title: The mitotic STAG3–cohesin complex shapes male germline nucleome

first: Yukihiro

last: Yabuta


title: The mitotic STAG3–cohesin complex shapes male germline nucleome [Hi-C]

status: Public on Jul 07 2025

city: Kyoto

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

summary: Germ cells are unique in that they tailor chromatin toward generating totipotency. Accordingly, mammalian spermatogonia, including spermatogonial stem cells (SSCs) which constitute the source for male gametes, acquire distinctive chromatin organization with weak insulation, but the underlying mechanism remains unknown.  Here, we show that STAG3, this far known to exclusively form meiotic cohesins, generates a mitotic cohesin for male germline nucleome programming in mice.  Due to its shorter chromatin residence, STAG3–cohesin attenuates topologically associating domains (TADs), rewires enhancer–promoter and Polycomb-mediated repressive interactions, and facilitates finer and more strengthened compartments, establishing a distinctive spermatogonial nucleome.  Moreover, in the absence of STAG3–cohesin, SSCs show an impaired differentiation priming for spermatogenesis.  Mitotic STAG3–cohesin is also expressed in human B cells and their malignant variations, promoting their propagation.  Our findings on mitotic STAG3–cohesin elucidate a principle of male germline nucleome programming, demonstrate an unexpected mitotic role for STAG3 and might potentially improve understanding of human malignancies.

overall_design: Hi-C for STAG3-cohesin characterization in Stag3 KO, Stag1-only, Stag2-only, and Stag3-only GSCs and Stag3-only ESCs for the comparison with WT GSCs and ESCs (Nagano et al., 2022).

first: Masahiro

last: Nagano

first: Bo

last: Hu

first: Kosuke

last: Ogata

first: Fumiya

last: Umemura

first: Yukiko

last: Ishikura

first: Shinnosuke

last: Suzuki

first: Christos

middle: C

last: Katsifis

first: Masanori

last: Yoshinaga

first: Gabriele

last: Litos

first: Kota

last: Nagasaka

first: Wen

last: Tang

first: Yoshiaki

last: Nosaka

first: Hiromichi

last: Sasada

first: Hanbo

last: Wang

first: Daichi

last: Kondo

first: Yoshitaka

last: Kato

first: Ken

last: Mizuta

first: Hiroshi

last: Ohta

first: Francisca

middle: N

last: de Luna Vitorino

last: Arima

first: Takafumi

last: Ichikawa

first: Michele

last: Gabriele

first: Jacek

last: Majewski

first: Benjamin

middle: A

last: Garcia

first: Osamu

last: Takeuchi

first: Shosei

last: Yoshida

first: Anders

middle: S

last: Hansen

first: Jan-Michael

last: Peters

first: Yasushi

last: Ishihama

first: Mitinori

last: Saitou


title: The mitotic STAG3–cohesin complex shapes male germline nucleome [ATAC-seq]

first: Yukihiro

last: Yabuta

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ATAC-seq for STAG3-cohesin characterization in Stag3 KO GSCs for the comparison with WT (Nagano et al., 2022).

first: Masahiro

last: Nagano

first: Bo

last: Hu

first: Kosuke

last: Ogata

first: Fumiya

last: Umemura

first: Yukiko

last: Ishikura

first: Shinnosuke

last: Suzuki

first: Christos

last: Katsifis

first: Masanori

last: Yoshinaga

first: Gabriele

last: Litos

first: Kota

last: Nagasaka

first: Wen

last: Tang

first: Yoshiaki

last: Nosaka

first: Hiromichi

last: Sasada

last: Wang


title: The mitotic STAG3–cohesin complex shapes male germline nucleome [ChIP-seq]

overall_design: ChIP-seq against RAD21, STAG1, STAG2, STAG3, CTCF, GFP, H3K27ac, H3K27me3, H3K9me3 for STAG3-cohesin characterization in Stag3 KO, Stag1-only, Stag2-only, Stag3-only, and WT GSCs, Stag3-only and WT ESCs, WT EpiLCs, d2 PGCLCs and d4c7 PGCLCs.

first: Hanbo

first: Daichi

last: Kondo

first: Yoshitaka

last: Kato

first: Ken

last: Mizuta

first: Hiroshi

last: Ohta

first: Francisca

last: de Luna Vitorino

last: Arima

first: Takafumi

last: Ichikawa

first: Michele

last: Gabriele

first: Jacek

last: Majewski

first: Benjamin

last: Garcia

first: Osamu

last: Takeuchi

first: Shosei

last: Yoshida

first: Anders

last: Hansen

first: Jan-Michael

last: Peters

last: Ishihama


title: 3' poly(A)-RNA-End sequencing of Aspergillus fumigatus strain CEA10

status: Public on Jul 04 2025

city: Jena

first: Matthew

middle: George

last: Blango

address: Adolf-Reichwein-Str. 23

department: Junior Resaerch Group RNA Biology of Fungal Infections

country: Germany

institute: Leibniz Institute for Natural Product Research and Infection Biology

summary: Experimantal validation for the 3' end of poly(A)-RNA in Aspergillus fumigatus is currently lacking. Therefore we performed 3'RNA-End sequencing from 24-h mycelium grown in AMM at 37°C and 42°C with a library kit purchased from Eclipse Bioinnovations.

overall_design: Total RNA from 24-h mycelium grown in AMM at 37°C and 42°C was subjected to the 3'RNA-End sequecing kit from Eclipse Bioinnovations

middle: G

first: Lukas

last: Schrettenbrunner


title: 5' poly(A)-RNA-End sequencing of Aspergillus fumigatus strain CEA10

summary: Experimantal validation for the 5' end of poly(A)-RNA in Aspergillus fumigatus is currently lacking. Therefore we performed 5'RNA-End sequencing from 24-h mycelium grown in AMM at 37°C and 42°C with a library prepration kit purchased from Eclipse Bioinnovations.

overall_design: Total RNA from 24-h mycelium grown in AMM at 37°C and 42°C was subjected to the 5'RNA-End sequecing kit from Eclipse Bioinnovations


title: Hepatic leukemia factor directs tissue residency of proinflammatory CD4+ T cells [bulk]

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

institute: Chiba univercity

type: Expression profiling by high throughput sequencing

summary: CD4+ tissue-resident memory T cells (TRM) contribute to both host defense and pathogenesis of chronic inflammatory diseases.  However, the molecular mechanisms that direct tissue residency and functional heterogeneity of CD4+ TRM remain unknown.  We herein show that the transcription factor, hepatic leukemia factor (HLF), directs the tissue residency program and functionality of CD4+ TRM. HLF simultaneously upregulates tissue retention receptors and downregulates tissue egress receptors via changes in chromatin accessibility, and drives proinflammatory CD4+ TRM by inducing Bhlhe40.  Genetic deletion of Hlf inhibits CD4+ TRM generation, consequently ameliorating airway tissue inflammation in vivo.  In humans, HLF-positive CD4+ TRM from inflamed airway tissue have a tissue residency signature and express inflammatory cytokines.  HLF is therefore a central regulator of proinflammatory CD4+ TRM development and function.

overall_design: This study employed RNA-seq, ChIP-seq, and ATAC-seq to investigate the transcriptional and epigenetic roles of Hlf in T cell populations. RNA-seq was used to compare gene expression profiles between circulating and tissue-resident memory T cells with or without Hlf expression. Total RNA was extracted using TRIzol, libraries were prepared with the TruSeq RNA Sample Prep Kit v2, and sequencing was performed on an Illumina NextSeq500. Reads were aligned to the mouse genome (GRCm38) using Bowtie 2 and TopHat, and expression levels were quantified with Cufflinks. ChIP-seq was conducted to identify genome-wide Hlf binding sites in Th2 and Th17 cells using anti-Flag antibodies, followed by library preparation with the NEBNext Ultra II DNA Library Prep Kit and sequencing on a NextSeq500. ATAC-seq was performed to assess chromatin accessibility in Hlf-positive and Hlf-negative cells. Cells were lysed and tagmented with Tn5 transposase, and the resulting libraries were sequenced on a NextSeq500. These approaches provided a comprehensive view of Hlf-mediated transcriptional regulation and chromatin dynamics in T cell subsets.

last: Nemoto

first: Hiroyuki

last: Yagyu

first: Ami

last: Aoki

first: Chiaki

last: Iwamura

first: Hikaru

last: Sugimoto

first: Yuki

last: Masuo

first: Hajime

last: Morita

first: Shuhe

last: Ma

first: Yukiko

last: Okuno

first: Takahisa

last: Hishiya

first: Kaori

last: Tsuji

first: Atsushi

last: Sasaki

first: Kota

last: Kokubo

first: Kanae

last: Ohishi

first: Rie

last: Shinmi

first: Yuri

last: Sonobe

first: Tomohisa

last: Iinuma

first: Syuji

last: Yonekura

first: Tomomasa

last: Yokomizo

first: Norio

last: Komatsu

last: Onodera

first: Shinya

last: Okumura

first: Takashi

last: Ito

first: Etsuro

last: Hatano

first: Tatsuaki

last: Tsuruyama

first: Yosuke

last: Kurashima

first: Naoko

last: Mato

first: Takuji

last: Suzuki

first: Motoko

middle: Y

last: Kimura

first: Shinichiro

last: Motohashi

first: Eiryo

last: Kawakami

first: Hideki

last: Ueno

first: Damon

middle: J

last: Tumes

first: Toyoyuki

last: Hanazawa

first: Toshinori

last: Nakayama

first: Kiyoshi

last: Hirahara


title: Poly(A)-RNA-Seq sequencing of Aspergillus fumigatus strain CEA10 at 37°C and 42°C

first: Matthew

last: Blango

summary: Experimantal validation for the 5' and 3' ends of poly(A)-RNA in Aspergillus fumigatus is currently lacking. The dataset here was used a total RNA-Seq control for poly(A)-enriched RNAs of Aspergillus fumigatus in comparison with 5' and 3' End-Seq data.

overall_design: Total RNA from 24-h mycelium grown in AMM at 37°C or 42°C was subjected to RNA-Seq

first: Lukas

last: Schrettenbrunner


title: Hepatic leukemia factor directs tissue residency of proinflammatory CD4+ T cells

first: Masahiro

last: Kiuchi

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Freshly isolated or thawed single-cell suspensions from human nasal polyps and peripheral blood as well as CD4(iv)-negative tissue-resident and CD4(iv)-positive circulating CD4⁺ T cells from murine lungs, were processed for scRNA-seq using Chromium Single Cell 3’ v3.1 (10x Genomics), and for scATAC-seq using Chromium ATAC v1.1 kits, with all libraries sequenced on a NovaSeq 6000 system (Illumina) using paired-end dual indexing and protocol-specific cycle numbers, at a depth of ≥20,000 read pairs per cell for scRNA-seq and ≥25,000 read pairs per nucleus for scATAC-seq.

