title: Vostok (CG11504):  A New Looping Factor for the Organization of the Regulatory Genome in the Drosophila Brain

status: Public on Jun 02 2025

city: Princeton

first: Michael

last: Levine

state: New Jersey

address: Icahn lab, Princeton University

institute: Princeton University

summary: The Drosophila regulatory genome is organized in a hierarchical series of topological associating domains (TADs) and intra-TAD regulatory loops.  High-resolution Micro-C maps identified ~645 such loops in the larval brain of Drosophila, spanning distances of 25 kb to 250 kb.  Many of these loops are associated with genes encoding neural adhesion proteins implicated in the formation of specific synapses, including Dprs, Dips, Sides and Beats.  They are formed by interactions of pairs of tethering elements that contain simple repeated sequence motifs, such as GAGAG.  Approximately 10% (64/645) of the loops are lost or diminished in larval brains obtained from homozygous mutants lacking the GAF (GAGA-associated factor) POZ oligomerization domain.  We also present evidence for a second looping factor, the MADF-containing Vostok protein, which recognizes a GCAACA motif that is over-represented in brain tethering elements.  There is a loss of 47 of the loops (7%) in larval brains obtained from Vostok mutants. These losses are associated with diminished expression of associated genes, suggesting impaired enhancer-promoter interactions.  Only 9 loops are disrupted in both Vostok and GAF mutants, raising the possibility of a combinatorial code for tether-tether interactions.  Support for this possibility stems from the observation that two previously identified meta-loops spanning 6 Mb rely on both GAF and Vostok. We discuss the prospects of using different combinations of looping factors to produce unlimited 3D associations of genetic loci in animal genomes.

overall_design: Micro-C and bulk RNA-seq on Vostok mutant to examine the gene function on chromatin organization and transcription

first: Jie

last: Hu

first: Xiao

last: Li

first: Lomaev

last: Dmitry

first: Nadezhda E.

last: Vorobyeva

first: Maksim

last: Erokhin

first: Darya

last: Chetverina


title: Profile in circulating neutrophils from COPD patients

status: Public on May 28 2025

city: Verona

first: Barbara

last: Mariotti

state: Verona

address: strada le grazie 8

department: Medicine

country: Italy

institute: University of Verona

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Characterization of the transcriptional profile of circulating neutrophils from COPD patients [RNA-Seq]

summary: The aim of this study is to comprehensively charatcterizethe transcriptional and epigenetic profile of circulating neutrophils from COPD patients and to explore correlations with neutrophils’ functional dysregulation and clinical disease parameters.

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data from circulating neutrophils purified from COPD patients and sex- and age-matched control donors.

first: Bazzoni

last: Flavia

first: Mariotti

last: Barbara


title: Large B-cell lymphoma microenvironment archetype profiles (LymphoMAPs). [macrophage]

status: Public on May 27 2025

city: Houston

last: Green

state: Texas

address: 7455 Fannin Street

department: Department of Lymphoma/Myeloma

country: USA

institute: The University of Texas MD Anderson Cancer Center

summary: Large B-cell lymphomas (LBCL) are clinically and biologically heterogeneous lymphoid malignancies with complex microenvironments that are central to disease etiology. Here we have employed single-nucleus multiome profiling of 232 tumor and control biopsies to characterize diverse cell types and subsets that are present in LBCL tumors, effectively capturing the lymphoid, myeloid, and non-hematopoietic cell compartments. Cell subsets co-occurred in stereotypical Lymphoma Microenvironment Archetype Profiles (LymphoMAPs) defined by; (i) a sparsity of T-cells and high frequencies of cancer-associated fibroblasts and tumor-associated macrophages [FMAC]; (ii) lymph node architectural cell types with naïve and memory T-cells [LN]; or (iii) activated macrophages and exhausted CD8 T-cells [TEX]. Divergent patterns of cell-cell communication underpinned the transcriptional phenotypes of archetype-defining cell subsets resulting in exclusion, support or suppression of T-cells, respectively. Consistent with this, LymphoMAPs were associated with significantly different clinical outcomes following CD19 CAR T-cell therapy.

overall_design: Peripheral blood-derived monocytes were isolated from cryopreserved peripheral blood mononuclear cells obtained from 3 different healthy donors (Stemcell) using pan-monocyte isolation kit (Miltenyi) with autoMACS Neo cell separator (Miltenyi) according to the manufacturer’s instructions. Cells were cultured in ImmunoCult SF Macrophage medium (Stemcell) containing 50 ng/mL of recombinant human M-CSF (Stemcell) in temperature-responsive polymer-treated UpCell plates (Thermo Fisher) for 4 days, followed by either supplementation with 50 ng/mL of recombinant human IFN-gamma (Stemcell) or replacement with supernatant of exhausted T-cells (Tex sup) for an additional 2 days. For Tex sup production, a serial killing assay was conducted using healthy donor-derived CAR T cells and HT cell line, starting at a 1:1 ratio in IMDM (Gibco) supplemented with 10% FBS (Gibco). HT cells were added every 2 days along with medium exchange. The supernatant was collected on day 10 and then cryopreserved until use. Tex sup and ImmunoCult SF macrophage medium were mixed at a 1:1 ratio and supplemented with 50 ng/mL rhM-CSF. RNA was extracted using RNeasy micro kit (QIAGEN) according to the manufacturer’s protocol after washing the cells with PBS, followed by library preparation for RNAseq.


title: Single cell RNA sequencing data obtained from aortic specimens of Fbn1G234D/G234D mouse model

status: Public on May 30 2025

city: Tsukuba

first: Erna

last: Raja

address: 1-1-1 Tennodai

department: TARA center

country: Japan

institute: University of Tsukuba

summary: We generated a novel genetic mouse model of fatal aortic dissection by introducing a pathogenic variant of Fbn1 (Fbn1G234D/G234D), identified in a patient with familial aortic dissection, into mice using the CRISPR/Cas9 system. To investigate the cellular heterogeneity underlying the progression of aortic dissection, we performed single cell RNA sequencing on aortic tissues obtained from Fbn1G234D/G234D (AD) and wild-type mice (WT).

overall_design: Following anesthesia, aortic tissues—including the ascending aorta and aortic arch up to the left subclavian artery—were collected from 3- and 5-week-old wild-type (WT) and Fbn1G234D/G234D mutant (AD) mice. The tissues were enzymatically digested to generate single-cell suspensions, which were then processed using the Chromium™ Single Cell Platform (10x Genomics) according to the manufacturer’s protocol. A total of eight single-cell suspensions were prepared for the study. For 3-week-old mice, the first batch included pooled samples from WT (n=2) and AD (n=2), and the second batch included another set of pooled WT (n=2) and AD (n=2). Similarly, for 5-week-old mice, the first batch consisted of WT (n=2) and AD (n=2), and the second batch included WT (n=3) and AD (n=3).

