title: Micro-C reveals MORC/ApiAP2-mediated links between distant, functionally related genes in the human malaria parasite [ChIP-seq]

city: Parul

first: Parul

last: Singh

address: 25-28, rue du Docteur Roux

institute: Institut Pasteur

summary: Genome organization plays a significant role in silencing heterochromatinized genes in the most virulent human malaria parasite, Plasmodium falciparum. However, it remains unclear how heterochromatinized genes spatially cluster or if active genes are also organized in a specific manner. We used Micro-C to achieve a near-nucleosome resolution DNA-DNA contact map, which revealed new inter- and intrachromosomal heterochromatic and euchromatic structures in the blood stage parasite. We observed subtelomeric fold structures that facilitate interactions amongst heterochromatinized genes involved in antigenic variation. In addition, we identified long-range intra- and interchromosomal interactions amongst active, stage-specific genes. Both structures are mediated by AP2-P, an ApiAP2 transcription factor, and a putative MORC chromatin remodeler, and functional specificity is achieved via combinatorial binding with other sequence-specific DNA-binding factors. This study provides unprecedented insight into the organizational machinery used by this medically important eukaryotic parasite to spatially coordinate genes underlying antigenic variation and to co-activate stage-specific genes.

sample_organism:
Plasmodium falciparum
Plasmodium falciparum 3D7

overall_design:
ChIP-Seq experiment was performed for AP2-P and MORC proteins in P. falciparum to map genome-wide binding in the late stage of red blood cell development.
ChIP-Seq experiment was performed for second replicate of MORC protein in P. falciparum to map genome-wide binding in the late stage of red blood cell development.

first: Jacques

last: Serizay

first: Justine

last: Couble

first: Sebastian

last: Baumgarten

first: Jessica

last: Bryant


title: The genes involved in histone deacetylation regulates lipid metabolism through H4K5 and H4K8

status: Public on Jul 31 2025

city: Kunming

first: Qinyi

last: Wu

state: Yunnan

address: No.1076 Yuhua Road

country: China

institute: Yunnan University of  Chinese Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To identify genes which were involved in histone deacetylation regulates lipid through H4K5 and H4K8. ChIP-seq and motif analysis of C. elegans which were fed with E. coli OP50 until reach to adult. After washing by M9 buffer for three times, worms were re-suspended in PBS, frozen immediately in liquid nitrogen for ChIP-seq which were carried out by Wuhan SeqHealth Tech Co.,Ltd (Wuhan, China). The chromatin was sheared into 0.2 to 1kb fragments then subjected to immunoprecipitation using antibodies for H4K5ac (Abcam, ab51997) or H4K8ac (Abcam ab45166). Indexed ChIP-seq libraries were prepared using the NEB Next Ultra DNA library prep kit (New England Biolabs) and pair-end sequences on iIIumina NovaSeq 6000. HOMER was used in motif analysis of deferentially enriched peaks 31.

overall_design: The worms which fed on E. coli OP50 were collected after reaching to adult stage. The chromatin was sheared into 0.2- to 1-kb fragments. The soluble chromatin fraction was immunoprecipitated using antibodies specific for H4K5ac (Abcam, ab51997) or H4K8ac (Abcam, ab45166). ChIP-seq libraries were prepared using the NEBNext UltraDNA library prep kit (New England Biolabs) followed with paired-end sequencing on an Illumina NovaSeq6000.

first: Qin-Yi

first: Yi-Cheng

last: Ma

first: Meng

last: Zhou

first: Rui

last: Zhu

first: Cheng-Gang

last: Zou


title: Cancer cells subvert ZNF93 to escape surveillance by L1 epigenetic sentinels and control APOBEC3B

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

department: School of Life Science

country: Switzerland

institute: EPFL

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: YAP1 and QSER1 are Key Modulators of Embryonic Signaling Pathways in the Mammalian Epiblast [scRNA-seq]

city: Philadelphia

first: Naiara

last: Akizu

state: PA

address: 3501 Civic Center Blvd

department: Pathology And Lab Medicine

country: USA

institute: Children's Hospital of Philadelphia

summary: The Hippo:YAP1 signaling pathway was long considered a master regulator of organ growth. However, recent evidence has challenged this view, showing that the loss of YAP1 does not prevent several organs from reaching their normal size. Hence, resolving the functions of YAP1 in the embryo has become a central question in the field. To shed light into this, we analyzed YAP1’s role in regulating pluripotency of the mammalian epiblast, using scRNAseq approaches. Conditional deletion of Yap1 in the mouse epiblast (Sox2-Cre) altered the expression of signaling and differentiation genes, including Nodal, Wnt3, Fgf8, and Nanog, without impairing cell proliferation. Instead, Yap1 loss led to hyperactivation of Nodal signaling and enhanced differentiation of the epiblast toward mesodermal fate.  Furthermore, an unbiased screening in human pluripotent stem cells revealed that YAP1 transcriptionally cooperates with QSER1 protein, to regulate multiple WNT and NODAL signaling genes. Mechanistically, QSER1 represses lineage enhancers of signaling genes by counteracting RNA Polymerase II recruitment on YAP1-targets.  Accordingly, QSER1 depletion, similar to YAP1, leads to hyperactive Nodal signaling in human 2D-gastruloids. Overall, our findings not only advance our understanding of YAP1’s role in early development but also open new avenues for exploring how the interplay with QSER1 could influence additional developmental processes.

overall_design: Single-cell RNA sequencing (scRNAseq) data were obtained from E7 mouse embryos, including cYAP KO (Sox2cre:Yapflox/flox) and control (Sox2cre:Yapflox/+).

first: Elizabeth

last: Abraham

first: Thomas

last: Roule

first: Aidan

last: Douglas

first: Emily

last: Megil

first: Alex

last: Morris

first: Mikel

last: Zubillaga

first: Conchi

last: Estaras


title: YAP1 and QSER1 are Key Modulators of Embryonic Signaling Pathways in the Mammalian Epiblast [ChIP-seq]


title: Evolutionarily recent TFs partake in human cell cycle regulation


title: Genetic mapping of lifespan and mitochondrial stress response in C. elegans

status: Public on Jul 30 2025

first: Xiaoxu

last: Li

address: Station 15 - CH

summary: The mitochondrial unfolded protein response (UPRmt) is one of the mito-nuclear regulatory circuits that restores mitochondrial function upon stress conditions, promoting metabolic health and longevity. However, the complex gene interactions that govern this pathway and its role in aging and healthspan remain to be fully elucidated. Here, we activated the UPRmt using doxycycline (Dox) in a genetically diverse C. elegans population comprising 85 strains and observed large variation in Dox-induced lifespan extension across these strains. Through multi-omic data integration, we identified an aging-related molecular signature that was partially reversed by Dox. To identify the mechanisms underlying Dox-induced lifespan extension, we applied quantitative trait locus (QTL) analyses and found one novel UPRmt modulator, fipp-1/FIP1L1, which was functionally validated in C. elegans and humans. In the human UK Biobank, FIP1L1 was associated with metabolic homeostasis, underscoring its translational relevance. Overall, our findings demonstrate a novel UPRmt modulator across species and provide insights into potential translational research.

overall_design: Synchronized worms from each strain were fed with E. coli HT115 treated with 15 µg/mL doxycycline (Dox; Sigma, Cat. D9891)

first: Weisha

first: Arwen

last: Gao

first: Johan

last: Auwerx


title: OXPHOS driven by glycolysis through the malate aspartate shuttle is required for cardiomyocyte re-differentiation and long-term fish heart regeneration

city: Oxford

first: Mathilda

last: Mommersteeg

address: | Institute of Developmental and Regenerative Medicine (IDRM) | IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Drive

department: Department off Physiology, Anatomy and Genetics

country: United Kingdom

institute: University of Oxford

sample_organism:
Danio rerio
Astyanax mexicanus

platform_organism:
Danio rerio
Astyanax mexicanus


title: Vaccination with an mRNA-encoded membrane-bound HIV envelope trimer induces neutralizing antibodies in animal models

city: La Jolla

first: Shane

last: Crotty

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

summary: A protective vaccine against HIV will likely need to induce broadly neutralizing antibodies (bnAbs) that engage relatively conserved epitopes on the HIV envelope glycoprotein (Env) trimer. We report the design of mRNA-delivered membrane-bound form of a stabilized native-like Env trimer (BG505 MD39.3) and comprehensive evaluation of B cell, T cell, and antibody responses in non-human primates.

overall_design: HIV Env-specific memory B cells from PBMCs were isolated by fluorescence-activated cell sorting (FACS) and analyzed by scRNA-seq, including VDJ and GEX libraries, using the 10X Genomics platform.

first: Parham

last: Ramezani-Rad


title: Altered mRNA transport and local translation in i3Neurons with RNA binding protein knockdown

city: Rockville

first: Veronica

last: Ryan

state: MD

address: 9000 Rockville Pike

department: Center for Alzheimer's and Related Dementias, Alzheimer's and Related Dementias Independent Scholar

institute: National Institute on Aging

summary: Neurons rely on mRNA transport and local translation to facilitate rapid protein synthesis in processes far from the cell body. These processes allow precise spatial and temporal control of translation and are mediated by RNA binding proteins (RBPs), including those associated with neurodegenerative diseases. Here, we use proteomics, transcriptomics, and microscopy to investigate the impact of RBP depletion on mRNA transport and local translation in iPSC-derived neurons. We find thousands of transcripts enriched in neurites and that many of these transcripts are locally translated, possibly due to the shorter length of transcripts in neurites. Loss of frontotemporal dementia/amyotrophic lateral sclerosis (FTD/ALS)-associated RBPs TDP-43 and hnRNPA1 lead to distinct alterations in the neuritic proteome and transcriptome. TDP-43 knockdown (KD) leads to slightly increased neuritic mRNA and translation. In contrast, hnRNPA1 leads to more moderate effects on local mRNA profiles, possibly due to compensation by hnRNPA3. These results highlight the crucial role of FTD/ALS-associated RBPs in mRNA transport and local translation in neurons and the importance of these processes in neuron health and disease.

overall_design: i3Neurons grown in Boyden chambers were split into soma- and neurite-fractions and had their transcriptomes assessed via RNA-seq. We include samples with no further treatment (no-treatment), as well as CRISPRi knockdown of hnRNPA1 or TDP-43, in addition to non-targeting sgRNA controls.

first: Rachael

last: Dargan

first: Alla

last: Mikheenko

first: Nicholas

middle: L

last: Johnson

first: Benjamin

last: Packer

first: Ziyi

first: Emma

middle: J

last: Craig

first: Christina

last: Como

first: Stephanie

last: Sarbanes

first: Colleen

last: Bereda

first: Ying

last: Hao

first: Puja

middle: R

last: Mehta

first: Matthew

last: Keuss

first: Mike

middle: A

last: Nalls

first: Yue

last: Qi

first: Cory

last: Weller

first: Pietro

last: Fratta

middle: H


title: Chemical reprogramming of human blood cells into hCiPS cells [bulk RNA-seq]

city: Beijing

first: Ruoqi

last: Cheng

state: Beijing

address: NO.5, Yiheyuan Road, Haidian District

department: School of Life Sciences

institute: Peking University

summary: Chemical reprogramming offers a fundamentally innovative approach for generating human pluripotent stem (hCiPS) cells using small molecules. Our recent studies showed that this approach was highly efficient in reprogramming human fibroblasts to hCiPS cells.  In this study, we established a robust method that successfully generated hCiPS cells from both cord blood and adult peripheral blood cells. This method achieved efficient reprogramming with both fresh and cryopreserved blood cells.

