disease and is enriched in microglia in the central nervous system. SHIP1 has been found to be highly expressed in plaque-associated microglia. However, how it regulates microglial function and influences brain physiology has been poorly investigated. Here we show that SHIP1 is not only enriched in microglia associated with amyloid beta plaques, but also in early stages of healthy brain development. By combining in vivo loss-of-function approaches and proteomics, we discovered that conditional knockout mice lacking microglial SHIP1 (cKO) display increased complement and synapse loss in the early postnatal brain. Additionally, SHIP1 KO microglia show reduced morphological complexity, altered transcriptional signatures, and abnormal synaptic pruning, which is dependent on the complement system. Single nucleus RNA-sequencing analysis of the entire hippocampus confirmed decreased interaction for synaptic structure related pathways in both excitatory and inhibitory neurons. Importantly, cKO mice show cognitive defects in adulthood only when microglial SHIP1 is depleted at early postnatal days, but not when depleted at later stages. Finally, using CRISPR/Cas9 we generated human iPSC-derived microglia lacking SHIP1, and validated the increased engulfment of synaptic structures. Altogether, these findings suggest that SHIP1 is essential for proper microglia-mediated synapse remodeling through the complement system in the early postnatal brain. Disrupting this process has lasting behavioral effects and may provide a link to vulnerability to neurodegeneration.

overall_design: We isolated YFP-positive microglia from the hippocampi of control and SHIP1 cKO mice at postnatal day 15, and performed Bulk-RNA sequencing.

first: Alessandro

last: Matera

first: Anne-Claire

last: Compagnion

first: Chiara

last: Pedicone

first: Janssen

last: Kotah

first: Katia

last: Monsorno

first: Gwenaël

last: Labouèbe

first: Loredana

last: Leggio

first: Marta

last: Pereira

first: Dieter

last: Beule

first: Virginie

last: Mansuy-Aubert

first: Tim

last: Williams

first: Nunzio

last: Iraci

first: Amanda

last: Sierra

first: Samuele

last: Marro

first: Alison

last: Goate

first: Bart

last: Eggen

first: William

last: Kerr

first: Rosa

last: Paolicelli


title: Respiratory viral infection promotes the awakening and outgrowth of dormant metastatic breast cancer cells in lungs

first: Andrew

last: Goodspeed

summary: Breast cancer is the second most common cancer globally. Most deaths from breast cancer are due to metastatic disease which often follows long periods of clinical dormancy. Understanding the mechanisms that disrupt the quiescence of dormant disseminated cancer cells (DCC) is crucial for addressing metastatic progression. Infection with respiratory viruses (e.g. influenza or SARS-CoV-2) is common and triggers an inflammatory response locally and systemically. Here we show that influenza virus infection leads to loss of the pro-dormancy mesenchymal phenotype in breast DCC in the lung, causing DCC proliferation within days of infection, and a greater than 100-fold expansion of carcinoma cells into metastatic lesions within two weeks. Such DCC phenotypic change and expansion is interleukin-6 (IL-6)-dependent. We further show that CD4 T cells are required for the maintenance of pulmonary metastatic burden post-influenza virus infection, in part through attenuation of CD8 cell responses in the lungs. Single-cell RNA-seq analyses reveal DCC-dependent impairment of T-cell activation in the lungs of infected mice. SARS-CoV-2 infected mice also showed increased breast DCC expansion in lungs post-infection. Expanding our findings to human observational data, we observed that cancer survivors contracting a SARS-CoV-2 infection have substantially increased risks of lung metastatic progression and cancer related death compared to cancer survivors who did not. These discoveries underscore the significant impact of respiratory viral infections on the resurgence of metastatic cancer, offering novel insights into the interconnection between infectious diseases and cancer metastasis.

overall_design: Lungs from MMTV-erbB2/neu/HER2 (MMTV-Her2) with or without depletion of CD4 cells: MMTV-Her2 mice were collected for scRNA-seq post IAV infection at 9 and 15 days.