first: Kenichi

last: Kimura

first: Eri

last: Motoyama

first: Keiichi

last: Asano

first: Ryutaro

last: Ishii

first: Hiromi

last: Yanagisawa


title: Large B-cell lymphoma microenvironment archetype profiles (LymphoMAPs). [tonsil frc]

overall_design: Tonsillar fibroblastic reticular cells (tFRCs) were isolated from fresh tonsils. The cells were passaged for six generations in Insulin-Transferrin-Selenium (Thermo Fisher) containing Dulbecco's Modified Eagle Medium (DMEM, Corning) supplemented with 10% fetal Bovine serum (FBS) and Penicillin (100 units/mL)-streptomycin (100 µg/mL). The tFRCs were stimulated with 10 ng/mL and 50 ng/mL TGFB (Peprotech). The cells were harvested after 48 hours post treatment and subjected to bulk RNA sequencing.


title: Single-cell sequencing of CD45+ cells isolated from nasal mucosa of mice

city: Shanghai

first: Jin

last: Hou

address: 800 Xiangyin Road

country: China

institute: Second Military Medical University

summary: To explore the impact of nasal commensal viruses on the onset and progression of allergic rhinitis, We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of CD45+ cells in the nasal mucosa of control and AR mice treated with Vehicle or Ribavirin.

overall_design: CD45+ cells were isolated from nasal mucosa of mice using magnetic beads .Using 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’V3.1 Reagent Kits (10X Genomics, Pleasanton, CA) to measure single-cell RNA sequence (3' scRNA-seq) to comprehensively characterize the lung immune mincroenvironment.

first: Ye

last: Zhou

first: Zhixuan


title: Enhanced Polar Auxin Transport and Reduced Brassinosteroid Activity Drive Internode Elongation in Chinese Fir (Cunninghamia lanceolata)

status: Public on May 25 2025

city: Fuzhou

first: Yu

last: Chen

state: Fujian

address: NO.15 Shangxiadian Road

institute: Fujian Agriculture and Forestry University

summary: Knot-free timber production in Cunninghamia lanceolata depends critically on internodal characteristics, yet the mechanisms governing internode elongation remain poorly understood, hindering breeding efforts for longer-internode varieties. In this study, we selected two clones with distinct internodal traits (the C1 clone exhibited a 25.03% longer internodal length than the C11 clone) as materials. Enzyme-linked immunosorbent assay (ELISA) and RNA sequencing were used to investigate dynamics in endogenous hormones and transcriptional regulation in internodal growth. Results showed that the difference in indole-3-acetic acid (IAA) rhythms in apical buds is a key factor of C1?s longer internodal growth; higher levels of IAA and cytokinins in the apical buds of C1 may support sustained internodal growth; upregulated IAA-related genes in upper phloem (PIN1 and SAURs), which are involved in polar transport and signal response, indicates a stronger capacity to establish apical dominance. Hormone transport may be regulated by very long-chain fatty acids (VLCFAs). Consistent with reduced brassinosteroid activity, genes involved in VLCFA biosynthesis and transport were generally lower in C1, implying excessive VLCFA accumulation in C11 may be negative to IAA transporting and internode growth. This study offers a preliminary insight into internodal growth mechanisms influenced by hormone biosynthesis and transport in C. lanceolata., providing a basis for genetic improvement, germplasm selection, and exogenous hormone applications in knot-free timber cultivation.

overall_design:
RNA-seq profiling of the Apical Bud (AB), Upper Phloem (UP) and Lateral Bud (LB) tissues of two Chinese fir clones (C1 and C11) with obvious differences in growth and branching characteristics.

UPDATE: [May-07-2026] The title and summary of GSE297964 were updated.

first: Chao

last: Wu

first: Fang-fang

last: Wang

last: Ma

first: Ling-peng

last: Ye

first: Shi-yan

last: Mu

first: Ya-ting

last: Yang

first: Xiao-yu

last: Qu

first: Ya-ling

last: Zhang

first: Shu-bin

last: Li

first: Shan-shan

last: Xu

first: Xiang-qing

first: Guang-qiu

last: Cao

first: Si-zu

last: Lin


title: Characterization of H3K4me3 profile in circulating neutrophils from COPD patients [ChIP-Seq]

first: Barbara

last: Mariotti

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modification H3K4me3 in circulating neutrophils from COPD patients and sex- and age-matched control donors.

first: Bazzoni

last: Flavia

first: Mariotti

last: Barbara


title: Tumor CD45+ cells and spleen LY6G+ PMNs isolated from Hdc-GFP mice with subcutaneous ACKP syngeneic GC line-established tumors and treated with TFF2-MSA and/or anti-PD-1 therapies.

status: Public on May 23 2025

city: Sydney

first: Chenkai

state: NSW

address: 11 Julius Avenue

country: Australia

institute: CSIRO

summary: We designed a novel TFF2-MSA peptide as a CXCR4 partial agonist, and used it either alone or in combination with anti-PD-1 to treat established ACKP tumors. PMNs are known to be highly heterogenous, thus these tumors are grown in Hdc-GFP host mice to trace Hdc+ PMN subsets. We then used single cell-RNA sequencing (scRNA-seq) to elucidate the effect of TFF2-MSA on tumor and spleen PMNs, and more broadly the tumor microenvironment.

overall_design: The CD45+ cells were isolated with subcutaneous syngeneic ACKP tumors following 3 cycles of treatment with vehicle, TFF2-MSA, anti-PD-1, or their combination. To detect the systemic effect of TFF2-MSA on PMNs, LY6G+ PMNs were isolated from the spleens of ACKP tumor-bearing mice following the vehicle, TFF2-MSA, and TFF2-MSA plus anti-PD-1 treatments. A spleen PMN sample from tumor-free mice was included to identify tumor-induced effects on PMNs. To increase the visibility of PMNs in scRNA-seq, given their low RNA content, we employed a strategy of mixing Ly6G+ tumor PMNs with total CD45+ cells isolated from the same tumors at a 1:2 ratio during sample preparation for scRNA-seq analysis.

first: Jin

last: Qian

first: Timothy


title: Therapy of allergic rhinitis using ribavirin spray to clear nasal commensal viruses

status: Public on May 20 2025

first: Ye

last: Zhou

address: Xiangyin Road

department: National Key Laboratory of Immunity & Inflammation

institute: Naval Medical University

summary: To elucidate the potential role of commensal viruses in the etiology of AR, we performed a metagenomic analysis of nasal mucosa to identify commensal viruses in the nose of mice. To evaluate the potential role of these commensal viruses in AR, we reduced them in the nose of mice by administrating intranasal drops of vehicle (Vehicle group) or broad-spectrum antiviral drug ribavirin daily, starting at 4-week-old and lasting for three weeks (Ribavirin group). These mice were also administrated with PBS, OVA, or HDM to induce AR.

overall_design: Nasal mucosa was obtained from mice that were administered intranasal drops of either vehicle or ribavirin, together with PBS, OVA, or HDM. The nasal tissue samples were then subjected to metatranscriptomic sequencing to assess the abundance of viruses.