overall_design: Total of 62 bulk RNAseq data were analyzed, which include EPC, hCiPSC, S1, S1-BI-7273, S1-NIBR, S1-BI-7273-NIBR, derived teratoma and 2 biological replicates for each condition.

first: Hongkui

last: Deng

first: Jingyang

last: Guan

first: Fangqi

last: Peng

first: Yanglu

last: Wang

first: Lin

first: Ruyi

last: Cai

first: Xiaodi

last: Fu


title: OXPHOS driven by glycolysis through the malate aspartate shuttle is required for cardiomyocyte re-differentiation and long-term fish heart regeneration [scRNA-seq]

first: Mathilda

last: Mommersteeg

summary: In contrast to humans after myocardial infarction, fish can fully regenerate their hearts. However, not all fish are equally able to regenerate, allowing comparative inter- and intra-species analysis to identify novel mechanisms controlling successful heart regeneration. Here, we report a differential regenerative response to cardiac cryo-injury between seven different wild-type zebrafish strains. Correlating this data to single cell and bulk RNAseq data, we identify oxidative phosphorylation (OXPHOS) as a positive regulator of long-term regenerative outcome. OXPHOS levels, driven by Glycolysis through the Malate aspartate shuttle (MAS), increase as soon as cardiomyocyte proliferation decreases, and this increase is required for cardiomyocyte re-differentiation and successful long-term regeneration. We confirm these findings in Astyanax mexicanus and link it to a dynamic temporal sarcomere gene expression programme during cardiomyocyte re-differentiation. These findings challenge the current stance that OXPHOS inhibits regeneration and provide new targetable pathways to enhance heart repair in humans after myocardial infarction.

overall_design: scRNA-seq data on FAC-sorted nppa-positive border zone cardiomyocytes at 1. 3 and 7dpci. Zebrafish underwent cryo-injury of the cardiac ventricle.

first: Jeroen

last: Bakkers

first: Phong

last: Nguyen

first: Hessel

last: Honkoop


title: Single-cell transcriptomic reconstruction of the human hair cycle: Capturing the temporal dynamics of skin tissue remodeling

city: Chuo-ku, Kobe

first: Hironobu

last: Fujiwara

state: Hyogo

address: 2-2-3 Minatojima-minamimachi

department: Center for Biosystems Dynamics Research

country: Japan

institute: RIKEN

summary: To investigate dynamic molecular and cellular changes associated with skin tissue remodeling during the human hair cycle, we aimed to obtain single-cell RNA sequencing (scRNA-seq) data from different hair cycle phases. We obtained scRNA-seq from randomly dissected human skin samples containing a single hair. Nineteen small skin pieces with a single hair were dissected from three female donors (single-hair samples). For comparison, we also collected three small skin pieces with no hairs from the same donors (non-hair samples). We enzymatically removed the interfollicular epidermis to focus our analysis on hair follicles and their surrounding dermis, which are the main areas of hair cycle-dependent tissue remodeling.

overall_design: We obtained human abdominal skin tissues from three healthy female donors who underwent a cosmetic surgery: donor A (40 years old), donor B (37 years old), and donor C (36 years old). After dissecting 19 single-hair samples (seven samples from each of donors A and B, and five samples from donor C) as well as three non-hair samples (one sample from each of the three donors), each sample was initially treated with dispase to remove the interfollicular epidermis and then treated with a collagenase and hyaluronidase mixture to make a single-cell suspension. Each sample was subjected to scRNA-seq using the 10X Genomics Chromium system (v3 chemistry). Cell quality control was performed for all 22 scRNA-seq data, and a total of 44,601 cells that passed our quality standards were integrated and used for subsequent analysis.

first: Jun

last: Yokota

first: Kazuyuki

last: Yo


title: A More Rapid Method for Culturing LUHMES-Derived Neurons Provides Greater Cell Numbers and Facilitates Studies of Multiple Viruses

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

country: Germany

institute: Ludwig-Maximilians-Universität München

summary: The ability to study mature neuronal cells ex vivo is complicated by their nature as non-dividing and difficulty in obtaining large numbers of primary cells from organisms. Thus, numerous transformed progenitor models have been developed that can be routinely cultured then scaled and differentiated to mature neurons. Here, we present a new method for differentiating one such model, the LUHMES dopaminergic neurons. This method is two days faster than some established protocols, results in nearly five times greater numbers of mature neurons, and involves fewer handling steps that could introduce technical variability. Moreover, it overcomes the problem of cell aggregate formation that commonly impedes high-resolution imaging, cell dissociation and downstream analysis. While recently established for herpes simplex virus type 1, we demonstrate that LUHMES neurons can facilitate studies of other herpesviruses, as well as RNA viruses associated with childhood encephalitis and hemorrhagic fever. This protocol provides an improvement in the generation of large-scale neuronal cultures, which may be readily applicable to other neuronal 2D cell culture models and provides a system for studying neurotrophic viruses. We name this method the Streamlined Protocol for Enhanced Expansion and Differentiation Yield, or SPEEDY method.

sample_organism:
Homo sapiens
Human alphaherpesvirus 1

platform_organism:
Homo sapiens
Human alphaherpesvirus 1

overall_design: rRNA depleted total RNA-seq and SLAM-seq of undifferentiated and differentiated LUHMES cells, with and without HSV-1 infection at given timepoints

first: Thomas

last: Hennig

first: Adam

middle: W

last: Whisnant

first: Arnhild

last: Grothey

middle: C

first: Lars

last: Dölken


title: Transcriptional alterations in the brain following Dot1l conditional knockout using the Emx1-Cre mouse line at embryonic day 16.5 [EmxDotRNAE16]

city: Freiburg

first: Tanja

last: Vogel

address: Albertstr. 23

institute: University of Freiburg

summary: During cerebral cortex development, neural stem cells (NSCs) require precise spatiotemporal signals to acquire the correct cell identity at the exact moment. Even though epigenetic regulation plays a central role in cell fate decisions, the exact mechanisms remain elusive. Thus, we focus our research on the H3K79 methyltransferase DOT1L, a key player in cell fate decisions. Our group has shown that DOT1L prevents NSC premature differentiation by increasing expression of genes that regulate asymmetric cell division (Franz et al. 2019). Using cell-lineage tracing and pharmacological inhibition, we confirmed that when DOT1L is inhibited apical progenitors (APs) switch to symmetric neurogenic divisions in detriment of asymmetric self-renewal (Appiah et al. 2023). We now analyse conditional knockout (cKO)  and control (WT) mice for DOT1L using Emx1-Cre line during cortical mid-neurogenesis (E14.5) using single cell RNA-seq to understand how the transcriptome changes.

overall_design: Emx1Dot cKO and control mouse embryos were harvested at E16.5. The cerebral cortex was dissected, dissociated into a cell suspension and analyzed using scRNA-seq.

first: Camila

last: Fullio


title: Real-time quantitative PCR analysis of human memory-like NK cells

city: Madison

first: Rithvik

last: Turaga

state: WI

address: Suite 3000, 1111 Highland Ave

institute: University of Wisconsin-Madison, Dept of Dermatology

summary: Human NK cells were purified from healthy whole blood and were differentiated to memory-like NK cells in vitro by culturing for one day in the presence of interleukin-12 (IL-12, 200µg/mL ), interleukin-15 (IL-15, 200µg/mL ) and interleukin-18 (IL-18, 200µg/mL ). After  24hrs media was changed to media containing only inteleukin-15 (IL-15, 200µg/mL). Cell were allowed to remain in culture for 6 days. RNA was extrated using Qiagen RNAEasy Plus Mico Kit. cDNA synthesis and RT-qPCR were perfromed using Qiagen cDNA synthesis kit and Human Glucose Metabolism RT2 Profiler PCR Array. 4 donors were used in gene expression analysis. Donor 4 was selected as the control to compare with samples from donors 1,2, and 3.

overall_design: qPCR gene expression profiling.  Memory-like NK cells from 4 donors were used for gene expression analysis. Each donor was run in triplicates. Donors 1,2 and 3 were compared to donor 4.

first: Jose

last: Ayuso


title: Bovine endometrium drives and responds to divergence of in vitro produced conceptus biochemistry

city: Knoxville

first: Daniel

last: Mathew

state: TN

address: 2506 River Drive

department: Animal Science

institute: University of Tennessee

summary: In vitro produced (IVP) bovine embryos are used to enhance herd genetics and support advanced reproductive technologies, however, less than 40% survive the first month of gestation after transfer to the surrogate. While the biochemical consequences of in vitro culture on the embryo before transfer have been well documented, less is known after transfer when the embryo interacts with the endometrium and pregnancy failure occurs. To investigate this, we utilized a Day 16 trophectoderm-endometrial mono-culture and co-culture system, integrating transcriptomic and proteomic analyses, to compare crosstalk between the IVP or in vivo derived (IVD) bovine conceptus and endometrium. We found that the IVP conceptus transcriptome (differentially expressed genes; DEG), diverged from the IVD conceptus but only after co-culture with endometrium (377 DEG; FDR < 0.05). Further, of the IVP conceptus DEG, 81 genes (21%) were associated with abnormal embryonic or fetal development. Significant biological processes associated with abundant endometrial DEG induced by IVP conceptuses were related to GTPase activity and the inflammatory response (FDR < 0.01), the latter of which may be associated with increased MHC class II expression, which was specific to IVP conceptuses. Proteomic analysis of the culture media identified 1,031 and 604 differentially abundant proteins (FDR < 0.05) associated with the IVD and IVP conceptus-endometrial co-cultures, respectively, compared to endometrium alone, indicating the proteomic environment surrounding the IVP conceptus may be suboptimal. Collectively, compared to the IVD conceptus, it appears the endometrium drives and responds to divergence of IVP conceptus biochemistry, likely contributing to pregnancy failure.

overall_design:
All procedures involving animals were approved by the University of Tennessee, Knoxville, Institutional Animal Care and Use Committee (IACUC 2020-67015-31617). Estrus synchronized Angus-Holstein heifers were used to generate cyclic Day 16 endometrial explants or elongated in vivo derived (IVD; artificial insemination) or in vitro produced (IVP) Day 16 bovine conceptuses. Endometrial explants (8 mm) and conceptus sections (5 X 2 mm) were cultured in medium separately (monoculture) or together in a co-culture system. After a 12 h incubation, the endometrial and conceptus tissue RNA was also isolated for RNA sequencing (RNA-Seq). Collectively, 13 cyclic uteri, 9 IVD conceptuses and 7 IVP conceptuses and were used to produce endometrial explants and conceptus sections for mono- and co-cultures.