first: Shi

last: Chia

first: Bryan

last: Johnson

first: Meher

last: Boorgula


title: Transcription promotes discrete long-range chromatin loops and 3D domains besides organizing cohesin-mediated folding

city: Toulouse

first: christophe

last: chapard

address: 118 route de Narbonne

department: CBI - MCD

institute: CNRS

summary: The multi-layered arrangement of eukaryotic genomes and chromosome spatial organization dynamics are of functional importance for gene expression, DNA replication and segregation. Cohesin is an essential instrument of chromosome folding by carrying out long range intra-chromatid DNA looping in addition to allowing timely chromosome segregation. Cohesin also ensures dynamic regulation of gene expression in mammals by promoting interaction between distal regulatory elements and promoters whereas transcription affects genome folding in multiple ways in multiple organisms. Here, we comprehensively dissect the relative contributions of transcription and cohesin complexes as well as their interplay on the yeast S.cerevisiae genome organization through DNA borders and loops. Transcription activation specifically induces apparition of DNA borders and loops, independently of cohesin, interfering in addition with cohesin mediated loop expansion.

overall_design: Examination of the interplay between transcription and SMC complexes such as cohesin on the genome 3D organization using HiC and ChIP-seq methods, yeast mutants, cell synchonisation, gene induction and protein depletion

first: Christophe

last: Chapard

first: Nathalie

last: Bastié

first: Laura

last: Chaptal

first: Romain

last: Koszul

first: Armelle

last: Lengronne

first: Frédéric

last: Beckouët


title: Patterns of intra- and inter-tumor phenotypic heterogeneity in men with lethal prostate cancer [scRNA-seq]

status: Public on May 22 2025

city: Seattle

first: Brian

last: Hanratty

state: WA

address: 1100 Fairview Avenue

department: Division of Human Biology

institute: Fred Hutchinson Cancer Cancer

summary: Metastatic prostate cancer (mPC) is a clinically and molecularly heterogeneous disease. While there is increasing recognition of diverse tumor phenotypes across patients, less is known about the molecular and phenotypic heterogeneity present within an individual. In this study, we aimed to define the patterns, extent, and consequences of inter- and intra-tumoral heterogeneity in lethal prostate cancer. By combining and integrating in situ tissue-based and sequencing approaches, we analyzed over 630 tumor samples from 52 mPC patients. Our efforts revealed phenotypic heterogeneity at the patient, metastasis, and cellular levels. We observed that intra-patient, inter-tumoral molecular subtype heterogeneity was common in mPC and showed associations with genomic and clinical features. Additionally, cellular proliferation rates varied within a given patient across molecular subtypes and anatomic sites. Single-cell sequencing studies revealed features of morphologically and molecularly divergent tumor cell populations within a single metastatic site. These data provide a deeper insight into the complex patterns of tumoral heterogeneity in mPC with implications for clinical management and the future development of diagnostic and therapeutic approaches.

overall_design: scRNA-seq of metastatic prostate cancer tissue samples.

first: Martine

last: Roudier

first: Roman

last: Gulati

first: Erolcan

last: Sayar

first: Radhika

last: Patel

first: Micah

last: Tratt

first: Helen

last: Richards

first: Paloma

last: Cejas

first: Miguel

last: Gomez Munoz

first: Xintao

last: Qiu

first: Yingtian

last: Xie

first: Samir

last: Zaidi

first: Jimmy

last: Zhao

first: Mohamed

last: Adil

first: Chitvan

last: Mittal

first: Yibai

first: Ruth

last: Dumpit

first: Ilsa

last: Coleman

first: Jin-Yih

last: Low

first: Thomas

last: Persse

first: Patricia

last: Galipeau

first: John

middle: K

last: Lee

first: Maria

last: Tretiakova

first: Meagan

last: Chambers

first: Funda

last: Vakar-Lopez

first: Lawrence

last: True

first: Marie

last: Perrone

first: Hung-Ming

last: Lam

first: Lori

last: Kollath

first: Chien-Kuang

last: Cornelia Ding

first: Stephanie

last: Harmon

first: Heather

middle: H

last: Cheng

first: Evan

middle: Y

last: Yu

first: Robert

last: Montgomery

first: Jessica

middle: E

last: Hawley

first: Daniel

last: Lin

first: Eva

last: Corey

first: Michael

middle: T

last: Schweizer

first: Manu

last: Setty


title: Cohesin supercoils DNA during loop extrusion

city: Vienna

first: Roman

last: Stocsits

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP - Research Institute of Molecular Pathology

summary: Cohesin extrudes genomic DNA into loops that promote chromatin assembly, gene regulation and recombination. Loop extrusion depends on large-scale conformational changes in cohesin, but how these translocate DNA is poorly understood. Here we provide evidence that cohesin negatively supercoils DNA loops during extrusion. Supercoiling requires engagement of cohesin’s ATPase heads, DNA clamping by these heads, and a DNA binding site on cohesin’s hinge, indicating that cohesin twists DNA when constraining it between the hinge and the clamp. A cohesin mutant defective in negative supercoiling forms shorter loops in cells, and a similar, although weaker, phenotype is observed after depletion of topoisomerase I. These results suggest that supercoiling is an integral part of the loop extrusion mechanism and that relaxation of supercoiled DNA is required for cohesin-mediated loop extrusion and genome architecture.