last: Hou


title: Comparative study of transcriptome expression in water extract and ethanol extract of Schisandra chinensis

status: Public on May 19 2025

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

country: South Korea

institute: Korean Institute of Oriental Medicine

summary: This study aimed to identify the mode of action of Schisandra chinensis water extracts (SCW) and  Schisandra chinensis ethanol extracts (SCE) in SW1783 cell line.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for SCW (500 ug/mL, 100 ug/mL, and 20 ug/mL, respectively), SCE (310 ug/mL, 62 ug/mL, and 12.4 ug/mL) and vehicle control (DMSO).


title: Whole genome bisulfite sequence in heat treated rice seeds

city: Fukuoka

first: Yushi

last: Ishibashi

state: Fukuoka

address: 744 Motooka, Nishi-ku

department: Department of Bioresource Sciences

institute: Kyushu University, Faculty of Agriculture

type: Methylation profiling by high throughput sequencing

summary: We report the relationship between transgenerational growth and  profiling of DNA methylation in rice seeds treated with heat.

overall_design: Examination of DNA methylation in seeds treated with heat.

first: Ishibashi

last: Yushi

first: Suriyasak

last: Chetphilin


title: The constitutive 20S proteasome is required for the maintenance and differentiation of spermatogonia in mice

city: Hang Zhou

first: Chao

last: Yu

address: 866 Yuhangtang Rd, Xi Hu Qu

institute: Zhejiang University

summary: Proteasomes undergo dynamic changes in their types and activities during mammalian spermatogenesis. While the spermatogenesis-specific 20S proteasome (s20S), characterized by PSMA8 substitution of PSMA7, is known to be essential for meiosis I completion, the functions of the constitutive PSMA7-containing 20S proteasomes (c20S) in spermatogenesis remain poorly understood. Here, we show that c20S proteasomes are required for the maintenance and differentiation of spermatogonia. PSMA7 is ubiquitously expressed in male germ cells beginning at the early spermatogonial stage, preceding PSMA8 expression. Conditional ablation of Psma7 using Stra8-Cre impairs proteasomal degradation in differentiating spermatogonia, leading to male infertility. Single-cell RNA sequencing analysis reveals that PSMA7-deleted germ cells are arrested at the differentiating spermatogonia stage and fail to enter meiosis. Notably, sufficient overexpression of PSMA8 restores normal spermatogenesis in Psma7-null germ cells, suggesting a potential complementarity of s20S to c20S. Therefore, our results add critical insights into the complex regulation of proteasomal degradation during spermatogenesis.

overall_design: Testes were collected from C57BL/6 mice at postnatal day 13 (PD13), comparing control (Psma7 F/+, WT) and conditional knockout (Psma7 F/-;Stra8-Cre KI/+, Psma7_s8ko) genotypes, and analyzed by scRNA-seq.

first: Anxuan

last: Fang

first: Huiwen

first: Ying

first: Jiangxu

last: Wu

first: Qianting

first: Liang


title: Mitochondrial fusion controls the development of specialized mitochondrial structure and metabolism in rod photoreceptor cells

status: Public on May 17 2025

city: Madison

first: Ryo

last: Hagimori

state: WI

address: 425-G Henry Mall

department: Department of Medical Genetics

institute: University of Wisconsin-Madison

summary: Mitochondria are dynamic organelles that undergo continuous morphological changes, yet exhibit unique, cell-type-specific structures. In rod photoreceptor cells of the retina, these structures include elongated mitochondria in the inner segments and a distinct, large, circular mitochondrion in each presynaptic terminal. The mechanisms underlying the establishment and maintenance of these specialized mitochondrial morphologies, along with their functional significance, are not well understood. Here, we investigate the roles of mitochondrial fusion proteins mitofusin 1 (MFN1) and mitofusin 2 (MFN2) in shaping these structures and maintaining photoreceptor cell health. Rod photoreceptor cell-specific ablation of MFN1 and MFN2 resulted in mitochondrial fragmentation by one month of age, suggesting that mitochondrial fusion is essential for the development of photoreceptor cell-specific mitochondrial structures. Notably, the layer structures of the retina examined by light microscopy appeared unaffected at this age. Following this time period, significant photoreceptor cell degeneration occurred by three months of age. Furthermore, we showed that impaired mitochondrial fusion perturbed the balance of proteins involved in glycolysis, oxidative phosphorylation (OXPHOS), and β-oxidation, highlighting the critical role of mitochondrial fusion in ensuring the proper levels of proteins necessary for optimal energy metabolism. Additionally, we identified upregulation of cellular stress pathways such as endoplasmic reticulum (ER) stress and unfolded protein response (UPR), which arise in response to energy deprivation, and cytoprotective biosynthetic pathways mediated by CCAAT/enhancer-binding protein gamma (C/EBPγ) and mammalian target of rapamycin complex 1 (mTORC1) signaling. In summary, our findings indicate that mitochondrial fusion through MFN1 and MFN2 is vital for the development of unique mitochondrial structures and proper energy production, underscoring the fundamental importance of mitochondrial dynamics in photoreceptor cell function and survival.

overall_design: RNA-seq profiles of neutal retina from one-month-old control (cre-/-) mice and rod-specific double cKO (Rho-Cre/Mfn1flx/flx/Mfn2flx/flx) mice

first: Michael

last: Landowski

first: Vijesh

middle: J

last: Bhute

first: Tetsuya

last: Takimoto


title: The LSD1 inhibitor RN1 rescues Congenital Dyserythropoietic Anemia type II

status: Public on May 15 2025

city: Ann Arbor

first: Kaiwen

last: Deng

state: Michigan

address: 3305 NCRC Building 520

institute: University of Michigan

summary: Congenital dyserythropoietic anemia type II (CDAII) is an autosomal recessive disease resulting from loss-of-function mutations in SEC23B, which encodes a component of coat complex protein II (COPII) vesicles. We have previously shown that the expression of SEC23A, a paralogous protein for SEC23B, is significantly lower than that of SEC23B in human erythroid cells and that increased SEC23A expression rescues CDAII. In this study, we generated a human erythroid cell line that expresses eGFP from the endogenous genomic locus of SEC23A and performed a small molecule screen to identify compounds that increase the SEC23A-eGFP level. The top compound passing all filters was an LSD1 inhibitor. We validated that LSD1 inhibition with RN1 i) results in increased SEC23A mRNA and protein levels in primary erythroid cells derived from CD34+ human hematopoietic stem and progenitor cells (HSPCs), at doses that do not impair erythroid cell growth or differentiation and ii) rescues the defect resulting from SEC23B deletion in primary human erythroid cells. We validated LSD1 as the target of RN1 by showing that genetic downregulation of LSD1 also led to a profound induction of SEC23A mRNA levels in HPSC-derived erythroid cells. Subsequently, we validated our findings in vivo, demonstrating that deletion of Lsd1 in mouse erythroid cells results in increased Sec23a expression and that RN1 treatment rescues the erythroid defect observed in CDAII mice. Finally, using CUT&RUN, we found that LSD1 occupies a sequence in the SEC23A promoter, which when deleted, results in increased SEC23A expression and rescue of CDAII. These finding suggest that LSD1 occupies the SEC23A promoter, repressing SEC23A transcription and that in the setting of LSD1 inhibition, SEC23A expression is de-repressed, resulting in CDAII rescue. Therefore, using an unbiased screen, we have identified and validated a novel promising therapeutic strategy for CDAII, using a compound that inhibit LSD1 or a genetic approach based on deleting the SEC23A promoter sequence that is occupied by LSD1.