last: Nemoto

first: Hiroyuki

last: Yagyu

first: Ami

last: Aoki

first: Chiaki

last: Iwamura

first: Hikaru

last: Sugimoto

first: Yuki

last: Masuo

first: Hajime

last: Morita

first: Shuhe

last: Ma

first: Yukiko

last: Okuno

first: Takahisa

last: Hishiya

first: Kaori

last: Tsuji

first: Atsushi

last: Sasaki

first: Kota

last: Kokubo

first: Kanae

last: Ohishi

first: Rie

last: Shinmi

first: Yuri

last: Sonobe

first: Tomohisa

last: Iinuma

first: Syuji

last: Yonekura

first: Tomomasa

last: Yokomizo

first: Norio

last: Komatsu

last: Onodera

first: Shinya

last: Okumura


title: Integrated profiling of iPSC-derived motor neurons carrying C9orf72, FUS, TARDBP, or SOD1 mutations

status: Public on Jun 24 2025

city: Shanghai

first: Guoming

address: 100 Haike Road, Zhangjiang Hi-Tech Park

department: Interdisciplinary Research Center on Biology and Chemistry

country: China

institute: Chinese Academy of Science

summary: We conducted temporal RNA-seq profiling of human induced pluripotent stem cells (hiPSCs) and iPSC-derived motor neurons (iMNs) carrying C9orf72, FUS, TARDBP, or SOD1 mutations in both patients with ALS and healthy individuals. We discovered dysregulated gene expression and alternative splicing (AS) throughout iMN development and maturation, and iMNs with mutations in ALS-associated genes displayed enrichment of cytoskeletal defects and synaptic alterations from the premature stage to mature iMNs. Our findings indicate that synaptic gene dysfunction is a common molecular hallmark of familial ALS, which may result in neuronal susceptibility and progressive motor neuron degeneration. Analysis of upstream splicing factors revealed that differentially expressed RNA-binding proteins (RBPs) in iMNs from patients with ALS may cause abnormal AS events, highlighting the importance of studying RBP defects in ALS research. Overall, our research provides a comprehensive and valuable resource for gaining insights into the shared mechanisms of familial ALS pathogenesis during motor neuron development and maturation in iMN models.

overall_design: We generated iPSCs from nine fibroblasts of patients with ALS carrying SOD1 (SOD1-1, SOD1-2, SOD1-3, and SOD1-4), TARDBP (TARDBP-1 and TARDBP-2), FUS (FUS-1 and FUS-2), or C9orf72 gene mutations, and four fibroblasts from healthy individuals. We performed RNA-seq from iPSCs (Day 0), NPCs (Day 6), young iMNs (Day 28), and mature iMNs (Day 50) derived from nine patients with ALS-causing gene mutations and four healthy donors.

first: Congcong

last: Xia

first: Boyu

last: Lyu

first: Jie

last: Liu

first: Wenyuan

last: Wang


title: LINE-1 retrotransposition in a mouse TDP-43 model of neurodegeneration marks motor cortex neurons for cell-intrinsic and cell non-autonomous programmed cell death.

status: Public on Jun 23 2025

city: New York

first: Oliver

middle: H

last: Tam

state: New York

address: 435 E 30th St

department: Institute for Systems Genetics

country: USA

institute: NYU Grossman School of Medicine

summary: A key pathological feature of Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Dementia (FTD) is the loss of nuclear localization and accumulation of cytoplasmic inclusions of TAR-DNA binding protein 43 (TDP-43). TDP-43 is a nucleic acid-binding protein involved in transcriptional repression, mRNA splicing, and the regulation of retrotransposable elements (RTEs) and endogenous retroviruses (ERVs). RTEs/ERVs are mobile virus-like genetic elements that constitute about 45% of our genome and encode the capacity to replicate through an RNA intermediate and insert cDNA copies at de novo chromosomal locations. A causal role of RTEs/ERVs has been demonstrated in Drosophila in mediating both intracellular toxicity of TDP-43 and the intercellular spread of toxicity from glia to neurons. RTEs/ERVs are inappropriately expressed in postmortem tissues from ALS, FTD, and Alzheimer's Disease (AD) patients, but the role of RTEs/ERVs has not yet been examined in a vertebrate model of TDP-43 pathology. We utilized established transgenic mouse models that overexpress moderate levels of human wild-type TDP-43 or a mutant version with a specific ALS-causal Q331K amino acid substitution, together with a LINE-1-EGFP retrotransposon indicator line. We found that TDP-43 animals exhibit broad expression of RTEs/ERVs with LINE-1 retrotransposition in glia and neurons in the motor cortex. Expression begins with onset of neurological phenotypes, earlier in hTDP-43-Q331K animals and later in hTDP-43-WT. The LINE-1-EGFP retrotransposition reporter transiently labels spatially clustered groups of neurons and glia at the time of onset of motor symptoms, while EGFP-labeled neurons undergo cell death and are therefore lost over time. Unlabeled cells also die as a function of distance from the clusters of LINE-1-EGFP labeled neurons and glial cells. Together, these findings support the hypothesis that TDP-43 pathology triggers RTE/ERV expression in the motor cortex, that such expression marks cells for programmed cell death, with cell non-autonomous effects on nearby neurons and glial cells.

overall_design: RNA sequencing was performed on the motor cortices of mice that are expressing human TDP-43 cDNA, human TDP-43 cDNA with Q331K mutation, or are non-transgenic. Samples were collected at various ages: 1.5 mth, 3 mth, 6 mth, 10 mth and 15 mth, and gene and TE expression were quantified and compared.

first: Shreevidya

last: Korada

first: Hunter

last: Greco

first: Molly

last: Gale Hammell

first: Josh

last: Dubnau

first: Roger

middle: B

last: Sher


title: TrAEL-seq captures DNA replication dynamics in mammalian cells

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

summary: Precise DNA replication is critical to the maintenance of genome stability, and the DNA replication machinery is a focal point of many current and upcoming chemotherapeutics. TrAEL-seq is a robust method for profiling DNA replication genome-wide that works in unsynchronised cells and does not require treatment with drugs or nucleotide analogues. Here, we provide an updated method for TrAEL-seq including multiplexing of up to 6 samples that dramatically improves sample quality and throughput, and we validate TrAEL-seq in multiple mammalian cell lines. The updated protocol is straightforward and robust yet provides excellent resolution comparable to OK-seq in mammalian cell samples, and does not require cell synchronisation, drug treatment, labelling or sorting. High resolution replication profiles can be obtained across large panels of samples and in dynamic systems, for example during the progressive onset of oncogene induced senescence. In addition to mapping zones where replication initiates and terminates, TrAEL-seq is sensitive to replication fork speed, revealing effects of both transcription and proximity to replication initiation zones on fork progression. Although forks move more slowly through transcribed regions, this does not have a significant impact on the broader dynamics of replication fork progression, which is dominated by rapid fork movement in long replication regions (>1Mb).  Short and long replication regions are not intrinsically different, and instead replication forks accelerate across the first ~1 Mb of travel such that forks progress faster in the middle of regions lying between widely spaced initiation zones. We propose that this is a natural consequence of fewer replication forks being active later in S phase when these distal regions are replicated and there being less competition for replication factors.

overall_design: TrAEL-seq applied to deiverse human cell lines, including HRASG12V induction timecourse in IMR90

first: Neesha

last: Kara

first: Alex

last: Whale

first: Aled

last: Parry

first: Paola

last: Garran Garcia

first: Jhanavi

last: Srinivasan

first: Peter

last: Rugg-Gunn

first: Simon

last: Andrews

first: Jonathan

last: Houseley


title: Plasticity of regulatory grammar in human promoters uncovered by MPRA-trained deep learning

status: Public on Jul 01 2025

city: Amsterdam

first: Noud

last: Klaassen

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Insitute

summary: One of the major challenges in genomics is to build computational models that accurately predict genome-wide gene expression from the sequences of regulatory elements. Promoters play a key role in gene regulation, yet their regulatory logic remains incompletely understood. Here, we present PARM, a cell-type specific deep learning model trained on specially designed massively parallel reporter assays that query human promoter sequences. PARM is computationally light-weight and reliably predicts autonomous promoter activity across the genome from DNA sequence alone, in multiple cell types. PARM can also design purely synthetic strong promoters. We leveraged PARM to systematically identify binding sites of transcription factors (TFs) binding sites that are likely to contribute to the activity of each natural human promoter, and to detect the rewiring of these regulatory interactions upon various stimuli to the cells. We also uncovered and experimentally confirmed striking positional preferences of TFs that differ between activating and repressive regulatory functions, as well as a complex grammar of motif-motif interactions. Our approach provides a foundation towards a deeper understanding of the dynamic regulation of human promoters by TFs

overall_design: Various cell lines were transfected with various different massively parrallel reporter assay (MPRA) libraries. Data contain raw read counts as well as normalized data.


title: HELLS is required for DNA methylation at human satellite repeats [RNA-seq]

city: Berlin

first: Helene

last: Kretzmer

address: Ihnestraße 63

department: Genome Regulation

institute: Max Planck Institute for Molecular Genetics

summary: HELLS is a known chromatin remodeler, but its specific genomic targets have not been sufficiently described. Here, we report the generation of HELLS knockout human pluripotent cells and through telomere-to-telomere mapping of whole genome bisulfite sequencing data combined with ATAC-sequencing, we discovered a striking loss of DNA methylation over inaccessible, satellite repeats. Our study further clarifies the role of HELLS and provides insights into functional consequences through its deregulation in diseases.

overall_design: RNA-seq was performed on iPSCs and iPSC-derived Endoderm cells in WT and HELLS KO conditions.

first: Philine

last: Guckelberger

first: Leah

last: Haut

first: Rosaria

last: Tornisiello

first: Alexander

last: Meissner


title: Drosophila single-cell expression data of enteroendocrine cell lineage-traced guts, and guts under control and Xrp1 overexpression conditions in enteroendocrine cells.

status: Public on Jul 05 2025

city: Tsukuba

first: Ryusuke

last: Niwa

state: Ibaraki

address: 1 Chome-1-1 Tennodai

institute: University of Tsukuba

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

overall_design: Refer to individual Series


title: A SOX2-VSX2 axis modulates a core cis-regulatory circuitry to safeguard retinal neural competence [RNA-seq]

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

summary: Retinal neurogenesis is mediated by the coordinated activities of a complex gene regulatory network (GRN) of transcription factors (TFs) in multipotent retinal progenitor cells (RPCs). How this GRN mechanistically guides neural competence remains poorly understood. Here, we describe integrated transcriptional, genetic, and genomic analyses to identify the regulatory mechanisms of SOX2, a critical factor for RPC neural competency. We show that SOX2 is preferentially enriched in the RPC-specific enhancer landscape associated with essential regulators of retinogenesis. Perturbation of SOX2 expression leads to a failure in retinogenesis initiation as a result of selective loss of enhancer activity near key genes underlying proliferation and lineage specification.  We identified the RPC transcription factor VSX2 as a binding partner for SOX2, and together they target a core retina-specific chromatin repertoire characterized by enhanced TF binding and robust chromatin accessibility. We delineate a SOX2-VSX2 common transcriptional code that promotes the expression of critical regulators of neurogenesis and suppresses the acquisition of alternative lineage cell fate. Our data illuminate fundamental biological insights on how transcription factors act in concert to drive chromatin-based genetic programs underlying retinal neural competence.

overall_design: Mouse retina samples with three repeats for wild-type (WT) and four repeats for Sox2 Knock-out (KO).

first: Fuyun

last: Bian

first: Kimia

last: Golestaneh

first: Emily

last: Davis

first: Abdullah

last: Khan

first: Marwa

last: Daghsni

first: Keevon

last: Flohr

first: Silvia

first: Susana

last: da Silva

first: Len

last: Pennacchio

first: Issam

last: Aldiri


title: A SOX2-VSX2 axis modulates a core cis-regulatory circuitry to safeguard retinal neural competence [CUT&RUN]

overall_design: Mouse retina samples with two repeats of paired input and treament samples, with an additional IgG CUT&RUN sample.

first: Brendan

last: Nicholson


title: A SOX2-VSX2 axis modulates a core cis-regulatory circuitry to safeguard retinal neural competence [ATAC-seq]

overall_design: Mouse retina samples with two repeats for wild-type (WT) and two repeats for Sox2 Knock-out (KO).