overall_design: Hi-C to analyze the effect of mutations on chromatin architectures in different conditions

first: Gordana

last: Wutz

first: Iain

middle: F

last: Davidson

first: Jan-Michael

last: Peters

first: Wen

last: Tang

first: Kota

last: Nagasaka


title: Acquisition of residency programs by T cells entering the human brain

city: Amsterdam

first: Jeen

last: Engelenburg

address: Meibergdreef 47

country: Netherlands

institute: Netherlands Institute for Neuroscience

summary: Surveillance by T cells is mandatory for maintaining a healthy state of the central nervous system (CNS), while aberrant accumulation of T cells is linked to neuroinflammatory diseases. To understand the phenotype of T cells recruited into distinct CNS compartments, we studied CD8+ and CD4+ T cells isolated from CNS border compartments (choroid plexus and meninges), intrathecal compartments (cerebrospinal fluid (CSF) and subcortical white matter (WM)), and paired peripheral blood of human brain donors. Flow-cytometric analyses revealed that T cells in all CNS compartments show an effector memory phenotype. Tissue residency-associated integrins (CD49a, CD103), chemokine receptors (CCR2, CCR5), and brain T cell-associated CD20, but not the canonical tissue resident memory T-cell marker CD69, were enriched in T cells from both CNS border compartments compared to blood. While small circulating fractions co-expressed these border-associated markers, the interaction of T cells with brain endothelium resulted in up-regulation of CD49a and CD103, with a further gain of CD20 upon trans-endothelial migration. In contrast to border compartments, intrathecal T cells were additionally characterized by a high expression of CD69. The transcriptomes of intrathecal T cells from CSF and WM were very similar and displayed a tissue residency-associated pattern. Still, WM-derived T cells showed a lower expression of markers associated with migratory potential (CRTAM, RGS1), recent activation (CD25, HLA-DR), and co-stimulation (CD28), which was associated with reduced Eomes expression. This work demonstrates the versatility of T-cell phenotypes across CNS compartments and provides insight into the programs regulating their recruitment and maintenance within the CNS.

overall_design: RNAseq profiling of primary isolated CD4 and CD8 T cells from control brain donors from circulation, CSF and white matter

first: Cheng-Chih

last: Hsiao

first: Hendrik

first: Jasper

last: Rip

first: Annet

last: Wierenga-Wolf

first: Fabiënne

last: van Puijfelik

first: Marvin

last: van Luijn

first: Inge

last: Huitinga

first: Jörg

last: Hamann

first: Joost

last: Smolders


title: Hinokiflavone, a novel CK2 inhibitor, promotes apoptosis and synergizes with chemotherapeutic agents in cisplatin-resistant bladder cancer cells.

city: Taipei

first: Tsung-Han

last: Hsieh

address: XinYi dist.,WuXing Street, No.250.

country: Taiwan

institute: Taipei Medical University

summary: Bladder cancer (BC) remains a major therapeutic challenge, particularly in patients with acquired resistance to platinum-based chemotherapy. In this study, we investigated the potential of hinokiflavone (HNK), a natural biflavonoid, as a therapeutic agent against cisplatin-resistant BC. Our results demonstrate that HNK differentially inhibits the proliferation of cisplatin-resistant BC cells while sparing normal uroepithelial cells. Mechanistically, HNK induces apoptosis through both intrinsic and extrinsic pathways, as evidenced by caspase activation and Annexin V staining. Next-generation sequencing and gene set enrichment analysis revealed that HNK affects genes associated with biosynthesis, metabolism, DNA replication and DNA repair. Additionally, HNK suppresses the transcription of MUTYH, OGG1, and XRCC1, key genes involved in base excision repair. We firstly identified that HNK as a novel CK2 inhibitor, and subsequent experiments confirmed that HNK inhibits CK2 activity, leading to decreased phosphorylation of Akt, Stat3, and XRCC1. The data suggest that the disruption of CK2-mediated signaling compromises BC cell survival and DNA repair capacity. Furthermore, combination treatment with HNK and chemotherapeutic agents such as doxorubicin or mitomycin C resulted in enhanced cytotoxic effects, suggesting a potential role of HNK as a chemo-sensitizing agent. These findings highlight HNK as a promising therapeutic candidate for cisplatin-resistant BC by targeting both DNA repair pathways and CK2-mediated survival signaling.