overall_design: To investigate the mechanism by which LSD1 inhibition induces SEC23A expression and rescues CDAII, we performed CUT&RUN using a well-established LSD1 antibody in day 11 and day 14 erythroid cells derived from human CD34+ HSPCs.

first: Lei

first: Yu

last: Wang

first: Rami

last: Khoriaty


title: Deciphering HAND Pathogenesis Using Single-Nucleotide Omics Approaches

status: Public on May 16 2025

city: Washington

first: Anelia

last: Horvath

state: DC

address: 2300 I St NW

department: Biochemistry and Molecular Medicine

institute: George Washington University

summary: Although antiretroviral therapy (ART) effectively suppresses HIV-1 replication to undetectable levels and restores many immune parameters in people living with HIV (PLWH), these individuals remain at elevated risk for HIV-associated comorbidities. Among the most prevalent is neurocognitive impairment—a mild form of HIV-associated neurocognitive disorders (HAND)—which affects up to 50% of PLWH. Despite extensive investigation, the precise mechanisms underlying HAND pathogenesis remain unclear, in part due to its multifactorial nature. To address this, we conducted a comparative single-nucleus multi-omics analysis—integrating RNA sequencing (RNA-seq) and chromatin accessibility profiling (ATAC-seq)—of post-mortem brain tissues from HIV-infected individuals with and without HAND, as well as uninfected controls. Our results reveal substantial dysregulation in genes involved in inflammation, innate immunity, glycosylation, and cholesterol metabolism in HIV-infected brains (HAND+ and HAND−) relative to uninfected controls. Notably, these changes were further accentuated in HAND+ samples compared to HAND−, with microglia and oligodendrocytes emerging as the most affected cell populations—highlighting their potential central role in sustaining neuroinflammation. Interestingly, we observed a disconnect between transcriptomic and epigenomic signals: many inflammation-related genes located in accessible chromatin regions in HAND+ brains were not transcriptionally upregulated. This epigenetic priming—particularly in microglia and astrocytes—is consistent with the concept of trained immunity (TRIM), wherein prior exposures epigenetically “train” innate immune cells to respond differently to subsequent stimuli. Our findings suggest that maladaptive TRIM may be a key contributor to persistent neuroinflammation and the pathogenesis of HAND in the ART era.

overall_design: paired single-nuclei multiomic RNA and ATAC sequencing profiling of HAND and Non-HAND flash frozen brain tissue samples

last: Bukrinsky

first: Dmitri

last: Sviridov

first: Tatiana

last: Pushkarsky

first: Siera

last: Martinez


title: RNA-seq data of 293T cells trasfected with long non-coding RNA Lnc#61 or vehicle pcDNA3.1, and then infected or non-infected with the H5N1 avian influenza virus CK10 strain

city: Yangzhou

first: Jiao

last: Hu

address: 48 Wenhui Road

institute: Yangzhou University

summary:
Lnc#61 is a Long non-coding RNA that inhibits the replication of H5N1 subtype of influenza A virus
However, the mechanism of  role of Lnc#61 against highly pathogenic avian influenza virus (HPAIV) H5N1 subtype in mammalian cells is largely unknown.
By functional analysis, we want to investigate host factors involved in Lnc#61's antiviral activity in infected or non-infected 293T cells

overall_design: Cell samples were collected 24h after CK10 infection, a total of three biological samples were analyzied, each of them had triplication.The samples are named 011-1-1, 011-1-2, 011-1-3,  C1-1-1,  C1-1-2, C1-1-3, wei011-1, wei011-2,  wei011-3,  weiC1, weiC2, weiC3, repectively. As for the sample name, 011-1means transfected with Lnc#61 and then infected with CK10, C1-1 means transfected with pcDNA3.1 and then infected with CK10, while wei011 means transfected with Lnc#61 but non-infection, weiC1 means transfected with pcDNA3.1 but non-infection.

first: Xinxin

last: Zheng


title: Malignant transformed cells of bladder epithelium: control CdC12-V2 vs NSUN6-knockout Malignant transformed cells of bladder epithelium

status: Public on May 13 2025

city: Guangzhou

first: Ying

last: Xiaoling

address: 250 Changgang east road, Guangzhou

institute: The second affiliated Hospital of Guangzhou Medical University

summary: m5C-specific methylated small RNA immunoprecipitation microarray analysis in CdC12-V2 vs NSUN6-knockout Malignant transformed cells of bladder epithelium

overall_design: 1-5 μg of each total RNA sample was immunoprecipitated by 4 μg anti-5-methylcytosine antibody (Mab-006-500) with 1 mg DynabeadsTM M-280 Sheep Anti-Mouse IgG (Invitrogen, 11201D) in 500 μL RIP buffer. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”. The “IP” and “Sup” RNAs were enzymatically labeled with Cy5 and Cy3 respectively in separate reactions using Arraystar’s standard protocols. The labeled RNAs were combined together and hybridized onto Arraystar Human small RNA Modification Microarray (8x15K, Arraystar) and the array was scanned in two-color channels by an Agilent Scanner G2505C.

first: Xiaoling

last: Ying

first: Yapeng

last: Huang


title: Bladder epithelial cells with different degrees of malignancy: SV1 vs SV1 Cdcl2 vs T24

summary: m5C-specific methylated small RNA immunoprecipitation microarray analysis in SV-HUC-1, Cd-SV-HUC-1 and T24 cells


title: Adipose-derived Stem cll and Stronal Vascular Fraction response to inflammation sc RNA seq

city: Providence

first: Eric

last: Darling

state: RI

address: 171 Meeting St

institute: Brown University

summary: The therapeutic potential of mesenchymal stem/stromal cells (MSCs) relies on their ability to modulate immune responses in disease and wound contexts. In this study, we present an analytical pipeline using established algorithms to better characterize the response of adipose-derived stem/stromal cells (ASCs) to in vitro inflammatory stimuli, which in turn has therapeutic benefit in the context of MSC cell therapies. By integrating single-cell RNA sequencing and bulk proteomics data of ASCs derived from the stromal vascular fraction of adipose tissue, we present a detailed characterization of the ASC response to inflammation and additionally introduce a method of relating phenotypes observed in exogenously stimulated culture conditions to subpopulations of in vivo cells. Our pipeline involves multiple benchmarks to establish concordance between single-cell and bulk assays to more comprehensively characterize the ASC response to inflammation. This study is the introduction of a practical and efficient approach to identify functionally homogeneous and therapeutically relevant cell populations from heterogeneous mixtures using computational strategies and provides deeper insight into the ASC response to inflammation.