title: Myeloid progenitor dysregulation fuels immunosuppressive macrophages in tumors [dataset 1]

first: Laszlo

last: Halasz

state: NY

address: 1470 Madison Avenue

department: Department of Oncological Sciences

institute: Mount Sinai Icahn School of Medicine

summary: Monocyte–derived macrophages (mo-macs) drive immunosuppression in the tumor microenvironment (TME) and tumor-enhanced myelopoiesis in the bone marrow (BM) fuels these populations. Here, we performed paired transcriptome and chromatin analysis over the continuum of BM myeloid progenitors, circulating monocytes, and tumor-infiltrating mo-macs in mice and in patients with lung cancer to identify myeloid progenitor programs that fuel pro-tumorigenic mo-macs. Analyzing chromatin accessibility and histone mark changes, we show that lung tumors prime accessibility for Nfe2l2 (NRF2) in BM myeloid progenitors as a cytoprotective response to oxidative stress. NRF2 activity is sustained and increased during monocyte differentiation into mo-macs in the lung TME to regulate oxidative stress, in turn promoting metabolic adaptation, resistance to cell death, and contributing to immunosuppressive phenotype. NRF2 genetic deletion and pharmacological inhibition significantly reduced mo-macs’ survival and immunosuppression in the TME, enabling NK and T cell therapeutic antitumor immunity and synergizing with checkpoint blockade strategies. Altogether, our study identifies a targetable epigenetic node of myeloid progenitor dysregulation that sustains immunoregulatory mo-macs in the TME.

overall_design:
Mouse: Gene expression and chromatin accessibility (scRNA-seq, n = 3; scATAC-seq, n = 4) of myeloid cells from lung, blood and bone marrow of naive and KP tumor-bearing mice.
Human: Gene expression and chromatin accessibility (multiome, n = 14; scATAC-seq, n = 27) of CD45-positive cells from PBMC, Tumor and Adjacent Normal tissues of 14 patients with non-small cell lung cancer (NSCLC).
Mouse: Chromatin accessibility (scATAC-seq, n = 4) from lung and bone marrow of naïve or KP tumor-bearing mice.

first: Samarth

last: Hegde

first: Miriam

last: Merad


title: HELLS is required for DNA methylation at human satellite repeats

first: Helene

last: Kretzmer

type: Methylation profiling by high throughput sequencing


title: Exploring the Transformative Effects of Calorie Restriction on the Lacrimal Gland in Adult Mice

status: Public on Jun 17 2025

city: Houston

first: EMRE

last: AKSAN

state: TX

address: 6501 Fannin St NB302

department: Ophthalmology

institute: Baylor College of Medicine

summary: Advanced age is one of the most recognizable risk factors for dry eye. Dry eye disease affects millions worldwide and can result from age-related lacrimal gland dysfunction, which correlates with a decline in lacrimal gland secretory cell function and chronic inflammation. This study investigated the potential of calorie restriction to maintain LG and ocular surface health. Adult female C57BL/6J mice were subjected to a 40% calorie restriction for four months, starting at 6–7 months and continuing until 10–11 months. These mice were compared to controls fed ad libitum. Bulk RNA sequencing of lacrimal glands, conjunctiva and cornea subjected to calorie restriction compared to ad libitum revealed significant differentially expressed genes (DEGs). Pathways enriched in the upregulated DEGs indicate enhanced circadian rhythm, secretory functions and lipid metabolism. These findings were confirmed using individual qPCR reactions and western blotting.  In contrast, pathways enriched in the downregulated DEGs were associated with immune cell activation, adaptive immune responses, extracellular matrix remodeling, and metalloproteinase activity. Histological sections of calorie-restricted lacrimal glands revealed reduced mononuclear cell infiltration and fewer positive cells for CD4, CD19, and MHC II compared to libitum lacrimal glands. Calorie restriction also prevented age-related corneal barrier dysfunction and mitigated age-related conjunctival goblet cell loss, hallmarks of dry eye disease. These findings suggest that calorie restriction supports lacrimal gland and ocular surface health by reducing inflammation and extracellular matrix remodeling and by enhancing the lacrimal glands secretory function.

overall_design: RNA-seq profiling of cornea and conjunctiva in young C57BL/6 mice under calorie-restricted and ad libitum feeding


title: Effect of different Trp53 allelic states on the response to etoposide treatment in ER-Hoxb8 cells

city: Zurich

first: Jonas

last: Fullin

address: Rämistrasse 100

department: Department  of Medical Oncology and Hematology

country: Switzerland

institute: University of Zurich

summary: Trp53 is an essential tumor suppressor gene that coordinates the response to cellular stress, including exposure to chemotherapeutic agents. We aimed to characterize the effect of various Trp53 allelic states (i.e. wild-type, monoallelic mutations and biallelic mutations) on the modulation of downstream pathways in the context of treatment with the chemotherapeutic agent etoposide. In order to obtain a cell model that represents key characteristics of the pre-malignant condition of clonal hematopoiesis, we utilized ER-Hoxb8 cells, which represent an immortalized, but otherwise genetically normal hematopoietic progenitor cell line. Generation of this cell model from a mouse strain carrying the inducible Trp53 missense mutation R245W in the endogenous locus and coupled to a GFP reporter, allows therefore to study the impact of the various allelic states of Trp53 on cellular consequences in a context that models clonal hematopoiesis.

overall_design: Er-Hoxb8 cells carrying the various Trp53 allelic configurations (wild-type: mono_GFPneg and bi_GFPneg; monoallelic mutated: mono_GFPpos; biallelic mutated: bi_GFPpos) were treated with DMSO or 10 uM etoposide for 3 hours, after which RNA was isolated and subjected to bulk RNA-seq.


title: The role of HELLS in human induced pluripotent stem cells II

summary: interactions that require remodeling proteins like the Helicase, Lymphoid-specific (HELLS). Here, we generate HELLS and de novo DNA methyltransferase 3 A and B (DNMT3A/B) knockout hu-man pluripotent stem cells and assemble telomere-to-telomere maps of whole genome bisulfite sequencing data combined with ATAC-sequencing. Disrupting HELLS induces a global loss of DNA methylation that is distinct from the de novo DNMTs, in particular over peri/centromeric satellite repeats as defined in the telomere-to-telomere genome assembly. However, HELLS is dispensable for local enhancer remodeling and the potential to differentiate into the three germ layers. Taken together, these findings further clarify the genomic targets and role of HELLS in human cells.

overall_design: ATAC-seq was performed on iPSCs and iPSC-derived Endoderm cells in WT and HELLS KO conditions.

first: Philine

last: Guckelberger

first: Leah

last: Haut

first: Alexander

last: Meissner

first: Rosaria

last: Tornisiello


title: Cellular imbalance in proximal and distal lung of CFTR-/- sheep in utero and at birth.

status: Public on Jun 18 2025

city: Cleveland

first: Ann

last: Harris

state: OH

address: 10900 Euclid Ave

department: Genetics and Genome Sciences

institute: Case Western Reserve University

summary: The lung is the major focus of therapeutic approaches for the inherited disorder cystic fibrosis (CF) as without treatment lung disease life-limiting. However, the initiating events that predispose the CF lung to cycles of infection, inflammation and resultant tissue damage are still unclear. Observations of inflammation in the CF lung prior to birth in human and several large animal models suggested an in utero origin for the disease and encouraged a detailed investigation of cell identity prior to birth. Here we used the sheep model of CF (CFTR-/-) and age-matched wild-type sheep to investigate the single cell transcriptomes of proximal and distal lung tissue at 80- and 120 days of gestation and at term (147 days).

overall_design: Single cells from sheep (WT and CF) distal and proximal lung tissue were isolated and analyzed using scRNA-seq.

first: Tkachenko

last: Svyatoslav

first: Paranjapye

last: Alekh

first: Leir

last: Shih-Hsing

first: Harris

last: Ann


title: A Single-Cell Atlas of DNA Methylation in Autism Spectrum Disorder Reveals Distinct Regulatory and Aging Signatures

city: Los Angeles

first: Nasser

last: Elhajjaoui

state: CA

address: 695 Charles E Young Dr S

department: Human Genetics

institute: University of California, Los Angeles

summary: Autism spectrum disorder (ASD) is a prevalent and heterogeneous condition that profoundly impacts health and behavior. Analysis of gene expression in the cortex broadly implicates decreased synaptic functioning in excitatory neurons and increased reactivity in glia in ASD; however, whether these phenotypes are reflected in epigenetic signatures is unknown. Here, we report on the first single-cell analysis of DNA methylation (DNAm) in ASD. We profile DNAm from over 60,000 nuclei derived from 49 donors and interpret our findings with gene expression from the same nuclei using snmCT-seq.

overall_design:
Single-nucleus joint profiling of postmortem cortical brain samples isolated from the prefrontal cortex (PFC; Brodmann area 9, BA9) of 26 autistic male donors and 23 non-autistic male  controls. 1 low RIN donor (5302) was excluded from RNA analysis.

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
The raw data (controlled-access, fastq files) is going to be submitted and available through NeMO.
***************************************************************

first: Katherine

middle: W

last: Eyring

first: Cuining

last: Liu

first: Kevin

middle: D

last: Abuhanna

first: Yi

last: Zhang

first: Zachary

last: von Behren

first: Eleazar

last: Eskin

first: Daniel

last: Geschwind

first: Chongyuan

last: Luo

first: Min

last: Tsai


title: Integrated single-cell chromatin and transcriptomic analyses of human peripheral immune cells in patients with alopecia areata.

city: Sevilla

first: Eloisa

last: Andujar

state: Sevilla

address: Avda Americo vespucio s/n

department: GENOMICS UNIT

country: Spain

institute: CABIMER-CSIC

summary: To investigate gene expression and epigenetic changes in circulating immune cells across varying levels of alopecia areata severity by scRNA-seq and scATAC-seq.

overall_design: We performed scRNA-seq and scATAC-seq on peripheral blood mononuclear cells (PBMCs) isolated by Ficoll-Paque density gradient centrifugation from severe and mild alopecia areata patients and healthy controls.

first: Jesus

last: Gay-Mimbrera

first: Juan

last: Ruano


title: Construction of a multi-tissue cell atlas reveals cell-type-specific regulation of molecular and complex phenotypes in pigs

status: Public on Jun 09 2025

city: Shenzhen

first: juan

middle: li

last: chen

address: Dapeng

institute: Chinese Academy of Agricultural Sciences

summary: Cells are the functional intermediaries linking genotypes to phenotypes. However, the systematic characterization of cellular heterogeneity among tissues and cell-type-specific regulation of complex phenotypes are still understudied in pigs. Within the Pig Genotype-Tissue Expression (PigGTEx) project, we present a single-cell atlas of adult pigs that encompasses 229,268 high-quality nuclei from 19 tissues. We further deconvolute bulk RNA-seq samples from 17 matching tissues in the PigGTEx project, dissecting thousands of genetic variants with cell-type interaction effects on gene expression (ieQTL) . Additionally, We colocalize ieQTL with variants associated with 268 complex traits.

overall_design: Expression profiling by high throughput sequencing

first: Guoqiang

last: Yi


title: The role of HELLS in human induced pluripotent stem cells

first: Helene

last: Kretzmer

summary: DNA methylation is essential for genome integrity and involves multi-layered chromatin interac-tions that require remodeling proteins like the Helicase, Lymphoid-specific (HELLS). Here, we generate HELLS and de novo DNA methyltransferase 3 A and B (DNMT3A/B) knockout human pluripotent stem cells and assemble telomere-to-telomere maps of whole genome bisulfite se-quencing data combined with ATAC-sequencing. Disrupting HELLS induces a global loss of DNA methylation that is distinct from the de novo DNMTs, in particular over peri/centromeric satellite repeats as defined in the telomere-to-telomere genome assembly. However, HELLS is dispen-sable for local enhancer remodeling and the potential to differentiate into the three germ layers. Taken together, these findings further clarify the genomic targets and role of HELLS in human cells.