overall_design: N/P(14) cells were plated in 6 cm dishes and treated with hinokiflavone (5 μM) for 24 hours, and collected the RNA to perform mRNA-sequencing.

first: Chun-Han

last: Chen


title: Sub-Lethal levels of Gentamicin impacts gonococcal gene expression

city: Decatur

first: Concerta

last: Holley

state: GA

address: 1670 Clairmont Rd, Research 5A181

institute: Emory University

summary: The continued emergence of Neisseria gonorrhoeae (Ng) isolates resistant to first-line antibiotics has focused efforts on understanding how alternative therapies such as expanded use of gentamicin (Gen) might counteract this global public health problem. Focusing on Gen as a possible alternative antibiotic for treatment of gonorrheal infections, we used RNA-Seq to determine if sub-lethal levels of Gen might impact gonococci on a transcriptional level. We found that sub-lethal Gen altered expression of a finite number of genes in gonococcal strain FA19. Many of the differentially regulated genes were associated with known stress responses elaborated by Ng under different harmful conditions. Within the Gen regulon, we found that the hicAB operon, which encodes the putative HicAB toxin-antitoxin system, was transcriptionally activated in response to Gen.

overall_design: To determine the Gen induced regulon in GC, an RNA-Seq analysis was performed using total RNA samples collected from wild-type (WT) strain FA19 grown in the presence or absence of sub-lethal Gen (2 µ g/mL, 0.25X MIC) for 4 hours in GC broth

first: William

last: Shafer


title: Multi-omics analysis reveals CMTR1 upregulation in cancer and roles in ribosomal protein gene expression and tumor growth

city: Detroit

first: Zeng-Quan

last: Yang

address: 4100 John R Street

institute: Wayne State University

summary: CMTR1 (cap methyltransferase 1), a key nuclear mRNA cap methyltransferase, catalyzes 2'-O-methylation of the first transcribed nucleotide, a critical step in mRNA cap formation. Previous studies have implicated CMTR1 in embryonic stem cell differentiation and immune responses during viral infection; however, its role in cancer biology remains largely unexplored. In this study, we conducted a comprehensive multi-omics analysis of CMTR1 across various human cancers using TCGA and CPTAC datasets. Functional studies were performed using CRISPR-mediated knockout and siRNA knockdown in human and mouse basal-like breast cancer models. Transcriptomic and pathway enrichment analyses were carried out in CMTR1 knockout/knockdown models to identify CMTR1-regulated genes. In silico screening and biochemical assays were employed to identify novel CMTR1 inhibitors.We found that CMTR1 is significantly upregulated at the mRNA, protein, and phosphoprotein levels across multiple cancer types. Functional studies demonstrated that CMTR1 depletion significantly inhibits tumor growth both in vitro and in vivo. Transcriptomic analysis of CMTR1 knockout cells revealed that CMTR1 primarily regulates ribosomal protein genes and other transcripts containing 5' Terminal Oligopyrimidine (TOP) motifs. Additionally, CMTR1 affects the expression of snoRNA host genes and snoRNAs, suggesting a broader role in RNA metabolism. Mechanistic studies indicated that CMTR1's target specificity is partly determined by mRNA structure, particularly the presence of 5'TOP motifs. Finally, through in silico screening and biochemical assays, we identified several novel CMTR1 inhibitors, including N97911, which demonstrated in vitro growth inhibition activity in breast cancer cells. In conclusion, our findings establish CMTR1 as a key player in cancer biology, regulating critical aspects of RNA metabolism and ribosome biogenesis. The study highlights CMTR1's potential as a therapeutic target across multiple cancer types and provides a foundation for developing novel cancer treatments targeting mRNA cap methylation.