overall_design: Stromal vascular fraction derived from human adipose tissue, as welll as passaged control (ctrl) and cytokine-stimulated (Stim) ASCs from one of the SVF donors. Stim cells were cultured in IFNg and TNFa fro 48 hours. Samples were all run on the 10x genomics single cell RNA sequencing platform.

first: Darling

last: Eric

first: Parsons

last: Adrienne

first: Ahsan

last: Nagib


title: Transcription factor NFYA directs male meiotic entry by facilitating accessible chromatin at meiotic promoters in mice

status: Public on May 10 2025

city: Stockholm

first: Masomeh

last: Askari

address: Svante Arrhenius väg 20C

country: Sweden

institute: Stockholm University

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

overall_design: Refer to individual Series


title: Transcription factor NFYA directs male meiotic entry by facilitating accessible chromatin at the promoters of genes expressed during meiosis [CUT&RUN]

summary: Meiotic prophase I characterized by homologous recombination and synapsis is an intricate step for spermatogenesis. This process entails extensive changes to chromatin and transcription. Recent studies have revealed that prior to prophase I, accessible chromatin bound by paused Pol II at meiotic gene promoters is essential for their timely activation during later stages of prophase I. However, the factor responsible for promoting accessible chromatin at meiotic gene promoters before entry into prophase I is unknown. Here, we discovered that NFYA expressed in pre-meiotic germ cells promotes accessible chromatin at meiotic gene promoters. Concordantly, conditional germline deletion of Nfya in male mice blocks meiotic entry. Functionally, our spatial and single-cell ATAC-seq data revealed that loss of NFYA in pre-meiotic cells disrupts accessible chromatin at meiotic gene promoters. Our study identifies a pioneer role for NFYA in facilitating permissive chromatin at meiotic gene promoters before meiosis, thereby controlling the timely activation of meiotic genetic program during later meiosis.

overall_design: CUT&RUN was performed to profile [H3K4me3 and  NFYA] binding sites in FACS-sorted cells from adult testis.

first: Martin

last: Säflund

first: Atiyeh

last: Eghbali

first: Mukhtar

last: Mohammed Abdi

first: Ann-Kristin Iréne

last: Östlund Farrants

first: Tianxiong

last: Yu

first: Deniz

middle: M

last: Özata


title: Haploid genome activation exposes genes with a specific chromatin signature for pollen selection

city: wuhan

first: zhu

last: bo

state: beijing

address: shi zi shan street

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

summary: Here, we obtained datasets of single cell and/or cell type transcriptomes and epigenomes of the rice male germ line isolated at the different developmental stages from hybrid and/or inbred varieties. Analysis of the data pinpoints to a premeiotic set-up of a chromatin state to instruct male germ cell-type specific gene expression during the gametogenesis, reveals that the male haploid genome activation occurs shortly after meiosis, and uncovers a specific chromatin signature for haploid gene expression which has implication in haploid and pollen selection.

sample_organism:
Oryza sativa Indica Group
Oryza sativa Japonica Group

overall_design: Germ cells were obtained by micromanipulation. DNA methylation and transcriptome libraries were constructed by scBS-seq and scRNA-seq techniques. Histone modification library was constructed using CUT&Tag technology.

first: Bo

last: Zhu

first: Feng

last: zhao


title: Sequencing de novo Mu transposon insertions across maize tissues

status: Public on May 09 2025

city: Athens

first: Brad

last: Nelms

state: GA

address: 120 E Green St

institute: University of Georgia

summary: We sequenced insertion sites for the maize Mutator (Mu) transposon in leaf, root, endosperm, and pollen from Mu-active plants and Mu-inactive controls. Inherited insertions were identified using matched tissues, and then the abundance of de novo (post-zygotic) insertions was quantified and converted to variant allele frequencies (VAF). This dataset provides insight into the abundance of new transposon insertions within heterogeneous tissues and factors that shape mutation accumulation in multicellular organisms.

overall_design: Matched tissues were collected from Mu-active plants. Endosperm samples were first obtained by seed chipping; then the chipped seed was grown to collect V2 seedling leaves, primary root, and pollen at maturity (collected between 9 and 11 AM). Two genotypes were used for these experiments: (1) Mu-active plants, generated by crossing a mu-active male parent to a mu-inactive female parent, both of the W22 maize inbred background, and (2) Mu-inactive plants, which was the W22 mu-inactive female parent of #1.

first: Justin

last: Scherer


title: Reprogramming breast cancer cells to breast cancer stem cells-like by the POU1F1 transcription factor

status: Public on May 06 2025

city: Santiago de Compostela

first: Leandro

middle: Avila

last: Concepcion

state: Coruña

address: Ave Barcelona

department: Department of Physiology, Center for Molecular Medicine and Chronic Diseases

country: Spain

institute: University  Santiago de Compostela

summary: POU1F1 (also named PIT-1) is a well-known transcription factor involved in embryonic and adult pituitary development that has also been analyzed for its role in breast cancer . This study provides compelling evidence of POU1F1 in reprogramming breast cancer cells into BCSC-like. Our data demonstrates that POU1F1 induces a BCSC-like phenotype in breast tumor cells by deregulating markers such as CD24, CD44, CD133, and ALDH. These phenotypic modifications are correlated with functional changes, i.e. higher clonogenicity, increased mammospheres formation, and increased glycolysis metabolism. In addition, using in vivo immunodeficient mice models we found that a subpopulation of ALDHhigh cells from the POU1F1 overexpressing MCF-7 cells possess high tumor-initiating capacity, high resistance to chemo- and radiotherapy, and reduced overall survival. Mechanistically, POU1F1 induces an increase in IL-6 mRNA expression and raises IL-6 in the culture medium. This activates the IL-6/JAK/STAT3 pathway, which in turn increases ALDH mRNA expression.

overall_design: RNA-seq profiling of wildtype MCF-7 cells and their overexpreesion of POU1F1 transcripcion factor.

last: Avila

first: David

last: Martinez-Delgado

first: Roman

last: Perez-Fernández


title: Single-cell gene expression profiles of mice lung tissue under PM2.5 exposure

city: Beijing

first: Guoqing

last: Feng

address: No. 30 Shuangqing Road, Haidian District

institute: Tsinghua University

summary: Numerous epidemiological studies have demonstrated a significant association between PM2.5 exposure and pulmonary diseases. PM2.5 may contribute to epithelial injury and immune dysregulation in lung cells. In this study, we provide single-cell level gene expression profiles of mouse lungs under PM2.5 exposure, offering insights into the microenvironmental alterations and physiological responses induced by PM2.5.