overall_design: Whole genome bisulfite sequencing was performed on proliferating and G2-arrested WT and HELLS KO iPSCs as well as on HELLS KO iPSC-derived Endoderm cells.

first: Philine

last: Guckelberger

first: Alexander

last: Meissner

first: Leah

last: Haut

first: Rosaria

last: Tornisiello


title: Promotion of Treg/Th17 Balance in MRL/lpr Mice by Jianpi-Zishen Formula Via Modulation of DNMT1-Mediated Foxp3 Methylation

status: Public on May 31 2025

city: Hefei

first: ming

last: Li

state: Anhui

address: No.117 Meishan Road, Shushan District

department: Department of Rheumatology

institute: The First Affiliated Hospital of Anhui University of Chinese Medicine

summary: A total of 48 female MRL/lpr mice were included in this study and divided into six groups: JPZS group (Low, medium, and high doses), 5-aza-CdR group, and DC_517 group, with eight mice in each group. Eight female C57BL/6 mice were used as controls. The mice were subjected to the corresponding intervention measures for eight weeks. The impact of JPZS on the disease progression of MRL/lpr mice was evaluated using enzyme-linked immunosorbent assay (ELISA) and serum biochemical parameters. Moreover, immunofluorescence staining and flow cytometry were employed to investigate alterations in the proportions of Tregs and Th17 cells. CD4+ T cells were isolated from the spleen for subsequent investigation, including quantitative real-time PCR, western blotting, and determination of DNA methylation levels. Furthermore, the enzymatic activity of CD4+ T cell-specific DNA methyltransferases was quantified using an EpiQuik DNMT detection kit.The results indicate that JPZS significantly improved the disease development of MRL/lpr mice in a dose-dependent manner. Immunofluorescence staining and flow cytometry suggest that JPZS can increase the ratio of Treg/Th17. Research has found that Foxp3 is at a high methylation level in CD4+ T cells of the model group, and the transcription level of Foxp3 mRNA is downregulated; JPZS can downregulate Foxp3 methylation levels of CD4+ T cells in the model group. Further research has found that the level of Foxp3 methylation is closely related to Dnmt1 enzyme activity, and JPZS can downregulate Dnmt1 enzyme activity, thereby upregulating the transcription level of Foxp3 mRNA.

overall_design: This study included a total of 48 female MRL/lpr mice, divided into six groups: JPZS group (low, medium, and high doses), 5-aza-CdR group, and DC_517 group, with 8 mice in each group. Use 8 female C57BL/6 mice as controls. The mice received corresponding intervention measures for eight weeks. CD4+T cells were isolated from the spleen and the DNA methylation level of Foxp3 gene was detected using MethylTarget sequencing technology (sulfite treatment combined with high-throughput sequencing).

first: Ming

first: Lijun

last: Pang

first: Yunfei

first: Junjie

last: Chen

first: Shuangshuang

last: Shang

first: Chuanbing

last: Huang


title: Comprehensive analysis of microRNAs in brain-derived extracellular vesicles (BDEV) from serum of mice subjected to acute stress.

status: Public on May 26 2025

city: Tokorozawa

first: Yusuke

last: Mizohata

address: Namiki 3-2

institute: National Defense Medical College

summary: An comprehensive analysis of 1900 miRNAs revealed an 8-fold increase in 65 miRNAs compared to the control group.

overall_design: Brain-derived extracellular vesicles were purified and microRNAs were extracted from the serum of 8 mice in the restraint water immersion stress (RWIS) group (n=2) and control group (n=2), respectively.

first: Yuji

last: Morimoto


title: Targeting HDAC8 sensitizes tyrosine kinase inhibitors in the elimination of B-cell acute lymphoblastic leukemia cells through degradation of HIF-1α

status: Public on Jun 05 2025

city: Beijing

first: Ke

address: 1 Tian Tan Xi Li

department: Institute of Medicinal Biotechnology

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analysis the differiational genes and pathways in Ph+ B-ALL cells treated with control, dasatinib, or 22d+dasatinib.

overall_design: Methods: mRNA profiles of Ph+ B-ALL cells treated with control, dasatinib, or 22d+dasatinib were generated by deep sequencing, in triplicate, using NovaSeq 6000 platform (Illumina)

first: Jiong

last: Hu

first: Guilin

last: Xu

first: Feng

last: Wang

first: Wenhui

last: Gao


title: Silencing KRIT1 Partially Reverses the Effects of Disturbed Flow on the Endothelial Cell Transcriptome

status: Public on May 29 2025

city: La Jolla

first: Miguel

middle: Alejandro

last: Lopez Ramirez

address: 9500 Gilman Dr

department: Medicine

institute: University of California, San Diego

summary: Endothelial cells respond to forces generated by laminar blood flow with changes in vasodilation, anticoagulant, fibrinolytic, or anti-inflammatory functions which preserve vessel patency.  These responses to flow are primarily mediated by the elevation of transcription factors Krüppel-like factors 2 and 4 (KLF2 and KLF4). Notably, turbulent flow patterns, which predispose to atherosclerosis, significantly reduce the endothelial expression of KLF2 and KLF4 and reulting changes in the transcriptome that exacerbate inflammation and thrombosis. The CCM complex, comprising KRIT1, CCM2, and CCM3 suppress expression of KLF2 and KLF4. Loss of function of the CCM complex has recently been suggested to protect from coronary atherosclerosis in humans. We thus hypothesized that silencing of KRIT1, the central scaffold of the CCM complex, can normalize the effects of turbulent flow on the human endothelial transcriptome. We conducted bulk RNA sequencing (RNA-seq) on human umbilical vein endothelial cells (HUVECs) after silencing KRIT1 expression using specific siRNAs. The endothelial cells were exposed to pulsatile shear stress (laminar flow), oscillatory shear stress (disturbed flow), or no flow for 24 hours.

overall_design: HUVECs transfected with siRNA for 48 hours were replated using 0.05% Trypsin/EDTA (Thermo Fisher, 25300054) on 38 mm × 76 mm glass plates at 95% confluence. A subset of the glass plates were then assembled into a parallel-plate flow channel as previously described22 for each condition: siScr+PS, siKrit1+PS, siSCr+OS, and siKrit1+OS. The flow system was maintained at 37°C and ventilated with 95% humidified air with 5% CO2. HUVECs were exposed to pulsatile flow (PS) (12 ± 4 dyn/cm2, 1 Hz) or oscillatory flow (OS) (1 ± 4 dyn/cm2, 1 Hz) for 24 hours as described previously23. Additional control plates of siScr- and siKrit1-transfected HUVECs were subject to static conditions (no flow) and maintained in the same culture medium and conditions described above in an adjacent incubator.

first: Amelia

last: Meecham

first: Sara

last: McCurdy

first: Helios

last: Gallego-Gutierrez

first: Mark

last: Ginsberg

last: Lopez-Ramirez


title: Rapid gain and loss of a chromosome drives key morphology and virulence phenotypes in Histoplasma, a fungal pathogen of humans

status: Public on May 30 2025

city: San Francisco

last: Voorhies

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

overall_design: Refer to individual Series


title: ABHD11 mediated deglutarylation regulates the TCA cycle and T cell metabolism

status: Public on May 23 2025

first: Niek

last: Wit

state: Not US or Canada

address: Puddicombe Way

department: Department of Medicine

institute: University of Cambridge

summary: Glutarate is an intermediate of amino acid catabolism and an important metabolite for reprogramming T cell immunity, exerting its effects by inhibition of histone demethylase enzymes or through glutarylation. However, how distinct glutarate modifications are regulated is unclear. Here, we uncover a deglutarylation pathway that couples amino acid catabolism to tricarboxylic acid (TCA) cycle function. By examining how glutarate can form conjugates with lipoate, an essential mitochondrial modification for the TCA cycle, we find that Alpha Beta Hydrolase Domain 11 (ABHD11) protects against the formation of glutaryl-lipoyl adducts. Mechanistically, ABHD11 acts as a thioesterase to selectively remove glutaryl adducts from lipoate, maintaining integrity of the TCA cycle. Functionally, ABHD11 influences the metabolic reprogramming of human T cells, increasing central memory T cell formation and attenuating oxidative phosphorylation. These results uncover ABHD11 as a selective deglutarylating enzyme and highlight that targeting ABHD11 offers a potential approach to metabolically reprogramme cytotoxic T cells.

overall_design: Activated CD8+ T cells were cultured in complete RPMI 1640 supplemented with 10% FBS and 30 U/ml IL-2 and treated with 1 uM ML226 for 11 days.

first: Minogue

last: Eleanor

first: Wit

last: Niek

first: Johnson

last: Randall

first: Nathan

last: James


title: The Chd4 chromatin remodeller controls temporal programs during retinal neurogenesis

city: Ottawa

first: Pierre

last: Mattar

state: ON

address: CCW6109, Box 511, 501 Smyth Rd.

country: Canada

institute: OHRI

summary: During retinal development, neurons and glia are produced in a highly stereotyped and evolutionarily conserved birth order. Landmark studies have demonstrated that the sequence of cell production is temporally encoded. Transcription factors and heterochromatic determinants have been elsewhere implicated in the temporal regulation of progenitor competence states, but the underlying mechanisms are not well understood. Since chromatin remodelling complexes interact with both transcription factors and heterochromatic complexes such as polycomb, we focused on the nucleosome remodeller Chd4. We generated conditional knockouts (cKOs) of Chd4 – a key chromatin remodelling enzyme in neural progenitors. Chd4 cKOs exhibited a marked expansion in early-born retinal ganglion cells. Postnatally, rod photoreceptors were drastically underproduced. As a result, progenitors failed to be exhausted during late phases of development, leading to a striking increase in the production of Müller glia. Clonal retroviral lineaging and histological marker analyses suggest that these effects were independent of alterations in cell death or proliferation. Next, we examined the effect of Chd4 on the genome and transcriptome, focusing on retinal progenitors at P0/P1. Multi-seq single-cell transcriptomics demonstrated that deletion of Chd4 created divergent gene expression profiles and developmental trajectories. ATAC-seq experiments performed on sorted P1 retinal progenitors revealed that chromatin accessibility was significantly increased at ~10 000 enhancer elements and ~4000 genes in the Chd4 cKO, demonstrating that Chd4 is required to repress gene expression and genome accessibility. Finally, to determine whether Chd4 regulates retinal cell-type production by altering competence windows, we performed EdU birthdating. These experiments revealed that cell fates were altered without affecting competence windows. Thus, despite a very strong shift in the production of early-born and late-born cell types, our data suggest that chromatin remodelling does not directly regulate competence windows.

overall_design:
Cut&run-seq was performed using the Cutana cut&run kit (14-0500; Epicypher), following the manufacturer’s instructions. Briefly, P0 retinas were dissected. Cells were dissociated with mechanical trituration in order to retain the glycoproteins necessary for adhering to the concavanalin beads. 500 000 cells were used in each reaction. Cut&run seq was performed using antibodies against Chd4 (Abcam ab72418) or Mbd3 (Fortis A302-529A). Non-specific IgG was used as a negative control. Libraries were prepared using the NEBNext® UltraTM II Library Prep Kit (New England Biolabs). Paired-end 150 sequencing was performed using the NextSeq 500 platform (Illumina) to a read-depth of ~20-35 million reads per sample.
For ATAC-seq, we followed Buenrostro et al. [54]. Briefly, 75,000 cells were sorted from Chx10-Cre-YFP animals using YFP to purify RPCs. Cells were lysed in cold lysis buffer (10 mM Tris-Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630). Lysed nuclei were tagmented using 6.5 µl of TDE1 transposase from the Nextera DNA Flex Library kit (Illumina). Samples were purified using Zymo-Spin IC columns (Zymo), and libraries constructed according to the Nextera workflow. Libraries were cleaned up using the AMPure XP kit (Beckman Coulter). PE 150 sequencing was performed using the NextSeq 500 platform.
Bioinformatic analysis was performed using Galaxy. FASTQ files were processed via Fastq Groomer and Trimmomatic, and then mapped to the mm9 genome using Bowtie2. Peak calling was performed with Macs2.