overall_design: RNA-seq of 4T1 wild-type and CMTR1 knockout (by CRISPR) cells

first: Yuanyuan

last: Jiang

first: Ion John

last: Campeanu


title: Patterns of intra- and inter-tumor phenotypic heterogeneity in men with lethal prostate cancer [scATAC-seq]

first: Brian

last: Hanratty

overall_design: scATAC-seq of metastatic prostate cancer tissue samples.

first: Martine

middle: P

last: Roudier

first: Roman

last: Gulati

first: Erolcan

last: Sayar

first: Radhika

middle: A

last: Patel

first: Micah

last: Tratt

first: Helen

last: Richards

first: Paloma

last: Cejas

first: Miguel

last: Gomez Munoz

first: Xintao

last: Qiu

first: Yingtian

last: Xie

first: Samir

last: Zaidi

first: Jimmy

last: Zhao

first: Mohamed

last: Adil

first: Chitvan

last: Mittal

first: Yibai

first: Ruth

last: Dumpit

first: Ilsa

last: Coleman

first: Jin-Yih

last: Low

first: Thomas

last: Persse

first: Patricia

last: Galipeau

first: John

last: Lee

first: Maria

last: Tretiakova

first: Meagan

last: Chambers

first: Funda

last: Vakar-Lopez

first: Lawrence

last: True

first: Marie

last: Perrone

first: Hung-Ming

last: Lam

first: Lori

last: Kollath

first: Chien-Kuang

last: Cornelia Ding

first: Stephanie

last: Harmon

first: Heather

last: Cheng

first: Evan

last: Yu

first: Robert

middle: B

last: Montgomery

first: Jessica

last: Hawley

first: Daniel

middle: W

last: Lin

first: Eva

last: Corey

first: Michael

last: Schweizer

first: Manu

last: Setty


title: ATAC-sequencing in untreated (UN), sodium arsenite (SA) and heat shock (HS) stressed THP-1 cells

first: Li

last: Yang

overall_design: We performed ATAC-seq in untreated (UN), sodium arsenite (SA) and heat shock (HS) stressed THP-1 cells. Two biological independent experiments in each condition were included.

first: Ling-Ling

last: Chen

first: Bao-Qing

last: Gao

first: Xiao-Qi

last: Liu

first: Pan

last: Li


title: Nanopore long-read RNA sequencing in untreated (UN), sodium arsenite (SA) and heat shock (HS) stressed HeLa cells

summary: Recent completion of the telomere-to-telomere (T2T) genome assembly has enabled a comprehensive characterization of pericentromeric SatⅠ, SatII, SatⅢ and centromeric α-satellite repeats. SatⅢ DNA constitutes ~1.56% of the genome with a reported localization across 16 chromosomes. The transcription activity of SatⅢ DNA across genome and the sequence of SatⅢ transcripts remained largely unclear. We performed nanopore long-read RNA sequencing (RNA-seq) in untreated (UN), sodium arsenite (SA: 0.1mM, 5 h) and heat shock (HS: 42°C, 2 h; 37°C, 1 h) stressed HeLa cells to characterize SatⅢ transcripts . Since a portion of SatⅢ transcripts is non-polyadenylated, We performed polyadenylated (poly(A)+) and rRNA-depleted (ribo-) nanopore cDNA long-read RNA-seq.

overall_design: We performed polyadenylated (poly(A)+) and rRNA-depleted (ribo-) nanopore long-read RNA-seq in untreated (UN), sodium arsenite (SA) and heat shock (HS) stressed HeLa cells. Two biological independent experiments in each condition were included.


title: Targeting the BCKDK/BCLAF1/MYC/HK2 axis to alter aerobic glycolysis and overcome Trametinib resistance in lung cancer

city: Tianjin

first: Hao

last: Wu

state: Tianjin

address: No. 22, Weidai Road, Heping District

department: Department of Immunology

institute: Tianjin Medical University

summary: BCKDK is a branched-chain amino acid metabolizing enzyme whose expression is up-regulated in tumors. BCKDK is closely associated with the development, progression, and metastasis of a wide range of tumors; however, the mechanisms behind this association remain poorly understood. To explore the pro-tumorigenic molecular mechanism of BCKDK, we performed RNA sequencing analysis of BCKDK-deficient H1299 cells.

overall_design: BCKDK stable knockout (KO) cell lines were generated by Clustered regularly interspaced short palindromic repeat (CRISPR) genome editing.Two monoclonal cell lines were obtained by limited dilution.Cells with lentiviral transduction of the lentiCRISPR v2 plasmid served as controls.