overall_design: C57BL/6 mice were housed and managed at the animal facility. Airborne PM2.5 was collected by air PM sampler and multi-nozzle cascade impactor (MCI) (Tokyo Dylec Co.). The collected airborne PM2.5 was exposed to mice via respiratory tract. The duration of ambient PM2.5 exposure was one month to investigate the relatively long-term physiological effects. Subsequently, fresh lung tissue of mice was cleaned and placed in tissue preservation solution. C57BL/6 mice were randomly assigned to the PM2.5 exposure group and the control group to minimize batch effects in the single-cell experiment.

first: Yu

last: Li

first: Bencheng

last: Lin

first: De

last: Hao

first: Weilai

last: Zhou

first: Wenke

last: Yuan

first: Yuwei

last: Chen

first: Qian

last: Di

first: Miao

last: He

first: Huaiyong


title: Study of epithelial-mesenchymal transition induced by POU1F1 in normal breast cells

first: Sandra

last: Rodríguez González

address: Campus Vida Avenida Barcelona, s/n, 15782, A Coruña

institute: CiMUS

summary: The failure of treatment to deal with intractable cancer cells has raised the question of whether there is a special population of cells in tumor heterogeneity that exhibit resistant phenotypes that favor micrometastasis and have the potential to cause recurrence. One of the current points of view is that most solid cancers, including breast cancer, are stem cell diseases, and that these CSCs are critical to dissemination and metastasis. Our objective is to study the role of POU1F1 in breast cancer cell plasticity. Specifically, we will evaluate whether POU1F1 could modify the phenotype of normal -epithelial- cells to induce its transformation into CSCs/BCSCs

overall_design: RNA-seq profiling of HMEC control and HMEC with POU1F1 overexpression

last: Rodríguez-González


title: Condensin Accelerates Long-Range Intra-Chromosomal Interactions

status: Public on May 05 2025

city: State College

first: Yi

state: PA

address: 406 SOUTH FREAR, UNIVERSITY PARK

institute: Penn State University

summary: The 3D genome organization plays a key role in regulating interactions among chromosomal loci. While Chromosome Conformation Capture (3C)-based methods have provided static snapshots of chromatin architecture, the kinetics of chromosomal encounters in live cells remain poorly characterized. In this study, we employ Chemically Induced Chromosomal Interaction (CICI) to measure encounter times between multiple loci pairs in G1-arrested budding yeast. Our results show that chromosome motion closely follows the Rouse polymer model, with similar diffusion parameters at all tested loci. Surprisingly, we find that long-range intra-chromosomal encounters occur significantly faster than inter-chromosomal encounters at similar 3D distances. Using targeted depletion experiments, we identify condensin, but not cohesin, as the complex responsible for these rapid intra-chromosomal interactions. This is further supported by Hi-C analysis, which reveals that condensin promotes long-distance intra-chromosomal interactions in G1 yeast. Through polymer simulations, we estimate that condensin extrudes chromatin at ~2 kb/s with a density of one complex per 1-2 Mb and a processivity of 120-220 kb. These findings uncover a novel role for condensin in shaping the interphase genome organization and provide new insights into chromosomal search dynamics in vivo.

overall_design: Hi-C experiments are performed on G1-arrested, WT yeast strain and SMC4-AID strains with/without auxin (IAA).

first: Fan

last: Zou

first: Timothy

last: Földes

first: Henrik

middle: D

last: Pinholt

first: Courtney

last: Smith

first: Leonid

last: Mirny

first: Lu

last: Bai


title: AAV-mediated silencing of Sox4 leads to long-term amelioration of liver phenotypes in mouse models of Alagille syndrome (scRNA-Seq)

status: Public on Apr 30 2025

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary: BACKGROUND & AIMS: In patients with Alagille syndrome (ALGS), bile duct paucity often leads to severe cholestatic phenotypes that can only be cured with liver transplantation. However, no mechanism-based strategies exist to enhance biliary development in ALGS or other diseases associated with bile duct paucity. We aimed to identify a therapeutic target to address this unmet clinical need. METHODS: Preclinical mouse models of ALGS lacking one copy of Jag1 in germline with or without conditional deletion of one or both copies of Sox9 with Albumin-Cre were used. Sox4 levels were reduced in these models genetically or by using adeno-associated virus serotype 8 (AAV8) vectors driving a Sox4-silencing sequence. Liver histology, biliary tree ink injection, serum chemistry, RNAscope, and single-cell RNA-sequencing (scRNA-Seq) were performed for phenotypic characterization and gene expression analysis. RESULTS: Conditional removal of one copy of Sox4 in the liver significantly improved the liver phenotypes in ALGS mouse models in a Sox9-dependent manner. RNAscope experiments showed an increase in Sox4 expression level and relative abundance of Sox4-Sox9 double-positive cells in early postnatal livers of Jag1-heterozygous mice. scRNA-Seq revealed the appearance of an intermediate hepatobiliary cluster co-expressing Sox4 and Sox9 in Jag1-heterozygous livers. AAV8-mediated Sox4 knockdown, ubiquitously or driven by the hepatocyte-specific TBG promoter, led to long-term improvement of ALGS liver phenotypes upon one injection at postnatal day 1 (P1). An AAV8 injection at P15, when the liver damage response is activated, also led to phenotypic improvement. CONCLUSIONS: Our preclinical studies provide proof of principle for AAV-mediated Sox4 knockdown in TBG+ cells as a therapeutic approach for ALGS liver disease.

overall_design: Single-cell RNA sequencing studies of preclinical mouse models of ALGS lacking one copy of Jag1 in germline compared to wild-type provide evidence of differences in cell-type distribution and differentially activated pathways.

first: Duncan

last: Fox

first: Jun

last: Xie

first: Jennifer

middle: L

last: Burwinkel

first: Josh

last: Adams

first: Kashish

last: Chetal

first: Marzieh

last: Keivandarian

first: Yaniv

last: Faingelernt

first: Sanjay

last: Subramanian

first: Mario

middle: F

last: Lopez

first: Neda

last: Zarrin-Khameh

first: Guangping

last: Gao

first: Stacey

middle: S

last: Huppert

first: Hamed

last: Jafar-Nejad


title: Trpv4 specifically inhibits p53-driven Dkk1 and Sost secretion in a novel Kcnk2+ osteolineage subpopulation to rejuvenate the aged osteo-brain axis

status: Public on Apr 23 2025

city: Shanghai

first: Kai

last: Yang

address: 197 Ruijin 2nd Road, Shanghai, 200025, China

department: Shanghai Institute of Traumatology and Orthopedics

institute: Shanghai Jiao Tong University School of Medicine

summary: This comprehensive study aims to elucidate the multi-dimensional transcriptional and epigenetic mechanisms underlying osteogenic lineage fate remodeling and bone homeostasis during aging, mechanical intervention, and targeted pharmacological therapy. Bulk RNA-sequencing (RNA-seq) was performed to evaluate global transcriptomic alterations in both brain and bone tissues across aging, treadmill exercise, and bone-targeted drug treatments. To complement the tissue-level analysis, single-cell RNA sequencing (scRNA-seq) of mouse bone models was integrated to map osteogenic heterogeneity at single-cell resolution. Additionally, CUT&Tag profiling was utilized to delineate the direct genome-wide binding landscapes of downstream transcriptional regulators orchestrating this lineage transition.