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

middle: D

last: Peterson

first: Mary

last: Oliver

first: Trevor

middle: F

last: Freeman

first: Shankar

last: Poudel

first: Susanta

middle: K

last: Behura

first: David

last: Kakhniashvili

last: Johnson

first: Rebecca

last: Payton

first: Tulio

middle: M

last: Prado

first: Lew

middle: G

last: Strickland

first: Lannett

last: Edwards

first: Elizabeth

last: Shepherd

first: Jonathan

middle: E

last: Beever

last: Spencer


title: Herceptin-conjugated liposomes loaded with lipocalin-2 siRNA for the treatment of Inflammatory Breast Cancer

city: San Juan

first: Mariela

last: Rivera-Serrano

state: PR

address: 601 Ave Universidad

institute: University of Puerto Rico Rio Piedras

summary: Inflammatory breast cancer (IBC) is a rare and aggressive subtype of breast cancer (BC) that regularly affects women younger than 40 years and accounts for 1 to 5% of all types of BC. There is not an optimal treatment for women with IBC. Approximately 40% of IBC patients are HER2+, which can be treated with the monoclonal antibody-based therapy, Herceptin (trastuzumab). However, more than 25% of patients become resistant to trastuzumab-based therapy in early stages and about 75% in late stages patients and effective second line targeted therapies are currently unavailable for IBC patients. Lipocalin-2 (LCN2) is a is a secreted protein involved in iron homeostasis, immune responses, transportation of siderophores for degradation, and epithelial cell differentiation.  LCN-2 is highly abundant in certain subtypes of aggressive cancers including IBC. Reports have shown that LCN-2 is a potential target therapy for IBC patients. Here, we developed a double targeted therapy of liposomal-Herceptin formulation loaded with LCN2-targeted small interference RNA (siRNA). Trastuzumab DSPE-PEG(2000)-maleimide conjugates were synthesized for liposomal formulation, resulting in sizes of 18.3 nm and 73.7 nm for free DSPE-PEG(2000)-trastuzumab and trastuzumab-liposome, respectively. This formulation was efficiently internalized into HER2+ IBC cells, and reduced cell proliferation and tumor emboli formation in IBC cells. To further understand the molecular mechanism downstream LCN-2, we performed RNA-sequencing (RNA-seq), and we identified 139 differentially expressed genes upon siRNA-mediated LCN-2 knockdown in IBC cells.  Ingenuity Pathway Analysis grouped the RNA-seq data into 25 canonical pathways altered downstream LCN-2. Together, this information suggests that LCN2-target siRNA within Herceptin-conjugated liposomes is a potential therapeutic strategy against IBC.

overall_design: To identify the downstream signaling effectors after siRNA-mediated LCN2 knockdown in inflammatory breast cancer to understand the underlying mechanisms related to the silencing. Wecarried out a transcriptome-wide analysis via RNA sequencing (RNA-seq) in IBC3 cells

first: Marienid

last: Flores-Colón

first: Fatma

last: Valiyeva

first: Pablo

last: Vivas-Mejia


title: Chemical reprogramming of human blood cells into hCiPS cells [scRNA-seq]

first: Ruoqi

last: Cheng

overall_design: Total of 5 scRNAseq samples were analyzed, which include PBMC EPC, S1D1, S1D3, S1D6, S1D8.

first: Hongkui

last: Deng

first: Jingyang

last: Guan

first: Fangqi

last: Peng

first: Yanglu

last: Wang

first: Lin

first: Ruyi

last: Cai

first: Xiaodi

last: Fu


title: Chemical reprogramming of human blood cells into hCiPS cells

type: Methylation profiling by high throughput sequencing

overall_design: Total of 12 WGBS data were analyzed, which include EPCs and ADSCs derived hCiPSCs.


title: Cutaneous T-Cell Lymphoma: Yin-Yang Effects of Transcription Factors HLF and NFIL3 in Regulation of Malignant T-cell Markers in the Context of HDAC Inhibitor Romidepsin Treatment

first: Priyankara

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: The drug romidepsin which is known to regulate gene expression has been shown to be an effective treatment in a subset of patient with cutaneous T-cell lymphoma (CTCL). We examined changes in gene expression that occurred through repeated romidepsin treatments using carefully collected blood cell samples from treated CTCL patients. Focusing on data from highly responsive CTCL patient through 12 months of treatment, including a period free from disease, we identified new markers that are characteristic of the malignant cells and markers of difficult to detect residual disease. We have identified functional effect and potential mechanisms of dysregulation through miRNA and DNA methylation and found significant impact of regulators HLF (activator) and NFIL3 (suppressor) that control expression of a significant number of malignant cell markers. We report new surface markers for the malignant cells, including markers identifiable in residual disease, and new potential therapeutic targets.

overall_design:
RNAseq on PBMC from CTCL patients treated with romidepsin

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

first: Andrew

last: Kossenkov

first: Louise

last: Showe


title: Comparing DNA methylation landscapes of peripheral blood from Myalgic Encephalomyeli-tis/Chronic Fatigue Syndrome and Long COVID patients

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

summary: We generated reduced representation bisulfite sequencing (RRBS) data of 15 samples (5 Healthy, 5 Long COVID and 5 ME patients) from PBMCs to understand key molecular events involved in Long COVID and ME/CFS.

overall_design: Methylation profiling by high throughput sequencing

first: Sayan

last: Sharma

first: Katie

last: Peppercorn

first: Christina

last: D. Edgar

first: Peter

last: A. Stockwell

first: Euan

last: J. Rodger

first: Warren

last: P. Tate


title: Chemical reprogramming of human blood cells into hCiPS cells [bulk ATAC-seq]

first: Ruoqi

last: Cheng

overall_design: Total of 8 bulk ATACseq data were analyzed, which include PBMC EPC, S1, S1-BI-7273, PBMC hCiPSC and 2 biological replicates for each condition.

first: Hongkui


title: Comparison of axicabtagene ciloleucel and tisagenlecleucel patient CAR-T cell products by single cell RNA sequencing

city: Tampa

first: Michael

last: Jain

address: 12902 Magnolia Dr

institute: Moffitt Cancer Center

summary: Background: Autologous CD19 CAR T cell therapy leads to durable responses and improved survival in patients with relapsed or refractory large B cell lymphoma (R/R LBCL). Among approved CAR T cell products, axicabtagene ciloleucel (axi-cel; CD19/CD28) has greater real-world efficacy and cytokine-associated toxicity than tisagenlecleucel (tisa-cel; CD19/4-1BB), for reasons that are poorly understood. Methods: Here we report single cell RNA sequencing (scRNA-seq) of 57 pre-infusion CAR T cell products from axi-cel (n=39) and tisa-cel (n=18) patients treated as standard-of-care for R/R LBCL, and their biological associations with clinical outcomes. In vitro CAR manufacturing conditions mimicking those known for axi-cel and tisa-cel were performed using CD19/CD28z or CD19/4-1BBz constructs. Results: ScRNA-seq revealed that axi-cel and tisa-cel are markedly different products. Axi-cel is comprised of more CD4 central memory, CD8 central memory, and CD8 effectors, whereas tisa-cel is comprised of more proliferative CD4 and CD8 cells. Across multiple T cell subsets, axi-cel had greater expression of immune response pathways and protein synthesis and trafficking pathways vs. tisa-cel. On comparison of infusion product CAR transgene-positive (CAR+) cells to CAR transgene-negative (CAR-) T cells, axi-cel CAR+ cells had vastly different gene expression than axi-cel CAR- cells. Unexpectedly, tisa-cel CAR+ cells were highly similar to tisa-cel CAR- cells. Under recapitulated CAR-T manufacturing conditions known to be utilized for axi-cel and tisa-cel, we found that CAR+ cells differed from CAR- cells early after manufacturing yet became more similar to CAR- cells after prolonged expansion. Prolonged time in expansion culture, as utilized during tisa-cel manufacturing, greatly decreased naïve and central memory T cell subsets. Conclusions: Following manufacture, axi-cel is less differentiated and has greater immune activation compared to tisa-cel, potentially accounting for its greater efficacy and toxicity in patients. Our data support the conclusion that tisa-cel is adversely affected by its manufacturing rather than by the CAR construct.

overall_design: Patients and samples: All patients were consented to prospective sample collection and research database protocols approved by the Institutional Review Board (IRB) of the University of South Florida (USF) or by Advarra. All patient samples were collected at Moffitt Cancer Center. Patient CAR T-cells were obtained by washes from commercial product infusion bags after patient infusion, and cryopreserved for batch analysis.

first: Frederick

last: Locke

first: Xiaoqing

last: Yu

first: Ling

last: Cen


title: Impact of Acute Exercise on Alternative Splicing in Skeletal Muscle

city: Ann Arbor

last: Ludlow

state: Education

address: 830 N University Ave

institute: University of Michigan

summary: Alternative RNA splicing (AS) is a highly conserved post-transcriptional mechanism, generating mRNA variants to diversify the proteome. Acute endurance exercise appears to transiently perturb AS in skeletal muscle, but transcriptome-wide responses are not well-defined. We aimed to better understand differential AS (DAS) in skeletal muscle by comparing short-read RNA sequencing (SRS) and long-read RNA sequencing (LRS) data. Publicly accessible SRS of clinical exercise studies were extracted from the Gene Expression Omnibus. Oxford Nanopore LRS  was performed on mouse gastrocnemius before and following treadmill exercise. Differential gene expression (DGE), DAS, and isoform switching were analyzed. Western blots were performed to validate expression changes of candidate genes. Both SRS and LRS illustrated significant DGE in skeletal muscle post-exercise, whereby 57 and 15 RNA-binding proteins (RBPs) were up-/down-regulated, respectively. rMATS analysis of SRS data revealed that exon-skipping and intron-retaining splicing events were the most common. Swan analysis of LRS data revealed 38 RBPs with significant isoform switching: one of these RBPs, Hnrnpa3, underwent a significant intron-retained to protein-coding switch. HnRNP-A3 protein levels validated nearly two-fold increases at 1 hour (p=.0043) and 24 hours (p=.0103) post-exercise. This study illustrates that acute endurance exercise can elicit changes in AS-related responses and RBP expression in skeletal muscle. SRS is certainly a powerful tool for analyzing DGE but lacks AS detection. As such, “hidden” genes with no transcriptional changes but significant DAS and protein expression changes pose a major gap in knowledge. Our work highlights how LRS can uncover previously unknown transcript diversity and mechanisms influencing AS.

overall_design:
To investigate the impact of acute endurance exercise on alternative splicing in skeletal muscle, 20 mice underwent acute treadmill running (60% of maximal speed) treadmill running at a constant pace for 30 minutes. The mice were sacrificed at four time points, whereby the gastrocnemius muscles were harvested, flash frozen in liquid nitrogen, and stored at –80°C for subsequent tissue processing and RNA isolation.
We then isolated poly(A)-containing RNA to synthesize barcoded PCR-cDNA libraries (Oxford Nanopore Technologies) for long-read RNA sequencing on the MinION™ Mk1C sequencer with a MinION™ R9.4.1 flow cell.

first: Alexander

last: Ahn

first: Jeongjin

last: Kim

first: Aaron

last: Slusher

first: Jeffrey

middle: Y

last: Ying

first: Eric

last: Zhang

middle: T


title: Immune Signaling Mediates Stromal Changes to Support Epithelial Reprogramming in Celiac Duodenum

city: Spring House

first: Dylan

middle: Jack

last: Richards

address: 1400 McKean Rd

institute: Johnson & Johnson

summary: Coeliac Disease (CeD) is a chronic autoimmune disorder affecting 0.5-1% of the general population with a wide geographical distribution. Despite recent efforts to deeply phenotype gluten-specific immune activation at the single cell level, recent clinical studies targeting gluten degradation and other immune tolerance mechanisms have been unsuccessful. To this end, a deeper understanding of immune and non-immune cellular dynamics and interactions are required to characterize tissue-specific mechanisms responsible for CeD pathogenesis, repair, and resolution. Here, we assembled the most comprehensive scRNAseq dataset in Coeliac Disease to date, including 203,555 cells across 21 active CeD and 11 control duodenal samples. Compared to control duodenum, CeD was characterized by single cell differential changes in abundance, gene expression and cell-cell interactions across cellular compartments. In the immune compartments, CeD samples showed expected increases in plasma cell abundance and shifts toward type 1 effector biology (e.g., increase in cycling CD8pos, γδ T cells and IFNG transcriptional shifts) and Tfh-related biology (e.g., increases in IL21 signaling to effector T cells). In addition, activated myeloid subsets, including DC2 and monocytes, were increased in disease and were characterized by increased pro-inflammatory pathway expression, including IL-1β. Non-immune compartments showed increased stem/crypt and secretory enterocytes in CeD samples with a decrease in absorptive enterocytes, reflecting the villus atrophy and crypt hyperplasia hallmarks of CeD epithelial dysfunction. Accompanying the epithelial changes, distinct changes in stromal populations were identified, particularly with increases in abundance and transcriptional activity of NRG1 and SMOC2 fibroblasts. Cell-cell interaction analysis across multiple cellular compartments proposed a distinct increased role of fibroblasts to support the epithelial reprogramming of the increased stem/crypt epithelial fraction in CeD, mediated by myeloid derived IL-1β signal and lymphoid-derived IFN-γ. This dataset reveals a previously unknown role for T-myeloid-stromal-epithelial cell communication in CeD, highlighting key mechanisms of the tissue-level cellular dynamics in response to gluten ingestion.