title: Investigation of common genes and regulatory mechanisms of hyperlipidemia and aortic dissection

status: Public on May 16 2025

city: Tianjin

first: Meng

state: --- Select One ---

address: No. 261, Taierzhuang South Road, Jinnan District, Tianjin

institute: Tianjin chest hospital

summary: This study aimed to elucidate the common genes and regulatory mechanisms underlying hyperlipidemia and aortic dissection.

overall_design: Transcriptome sequencing of dissected and normal ascending aorta tissues was performed. Differentially expressed genes (DEGs) associated with aortic dissection were also identified. Moreover, DEGs related to hyperlipidemia were analyzed using a publicly available dataset. The hub common genes of the two diseases were identified by external dataset validation, followed by efficacy evaluation, protein-protein interaction (PPI) network analysis, immune infiltration association analysis, transcription factor (TF) prediction, and small-molecule drug analysis. Based on transcriptome sequencing data and publicly available datasets, 99 common DEGs between two diseases were identified

first: Qingliang

last: Chen

first: Chao

last: Chang


title: Comprehensive transcription factor perturbation responses for Cryptococcus neoformans

status: Public on May 27 2025

city: St Louis

first: Chase

last: Mateusiak

state: MO

address: 4515 McKinley Ave

department: Genetics

institute: Washington University, St Louis

summary: Cryptococcus neoformans is a deadly fungal pathogen. Upon entering a mammalian host, it deploys a voluminous polysaccharide capsule that is necessary for it to survive host defenses and maintain an infection. Capsule expansion is regulated transcriptionally, as deletion of many transcription factors alters capsule. Thus, we set out to map the transcriptional regulatory network of C. neoformans – that is, to identify the TFs that directly regulate each gene in the genome. First, we carried out RNA-seq of 120 single-TF-deletion strains, together with wild-type controls. We then applied NetProphet3, a TF network mapping algorithm, to predict the direct functional targets of each TF. Unexpectedly, analysis of this network indicated that there are no TFs that primarily regulate genes involved in capsule formation. Rather, the TFs that play a role in deploying capsule also regulate many other genes and processes. Comparison to a TF network map we built for Saccharomyces cerevisiae, a distantly related model yeast, identified pairs of TFs that are functionally orthologous – that is, their targets are enriched for orthologous genes. In many cases, these pairs are different from the ones identified by sequence homology alone. We suggest that network analyses should be used to complement sequence comparison when searching for functionally orthologous transcription factors. Our network map can be searched and visualized at http://cryptococcus.net.

overall_design: After growth in YPD at 30C, WT cells and deletion cells were washed in PBS and transferred to DMEM medium at 37C. Samples were taken for RNA-Seq at 90 minutes after transfer. We aimed for at least four replicates of each concentration at each time point. Replicates were grown and library-prepped on separate days to account for day-to-day variability.

first: Michael

middle: R

last: Brent

first: Tamara

middle: L

last: Doering


title: BLIMP1 negatively regulates IL-2 signaling in T cells

status: Public on May 18 2025

city: Bethesda

first: Jyothi

last: Padiadpu

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

summary: IL-2 signaling sustains immune homeostasis by fine-tuning the balance between effector and regulatory T cells. Our genome-wide CRISPR knockout screen using IL-2-dependent cells derived from a patient with Adult T-cell Leukemia (ATL) showed enriched sgRNAs targeting PRDM1 (encoding BLIMP1). BLIMP1 inhibits IL-2 production in T cells; however, its role in IL-2 signaling remains unknown. Here, we show that Prdm1 overexpression decreased IL-2 signaling in CD4+ T cells, while its deletion enhanced IL-2 signaling during influenza infection. Adoptive transfer of Prdm1 CKO Tregs into Rag2-/- mice elevated IL-2 signaling in T-cell induced colitis. Moreover, CRISPR/Cas9-mediated PRDM1 deletion augmented IL-2 signaling in human CD4+ T cells and natural Tregs with BLIMP1 binding to key genes affecting IL-2 signaling. Furthermore, ATL cells from acute patients exhibited increased IL-2 signaling but reduced BLIMP1 induction. Thus, BLIMP1 represses IL-2 signaling in T cells which is critical in orchestrating normal and pathophysiological immune responses.

overall_design: CD4+ T cells were purified from frozen PBMCs of healthy donors and acute ATL patients then analyzed using scRNA-seq.

first: Suyasha

last: Roy

first: Min

last: Ren

first: Peng

last: Li

first: Kairong

last: Cui

first: Yaqiang

last: Cao

first: Bryan

last: Fisk

first: Tovah

middle: E

last: Markowitz

first: Neelam

last: Redekar

first: Keiko

last: Sakamoto

first: Keisuke

last: Nagao

first: Jangsuk

last: Oh

first: Rosanne

last: Spolski

first: Wei

last: Liao

first: Sigrid

middle: P

last: Dubois

first: Brian

last: Kelsall

first: Keji

last: Zhao

first: James

last: Phelan

first: Warren

last: Leonard


title: Identification of differentially expressed genes involved in the enhancement of mild hyperthermia sensitivity by chroloquine in HSC-3 human oral squamous cell carcinoma cells.

status: Public on May 10 2025

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

institute: University of Toyama

summary:
Hyperthermia (HT) is an effective treatment for cancer. When combined with chemotherapy, radiotherapy, or both, HT is expected to show high therapeutic efficacy against various tumors. Chloroquine (CQ), a clinically used treatment for malaria, has been found to inhibit autophagy. CQ has also been reported to enhance thermosensitivity in cancer cells. However, the molecular mechanisms underlying CQ-induced enhancement of thermosensitivity remain unclear.
Here, we identified the differentially expressed genes involved in the enhancement of mild HT (MHT) sensitivity by chroloquine in HSC-3 human oral squamous cell carcinoma (OSCC) cells using GeneChip oligonucleotide microarrays.

overall_design: Human OSCC HSC-3 cells were treated with mild hyperthermia (MHT) at 42°C for 90 min, followed by incubation at 37°C for 3 h. Chloroquine (CQ) was added to the culture medium 30 min prior to MHT treatment. Total RNA samples were prepared from the cells, and quality of the RNA was analyzed using a Bioanalyzer 2100. Gene expression was analyzed by an Affymetrix GeneChip system with a GeneChip Human Genome U133 Plus 2.0 array. Sample preparation for array hybridization was carried out as described in the manufacturer’s instructions.


title: Maternal Med12 safeguards trophoblast pluripotency and placental development

status: Public on May 13 2025

city: Fort Collins

first: Michelle

middle: M

last: Halstead

state: CO

address: 200 West Lake Street

department: Biomedical Sciences

institute: Colorado State University

summary: For a brief but critical period post-fertilization, the mammalian embryo is entirely dependent on maternal products inherited from the oocyte. Previous research showed that oocyte-specific loss of Med12, an X-linked gene and Mediator complex subunit, leads to female sterility despite normal folliculogenesis and ovulation. Here, we show that loss of maternal Med12 has minimal effect on the oocyte transcriptome and does not manifest in embryonic lethality until post-implantation. Implants derived from Med12-null oocytes demonstrate abnormal placentation at E9.5, with an overabundance of trophoblast giant cells (TGC). This phenotype associates with downregulation of trophoblast pluripotency markers (e.g. Cdx2) and activation of drivers of TGC identity (e.g. Stra13) in the E7.5 extraembryonic ectoderm, revealing a previously undescribed role for Med12 in trophoblast pluripotency maintenance. Notably, we find consistently low Med12 expression in embryos derived from Med12-null oocytes, potentially due to programmed paternal X chromosome inactivation (XCI). To isolate the consequences of maternal Med12 depletion, we introduced an autosomal Med12 transgene and show that embryonic expression of the transgene rescues development of Med12-null oocytes. We conclude that oocyte-specific deletion of Med12 produces a maternal-zygotic double knock-out in extraembryonic tissues due to paternal XCI, leading to loss of pluripotency in the trophoblast, placental malformation, and embryonic death.

overall_design: To investigate the role of oocyte-derived Med12 in mouse oogenesis and embryogenesis, we used a conditional knock-out strategy via Zp3-Cre-mediated recombination to ablate Med12 from oocytes. We then performed comparative gen expression profiling using data obtained from RNA-seq of growing oocytes from 12-day-old females (D12), germinal vesicle (GV) oocytes, metaphase-II stage (MII) oocytes, and E7.5 embryonic tissues from individual implants (ectoplacental cone - EPC, extraembryonic ectoderm - ExE, epiblast - EPI) collected from either (1) Zp3-Cre;Med12fl/fl dams, in which Med12 is ablated from oocytes ("Med12KO"); or  (2)  Med12fl/fl control ("WT") females. Embryonic implants were collected after timed-mating of experimental dams with wild-type male studs of proven fertility.

first: Aleksandar

last: Rajkovic


title: Impact of Hypoxia on Epstein-Barr Virus–Mediated B Cell Transformation

status: Public on May 07 2025

city: Boston

first: Rui

last: Guo

state: Massachusetts

address: 150 Harrison Ave.

department: School of Medicine

institute: Tufts University

summary: Epstein-Barr virus (EBV) contributes to over 200,000 cancers annually, predominantly aggressive lymphomas originating from hypoxic germinal centers (<1% O2). However, conventional models fail to recapitulate the physiologically relevant hypoxic microenvironment which profoundly influences B-cell metabolic remodeling during transformation. Here, we establish an ex vivo model of EBV-driven B-cell transformation under 1% O2, demonstrating robust transformation and super-enhancer activation of oncogenic regulators, including MYC. Multi-omic analyses reveal distinct metabolic adaptations to hypoxia. Unlike normoxic B-cells, which rely on stearyl desaturase 1 and fatty acid oxidation to mitigate lipotoxicity, hypoxically transformed B-cells suppress fatty acid synthesis while upregulating glycerophospholipid metabolism and lipid droplet formation to buffer excess saturated lipids. Consequently, these cells exhibit heightened dependence on extracellular unsaturated fatty acids to support membrane biogenesis for proliferation. Our findings provide the first physiologically relevant model of EBV-driven B-cell transformation under hypoxia, uncovering metabolic vulnerabilities that could inform targeted therapeutic strategies for EBV-associated malignancies.

overall_design: Newly isolated human primary B cells were transformed by Epstein-Barr virus under either 21% O2 or 1% O2 conditions. After 28 days in culture, the infected B cells were fully transformed into lymphoblastoid cell lines (LCLs). These LCLs, generated under 21% O2 (referred to as 21% O2 LCLs) or 1% O2 (1% O₂ LCLs), were subsequently used for RNA-seq and ChIP-seq analysis targeting H3K27ac and H3K4me3.