first: Zhi

last: Yao

first: Zheng

last: Fu


title: The nucleolar granular component is required for NAD association with nucleoli  and the establishment of repressive chromatin architecture [RNAseq_NPM1KD]

city: Zurich

first: Raffaella

last: Santoro

address: Winterthurerstrasse 190

department: Dep. of Molecular Mechanisms  of Disease

institute: University of Zurich

summary: Repressive chromatin domains often localize to the nuclear lamina or nucleolus. Although nucleolar-associated domains (NADs) have recently been mapped, their mechanisms of nucleolar association and functional significance remain unclear. Here, we show that nucleophosmin (NPM1), a factor located in the granular component of the nucleolus, mediates NAD association in mouse embryonic stem cells. NPM1 binds NADs, interacts with the histone methyltransferase G9a (EHMT2), and is required for establishing H3K9me2 at NADs. Loss of NPM1 or expression of a DNA-binding-deficient mutant disrupts NAD-nucleolus association and reduces H3K9me2 specifically at NADs. G9a is dispensable for NAD-nucleolus contacts, indicating that H3K9me2 is acquired after NADs associate with NPM1 at nucleoli. These findings reveal mechanistic insights into how genomic domains associate with nucleoli and form repressive chromatin and indicate that the nucleolus not only serves as a scaffold for positioning repressive domains but also plays a direct role in establishing their repressive chromatin states.

overall_design: RNAseq in mouse ESCs.

first: Shivani

last: Gupta

first: Cristiana

last: Bersaglieri

first: Dominik

last: Bär

first: Mathieu

last: Raingeval

first: Luana

last: Schaab


title: The nucleolar granular component is required for NAD association with nucleoli  and the establishment of repressive chromatin architecture [CHIPSeq_H3K9me2uponNPM1KD]


title: The nucleolar granular component is required for NAD association with nucleoli  and the establishment of repressive chromatin architecture [RNAseq_EHMT2KD]


title: The nucleolar granular component is required for NAD association with nucleoli  and the establishment of repressive chromatin architecture [CHIPseq_NPM1]


title: Cell-Surface LAMP1 is a Senescence Marker in Aging and Idiopathic Pulmonary Fibrosis

status: Public on May 21 2025

city: Mountain View

first: Gabriel

last: Meca-Laguna

state: CA

address: 110 Pioneer Way, Suite J

institute: Lifespan Research Institute

summary: The accumulation of senescent cells (SEN) with aging produces a chronic inflammatory state that accelerates age-related diseases. Eliminating SEN has been shown to delay, prevent, and in some cases reverse aging in animal disease models and extend lifespan. There is thus an unmet clinical need to identify and target SEN while sparing healthy cells. Here, we show that Lysosomal-Associated Membrane Protein 1 (LAMP1) is a membrane-specific biomarker of cellular senescence. We have validated selective LAMP1 upregulation in SEN in human and mouse cells. Lamp1+ cells express high levels of prototypical senescence markers p16, p21, Glb1, and have low Lmnb1 expression as compared to Lamp1- cells. The percentage of Lamp1+ cells is increased with age and in mice with fibrotic lungs due to bleomycin instillation. The RNA-Seq. analysis of the Lamp1-enriched populations in sham and BLM mice lung tissue revealed enrichment of several senescence-related genes in both groups when compared to the SenMayo gene set derived from transcriptomic profiling of senescence markers in Mayo Clinic research datasets. Finally, we use a dual antibody-drug conjugate (ADC) strategy to eliminate senescent cells in cell culture assay.

overall_design: Lungs from Sham- and Bleomycin-treated mice were harvested. Cells were sorted  to enrich or depleted cells expressing surface Lamp1. There are 6 conditions in total. For each Sham and Bleomycin, there are unsorted single cells (whole lung population, all), enriched cells (Lamp1-positive), depleted cells (Lamp1-negative).