overall_design: Single cells were isolated from cryopreserved duodenal biopsies. Briefly, biopsies were dissociated using liberase/dnase solutions combined with removal of dead cells using EasySep™ Dead Cell Removal (Annexin V) Kit.

first: Darren

last: Ruane

first: Patrick

last: Walsh

first: Seamus

last: Hussey


title: IWS1 Stimulates Pol II Transcription Elongation In Vivo [ChIP-Seq]

city: Göttingen

first: Kristina

last: Žumer

address: Am Faßberg 11

department: Department of Molecular Biology

institute: Max Planck Institute for Multidisciplinary Sciences

summary: Interacts with SPT6 1 (IWS1) has been implicated in various co-transcriptional processes, yet its direct role in RNA Polymerase (Pol) II transcription in vivo remains elusive. In this study, we utilized a rapid depletion system of IWS1 in human cells, followed by multi-omics analysis and biochemical assays, to elucidate its function. We show that IWS1 depletion results in a global decrease of RNA synthesis, but does not affect the chromatin recruitment of the histone methyltransferase SETD2. In vivo and in vitro analyses of nascent transcription and histone modifications revealed that the observed decrease in methylation is a secondary effect of the transcription defect caused by IWS1 depletion. Whereas these results show that IWS1 is essential for maintaining normal RNA Pol II elongation velocity in vivo, and that it can directly stimulate transcription.

overall_design: Samples for each condition were collected in biological duplicates. Cells were treated with dTAG7 for 1 or 4 hours, the corresponding control cells were treated for the same duration with the solvent only (DMSO) at the same vol/vol dilution.

first: Aiturgan

last: Zheenbekova

first: James

last: Walshe

first: Moritz

last: Ochmann

first: Ute

last: Neef

first: Kerstin C.

last: Maier

first: Petra

last: Rus

first: Yumeng

last: Yan

first: Henning

last: Urlaub

last: Zumer

last: Cramer


title: NASP modulates histone turnover to drive PARP inhibitor resistance

status: Public on Jul 29 2025

city: Amsterdam

first: Judith

last: Haarhuis

address: Plesmanlaan 121

country: Netherlands

institute: The Netherlands Cancer Institute

summary: PARP inhibitors (PARPi) present a remarkable advance in the treatment of patients with homologous recombination (HR)-deficient tumors but resistance remains a challenge1-5. While most research has focused on the downstream consequences of PARPi exposure to tackle resistance, the immediate impact of PARP inhibition on the chromatin environment and its contribution to PARPi toxicity remains elusive. Here, we show that PARP inhibition induces histone release from the chromatin. This presents a vulnerability of PARPi-resistant cancer cells, which are addicted to histone homeostasis mechanisms to sustain elevated DNA replication rates and survival. Through functional genetic screens, we identified NASP as a key factor in maintaining the stability of evicted histones via its TPR motifs. NASP loss renders tumor cells hypersensitive to PARPi treatment in vitro and in vivo, impairs replication fork progression and elevates levels of replication-associated DNA damage. Moreover, NASP acts together with the INO80 complex and the chaperoning activity of PARP1 to ensure efficient histone turnover and prevent the accumulation of lethal DNA damage following PARPi exposure. Collectively, our work reports on histone eviction as an immediate cellular response to PARPi treatment and provides a promising avenue for targeting histone supply pathways to overcome PARPi resistance.

overall_design: Hi-C was performed on the following genotypes: Wild Type , ∆BRCA1/53BP1 HAP1 cells. Cells were untreated or exposed to 1μM olaparib for 24 hours.

first: Sarah

last: Moser

first: Anna

last: Khalizieva

first: Josef

last: Roehsner

first: Elisabeth

last: Pottendorfer

first: Milo

last: Kaptein

first: Giulia

last: Ricci

first: Vivek

last: Bhardwaj

first: Onno

middle: B

last: Bleijerveld

first: Liesbeth

last: Hoekman

first: Ingrid

last: van der Heijden

first: Simone

last: di Sanzo

first: Alexander

last: Fish

first: Aleksandra

last: Chikunova

first: Roel

last: Oldenkamp

first: Luisa

last: Robbez-Masson

first: Justin

last: Sprengers

first: Daniel

last: Vis

first: Lodewyk

last: Wessels

first: Marieke

last: van de Ven

first: Stephen

last: Pettitt

first: Andrew

middle: N

last: Tutt

first: Christopher

last: Lord

first: Benjamin

last: Rowland

last: Voelker-Albert

first: Francesca

last: Mattiroli

first: Thijn

last: Brummelkamp

first: Abdelghani

last: Mazouzi

first: Jos

last: Jonkers


title: IWS1 Stimulates Pol II Transcription Elongation In Vivo [mNET-seq]

first: Kristina

last: Žumer

type: Non-coding RNA profiling by high throughput sequencing

overall_design: Samples for each condition were collected in biological duplicates. Cells were treated with dTAG7 for 1 hour, the corresponding control cells were treated for the same duration with the solvent only (DMSO) at the same vol/vol dilution.

first: Aiturgan

last: Zheenbekova

first: James

last: Walshe

first: Moritz

last: Ochmann

first: Ute

last: Neef

first: Kerstin C.

last: Maier

first: Petra

last: Rus

first: Yumeng

last: Yan

first: Henning

last: Urlaub

last: Zumer

first: Patrick

last: Cramer


title: Induction of meiosis from human pluripotent stem cells [Bisulfite-seq]

city: Boston

first: Merrick

middle: Pierson

last: Smela

state: MA

address: 3 Blackfan Circle

institute: Harvard University

summary: An in vitro model of human meiosis would accelerate research into this important reproductive process and development of therapies for infertility. We have developed a method to induce meiosis starting from male or female human pluripotent stem cells. We demonstrate that DNMT1 inhibition, retinoid signaling activation, and overexpression of regulatory factors (anti-apoptotic BCL2, and pro-meiotic HOXB5, BOLL, or MEIOC) rapidly activates meiosis, with leptonema beginning at 6 days, zygonema at 9 days, and pachynema at 12 days. Immunofluorescence microscopy shows key aspects of meiosis, including chromosome synapsis and sex body formation. The meiotic cells express genes similar to meiotic oogonia in vivo, including all synaptonemal complex components and machinery for meiotic recombination. These findings establish an accessible system for inducing human meiosis in vitro.

overall_design: Plasmids for constitutive expression of BCL2 and doxycycline-inducible expression of HOXB5, BOLL, and MEIOC were integrated into F2 D4TDZG, F3 D4TT2G, and PGP1 D4TR8G reporter hiPSCs. The iPSCs were seeded at 50,000 cells/cm2 on Matrigel-coated plates in mTeSR1 supplemented with 5 µM GSK3484862, 1 µg/mL doxycycline, and 10 µM Y-27632. For 6-well plates, 1.5 mL of medium was used per well. After one day, the media was replaced with APEL2 containing 5 µM GSK3484862 and 1 µg/mL doxycycline. A 50% media change was performed every 2 days, and GSK3484862 was withdrawn starting on day 7. Cells were harvested at each day from day 0 (hiPSC) to day 15. For the pilot experiment, methyl-seq was performed on cells that had been fixed using the Parse Biosciences scRNAseq fixation kit. For the follow-up experiment, methyl-seq was performed on unfixed cells, some of which were sorted based on DDX4-tdTomato reporter expression. Library preparation was performed using the NEB Enzymatic Methyl-Seq kit. For the pilot experiment, sequencing was performed using a MiSeq Micro kit. For the follow-up experiment, sequencing was performed on two lanes of a Novaseq X Plus 25B PE150 flowcell.

middle: P

first: Jessica

last: Adams

first: Carl

last: Ma

first: Laura

last: Breimann

first: Ursula

last: Widocki

first: Ting

last: Wu

first: Toshi

last: Shioda

first: George

last: Church


title: H2A.Z regulates memory CD8+ T cell recall response [4]

first: Mingzhao

last: Zhu

address: 15 Da Tun Rd, Chaoyang District

department: Key Laboratory of Infection and Immunity

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: The rapid response of memory CD8+ T cells is crucial for the body's defense against infection and cancer. However, the mechanisms underlying memory recall responses remain unclear. Here we show that the rapid response of memory T cells is accompanied by the induction of gene expression associated with memory CD8+ T cell activation-recalled genes, which participate in various biological functions, such as response to antigen signals, intracellular phosphorylation kinase signaling pathways, and cytokine production. And the expression of ARGs in memory T cells is closely associated with their epigenetic features. We found that the genomic loci of ARGs in memory T cells exhibit active epigenetic marks, such as increased H2A.Z binding, elevated levels of H3K27 acetylation, enhanced binding of Pol II S5P, and reduced levels of repressive histone mark H3K27me3. Interestingly, H2A.Z plays a crucial role in modulating these epigenetic features. Depletion of H2A.Z results in a reduction in H3K27ac levels, decreased binding of Pol II, increased levels of H3K27me3, and a decrease in chromatin accessibility. Functionally, H2A.Z is essential in quiescent memory CD8+ T cells for generating effector CD8+ T cells, producing effector molecules and effectively eliminating pathogens during recall responses. In addition, H2A.Z deposition at specific ARG gene loci in the genome is mainly regulated by TCR/CD28 signals, and may be partly regulated by IL-7 and IL-15. Overall, these findings demonstrate that H2A.Z orchestrates the epigenetic landscape at ARG gene loci to regulate the recall responses of memory T cells.

overall_design: CD45 congenically distinct OT-I naïve CD8+ T cells sorted from the spleens of WT (OT-I H2A.Zf/f or OT-I) or cKO (OT-I H2A.Zf/f GzmB-cre) mice were transferred into hosts followed by infection with LM-OVA.  Naïve (CD62LhiCD44lo) OT-I CD8+ splenocytes and day 30 post-infection TM (CD127hiKLRG1lo) cells were purified from spleens. ATAC-seq, CUT&Tag and ChIP-seq were performed (2 biological replicates pooling 3-5 mice).

first: Wei

last: Liang

first: Jiyu

last: Ding


title: Systematic analyses of transposable element expression dynamics using long read RNA-seq in pluripotent stem cells and germ lineage cells [subcellular RNA-seq]

city: Shenzhen

first: Andrew

last: Hutchins

address: 1088 Xueyuan Rd

institute: Southern University of Science and Technology

summary: Transposable elements (TEs) are genomic elements that are found in multiple copies in mammalian genomes. Previously thought to have little functional relevance, recent studies have reported roles for TEs in multiple biological processes, and particularly in embryonic development. However, due to their repetitive nature it has been hard to fully account for the contributions of TEs to the transcriptome. To study the expression dynamics of TEs in human early development (hED), we performed in vitro differentiation of human pluripotent stem cells (hPSCs) to endoderm, mesoderm and ectoderm lineages, and constructed lineage-specific transcriptome assemblies using long-read sequence data to accurately place TE sequences in their transcript context. The analyses of specific TE types and genomic loci revealed lineage-specific expression patterns reflecting dynamic expression trajectories with an expression outburst of multiple TEs, including multiple LINEs and LRTs in the ectoderm lineage. We found several LTRs, including HERVH and LTRY7, to be highly expressed in hPSC and the endoderm, including endoderm-specific LTR6A. Indeed, a common feature of germ lineage-specific expression is the lineage-specific regulation of TE-containing transcripts with highly dynamic stability and subcellular localization. Chromatin association with TEs increased with differentiation. This study suggests that TEs contribute to hED via the regulation of chromatin structure.