first: Larissa

last: Havey


first: Jyothi

last: Padiadpu

overall_design: Splenic Tregs from WT (Foxp3YFP-cre) and Prdm1-CKO (Prdm1fl/flFoxp3YFP-cre) mice were isolated, pre-activated with anti-CD3 + anti-CD28, rested overnight, cultured with IL-2 for 24 hours

first: Suyasha

last: Roy

first: Tovah

last: Markowitz


title: Arabidopsis lines with modified ascorbate concentrations reveal a link between ascorbate and auxin biosynthesis

status: Public on May 17 2025

city: Málaga

first: Vitor

last: Amorim-Silva

address: Av. Louis Pasteur, 49

institute: University of Malaga

summary: Ascorbate is the most abundant water-soluble antioxidant in plants and an essential molecule for normal plant development. Although present in all green plants, ascorbate concentrations vary among plant species and tissues. While ascorbate accumulation is a trait of nutritional, and therefore, agronomical interest, the impact of different concentrations on cellular homeostasis remains elusive. To shed light on this question, we compared Arabidopsis (Arabidopsis thaliana) lines with very low (vtc2 mutant, 20% of wild-type (WT) levels), low (vtc4 mutant, 65% of WT levels), and high (vtc2/OE-VTC2, 165% of WT levels) ascorbate concentration in four-week-old rosette leaves. An 80% reduction of ascorbate increased the expression of genes implicated in defense against pathogens but repressed genes associated with abiotic stress responses. Unexpectedly, lines with increased (165% of WT) and decreased (65% of WT) ascorbate levels shared 85% of induced transcription factors and the gene ontology terms associated with their transcriptional programs. We identified TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS 1 (TAA1), a gene encoding the enzyme that catalyzes the first step of auxin biosynthesis, among the group of genes whose expression was positively correlated with ascorbate content. Using a combination of genetic and pharmacological approaches in fluorescent and histochemical reporter lines for auxin biosynthesis and signaling activity, we revealed that TAA1- and TAA1 RELATED 2 (TAR2)-mediated auxin biosynthesis is necessary for plants to cope with increased ascorbate concentration in a light-dependent manner, revealing a layer of complexity in the regulatory landscape of redox homeostasis.

overall_design: RNA-seq profilling of 4-week-old wild type (WT), vtc2-4 (vtc2), vtc4-4 (vtc4), and vtc2/OE-VTC2 L15 (OE) rosettes of Arabidopsis. Four-weeks old Arabidopsis rosettes grown under short day photoperiod (8-h light/16-h darkness cycle, 22±1ᵒC, 300±70 μmol photons m-2 s-1) were collected 30 minutes after the lights turned on and flash-frozen in liquid nitrogen. RNA from three independent replicates per genotype (WT, vtc2, vtc4 and OE) was used in this experiment.

first: Mario

last: Fenech

first: Viviane

last: Zulian

first: José

last: Moya-Cuevas

first: Dominique

last: Arnaud

first: Ian

last: Morilla

first: Nicholas

last: Smirnoff

first: Miguel

middle: A

last: Botella

first: Anna

middle: N

last: Stepanova

last: Alonso

first: Carmen

last: Martin-Pizarro


title: Heterologous expression of HCoV-HKU1 ORF 7b by mouse hepatitis virus protects against severe disease during murine infection

status: Public on Apr 23 2025

city: Newark

first: Adriana

last: Messyasz

address: 185 South Orange Avenue

institute: Rutgers-New Jersey Medical School

summary: Coronaviruses express a repertoire of accessory proteins for evading host immune responses. A small internal (I) accessory gene overlaps with the nucleocapsid (N) gene in an alternative reading frame of viruses that belong to the genus Betacoronavirus. Previous studies reported that I proteins of SARS-CoV (9b), MERS-CoV (8b) and SARS-CoV-2 (9b) inhibit type I interferon (IFN-I) expression through distinct mechanisms and have different roles in pathogenesis. In contrast, the functions of the I proteins of human coronaviruses HCoV-HKU1 (7b) and HCoV-OC43 (8b) have not been previously reported. Although HCoV-HKU1 and HCoV-OC43 predominantly cause common cold in healthy adults (common cold CoVs, CCCoVs), susceptible individuals infected with these viruses can develop severe disease. The lack of robust reverse genetic systems, tissue culture and animal models limit the study of HCoV-HKU1 and HCoV-OC43 pathogenesis. Here, we examined how the heterologous expression of the HCoV-HKU1 and HCoV-OC43 I proteins impact pathogenesis in a mouse model of infection using a prototypic betacoronavirus. We inserted the I gene of HCoV-HKU1 (ORF 7b) and HCoV-OC43 (ORF 8b) independently into the genome of a neurotropic strain of mouse hepatitis virus (J2.2). J2.2 infection is well characterized with clearly defined immune responses which allows the study of these genes in the context of authentic coronavirus infection. We showed that ORF 7b of HCoV-HKU1, but not ORF 8b of HCoV-OC43, ameliorated MHV-J2.2 pathogenesis while ORF 8b of MERS-CoV exacerbated disease. The presence of HCoV-HKU1 ORF 7b decreased virus titers and cytokine expression while ORF 8b of MERS-CoV led to increased immune cell infiltration and virus titers in mice after J2.2 infection. Moreover, proteins expressed by ORF 7b of HCoV-HKU1 and ORF 8b of HCoV-OC43 showed different patterns of subcellular localization. Overall, our findings suggest that the I genes of different betacoronaviruses play unique roles in pathogenesis.

overall_design: Mouse brains were homogenized in TRIZOL 3 days after infection with J2.2 virus expressing HKU1 protein or its control.

first: Roy

last: Wong


title: Single cell RNA sequencing of placenta in patients with gestational diabetes during term pregnancy

status: Public on Apr 16 2025

city: Changchun

first: Peng

last: Xu

state: Jilin

address: No.1 Xinmin Street

institute: The First Hospital of Jilin University

summary: We performed  the single cell RNAsequencing in the placental tissues of term pregnancies with  gestational diabetes mellitus complicated with macrosomia after cesarean section to explore the transcriptome differences and potential mechanisms of placenta in the process of macrosomia in patients with gestational diabetes. Our research helps to understand placental overgrowth in GDMM and its impact on fetal development, providing new insights into the pathogenesis of GDMM and predicting potential therapeutic interventions.

overall_design: After collecting placental tissues, they were immediately processed into single-cell suspensions. The process involved washing, cutting, digesting, filtering, lysing red blood cells, removing dead cells, staining, and finally suspending the cells in a solution. The single-cell suspension was loaded onto the Chromium Controller to generate single-cell gel beads, followed by single-cell RNA sequencing using the Illumina Novaseq6000 sequencer.

first: Chang

last: Shu

last: Chen

first: Zewen

last: Sun


title: Maturation of human cardiac organoids enables complex disease modelling and drug discovery

status: Public on Apr 14 2025

city: Brisbane

first: James

last: Hudson

state: Queensland

address: 300 Herston Rd, Herston QLD 4006

country: Australia

institute: QIMR Berghofer Medical Research Institute

summary: Cardiac maturation is an important developmental phase culminating in profound biological and functional changes to adapt to the high demand environment after birth. Maturation of human pluripotent stem cell-derived human cardiac organoids (hCO) to more closely resemble human heart tissue is critical for understanding disease pathology. Herein, we profile human heart maturation in vivo to identify key signalling pathways that drive maturation in hCOs. Transient activation of both the 5’ AMP-activated kinase (AMPK) and estrogen-related receptor (ERR) promoted hCO maturation by mimicking the increased functional demands of post-natal development. hCOs cultured under these directed maturation (DM) conditions (DM-hCOs) display robust transcriptional maturation including increased expression of mature sarcomeric and oxidative phosphorylation genes resulting in enhanced metabolic capacity. DM-hCOs have functionally mature properties such as sarcoplasmic reticulum-dependent calcium handling, accurate responses to drug treatments perturbing the excitation-coupling process and ability to detect ectopy CASQ2 and RYR2 mutants. Importantly, DM-hCOs permit modelling of complex human disease processes such as desmoplakin (DSP) cardiomyopathy, which is driven by multiple cell types. Subsequently, we deploy DM-hCOs to demonstrate that bromodomain extra-terminal inhibitor INCB054329 rescues the DSP phenotype. Together, this study demonstrates that recapitulating in vivo development promotes advanced maturation enabling disease modelling and the identification of a therapeutic strategy for DSP-cardiomyopathy.

overall_design: hCO were matured using serum-free (SF) (PMID: 37105170) or directed maturation (DM) protocols. Single Nuceli RNA-seq (snRNA-seq) was conducted to evaluate cell-type specific changes in the DM maturation protocol.

first: Mark

last: Pocock

first: Janice

last: Reid


title: HIV-1 m6A methylome investigation by m6A-SAC-seq [CD4+ T cells]

status: Public on May 01 2025

city: Chicago

first: Chuan

last: He

state: IL

address: 929 E 57th St

department: Chemistry Department

institute: University of Chicago

summary: N6-methyladenosine (m6A) is the most prevalent cellular mRNA modification and plays an important role in RNA stability, localization, and gene expression. There are several papers reported that HIV-1 infection upregulates cellular RNA m6A in CD4+ T cells, and this upregulation occurs without changes to the expression levels of the cellular enzymes which add or remove m6A. However, the mechanism of HIV-1 inducing cellular mRNA m6A upregulation is unknown. Here we show that HIV-1 infection upregulates m6A of cellular mRNA and promotes METTL3/METTL14 interaction. We found that HIV-1 infection resulted in increased cellular mRNA m6A level in activated primary CD4+ T cells detected by m6A dot blot and m6A ELISA. We found that HIV-1 infection of CD4+ T cells promotes METTL3/METTL14 interaction compared to mock control using co-immunoprecipitation (co-IP). Our ongoing studies will determine the transcriptomic, epitranscriptomic, and proteomic profiles of CD4+ T cells infected with HIV-1 for 4 days. These studies will facilitate the elucidation of the mechanisms by which HIV-1 infection leads to increased levels of cellular m6A and methyltransferase writers comlex.

overall_design: Primary activated CD4+ T cells were either infected with Mock or HIV-1NL4-3 for 96 hours and total RNA was isolated from three individual healthy donors. Poly-A RNA was enriched using oligodT beads and used for m6A-SAC-seq and RNA-sequencing.

first: Zhao

last: Yutao

first: Huang

last: Siyu

first: Wu

last: Li

first: He

last: Chuan


title: Single cell RNA sequencing of placenta in patients with early onset preeclampsia

first: Shu

last: Zheng

state: 吉林Jilin

address: Xinmin Road

institute: Jilin University

summary: Early-onset preeclampsia (EOPE) is a severe hypertensive disorder of pregnancy, frequently associated with fetal growth restriction (FGR) and reduced estrogen levels due to placental dysfunction. We employed single-cell RNA sequencing (scRNA-seq) to profile placental trophoblasts from EOPE patients complicated by FGR.


title: Single-Cell Transcriptomics Matrix of all PBMC samples used in “Single-Cell Transcriptomics Reveals Immune Dysregulation in HIV-MTB Co-Infection: CD4+ T Cells Exhaustion and CD8+ T Cells Hyperactivation”

status: Public on Apr 12 2025

city: Shanghai

first: Zihui

last: Zhao

address: Dongan Road No.130

institute: Shanghai Institute of Infectious Disease and Biosecurity, Fudan University

summary: To investigate the early immune profiles of patients, particularly those with HIV and tuberculosis co-infection, we collected blood samples from three individuals in the HIV/MTB co-infection group, three HIV/AIDS patients, and three healthy controls. Peripheral blood mononuclear cells (PBMCs) were isolated, and the MobiNova®-100 Single Cell System (MobiDrop (Zhejiang) Co., Ltd.) was employed to prepare single-cell sequencing libraries. Subsequently, a single-cell RNA expression matrix was generated using the Illumina NovaSeq 6000 System, yielding a total of 113,816 cells for further analysis.

overall_design:
The inclusion criteria for patients were as follows: (1) newly diagnosed with HIV infection/AIDS; (2) newly diagnosed with tuberculosis, receiving initial treatment. The exclusion criteria were: (1) prior use of antiretroviral therapy (ART) or anti-tuberculosis drugs; (2) detection of drug resistance in HIV susceptibility tests; (3) severe liver and/or kidney dysfunction; and (4) presence of underlying conditions such as pancreatitis or malignant tumors. Based on these criteria, a total of 6 patients were enrolled in the study, including 3 HIV/AIDS patients with M. tuberculosis co-infection (none of whom had received either anti-tuberculosis or antiviral treatment) and 3 early-diagnosed HIV/AIDS patients (none of whom had received antiretroviral treatment). This study also included three healthy control individuals.