overall_design:
A total of 44 bulk RNA-sequencing samples were analyzed in this study, comprising two distinct logical sub datasets: 18 samples derived from cortical bone and brain tissues of young, aged, and exercise-trained mice to define mechanical responsiveness; and 26 samples derived from bone and brain tissues subjected to targeted pharmacological treatment and its corresponding vehicle control to evaluate therapeutic efficacy. For bone tissue isolation, an optimized cortical bone enrichment protocol was deployed: long bones were first digested with Collagenase A to remove the periosteum, followed by sagittal splitting and extensive flushing to completely eliminate bone marrow cells. The remaining purified bone fragments, enriched for endosteal and cotical bones, alongside brain cortical regions, were subjected to polyA mRNA isolation and subsequent high-throughput bulk RNA-seq profiling to evaluate systemic transcriptomic shifts.
Following the initial preparation steps, including Collagenase A digestion to completely remove the periosteum, sagittal splitting, and thorough flushing of the bone marrow cavities, the remaining long bone fragments from an 8-month-old (8M) mouse were mechanically fragmented into fine pieces. The tissue was then enzymatically dissociated with a combination of EDTA and Collagenase A for a total of 20 minutes under continuous agitation at 37°C. The resulting cell suspension was filtered through a 20-μm cell strainer to yield a high-quality, viable single-cell suspension without FACS pre-sorting, which was immediately subjected to library preparation.
Differentiating IDG-SW3 osteolineage cells were treated with Nutlin-3 for 4 hours prior to harvest to stabilize the intracellular pool. The treated cells were subsequently collected and subjected to the CUT&Tag protocol utilizing a highly specific antibody to profile the direct genome-wide chromatin binding landscape of the transcription factor p53.

first: Rong

last: Zhou

first: Xinrui

last: Li

first: Yuxin

last: Zhang

first: Jiahui

first: Yichen

last: Zhao

first: Ruonan

last: Ning

first: Longyu

last: Xu

first: Xin

first: Wei

last: Yan

first: Huitong

last: Ruan

first: Min

last: Jiang

first: Lianfu

last: Deng


title: Bacillus subtilis root biofilm social interactions influence on potato transcriptome

status: Public on Apr 24 2025

city: Ljubljana

first: Marko

last: Petek

address: Večna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

summary: To investigate bacteria-plant social interactions and their influence on plant growth and immunity on transcriptional level, we performed RNA-seq analysis in plants inoculated with B. subtilis monocultures and their combinations. The results show differences in regulation in various social interactions both at the level of processes and at the level of individual genes.

overall_design: potato shoots and roots, non-inoculated control (incubated in MS30 medium without bacteria) and Bacillus subtilis inoculated samples. B. subtilis inoculations. Two experiments were performed: 'Monocultures', with individual strains (PS-216 YFP and PS-218 YFP), and control; and 'Interactions', with individual strains (PS-216 YFP, PS-218 YFP, PS-218 mKate2), an isogenic mixture of two strains (PS-218 mKate2 + PS-218 YFP), a non-kin mixture of strains (PS-218 mKate2 + PS-216 YFP), and control. Sampling was performed in 4 biological replicates per treatment group.

first: Tim

last: Godec

first: Katja

last: Stare

first: Tjaša

last: Lukan

first: Kristina

last: Gruden


title: Microbial cancer immunotherapy reprograms hematopoiesis to enhance myeloid-driven anti-tumor immunity [Human_Multiome_Cohort2

status: Public on Apr 22 2025

city: New York City

first: Andrew

middle: Wayne

last: Daman

state: NY

address: 1300 York Avenue

department: Pathology

institute: Weill Cornell Medical College

summary: Mycobacterium bovis Bacillus Calmette-Guérin (BCG) is the vaccine against tuberculosis and an immunotherapy for bladder cancer. When administered intravenously, BCG reprograms bone marrow hematopoietic stem and progenitor cells (HSPCs), leading to heterologous protection against infections. Whether HSPC reprogramming contributes to the anti-tumor effects of BCG administered into the bladder is unknown. We demonstrate that BCG administered in the bladder colonizes the bone marrow and, in both mice and humans, reprograms HSPCs to alter and amplify myelopoiesis. BCG-reprogrammed HSPCs are sufficient to confer augmented anti-tumor immunity through production of neutrophils, monocytes, and dendritic cells that broadly remodel the tumor microenvironment, drive T cell-dependent anti-tumor responses, and synergize with checkpoint blockade. We conclude that bladder BCG acts systemically through hematopoiesis, highlighting the broad potential of HSPC reprogramming to enhance the innate drivers of T cell-dependent tumor immunity.

overall_design: Single Cell Multiomics (paired scRNA and scATACseq) on human PBMC enriched for circulating CD34+ cells. Longitudinal human samples, pre or post the 6th consecutive bladder BCG administration as treatment for bladder cancer.

middle: W

first: Anthony

middle: C

last: Antonelli

first: Gil

last: Redelman-Sidi

first: Michael

last: Glickman

first: Steven

middle: Z

last: Josefowicz


title: Microbial cancer immunotherapy reprograms hematopoiesis to enhance myeloid-driven anti-tumor immunity [Human_Mulitome_Cohort1]


title: Microbial cancer immunotherapy reprograms hematopoiesis to enhance myeloid-driven anti-tumor immunity [Mouse_LSK_ATAC]

overall_design: ATAC-seq on sorted mouse Lin- cKIT+ Sca1+ (LSKs) from either PBS or intra-bladder BCG administered animals after 5 doses of BCG.


title: Microbial cancer immunotherapy reprograms hematopoiesis to enhance myeloid-driven anti-tumor immunity [Mouse_Multiome]

overall_design: Single Cell Multiomics (paired scRNA and scATAC seq) on sorted Lineage negative (Gr1-, CD19-, CD3-, NK1.1-, CD11b-) cells from mouse bone marrow treated with PBS or BCG with 3 weekly doses.