overall_design: RNA-seq data for human pluripotent stem cells, and mesoderm, endoderm, and ectoderm differentiated cells, in cells treated with actinomycin D to block transcription and measure transcript half-life

first: Isaac

middle: A

last: Babarinde

first: Xiuling

last: Fu


title: Systematic analyses of transposable element expression dynamics using long read RNA-seq in pluripotent stem cells and germ lineage cells [bulk RNA-seq]

overall_design: Bulk short-read RNA-seq data for human pluripotent stem cells, and mesoderm, endoderm, and ectoderm differentiated cells.


title: Systematic analyses of transposable element expression dynamics using long read RNA-seq in pluripotent stem cells and germ lineage cells [RNA-seq half-life]


title: Integration of multi-modal measurements identifies critical mechanisms of tuberculosis drug action

first: Bree

last: Aldridge

state: Massachusetts

address: 136 Harrison Ave

department: Molecular Biology and Microbiology

institute: Tufts University

summary: Treatments for tuberculosis remain lengthy, motivating a search for new drugs with novel mechanisms of action. However, it remains challenging to elucidate the direct targets of a drug, and even more so, to determine which disrupted cellular processes lead to bacterial killing. We developed a computational tool, DECIPHAER (Decoding Cross-modal Information of Pharmacologies via AutoEncodeRs), to select correlated transcriptional and morphological responses of Mycobacterium tuberculosis to drug treatments. By finding a latent space from these measurements, DECIPHAER highlighted important features of Mtb cellular damage such as phosphosugar stress and inhibition of translation and DNA replication. After training, DECIPHAER provides cell-death-relevant insight into even single-modal datasets, enabling interrogation of drug treatment responses for which transcriptional data are not available. Using only morphological data with DECIPHAER, we discovered that respiration inhibition by the poly-pharmacological drugs, SQ109 and BM212, can be their primary mechanism influencing cell death, not their effect on the cell wall. This study demonstrates that DECIPHAER can extract the critical shared information from multi-modal measurements to identify cell death-relevant mechanisms of TB drugs.

overall_design: Mtb strain Erdman with plasmid pMV306hsp+LuxG13 were adapted to a cholesterol in-vitro growth condition prior to drug exposure and RNA extraction. Briefly, Mtb were first cultured in standard growth medium consisting of 7H9 broth, (ThermoFisher; DF0713-17-9), 0.2% glycerol, 10% OADC (0.5g/L oleic acid, 50g/L albumin, 20g/L dextrose and 0.04g/L catalase), and 0.05% Tween-80 and then subcultured at least once prior to cholesterol adaptation. Once the bacterial cultures reached an OD600nm ~0.5, the cultures were diluted to an OD600nm of 0.05 in cholesterol growth medium consisting of 7H9 powder (4.7g/L), fatty acid-free BSA (0.5g/L), NaCl (100mM) and tyloxapol (0.05%). Cultures were then subcultured once more in the same media after reaching mid-log phase (OD600nm ∼0.5-0.7). Then, the cultures were subcultured to 0.05 OD in 50ml conical tubes containing the cholesterol growth media and drug treatment at a concentration of 1x the IC90. Drug-treated cultures and untreated controls were then harvested by centrifugation at timepoints 4, and 24 hours post drug treatment. All cultures were buffered with 100 mM 3-(N-morpholino)propanesulfonic acid at pH 7.

first: William

last: Johnson


title: Skeletal muscle expression profile changes in early stages of sepsis.

city: fuzhou

first: siming

last: lin

state: fujian

address: 20 Chazhong Road

institute: The First Affiliated Hospital of Fujian Medical University

summary: Purpose: RNA sequencing was employed to analyze the alterations in gene expression profiles within the gastrocnemius muscle of mice suffering from early sepsis.Methods: RNA sequencing was conducted on the gastrocnemius muscle of sepsis mice induced by LPS, as well as normal control mice.Results:The gene expression of the gastrocnemius muscle varied between early sepsis mice and normal control mice.Conclusions: Early sepsis mice exhibit significant differential gene expression in the gastrocnemius muscle, providing a promising avenue for early detection and treatment of sepsis-induced myopathy.

overall_design: Male C57BL/6J mice with SPF were selected for a single intraperitoneal injection of LPS at a dose of 10 mg/kg, while control mice were replaced with the same amount of saline. The mice were respectively executed at 18 h after LPS injection, and the gastrocnemius muscle was immediately taken. When the gastrocnemius muscle tissues were collected from all groups (sepsis group=8, control group=7), RNA sequencing was performed.

first: Siming

last: Lin

first: Shaodan

last: Feng

first: Guili

last: Lian

first: Liangdi

last: Xie


title: Genome-wide DNA methylation analysis of driver genes in blood of high-altitude pulmonary edema

city: Nanjing

first: Qiong

last: Li

state: Jiangsu

address: Dingjiaqiao Road 87#

institute: Southeast University

type: Methylation profiling by genome tiling array

summary: High Altitude Pulmonary Edema (HAPE) is a disease that interacts with environmental and epigenetic factors with a severe clinical course and high mortality rate. This study aims to investigate DNA methylation alterations of HAPE and identify the driver genes. The Illumina Infinium MethylationEPIC BeadChip (850K) was used to obtain DNA methylation profiles across 860,000 CpGs in blood of 6 HApe patients and 6 healthy volunteers.

overall_design: We identified differentially expressed of DNA methylation regions and CpG sites in a discovery set (6 HAPE patients and 6 healthy controls) using 850k high-throughput sequencing.All of the participants and health care volunteers were Han Chinese people between the ages of 18 and 65 who had travelled to Tibet.

first: Yan

last: Shen

first: Fujin

last: Fang

first: Chuanli

last: Yang

first: Yu

last: Dong


title: Systematic analyses of transposable element expression dynamics using long read RNA-seq in pluripotent stem cells and germ lineage cells


title: H2A.Z regulates memory CD8+ T cell recall response [RNA-Seq 3]

city: Beijing

first: Mingzhao

last: Zhu

overall_design: For TN, TCM and TEM in vitro activation transcriptome, OT-I naïve CD8+ T cells sorted from the spleen of WT (OT-I H2A.Zf/f) or cKO (OT-I H2A.Zf/f GzmB-cre) mice were transferred into hosts followed by infection with LM-OVA. TCM (CD127hiKLRG1loCD62LhiCD44hi)  and TEM (CD127hiKLRG1loCD62LloCD44hi) cells were purified from spleens on day 30+ post-infection . Naive, WT and cKO memory OT-I cells were stimulated in vitro with 2ug/ml coated anti-CD3 Ab and 1ug/ml soluble anti-CD28 Ab for 6 h, RNA was extracted for transcriptome analysis. For TM (day30+) and TM-response cells (day7 post-reinfection) transcriptome, CD45 congenically distinct OT-I naïve CD8+ T cells were transferred into hosts followed by infection with LM-OVA. TM (Day 30 post-infection, CD127hiKLRG1lo) and TM-response (Day 7 post-reinfection, CD44+) cells were purified from spleens. RNA-seq were performed (2 biological replicates pooling 3 mice).

first: Wei

last: Liang


title: The comparative methylome analysis of tumor microenvironment from African American and Non- White Hispanic American prostate cancer

city: Irvine

first: Farah

last: Rahmatpanah

state: CA

address: Med  scie 1 RM C220

institute: UCI

summary: We investigated differences in DNA methylation in tumor-adjacent stroma (TAS) of African Americans (AA) (n=17) and European Americans (EA) (n=15) to uncover differences that might contribute to a higher rate of aggressive prostate cancer (PCa) in AA men. We performed methyl binding domain sequencing (MBD-seq) on dissected FFPE tumor-adjacent stroma of both cohorts. To further investigate the tumor microenvironment methylome between AA and EA cohorts, we prepared carcinoma associated fibroblasts (CAFs) from fresh prostatectomy tissue of 3 AA and 4 EA patients. Prostate cancer tissues were examined to confirm the location of tumor and a 1-2 mm cube of tumor-adjacent stroma was removed. Frozen stocks of passages 1 to 6 primary cultures were prepared. At passage 6, a portion of the cells were placed in serum-free medium and incubated for 1 day. CAFs  were cultured in the presence of PBS or low-dose (0.5 µM) 5AzaC . CAFs were treated with 5AzaC for 1 day, followed by culture for 10 days in drug-free medium.

overall_design: To investigate DNA methylation differences in TAS, PCa FFPE tissues from AA and EA cohorts were collected using IRB-approved protocols at the Baylor College of Medicine (BCM). Fresh prostatectomy tissue was obtained from Medical University of South Carolina (MUSC) to develop the cultured CAFs. Patient and clinical information was provided to study members as de-identified data elements.

first: Vinay

last: Kumar

first: Tara

last: Jennings

first: James

last: Nguyen

first: Liankun

last: Song

first: Michael

last: McClleland

first: Weiping

last: Chu

last: Lilly

last: Ittmann

first: Patricia

last: Castro

first: Arash

last: Rezazadeh

first: Dan

last: Mercola

first: Omid

last: Yazdanpanah

first: Xiaolin

last: Zi


title: Microbiota of Breast cancer in Algerian females

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

summary: v3-v4 16S rRNA sequencing was used to characterize the differences in microbiota between specimens of breast cancer and healthy surrounding tissue in adult Algerian females

overall_design: Total DNA was extracted from stool and saliva of 9 patients and 10 healthy subjects, amplified to collect amplicons of variable V3–V4 regions (primers 341F and 805R) of the bacterial 16s rRNA gene and sequenced with MiSeq (2x300bp) Illumina platform.

first: Amedeo

last: Amedei

first: Simone

last: Baldi

first: Leandro

last: Di Gloria


title: AS04 drives superior cross-protective antibody response by increased NOTCH signaling of Dendritic Cells and proliferation of memory B cells

city: Gent

first: Valentino

last: D'Onofrio

address: Corneel Heymanslaan 10

department: Department of Diagnostic Sciences

country: Belgium

institute: Ghent University

summary: The Gardasil-4® vaccine targets HPV types 6, 11, 16 and 18 and is formulated with amorphous alum. Cervarix® targets HPV types 16 and 18 using AS04 (Al(OH)3 + TLR4 agonist MPL) to enhance immune response. Cervarix elicits higher cross-protection against other high-risk HPV types, likely mediated by AS04. To investigate mechanisms of cross-neutralizing potential, six monozygotic twins (12 females aged 9-13 years) were vaccinated with either Cervarix or Gardasil-4 (2 doses, 6 months apart). Serum neutralizing antibody titers against HPV 6,16,18,31,33,45,52, and 58 were assessed pre-vaccination and 7 days post-second dose. Multi-omic single cell RNA and ATAC sequencing of PBMCs was performed at the latter timepoint. Cervarix generated higher cross-neutralizing antibody titers than Gardasil-4. Higher frequencies of dendritic cells and memory B cells were observed. Gene Set Enrichment Analysis (GSEA) indicated enhanced pathways related to NOTCH2 signaling in DCs and cell cycling/RNA translation in B cells, correlating positively with cross-neutralizing antibody titers. Increased chromatin accessability in genes related to NOTCH signaling in cDC1 was also observed. Cervarix-vaccinated subjects showed increased DC-to-memory B signaling, through upregulation of NOTCH ligands. Engagement of NOTCH was associated to BCL2 expression in memory B cells, supporting an anti-apoptotic state, and resulted in increased IgG4 expression by B memory cells. Increased DC signaling, including NOTCH, through AS04 in Cervarix supports cell survival and sustained RNA translation in memory B cells, 7 days post-vaccination. This may enhance adaptive immune cell maturation, providing a mechanism that can lead to improved cross-reactivity.