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

first: Suyue

last: Huang


title: The micro-RNA signature of hypertrophic callus-formation in bone fractures accompanied with traumatic brain injury.

status: Public on Apr 21 2025

city: Salzburg

first: Andreas

last: Traweger

state: Salzburg

address: Strubergasse 22

department: Tendon and Bone Regeneration

country: Austria

institute: Paracelsus Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: Long-bone-fractures occasionally heal with hypertrophic callus formation when patients suffer a concomitant traumatic brain injury. Although this phenomenon is known for decades, the causal factors are still poorly understood and no feasible markers are currently available to predict the exuberant bone-mass-formation at an early timepoint after injury. In this study, we used small-RNA-seq, bioinformatic analyses and in vitro assays to identify a set of micro-RNAs in serum of hypertrophic callus patients that serve as potential biomarkers. The identified miRNAs are highly expressed in the human brain, primarily in the pituitary gland, they are differentially expressed during osteogenic differentiation of bone-marrow-derived mesenchymal stem cells and they regulate mRNA-targets, involved in bone-related pathways, such as RANK/RANKL, BMP/RUNX2, PI3K-AKT and Wnt/beta-catenin.

overall_design: Small RNA-seq profiling of human blood samples of four patient groups: fracture (Fx), traumatic brain injury (TBI), fracture accompanied with traumatic brain injury and normal bone healing (TBI+Fx) and fracture accompanied with traumatic brain injury and hypertrophic callus formation (TBI+Fx+Call). Blood sampling was performed 24h, 72h and 7 days after injury from three patients of each group.


title: A Bivalent Molecular Glue Linking Lysine Acetyltransferases to Oncogene-directed Cell Death [ChIP-seq]

status: Public on Apr 09 2025

city: Stanford

first: Sai

last: Gourisankar

address: 240 Pasteur Dr, Rm 4700

department: Chemical Systems Biology

institute: Stanford

summary: Lysine acetyltransferases (KATs) such as p300 and CBP regulate gene networks in healthy and malignant cells by scaffolding transcriptional machinery and by acetylating chromatin and transcription factors (TFs). In certain cancers including diffuse large B cell lymphomas, they contribute to tumor suppression and are therapeutic vulnerabilities when deregulated. Inhibitors and degraders of KATs are limited by potential toxicity associated with targeting these essential proteins. We introduce KAT-TCIPs (lysine acetyltransferase transcriptional/epigenetic chemical inducers of proximity), bivalent molecules that redirect the KAT and co-activating activity of p300 and CBP towards programmed cell death signaling repressed by the oncogenic TF BCL6. The lead KAT-TCIP molecule kills lymphoma cells at ~0.8 nM by redistributing chromatin acetylation, activating the pro-apoptotic protein PUMA, and repressing c-MYC. Analysis of the ternary co-crystal structure containing p300 and BCL6 reveals fortuitous interactions that drive the potency and specificity of KAT-TCIPs and sets a precedent for KAT-targeting induced proximity therapeutics.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone acetylation (H3K27ac and H2BK20ac) after TCIP3 treatment in SUDHL5 cells

first: Meredith

last: Nix

first: Roman

middle: C

last: Sarott

first: Brendan

last: Dwyer

first: Sabin

last: Nettles

first: Michael

last: Martinez

first: Hind

last: Abuzaid

first: Yanlan

last: Wang

first: Haopeng

last: Yang

first: Juste

last: Simanauskaite

first: Bryan

last: Romero

first: Hannah

last: Jones

first: Andrey

last: Krokhotin

first: Tara

last: Loewinson

first: Lei

last: Davis

first: Daniel

last: Fernandez

first: Tinghu

last: Zhang

last: Green

first: Stephen

last: Hinshaw

first: Nathanael

middle: S

last: Gray

first: Gerald

last: Crabtree


title: A Role for CAF1 in the Incorporation of H3.3 in Arabidopsis [ChIP-seq]

city: Yangling

first: Su

middle: Ying

last: Pei

state: Shaanxi

address: No. 3 Taicheng Road

department: College of Life Sciences and Institute of Future Agriculture

institute: Northwest A&F University

summary: Eukaryotic organisms organize their genetic material in chromatin rather than unprotected DNA. Efficient chromatin assembly is essential for all DNA-templated processes, including replication, transcription, and DNA repair. Our research focused on two major histone H3 deposition complexes: Chromatin Assembly Factor (CAF1), which deposits canonical H3 on naked DNA immediately after replication during the S-phase in yeast and metazoans, and the Histone Regulator A (HIRA) complex, which is thought to incorporate the H3.3 variant in a transcription-dependent manner. By combining biochemical, genetic, genomic, and proteomic data, we surprisingly discovered that CAF1 incorporates the histone variant H3.3 into Arabidopsis chromatin. Moreover, CAF1's role inH3.3 deposition is particularly pronounced in the transcribed regions of the genome.

overall_design:
ChIP-seq of FAS2 in fas2-4 and hira-1,fas2-4 backgrounds and ChIP-seq of histone H3.1 and histone H3.3 in Columbia-0 (WT), as well as in fas2-4 and hira-1 mutant backgrounds.The experimental tissues were collected form 12 day after germination (12DAG) from seedlings cultured on GM medium (1x MS salts, 1% sucrose, pH=5.7).
ChIP-seq of histone H3 in in Columbia-0 (WT), as well as in fas2-4 and hira-1 mutant backgrounds.The experimental tissues were collected form 12 day after germination (12DAG) from seedlings cultured on GM medium (1x MS salts, 1% sucrose, pH=5.7).

first: Israel

last: Ausin

first: Yafei

first: Fan

first: Yingpei

last: Su

first: Weijie

last: Xi


title: Decoding the molecular complexity governing corneal wound closure in vivo

status: Public on Apr 04 2025

city: Montpellier

first: Frederic

last: Michon

address: 80, rue Augustin Fliche

department: Institute for Neurosciences of Montpellier

country: France

institute: Inserm

summary: The cornea, the transparent outermost layer of the eye, possesses exceptional wound healing capabilities essential for vision preservation. The complexity of the corneal microenvironment is central to its rapid healing; however, the molecular mechanisms orchestrating this process remain poorly defined, limiting therapeutic advancements. Here, we elucidate the extensive remodeling of the corneal molecular landscape following physical injury. Multi-omics analyses—including transcriptomic, epitranscriptomic, and proteomic profiling—uncover significant induction of epithelial cell plasticity driving wound closure. Moreover, lacrimal gland ablation further suppresses Pax6 expression, highlighting its regulatory role. Our multi-omic approach uniquely reveals bilateral remodeling of the molecular environment, a phenomenon constrained by an intact tear film. Collectively, our findings identify novel molecular factors critical to corneal healing, significantly advancing the understanding of epithelial plasticity. These insights will facilitate the translation of cell plasticity research into innovative strategies for tissue and organ regeneration.

overall_design: We compared the transcriptomic signatures of murine corneas during wound healing

first: Feret

last: Nadege

first: Michon

last: Frederic


title: m5C methyltransferase NSUN3 regulates variant gene expression and development in blood-stage Plasmodium falciparum [RIP-seq]

status: Public on Apr 08 2025

city: Changsha

first: Xiaomin

last: Shang

state: Hunan Province

address: 172 Tongzipo Road

department: Department of Parasitology

institute: Central South University

summary: C5 methylation of cytosine is a relatively abundant post-transcriptional modification in eukaryotes, and the NSUN family has been identified as an important executor of m5C modification. Currently, little is known about this family in Plasmodium spp. Therefore, we constructed a pfnsun3 gene knockdown strain and the knockdown efficiency was confirmed through growth curves and western blot experiments. The target genes of PfNSUN3 was obtained by RNA immunoprecipitation and high-throughput transcriptome sequencing experiments. Our data reveal that pfnsun3 is an indispensable post-transcriptional RNA modification in regulating variant gene expression in Plasmodium falciparum.

overall_design: To explore the target genes of PfNSUN3 protein, we collected ring stage sample of pfnsun3-ty1-glmS strain to identify its direct-binding RNAs by RIP-seq experiments.

first: Yanting

last: Fan


title: Hematopoietic Progenitor Cell Genome Sensing of Inflammation [RNA-Seq]

status: Public on Apr 02 2025

city: Madison

first: Emery

last: Bresnick

address: 1111 Highland Avenue

institute: University of Wisconsin-Madison

summary: Genomes must adapt dynamically to alterations in the signaling milieu, including acute and chronic inflammation that transiently or permanently disrupt genome function. We investigated this problem with a human disorder caused by heterozygous mutations in GATA2, encoding a hematopoietic stem/progenitor cell regulator. GATA2 deficiency causes bone marrow failure in humans and mice and predisposes to leukemia in humans. GATA2-deficient murine progenitors are hypersensitive to Toll-Like Receptor (TLR)- and interferon-g-mediated inflammatory signaling, and downregulating the cell type-specific transcription factor PU.1 reduced TLR1/2- and IFNg-induced transcriptional responses. Genome sensing of inflammation involved inflammation-dependent recruitment of PU.1 to chromatin and PU.1 pre-occupying specific loci. Motifs for RUNX developmental regulators were enriched at TLR1/2-IFNg-activated genes in GATA2-deficient progenitors. Contrasting with the paradigm in which GATA2 and RUNX1 function cooperatively, their opposing activities were vital for integrating signaling and transcriptional mechanisms to endow a progenitor genome with the capacity to sense the inflammatory environment.

overall_design: For RNA-seq experiment: ER-HOXB8-immortalized hi-77-/- and hi-77-/-;Spi1URE-/- cells were treated with vehicle (0.1%BSA in PBS), IFNg, Pam3CSK4, or both agonists for 4 h. hi-77+/+ cells were treated with vehicle or combination of IFNg and Pam3CSK4 as controls. For CUT&Tag experiment: hi-77+/+, hi-77-/-, and hi-77-/-;Spi1URE-/- cells were treated with vehicle or combination of IFNg and Pam3CSK4 for 4 h.


title: Hematopoietic Progenitor Cell Genome Sensing of Inflammation [CUT&Tag]


title: A Bivalent Molecular Glue Linking Lysine Acetyltransferases to Oncogene-directed Cell Death [RNA-seq]

first: Sai

last: Gourisankar

state: CA

overall_design: RNA-seq of SUDHL5 cells treated with TCIP3 to examine effects on gene expression.

first: Meredith

last: Nix

first: Roman

last: Sarott

first: Brendan

middle: G

last: Dwyer

first: Sabin

last: Nettles

first: Michael

last: Martinez

first: Hind

last: Abuzaid

first: Yanlan

last: Wang

first: Haopeng

last: Yang

first: Juste

last: Simanauskaite

first: Bryan

last: Romero

first: Hannah

last: Jones

first: Andrey

last: Krokhotin

first: Tara

last: Loewinson

first: Lei

last: Chen

first: Mark

last: Davis

first: Daniel


title: m5C methyltransferase NSUN3 regulates variant gene expression and development in blood-stage Plasmodium falciparum [RNA-seq]

first: Xiaomin

last: Shang

overall_design: To explore the function of PfNSUN3 protein in regulating of gene expression in Plasmodium falciparum, we performed strictly synchronization and divided the parasites into GlcN-added and non-GlcN groups, then collected the total RNA samples in the next growth cycle at ring, trophozoite and schizont stages, respectively.