first: Amit

last: Sharma


title: ADAR1 expression is associated with cervical cancer progression and negatively regulates NK cell activity

city: Rome

first: Alessandra

last: Soriani

address: Viale Regina Elena 291

institute: Sapienza University of Rome

summary: ADAR1 edits double-stranded (ds) RNAs by deaminating adenosines into inosines preventing aberrant activation of innate immunity by endogenous dsRNAs, which may resemble viral structures. Several tumors exploit ADAR1 to evade immune surveillance; indeed, its deletion reduces tumor viability and reshapes infiltrating leukocytes. Here, we investigated the role of ADAR1 in immune evasion mechanisms during cervical cancer (CC) progression. Patients’ biopsies showed higher ADAR1 expression already in pre-malignant (SIL) lesions, and a substantially reduced percentage of infiltrating CD7+ innate cells in in situ and invasive carcinomas, compared to normal mucosa, with CD56+ NK cells showing phenotypic alterations that might impact their functional responses. In CC-derived cell lines (SiHa, CaSki), ADAR1 silencing reduced cell proliferation, an effect further enhanced by exogenous IFNbeta administration. It also induced pro-inflammatory gene expression, as demonstrated by RNAseq analysis, and conditioned supernatants collected from these cells activated several NK cell effector functions. NK cell infiltration and activation was also confirmed in organotypic 3D tissue models of SiHa cells knocked-out for ADAR1. In conclusion, ADAR1 expression increases with CC progression and is accompanied by alterations of tumor-infiltrating NK cells, but its silencing in CC-derived cell lines potentiated anti-tumor NK cell activities. Thus, ADAR1 inhibition may represent a therapeutic perspective for CC and possibly other malignancies.

overall_design: RNA library was prepared using 1,5 micrograms of RNA with Kapa RNA HyperPrep with RiboErase (total RNA) and Kapa Globin Depletion Hybridization Oligos (Roche), from CaSki and SiHa cells. We compared two conditions (siCtr and siADAR). Samples were sequenced by NovaSeq 6000 Sequencing System, RUN 2x101 bp, Illumina Instrument, with an average number of reads from each sample of 140 M.

first: A

first: C

last: Cerboni


title: An extracellular matrix niche secreted by epithelial cells drives intestinal organoid formation (RNA-seq)

city: Lausanne

first: Antonius

last: Chrisnandy

state: Vaud

address: Route Cantonale

department: SV

institute: EPFL

summary: An ill-defined laminin-rich three-dimensional (3D) extracellular matrix (ECM) is typically used for the generation of organoids, but little is known about its function. Here, using tunable and chemically defined 3D hydrogels, we systematically explored the role of the ECM during murine intestinal organoid development. Our results highlight the utility of chemically defined matrices for studying ECM biology in tissue engineering and pave the way for the replacement of animal-derived matrices in organoid culture.

overall_design: Expression profiling by high throughput sequencing of mouse intestinal organoids that were cultured within different hydrogel (Matrigel, PEG with Laminin 1 and PEG only) and  different culture media (ENR,ENRCV, ENRCD and ENRD) at day 04 and 06 from single cells.

first: Matthias

last: Lütolf


title: Piezo1 initiates host immune defense against pathogenic fungi through mechanosensory recognition of Candida albicans hyphae

city: Xiamen

first: Lanfen

last: Chen

state: Fujian

address: Xiang'an south rd, Xiang'an district

department: Life Science

institute: Xiamen University

summary: Candida albicans metamorphoses from benign yeast to a rigid hyphae , becoming an opportunistic pathogen in immunocompromised patients. The process by which immune cells discern fungal transformations remains elusive. Here we report that the mechanosensitive ion channel Piezo1 is indispensable for recognizing fungal hyphae and triggering anti-fungal innate immune responses. Hyphae-triggered Piezo1 activation increased CLRs expression in innate immune cells by inducing the expression of C/EBPb via the Piezo1/CaMKs/CREB axis. In addition, Piezo1/CaMKs signaling activated kinases NDR1/2, which augmented NLRP3 inflammasome assembly and promoted hyphae-induced inflammation. Abolishing the yeast-to-hyphae transition dampens CLR and NLRP3 activation. Piezo1-deficient mice exhibit compromised clearance of C. albicans infection, whereas Piezo1 agonist amplifies C. albicans clearance. In addition, CaMKs, CREB or NDR1/2 inhibition exacerbates hyphae infections, like Piezo1 deficiency. Therefore, we ascertain Piezo1-mediated mechanotransduction as vital for immune surveillance and control of hyphal C. albicans, heralding Piezo1 agonist as a potential remedy for fungal infections.

overall_design: RNA-seq analysis of WT and Piezo1KO BMDMs, with or without Candida albicans.

first: Yiran

last: Shi

first: Dawang

last: Zhou