overall_design: six monozygotic twins (12 females aged 9-13 years) were vaccinated with either Cervarix or Gardasil-4 (2 doses, 6 months apart). Multi-omic single cell RNA and ATAC sequencing of PBMCs collected 7 days after the second dose was performed.

first: Ana Carolina

last: Santana

first: Marthe

last: Pauwels

first: Gwenn

last: Waerlop

first: Anthony

last: Willems

first: Fien

last: De Boever

first: Martin

last: Müller

first: Peter

last: Sehr

first: Tim

last: Waterboer

first: Isabel

last: Leroux-Roels

first: Ashish

last: Sharma

first: Rafick

last: Sékaly

first: Geert


title: L1, a 3,3′-diindolylmethane-derivative,induced ER stress-mediated apoptosis and suppressed growth through the FLI1/AKT pathway in erythroleukemia HEL cells

status: Public on Jul 28 2025

city: Guiyang

first: Xiao

last: Xiao

address: Gaohai street

institute: Guizhou Medical University

summary: Introduction: 3,3’-Diindolylmethane (DIM) is a major phytochemical product derived from ingestion of cruciferous vegetables. As an effective cancer chemopreventive agent, DIM has been used in preclinical and clinical trials. Recently, our group synthesized and modified a novel DIM derivative, L1, and demonstrated its significant antileukemic activities. Methods: MTT assay was used to confirm the inhibition rates and IC50 value of L1 in erythroleukemia HEL cells. Flow cytometry analysis was used to reveal cell cycle arrest and apoptosis. RNAseq data with KEGG pathway enrichment analysis was performed to predict the anticancer mechanism of L1. RT-qPCR and Western blotting were carried out to verify the mechanism in the ER stress-mediated apoptosis and FLI1/AKT pathway. FLI1 knockdown in HEL cells was performed to confirm the mechanism of L1 in the FLI1/AKT pathway. AutoDocking analysis and PPI analysis via the STRING database were used to discover the potential target of L1. HSPA1A knockdown and treatment with HSP70 inhibitor were used to further evaluate the L1 target. Results: L1 significantly inhibited the growth of erythroleukemia HEL cells, with an IC50 value of 1.15±0.03 µM.  L1 induced G2/M cell cycle arrest and cell apoptosis.  RNA sequencing analysis revealed that differentially expressed genes (DEGs) mainly enriched in protein processing of endoplasmic reticulum (ER). L1 increased the protein expression level of GRP78 (BIP) and the RNA transcription of XBP1 and DDIT3 to induce ER stress-mediated apoptosis. Meanwhile, PPI analysis suggested that HSP70 (HSPA1A and HSPA1B) is a pivotal gene that may be involved in the ER stress. AutoDocking analysis also revealed that L1 may bind to the HSP70 protein (HSPA1A and HSPA1B) . The apoptosis rate was  reduced by cotreatment of L1 and the Hsp70 inhibitor VER155008.Moreover,the inhibition rate  was decreased in the HSPA1A knockdown HEL cells, suggesting that L1-induced apoptosis was related to HSP70 activity. Moreover, FLI1 is a crucial target for mediating cell differentiation, apoptosis, inflammation and displays abnormal expression in HEL cells. Here, we showed that the protein expression levels of FLI1 and AKT/p-AKT decreased with L1 treatment and that the RNA expressions of their downstream genes GATA1, TFRC, GYPA, CDKN1A and CDKN1B were also regulated by L1. Conclusion: This study revealed that the DIM-derivative molecule, L1, induced ER stress-mediated apoptosis and suppressed cell growth by inhibiting the FLI1/AKT pathway in erythroleukemia HEL cells.

overall_design: RNAseq was performed using HEL cells treated with L1(1 µM) or 0.5% DMSO for 24 h.RNA  was harvested using MagZolTM Reagent（Axygen, USA） , adding chloroform, and centrifuging to collect the RNA. Total RNA was usde for the construction of sequencing libraries.

first: Yi

last: Kuang


title: SnoRNA:U3:9B is required for the activation of immune response genes in Drosophila melanogaster [ATAC-Seq]

city: Stockholm

first: Neus

last: Visa

address: Svante Arrhenius väg 20c

country: Sweden

institute: Stockholm University

summary: Small nucleolar RNAs (snoRNAs) are prevailing components of the chromatin-associated transcriptome. We have studied a specific chromatin-associated snoRNA, snoRNA:U3:9B, that binds to a large number of protein coding genes in the genome of Drosophila melanogaster, including immune response genes. We have used CRISPR/Cas9 to delete snoRNA:U3:9B. SnoRNA:U3:9B-deficient larvae were viable in control conditions but failed to develop into pupae when challenged by expression of a Sindbis virus replicon, which suggests that snoRNA:U3:9B is required for the activation of an effective antiviral response. Consistent with this hypothesis, the chromatin decompaction and gene activation typically observed at immune response genes in response to Sindbis replicon expression were abolished in snoRNA:U3:9B-deficient larvae. Moreover, snoRNA:U3:9B was required for the recruitment of the ATP-dependent helicase brm to a set of target immune genes. The association of snoRNA:U3:9B with immune response genes in vivo shown by ChIRP-qPCR suggests that the chromatin and gene expression defects observed in the snoRNA:U3:9B knock-out strains are due to direct regulatory events. In summary, our findings reveal an immune defence mechanism that relies on a snoRNA for the recruitment of chromatin remodelling factors to immune genes, thereby modulating local chromatin accessibility to facilitate immune gene activation.

overall_design: accessible chromatin (ATAC-seq) from Drosophila melanogaster were extracted. Tagmentation reaction in S2 cells was performed according to ATAC-seq method79 using Nextera DNA library kit (FC-121-1030). Tagementation reaction from 5 brains of third instar larvae was performed according to Dhall et al

first: Jain

last: Shruti

first: Planells

last: Jordi

first: Regads

last: Isabel

first: Sinha

last: Indranil

first: Mannervik

last: Mattias

first: Visa

last: Neus


title: SnoRNA:U3:9B is required for the activation of immune response genes in Drosophila melanogaster

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

overall_design: Refer to individual Series


title: H2A.Z regulates memory CD8+ T cell recall response [CUT&Tag]

first: Mingzhao

last: Zhu

overall_design: OT-I CD8 TN cells (Naive) were stimulated by 1 µg/ml coated anti-CD3/CD28 Abs for 24 h (Activated T cells, TA), and then stimulated with 50 ng/ml IL-7 or IL-15 for another 24 h, respectively. Collected all subsets and then detected the deposition of H2A.Z via CUT&Tag-seq.

first: Wei

last: Liang

first: Jiyu

last: Ding


title: SnoRNA:U3:9B is required for the activation of immune response genes in Drosophila melanogaster [RNA-Seq]

overall_design: Total RNA was extracted using Trizol (Ambion). Total RNA samples consist in pooled biological triplicates. For chromatin-associated RNA extraction, S2 cells were crosslinked with formaldehyde for 10 min at RT and the cross-linking was stopped by addition of 1 M glycine for 10 additional min. RNAs from chromatin fraction were size fractionated into 0-500bp and > 500bp with AMPure beads (1.6X and 0.6X concentration respectively). 0-500bp were directly used for library preparation and > 500 bp RNAs were sonicated prior library preparation. Chromatin samples consist of 3 biological triplicates.


title: H2A.Z regulates memory CD8+ T cell recall response [RNA-Seq 2]

overall_design: OT-I naïve CD8+ T cells sorted from the spleen of WT (OT-I H2A.Zf/f) or cKO (OT-I H2A.Zf/f GzmB-cre) mice were transferred into hosts followed by infection with LM-OVA. TM (CD127hiKLRG1lo) cells were purified from spleens on day 30 post-infection . WT and cKO TM cells were stimulated in vitro with 200 nM OVA254-264 for 24 h, RNA was extracted for transcriptome analysis.


title: H2A.Z regulates memory CD8+ T cell recall response [RNA-Seq 1]

overall_design: CD45 congenically distinct OT-I naïve CD8+ T cells were transferred into hosts followed by infection with LM-OVA. Naïve (CD62LhiCD44lo) OT-I CD8+ splenocytes and day 30 post-infection TM (CD127hiKLRG1lo) cells were purified from spleens. RNA-seq were performed before or after stimulation (2 biological replicates pooling 3 mice).


title: Infection of LUVA mast cells with Salmonella Typhimurium wt and S.Tm ∆invG

city: Uppsala

first: Christopher

last: von Beek

address: Husargatan 3

department: IMBIM

institute: Uppsala University

summary: Human LUVA mast cells were infected for 4 h with Salmonella Typhimurium SL1344 wildtype (wt) and S.Tm ∆invG to explore LUVA mRNA expression levels upon infection and the role of type-3-secretion-system mediated invasion.

overall_design: mRNA from 0.5x10^6 LUVA cells per group, infected with S.Tm wt or ∆invG, as well as uninfected control cells, was analyzed by RNA seq. Every experimental group has 3 replicates. Each replicate derives from a separate bacterial subculture.

first: Gunnar

last: Pejler

first: Mikael

last: Sellin


title: BMI1 regulates human erythroid self-renewal through both repressive and activating chromatin associations [Cut&Run]

city: Rochester

first: Laurie

last: Steiner

state: NY

address: 601 Elmwood Ave

department: Pediatrics

institute: University of Rochester

summary: To gain insights into the mechanisms underlying BMI1 activity we assessed binding of BMI1, the PRC1 member RING1B, and the PRC-associated histone marks H3K27me3 and H2AK119ub in SREs and in iSREs.

overall_design: Cut&Run was used to profile PRC1 complex members Bmi1, Ring1b, H2AK119Ub, and H3K27me3 in SRE cells (untransduced) and iSRE cells (overexpressing Bmi1)

first: Jayme

last: Olsen

first: Kathleen

last: McGrath

first: Michael

last: Getman

first: Kristin

last: Murphy

first: Hyun

middle: H

last: An

first: Vincent

last: Schulz

first: Ah

middle: R

last: Kim

first: Bin

last: Zhang

first: Taylor

last: Schofield

first: Julien

last: Papoin

first: Lionel

last: Blanc

first: Paul

last: Kingsley

first: Connie

last: Westhoff

first: Patrick

last: Gallagher

first: Stella

last: Chou

first: James

last: Palis


title: Single-nucleus transcriptomics reveals distinct myelin-enriched microglia and increased MSR1-mediated phagocytosis as common features across dementia subtypes

city: Singapore

first: Li

last: Zeng

address: 11 Jln Tan Tock Seng

country: Singapore

institute: National Neuroscience Institute

summary: Alzheimer’s disease (AD), dementia with Lewy bodies (DLB), and Parkinson’s disease dementia (PDD) collectively represent the majority of dementia cases worldwide. While these subtypes share clinical, genetic, and pathological features, their transcriptomic similarities and differences remain poorly understood. We applied single-nucleus RNA-sequencing (snRNA-seq) to prefrontal cortex samples from individuals with non-cognitive impairment control (NCI), and dementia subtypes (AD, DLB, and PDD) to investigate cell type-specific gene expression patterns and pathways underlying pathological similarities and differences across dementia subtypes. SnRNA-seq findings were validated through RNAscope, immunohistochemistry, and additional biochemical analyses in human tissues and cellular models. snRNA-seq analysis revealed elevated microglial proportions across all dementia subtypes compared to NCI. Further analysis of cell type-specific transcriptomes identified overlapping differentially expressed genes (DEGs) between microglia and oligodendrocytes across all dementia subtypes. While AD showed molecular similarities to NCI, PDD and DLB were clustered more closely together, sharing a greater number of DEGs and related pathways, predominantly associated with microglia. Investigation of interactions between microglia and oligodendrocytes revealed a distinct myelin-enriched microglia (MEM) subcluster in all dementia subtypes. MSR1, a gene encoding a scavenger receptor, was upregulated in microglia across all dementia subtypes, along with its associated gene HSPA1A in oligodendrocytes. RNAscope supported the potential interaction between microglia and oligodendrocytes, where these cells were in closer proximity to each other in human cortical tissues of PDD compared to NCI. MSR1 expression was significantly increased in cortical primary microglia from PD mice compared with non-transgenic (NTg) mice. Additionally, the expression of myelin-associated genes (MBP, MOBP and PLP1) was significantly upregulated in PD microglia compared to NTg, supporting the presence of MEM. Furthermore, MSR1-positive microglia colocalised with MBP in cortical tissue of PDD patients, suggesting a functional role of MSR1 in myelin debris clearance. Overexpression of MSR1 in microglial cells enhanced their phagocytic activity toward myelin, and reciprocally, myelin treatment upregulated MSR1 protein levels, indicating enhanced MSR1-mediated myelin phagocytosis.