first: Yanting

last: Fan


title: Impaired cell interactions at the pre-eclamptic maternal-fetal interface

status: Public on Mar 31 2025

city: Berlin

first: Florian

last: Herse

state: FOREIGN

address: Lindenberger Weg 80

department: Experimental and Clinical Research Center (ECRC)

institute: Max-Delbrueck Center for Molecular Medicine

summary: Hypertensive disorders in pregnancy, of which the multisystem pathology pre-eclampsia is most severe, often lead to preterm delivery, maternal mortality and life-long complications. Pre-eclampsia lacks early screening tools and causal therapies, illustrating the urgent need for a better understanding of early disease dynamics. Here, we present the first study comparing single-nuclei transcriptomes of human diseased preterm preeclamptic placentae and healthy controls, embedding the characterization of the maternal-fetal barrier dysfunction in the context of a comprehensive spatio-temporal study including early and late gestational placentae. Our results highlight and contextualize a perturbed communication from fetal to maternal side during the development of pre-eclampsia starting with a dysregulated trophoblast stem-cell maturation. We provide new targets for potential early disease prevention in order to protect mother and child from increased gestational mortality and morbidity but also from life-long increased cardiovascular disease risk.

overall_design:
Single nuclei profiling of maternal-fetal interface in early and late gestational vs preeclamptic pregnancies
>>> Submitter declares that the raw data will be deposited in the European Genome-phenome Archive (EGA) due to patient privacy concerns. <<<

first: Olivia

last: Nonn

first: Anne

last: Staff

first: Cornelius

last: Fischer

last: Debnath

first: Naveed

last: Ishaque


title: Establishment and characterization of Bovine trophoblast stem cells (bTSCs) growing as adherent cells or vesicles

city: Bron

first: Bertrand

middle: Pierre-Yves

last: PAIN

address: 18, Avenue du  Doyen Lépine

institute: U1208, INSERM

summary: Understanding embryonic development still remains one of the main challenge in developmental biology. Using 3D in vitro models of early embryonic development in the mouse and human, scientists hope to decipher embryonic mechanisms, in particular the initial arrangement and interaction of cells within the embryonic structure. To date, there are very few models established for livestock species. In this study, we have derived and characterized bovine trophoblastic stem cells (bTSCs) that we further used to establish with bESCs (bovine embryonic stem cells) the first in vitro model of bovine blastoïds.

overall_design: The bTSCs were esablished using IVF embryos grown on inactivated BEF (bovine embryonic fibroblasts) in 2iTS medium composed of DMEM/F12 as a basis supplemented with Neurobasal, supplements WNT3A and small molecules as inhibitors of signaling pathways.  Once established, the 2iTS cells were routinely passaged every 3-4 days for adherent ones with a splitting ratio of around 1/6 and by dilution of 1/6 for the cells in suspension.

first: Camille

last: Baquerre

first: Christian

last: Jean

last: Pain


title: Tandem inactivation of inositol pyrophosphatases Asp1, Siw14, and Aps1 illuminates functional redundancies in inositol pyrophosphate catabolism in fission yeast

status: Public on Mar 26 2025

city: New York

first: Ana

last: Sanchez

state: NY

address: 430 E 67th Street, RRL-865

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

summary: RNA-seq anaysis compares gene expression of the asp1-H397A aps1∆ siw14∆ spx1∆ (HASX) mutant to the wild-type fission yeast (Schizosaccharomyces pombe)

overall_design: 1 test sample and 1 control sample were processed (each sample has 3 replicate experiments).

first: Beate

last: Schwer

first: Jill

last: Babor

first: Isabel

last: Prucker

first: Henning

middle: J

last: Jessen

first: Stewart

last: Shuman


title: Regeneration Alters Open Chromatin and Cis-Regulatory Landscape of Erythroid Precursors

status: Public on Mar 24 2025

city: Omaha

first: Venkatasai Rahul

last: Dogiparthi

state: NE

address: 985805 Nebraska Medical Center

department: Genetics Cell Biology and Anatomy

institute: University of Nebraska Medical Center

summary: Stress erythropoiesis elevates the rate of red blood cell (RBC) production as a physiological response to stressors such as anemia or hypoxia. To identify cis-regulatory changes that underlie anemia-specific gene expression and cellular responses, we analyzed chromatin accessibility in populations of cells enriched for red blood cell precursors isolated from mice at a range of time points after anemia induction. The representation of red blood cell trait-associated loci in ATAC-seq data remained durably elevated more than 1 month after anemia resolution. Together, these findings provide a framework to understand the early establishment and late resolution of a regeneration-dependent transcriptome in RBC progenitors and precursors.

overall_design: We used ATAC-seq to map chromatin accessibility in populations of cells enriched for red blood cell precursors isolated from mice at a range of time points (0, 1, 3, 7, 14, 21, 35 days) after anemia induced by the red blood cell lysing chemical phenylhydrazine

first: Kyle

last: Hewitt

first: Yichao

last: Zhou

first: Venkatasai

first: M

last: Rowley


title: Anti-CD3 mAb treatment reshapes infiltrating T and beta cells in the islets in autoimmune diabetes

city: New Haven

first: Ying

last: Wu

state: CT

address: 300 George St

institute: Yale University

summary: Anti-CD3 mAb delays or prevents type 1 diabetes (T1D) by modulating the immune mediated destruction of beta cells. Our findings described the reshaping of islet-infiltrating T cells and beta cells that lead to operational, but tenuous tolerance to autoimmune diabetes following anti-CD3 mAb treatment.

overall_design: Islets and paired pancreatic draining lymph nodes were isolated from anti-CD3 treated NOD mice in remission and processed for single-cell 5' RNA sequencing. Each scRNAseq dataset is multiplexed and contains islet cells or pancreatic draining lymph nodes of 3 mice, each individually labeled by hashtag barcode.

first: Maxwell

last: Spurrell

last: Lledó-Delgado

first: Songyan

last: Deng

first: Dejiang

last: Wang

first: Yang

last: Liu

first: Mahsa

last: Nouri Barkestani

first: Ana Luisa

last: Perdigoto

first: Kevan

last: Herold


title: An inherited predisposition allele promotes gastric cancer via enhancing deubiquitination-mediated activation of epithelial-to-mesenchymal transition signaling

status: Public on Mar 18 2025

first: Aixia

last: Song

address: Dong'an Road

institute: Fudan University

summary: Genome-wide human genetic studies have identified inherited cis-regulatory loci variants that predispose to cancers. However, the mechanisms by which these germline variants influence cancer progression, particularly through gene expression and proteostasis control, remain unclear. By analyzing genomic data from a gastric cancer (GC) case-control study (2,117 individuals), focusing on the ubiquitin-specific protease (USP) family, we identify the single nucleotide polymorphism (SNP) rs72856331 (G>A) in the promoter region of the proto-oncogene USP47 as a susceptibility allele for GC (OR = 0.78, P = 0.015). Mechanistically, the risk allele G is associated with enhanced USP47 expression, mediated by altered recruitment of the transcription factor GLI3 and changes in the epigenetic status at promoter. CRISPR/Cas9-mediated single-nucleotide conversion into risk allele G results in increased GLI3 binding and subsequent USP47 upregulation. The depletion of GLI3 results in a reduction of cancer-related phenotypes, similar to those observed following USP47 knockdown. Furthermore, we identify Snai1 as a deubiquitination target of USP47, explaining USP47-dependent activation of epithelial-mesenchymal transition pathway and tumor progression. Our findings identify a pivotal genetic predisposition that implicates the perturbation of transcription and proteostasis programs in GC, offering insights for novel prevention and therapeutic avenues for genetically stratified patients.

overall_design: We performed  RNA-seq to investigate the impact of USP47 deficiency on cellular pathways.We also performed  Cut&Tag to investigate allele-specific enrichment of H3K27ac at rs72856331 region in gastric cancer cells  In this study, samples for each condition were collected in biological duplicates. The corresponding control cells were treated with vehicle only (DMSO) at the same vol/vol dilution.

first: Bolin

last: Tao

first: Fei

middle: X

last: Chen


title: Pathogen-derived glyoxylate inhibits Tet2 DNA dioxygenase to facilitate bacterial persister formation

summary: Resistance, tolerance and persistence enable pathogenic bacteria to survive antibiotic treatment and are associated with an elevated risk of treatment failure and relapsing infections. The mechanism underlying bacterial antibiotic persister formation is not well understood. Here, we show that glyoxylate, a metabolite originally evolved to allow bacteria to utilize alternative carbon sources for optimal growth and pathogenicity, also serves as a signaling molecule to alter host gene expression and support persister formation. Specifically, we discovered glyoxylate interacting with TET2 DNA dioxygenase through an in-silico screen of human metabolome. We further show that Salmonella-produced glyoxylate inhibits the activity of Tet2 to suppress the expression of pro-inflammatory genes and attenuate host immune defense. Catalytic inactivation of Tet2, by genetic knock-in mutation, glyoxylate production by Salmonella, or exogenous glyoxylate treatment, facilitates bacterial persister formation in both murine and human macrophages. Conversely, stimulating TET2 with vitamin C or blocking Salmonella production of glyoxylate counters bacterial antibiotic resistance and improves the infection treatment outcomes. In conclusion, our study reveals a novel signaling function of glyoxylate in gene regulation beyond energetic and biosynthetic metabolism. Our findings also suggest that stimulating TET activity within host cells represents a potential therapeutic strategy to combat bacterial persistence.

overall_design: We performed TT-seq in BMDMs infected with different S. Tm strains to investigate the role of  glyoxylate-Tet2 in regulating transcription. The reads passed the quality check were aligned to the mouse mm10 genome. In this study, samples for each condition were collected in biological triplicates.

first: Zhenning

first: Zhouli

last: Cheng

first: Dan

last: Ye


title: DAXX is required for spermatogenesis and governs the silencing of LINE1 during meiosis in male

status: Public on Apr 01 2025

city: Wuhan

first: shen

last: jin

state: Hubei

address: No. 299, Bayi Road, Wuchang District, Wuhan City

institute: Wuhan university

summary: The disinhibition of transposon elements (TEs) is a significant threat to male reproduction, particularly during the delicate process of spermatogenesis. Here we identify that Death associated protein 6 (Daxx), a potent transcription repressor and an H3.3 chaperone essential for the TEs silencing during spermatogenesis. DAXX-deficient mouse display delayed meiotic progression, reduced production of spermatids, deformed spermatozoa and age-dependent decline in male fertility. We demonstrate that young long-interspersed nuclear elements (LINE1) and endogenous retroviral elements (ERVs) subfamilies, were upregulated in meiotic spermatocytes of Daxx null testes. Further study found that the Daxx mutant meiotic cells exhibit DNA hypomethylation in TEs. In summary, we have identified DAXX as a previously unknown key regulator of spermatogenesis that may function as an epigenetic regulator to silence young LINE1 by DNA methylation.

overall_design: This submission includes RNA-Seq(3 replicates), smallRNA-Seq(2 replicates), ATAC-seq(3 replicates), and WGBS sequencing(2 replicates) data from testicular spermatogonia and round sperms derived from wild-type and DAXX gene knockout mice. The samples aim to investigate the effects of DAXX gene deletion on reproductive health. The dataset comprises biological replicates for each condition, including both control (wild-type) and experimental (knockout) groups, to ensure statistical robustness and reproducibility of results

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