overall_design:
Postmortem prefrontal cortical tissues from 6 individuals with DLB (three males and three females), 6 individuals with PDD (three males and three females), 4 individuals with AD (one male and three females) and 4 age-matched healthy non-cognitive impairment controls (NCI, two males and two females), whose ages ranged from 73 to 92, were analysed by snRNA-seq.
Submitters state that individual-level de-identified age and gender data (for each sample) is unavailable.

first: Sook-Yoong

last: Chia

first: Mengwei

last: Li

first: Zhihong

first: Haitao

last: Tu

first: Jolene Wei Ling

last: Lee

first: Lifeng

last: Qiu

first: Jingjing

last: Ling

first: Richard

last: Reynolds

first: Salvatore

last: Albani

first: Eng-King

last: Tan

first: Adeline Su-Lyn

last: Ng

first: Jinmiao

last: Chen


title: LONG-TERM EFFECTS OF BCG VACCINATION ON TELOMERE LENGTH AND TELOMERASE ACTIVITY

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

institute: Radboud University

summary: Vaccination with Bacillus Calmette-Guérin (BCG) induces long-term innate immune memory, also called trained immunity, characterized by metabolic and epigenetic changes leading to enhanced responsiveness upon exposure to heterologous pathogens. BCG vaccination was also shown to reduce systemic inflammation. Thus, BCG counteracts two significant immunological changes associated with aging: impaired responsiveness and elevated systemic inflammation. However, if and how BCG impacts other aging-related processes in immune cells, such as telomere shortening, remains unexplored. In this study, we investigated the transcriptional impact of BCG training on telomere maintenance-related genes through RNA sequencing and determined average telomere length from whole blood via RT-qPCR before and three months after BCG vaccination in two independent human cohorts. Trained immunity response was measured by ex-vivo cytokine production induced by a heterologous stimulus three months after vaccination compared to baseline. In addition, we examined the effects of BCG on telomerase activation using an in vitro trained immunity model. In vitro BCG training upregulated processes related to telomere maintenance and telomerase localization. In vivo, we observed shorter telomeres three months after BCG vaccination in both studies. Interestingly, the induction of a trained immunity response by BCG was correlated to the change in telomere length: more telomere shortening was observed in trained immunity non-responder individuals, particularly in males. Higher testosterone concentrations before vaccination were linked to more telomere loss. In vitro, BCG training of human monocytes activated the telomerase enzyme, predominantly in females, an effect that was blocked by exogenous testosterone treatment. Overall, this study reports sex-specific long-term impacts of BCG vaccination on telomerase activity and telomere maintenance. These data add to the arguments that BCG vaccination impacts aging mechanisms, which warrants more investigation.

overall_design: Pathway analysis of genes detected as differential in RNA sequencing data from in vitro BCG-trained and control adherent PBMCs of healthy donors.

first: Ozlem

last: Bulut

first: V

last: Koeken

first: S

last: Moorlag

first: L

last: de Bree

last: Mourits

first: G

last: Kilic

first: P

last: Debisarun

first: Marijke

last: Baltissen

first: J

last: Dominguez-Andres

last: Joosten

first: Mihai

last: Netea


title: An automated ATAC-seq method reveals sequence determinants of transcription factor dose sensitivity [RNA-seq]

status: Public on Jul 27 2025

city: Stanford

first: Betty

last: Liu

address: 279 Campus Dr W

department: Genetics

institute: Stanford University

summary: Transcription factor (TF) dosage is a critical determinant of cellular identity. However, the quantitative relationship between TF dosage and its regulation of chromatin accessibility and gene expression remains poorly understood. To address this, we developed RoboATAC, a scalable, automated ATAC-seq platform for high-throughput accessibility profiling. We then systematically profiled genome-wide chromatin accessibility and gene expression changes induced by graded overexpression of 22 TFs in HEK293T cells (246 total samples), observing dose-dependent changes in accessibility and aggregate TF footprints. Modeling accessibility as a function of sequence and chromatin states revealed that DNA sequence alone accurately predicts dosage sensitivity at elements that become accessible, with low-affinity motifs requiring higher TF levels to induce accessibility. Interpretable deep learning models revealed contributions of motif orientation, spacing, and flanking bases to accessibility, both recapitulating known motifs and nominating novel dosage-sensitive motif arrangements. Nucleosome positioning analysis uncovered two distinct, TF identity dependent patterns by which accessibility is established by changing nucleosome position and occupancy.

overall_design: TF dose RNA-seq datasets overexpress 22 TFs in HEK293T cells at 5 different doses (0.05, 0.25, 0.5, 0.75, 1 ug per well) in duplicates, including GFP controls as dose 0

first: Masaru

last: Shimasawa

first: Sidney

last: Vermeulen

first: Samuel

last: Kim

first: Nika

last: Iremadze

first: Doron

last: Lipson

first: Zohar

last: Shipony

first: William

middle: J

last: Greenleaf


title: Trans-omics analyses identify the biochemical network of LPCAT1 associated with coronary artery disease

city: Miaoli County

first: Paul

middle: Wei-Che

last: Hsu

state: Taiwan

address: Zhunan: 35, Keyan Road, Zhunan Town

department: National Health Research Institutes

country: Taiwan

institute: National Health Research Institutes

summary: This study used a trans-omics approach—combining genome-wide SNP analysis and metabolomics—to distinguish coronary artery disease (CAD) patients from high-risk and healthy individuals. It identified declining plasma phospholipids as potential biomarkers, linked key SNPs and genes (notably LPCAT1) to lipid changes, and developed a machine-learning model that accurately predicts CAD (AUC = 0.917). The results highlight the role of phospholipid metabolism and genetic variation in CAD progression.

overall_design: The genomic DNA was collected from peripheral white blood cells using the phenol/chloroform DNA extraction method after lysis of red blood cells. Each subject was genotyped using Axiom Genome-Wide TWB 2.0 array plates. SNPs were excluding with a minor allele frequency rate of 0 or SNPs with a missing rate of more than 10%.

first: Paul Wei-Che

first: Chi-Hsiao

last: Yeh

first: Ting-Fen

last: Tsai


title: An automated ATAC-seq method reveals sequence determinants of transcription factor dose sensitivity [ATAC-seq]

overall_design: Benchmarking ATAC-seq datasets comparing RoboATAC vs OmniATAC in 5 different cell lines, also comparing Illumina to Ultima sequencing of selected RoboATAC libraries.  TF dose ATAC-seq datasets overexpress 22 TFs in HEK293T cells at 5 different doses (0.05, 0.25, 0.5, 0.75, 1 ug per well) in duplicates, including GFP controls as dose 0


title: Targeted deletions of large syntenic regions in Arabidopsis thaliana

city: La Jolla

first: Allen

last: Mamerto

address: 10010 N Torrey Pines Rd

department: Plant Molecular and Cellular Biology Laboratory

institute: Salk Institute for Biological Studies

summary: Plant genomes have undergone multiple rounds of whole genome duplication and polyploidy over time. As a result, many plant species, including Arabidopsis thaliana, have numerous retained duplicate blocks or syntenic regions within their genomes, resulting in the retention of paralogous genes. We deleted four large duplicated blocks, ranging from ~115 kb to ~684 kb using Staphylococcus aureus Cas9 (SaCas9) to explore the effects of knocking out these retained blocks in Arabidopsis. Deletions were subsequently verified using whole genome sequencing, which revealed that there were limited off-target effects. The number of deleted genes ranged from 16 to 60, and deleted transposable element (TE) genes ranged from 4 to 112 among the four deleted retained blocks. Two deletion lines showed distinct phenotypes resulting from the loss of many genes, while two other deletions displayed no obvious defects for flowering time or hypocotyl elongation. Moreover, RNA sequencing (RNA-seq) analysis of the deleted lines revealed that expression compensation was not a general response to the deleted regions. Thus, it is possible to obtain viable plants when deleting large genomic regions that may be redundant or regions that contain non-essential genes. These results demonstrate that large chromosomal deletions can be used as a tool for various genome engineering approaches, such as genome minimization in plants and allele replacement using homology-directed repair mechanisms and other precision editing methods. Targeted deletions of large chromosome fragments will be a valuable tool for research and biotechnology applications.

overall_design: RNA-seq of pAP141 and pAP142 deletion lines including evening and morning timepoints; RNA-seq of pAP146 wild type, sibling controls, heterozygous, and homozygous lines.

first: Ashot

last: Papikian

first: Rachel

last: Rattner

first: Jenni

last: Kao

first: Neil

last: Hauser

first: Nicholas

last: Allsing

first: Nolan

last: Hartwick

first: Kelly

last: Colt

first: Todd

last: Michael


title: Heterochronic transcription factor expression drives cone-dominant retina development in 13-lined ground squirrels.

city: Baltimore

first: Pin

last: Lyu

address: 400 N Broadway

institute: JHU

sample_organism:
Mus musculus
Ictidomys tridecemlineatus

platform_organism:
Mus musculus
Ictidomys tridecemlineatus


title: Single-Cell transcriptomics reveals biomarker heterogeneity linked to CDK4/6 Inhibitor resistance in breast cancer cell lines

first: Matteo

last: Benelli

state: FI

department: Department of Experimental and Clinical Biomedical Sciences "Mario Serio"

summary: Cyclin dependent kinases 4 and 6 inhibitors have brought great improvements in the treatment of luminal breast cancer, but resistance is a major clinical hurdle. Multiple biomarkers of resistance have been proposed, but none is currently utilized in clinical practice. By performing single-cell RNA sequencing of seven palbociclib-naïve luminal breast cancer cell lines and palbociclib-resistant derivatives, we show that established biomarkers and pathways related to CDK4/6i resistance present marked intra- and inter- cell-line heterogeneity. Transcriptional features of resistance could be already observed in naïve cells correlating with levels of sensitivity (IC50) to palbociclib. Resistant derivatives showed transcriptional clusters that significantly varied for proliferative, estrogen response signatures or MYC targets. This marked heterogeneity was validated in the FELINE trial where, compared to the sensitive ones, ribociclib-resistant tumors developed higher clonal diversity at genetic level and showed greater trascriptional variability for genes associated with resistance . A potential signature of resistance inferred from the cell-line models, positively enriched for MYC targets and negatively enriched for estrogen response markers, was probed on the FELINE trial, separating sensitive from resistant tumors and revealing higher heterogeneity in resistant versus sensitive cells. These data suggest that heterogeneity for CDK4/6 inhibitors resistant markers might facilitate the development of resistance and challenge the validation of clinical biomarkers.

overall_design: Seven luminal BC cell lines and their respective established derivatives resistant to palbociclib were analysed using scRNA-seq: specifically three ER+/HER2- models, MCF7, T47D and ZR751, two endocrine resistant derivatives of MCF7 resistant to estrogen deprivation, the MCF7/EDR (EDR), or to tamoxifen, the MCF7/TamR (TamR), and two ER+/HER2+ models, BT474 and MDAMB361.

first: Ilenia

last: Migliaccio

first: Martina

last: Bonechi

first: Dario

last: Romagnoli

first: Giulia

last: Boccalini

first: Francesca

last: Galardi

first: Cristina

last: Guarducci

first: Agostina

last: Nardone

last: Schiff

first: Laura

last: Biganzoli

first: Luca

last: Malorni


title: High-fidelity and differential nonsense suppression in live cells and a frontotemporal dementia allele with human transfer RNAs

city: London

first: Patrick

last: O'Donoghue

state: Ontario

address: Middlesex Dr.

department: Biochemistry

country: Canada

institute: University of Western Ontario

summary: Nonsense mutations generate premature termination codons (PTCs) that are responsible for 11% of genetic disease alleles. The arginine (Arg, CGA) to stop (UGA) mutation is the most common PTC. Humans encode >600 tRNA genes with many identical and similar copies. We developed a dual fluorescent reporter to quantify PTC readthrough in live cells and found single nucleotide mutations of human tRNAArg gene variants enabled differential nonsense suppression that depended on the tRNA sequence and the cell type. We investigated G36A variants of all six human tRNAArgUCG isodecoders, and only the TCG-6-1 tRNA, where G36A occurs in 0.01% of human genomes, was unable to translate nonsense codons. With tRNA sequencing, we showed that a suppressor tRNA derived from the TCG-3-1 gene was expressed 2.1-fold higher and generated 1.8-fold more nonsense suppression than a tRNA derived from the TCG-4-1 gene. In a neuroblastoma model of frontotemporal dementia (FTD), we observed >70% readthrough of progranulin R493X with a suppressor tRNA that represented 5% of the total tRNAArg pool. The tRNAs outperformed aminoglycoside induced nonsense suppression in efficacy, tolerability to the cells, and translation fidelity according to mass spectrometry. Our studies show that human nonsense suppressor tRNAs can correct genetic defects that cause disease.

overall_design: Bulk RNA-Seq profile of SH-SY5Y cells transfected with an empty WT Pan vector or WT Pan expressing either suppressor tRNA-Arg-TCA-3-1 or tRNA-Arg-TCA-4-1

first: Aruun

last: Beharry

first: Cian

last: Ward

first: Henry

last: Moore

first: Kyle

middle: S

last: Hoffman

first: Patricia

last: Chan

last: Lowe


title: BMI1 regulates human erythroid self-renewal through both repressive and activating chromatin associations

first: Laurie

last: Steiner


title: Proteomics analysis of the bromodomain protein IBD2 reveals mechanistic insights into H2A.Z (Hv1) dynamics in Tetrahymena

city: Toronto

first: Alejandro

last: Saettone

address: 686 Bay Street

department: Genetics & Genome Biology

institute: The Hospital for Sick Children

summary: INO80 and SWR1 are evolutionarily related ATP-dependent chromatin remodeling complexes that regulate the chromatin occupancy of the histone variant H2A.Z, playing critical roles in transcriptional regulation, genome replication, and DNA repair. While INO80 and SWR1’s H2A.Z-related functions are well characterized in budding yeast and metazoans, much less is known about their composition and conserved roles outside the Opisthokonts. Here, we report that in the ciliate protozoan Tetrahymena thermophila, a distinct bromodomain-containing protein, IBD2, functions as a component of a putative INO80 complex. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) demonstrates that IBD2 is enriched near transcription start sites and promoter regions. Notably, the IBD2 genomic binding profile strongly correlates with that of H2A.Z (Hv1), supporting its association with the INO80 complex.

overall_design: Examination of ChIP DNA for Ibd2-FZZ cells (biological duplicates) during vegetative growth. Examination of RNA of Wild type cells (biological duplicates) and Ibd1 KO cells (biological triplicates) during vegetative growth

first: Alexandra

last: Petrova

first: Abdul

last: Hadi Khalid

first: Sherin

last: Shibin

first: Jack

last: Greenblatt

first: Jeffrey

last: Fillingham


title: Nrf2 ablation abolishes liver tumorigenesis by suppressing L-2-hydroxyglutarate-driven regulation of ferroptosis in a spontaneous liver tumor model induced by hepatic Tsc1 deletion

status: Public on Jul 26 2025

city: Augusta

first: Xingguo

last: Zhu

state: Georgia

department: Cancer Center

institute: Augusta University

summary: The metabolite L-2-hydroxyglutarate (L2HG) regulates liver tumor development through both anti- and pro-ferroptotic mechanisms, mediated via the Nrf2/Slc7a11 and Atf4/Chac1 signaling axes. To investigate the essential role of Nrf2 in L2HG-driven ferroptosis regulation, we analyzed gene expression profiles in liver tumors from Tsc1f/f wild-type, Tsc1f/fAlbCre+, and Tsc1f/fAlbCre+/Nrf2-/- mice. We found that the ferroptosis-related transcriptome in Tsc1f/fAlbCre+/Nrf2-/- mice more closely resembled that of tumor-free Tsc1f/f wild-type mice than the tumor-bearing Tsc1f/fAlbCre+ cohort. These findings demonstrate that Nrf2 ablation disrupts L2HG-induced cystine uptake via the xCT antiporter system, rewires metabolic pathways, and restores ferroptotic sensitivity. This metabolic reprogramming effectively suppresses liver tumor development in vivo, underscoring the critical oncogenic interplay between L2HG metabolism and Nrf2-mediated ferroptosis resistance.

overall_design: RNA-seq were conducted for the liver tissues or tumros of 10-month-old Tsc1f/f wild-type, Tsc1f/fAlbCre+, and Tsc1f/fAlbCre+/Nrf2-/- mice.

first: Caixia

last: Xi

first: Junfeng

last: Pang


title: Gene expression change after inactivation of ARHGAP45 by CRISPR-Cas9 and/or treatment of MBQ-167

city: PHILADELPHIA

first: Zhendong

last: Cao

state: PA

address: BRB Rm620, 421 Curie Blvd

department: Cancer biology

institute: university of pennsylvania

summary: GTPase-activating proteins (GAPs) and guanine nucleotide exchange factors (GEFs) function as negative and positive regulators of small GTPases, orchestrating GDP/GTP-bound binary activity switches. Yet their functional significance in hematopoietic malignancies remains largely uncharted.  In our study, guided by single-cell transcriptomic analysis  and functional CRISPR screens in primary AML specimens and their derived models, we uncover an unexpected and selective oncogenic role for ARHGAP45 in AML. ARHGAP45 is upregulated in malignant cells while notably absent in healthy counterparts. Depletion of ARHGAP45 impedes AML growth and triggers myeloid differentiation but is dispensable for normal CD34+ hematopoietic stem/progenitor cells (HSPC) development. Using CRISPR-mediated epistasis screens, we further show that the ARHGEF1-RhoA-PKN1 axis is responsible for the ARHGAP45 phenotype. In addition, we further found that ARHGAP45 prevents RhoA overactivation, loss of cell polarity, and lineage commitment. On the other hand, our screens also unveil the synergistic effect of combinatorial ARHGAP45 and CDC42 inhibition, which we further validate in vitro and in vivo. Collectively, our studies reveal that ARHGAP45 is indispensable for leukemia stemness and aggressiveness and rationalize therapeutic strategies for modulating GAP and GTPase activity in AML.

overall_design: mRNA profiles of Cas9 sgRNA-expressing human cell lines and PDX cells

first: Pu

last: Zhang


title: Effect of hemin on gene expression in erythroid progenitors derived from human sickle cell disease peripheral blood mononuclear cells (PBMC)

summary: Sickle cell disease endured chronic hemolysis and systemic hypxic conditions. SCD patients have aberrant metabolic regulation of fumarate, glutamate, glycine, malate, and other metabolites involved in glycolysis, nucleotide catabolism, and glutathione metabolism. To investigate the effect of hemin on the erythroid progenitors (EPs) derived form SCD PBMC, the transcriptome of hemin treated SCD EPs were explored under hypxoic condition (1% O2). Meanwhile, to explore chemical compounds that can alleviate hemin effect,gene expression profiles of dimethyl alpha ketoglutarate (DMKG), dimethyl fumarate (DMF) were studied. We found that DMKG and DMF showed protection effect against hemin through inducing the expression of NRF2-mediated antioxidantive signaling. NRF2 activation induced cellular anti-ferroptosis response to increase the SCD EPs viability and proliferation. Our findings suggest DMF and DMKG could be explored as novel SCD treatment options.

overall_design: SCD patient EPs were cultured under two-phase culture system, and on day 8 of culture, EPs were treated with PBS, hemin (75uM), DMF (75uM), DMKG (1mM) or their combination for 48 hours while cultured under hypoxic condition (1% O2).  RNA samples were collected on Day 10 of culture.


title: RNA-Seq analysis of GPR68 on basal and acute ischemia-induced transcriptome changes in mouse brain

city: New Orleans

first: XIANGMING

last: ZHA

state: LA

address: 1324 Tulane Ave

department: Neurosurgery

institute: Tulane University

summary: Brain acid signaling plays important roles in both physiological and disease conditions. One key neuronal metabotropic proton receptor in the brain is GPR68, which contributes to hippocampal long-term potentiation (LTP) and mediates neuroprotection in acidotic and ischemic conditions. Here, to gain greater understanding of GPR68 function in the brain, we performed mRNA-Seq analysis in mice. First, we studied sham-operated animals to determine baseline expression. Compared to wild type (WT), GPR68−/− (KO) brain downregulated genes that are enriched in Gene Ontology (GO) terms of misfolding protein binding, response to organic cyclic compounds, and endoplasmic reticulum chaperone complex. Next, we examined the expression profile following transient middle cerebral artery occlusion (tMCAO). tMCAO-upregulated genes cluster to cytokine/chemokine-related functions and immune responses, while tMCAO-downregulated genes cluster to channel activities and synaptic signaling. For proton-sensitive receptors, tMCAO downregulated ASIC1a and upregulated GPR4 and GPR65, but had no effect on ASIC2, PAC, or GPR68. GPR68 deletion did not alter the expression of these proton receptors, either at baseline or after ischemia. Lastly, we performed GeneVenn analysis of differential genes at baseline and post-tMCAO. Ischemia upregulated the expression of three hemoglobin genes, along with H2-Aa, Ppbp, Siglece, and Tagln, in WT but not in KO. Immunostaining showed that tMCAO-induced hemoglobin localized to neurons. Western blot analysis further showed that hemoglobin induction is GPR68-dependent. Together, these data suggest that GPR68 deletion at baseline disrupts chaperone functions and cellular signaling responses and imply a contribution of hemoglobin-mediated antioxidant mechanism to GPR68-dependent neuroprotection in ischemia.

overall_design: Wild type and GPR68-/- mice are subjected to transient MCAO. The brain were isolated from sham operated or MCAO mice. mRNA-Seq was performed to determine the changes in gene expression.

first: Guokun

last: Zhou

first: Tao

last: Wang

first: Xiang-Ming

last: Zha