title: Microbial cancer immunotherapy reprograms hematopoiesis to enhance myeloid-driven anti-tumor immunity [Mouse_CD45_scRNA]


title: A whole genomic CRISPR-Cas9 screen identifies the amino acid transporter SLC43A1 (LAT3) as a major determinant of oxaliplatin sensitivity in colorectal cancer cells

city: Bethesda

first: Robert

last: Robey

state: MD

address: 37 Convent Drive Rm 2112

institute: NCI

summary: Colorectal cancer (CRC) is the second leading cause of cancer deaths in the United States, with a five-year survival rate of 65%. Oxaliplatin was the first platinum drug shown to improve CRC patient outcomes and is now a common adjuvant therapy for advanced disease, yet 90% of patients develop resistance. Oxaliplatin was developed as a third-generation derivative of cisplatin, but recent evidence points to divergent modes of action. Here, genome-wide CRISPR activation and knockout screens were conducted to identify genetic changes that confer resistance to oxaliplatin in two CRC cell lines with distinct molecular backgrounds (SW620 and RKO). Guide RNAs corresponding to the neutral amino acid transporter SLC43A1 (LAT3) were the most significantly enriched in knockout screens and depleted in activation screens, suggesting a potential role for LAT3 in modulating oxaliplatin resistance. In vitro CRISPR knockout and overexpression of LAT3 in SW620 and RKO cell lines confirm increased resistance or sensitivity to oxaliplatin, respectively. Further analysis demonstrates that increased LAT3 levels corrrelate with increased intracellular levels of oxaliplatin, increased levels of DNA-platinum adducts and DNA damage, demonstrating that enhanced LAT3-mediated uptake of oxaliplatin can exert its expected mechanism of action and induce cytotoxicity. These findings may lead to a better understanding of oxaliplatin’s mode of action in CRC and can provide new insights into the interplay between essential nutrient uptake and drug transport.

overall_design: Profiling of sgRNA counts in colorectal cancer cells (SW620 and RKO) after 20 days of oxaliplatin treatment or untreated controls in whole-genome CRISPR knockout or activation screens.

first: Nisha

middle: R

last: Pawar

first: Heidi

last: Wade

first: Zoe

last: Jackson

last: Poungpeth

first: Allison

middle: V

last: Mitchell

first: Connor

middle: P

last: Jewell

first: Dalen

last: Chan

first: Pedro

last: Batista

first: Lisa

last: Jenkins

last: Gottesman


title: Human iPS cell-derived respiratory organoids as a model for respiratory syncytial virus infection

status: Public on Apr 21 2025

city: Kyoto

first: Kazuo

last: Takayama

state: Kyoto

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Center for iPS Cell Research and Application

institute: Kyoto University

summary: Respiratory syncytial virus (RSV) is a seasonal respiratory pathogen that primarily affects young children, potentially causing severe lower respiratory tract disease. Despite the high disease burden, understanding of RSV pathophysiology remains limited. To address this, advanced RSV infection models are needed. While HEp-2 cells are widely used due to their high susceptibility to RSV, they do not accurately reflect the host response of the human respiratory tract. In this study, we evaluated human induced pluripotent stem cell-derived respiratory organoids, which contain respiratory epithelial cells, immune cells, fibroblasts, and vascular endothelial cells, for their potential to model RSV infection and support pharmaceutical research. RSV-infected organoids exhibited high viral genome and protein expression, epithelial layer destruction, and increased collagen accumulation. Pro-inflammatory cytokine levels in culture supernatants also increased post-infection. Furthermore, RSV infection was significantly inhibited by monoclonal antibodies (nirsevimab, palivizumab, suptavumab, or clesrovimab), while ribavirin showed limited efficacy. These findings highlight the utility of respiratory organoids for RSV research.

overall_design: The human respiratory organoids were mechanically recovered from the culture plates, and then total RNA was collected and RNA-seq was performed.


title: Optimized low-volume Plasmodium blood sample processing protocols for untargeted transcriptomics

status: Public on Apr 16 2025

city: Antwerp

first: Anna

last: Rosanas-Urgell

address: Nationalestraat 155

department: Department of Biomedical Sciences

country: Belgium

institute: Institute of Tropical Medicine Antwerp

summary: As the importance of transcriptional variation and regulation for Plasmodium becomes more apparent, advances for non-falciparum species are hindered by our reliance on natural infections to study parasite biology. Untargeted transcriptomic research is also complicated by low parasite densities and high proportions of human genetic material, highlighting the need for optimized sample processing protocols. In this study, we used a P. knowlesi culture diluted in whole blood as a mock P. vivax natural infection to compare white blood cell, rRNA-, and globin depletion methods and RNA-seq library preparation kits to create an optimized protocol for low-volume sample processing.

overall_design:
Bulk RNA-seq of P. knowlesi mock natural infection samples (5,000 parasites/ul) processed using different combinations of white blood cell depletion methods (buffy coat removal after centrifugation (cent/pipette), Plasmodipur filter (plasmo), Plasmodipur filter + MACS column (PMACS), cellulose column (cellulose)) in comparison to a no filter control, library preparation kits (mRNA Illumina / Qiagen, total RNA Qiagen) and globin/rRNA depletion methods.
Please note that, since there was no ethical approval for sharing the human component,  filtered parasite-only fastq files are provided as raw data and the count tables do include the human component as described in the data processing description.

first: Erin

last: Sauve

first: Johanna Helena

last: Kattenberg

first: Pieter

last: Moris

last: Guetens

last: Monsieurs


title: Cutaneous lupus features specialized stromal niches and altered retroelement expression

status: Public on Apr 14 2025

city: New Haven

first: Jeff

last: Gehlhausen

state: CT

address: 333 Cedar St LCI 501

department: Yale Dermatology

institute: Yale School of Medicine

summary: Single-cell RNA and spatial sequencing of lesional and non-lesional cutaneous lupus skin compared to healthy controls. The study includes 12 single-cell samples (cutaneous lupus patients with non-lesional (5) and lesional (4) skin biopsies with healthy controls (3)) and 4 spatial transcriptomics samples (cutaneous lupus patient pre/post-Anifrolumab treatment, 1 additional CLE patient, and 1 healthy control).

overall_design: Overall design: Single-cell RNA-seq was performed on 12 samples: 5 non-lesional cutaneous lupus (CLE) samples, 4 lesional (NL) skin samples from CLE patients, and 3 healthy control (HC) samples. Additionally, 10x Visium spatial transcriptomics was performed on 4 samples: 1 from a patient with subacute cutaneous lupus (SCLE) before and after Anifrolumab treatment, 1 from a patient with discoid lupus erythematosus (DLE), and 1 healthy control sample. The study aims to investigate pathophysiology of cutaneous lupus, including interferon signatures, specialized fibroblast populations, and retroelement expression.


title: MapID-based Quantitative Mapping of Chemical Modifications and Expression of Human Transfer RNA

city: Chestnut Hill

first: Huiqing

last: Zhou

state: Massachusetts

address: 2609 Beacon St.

department: Chemistry

institute: Boston College

type: Non-coding RNA profiling by high throughput sequencing

summary: Transfer RNAs (tRNAs) carry abundant chemical modifications, and growing evidence shows dysregulation of chemical modifications on human tRNAs causes an expanding number of diseases including cancers, diabetes, neurological diseases, and mitochondrial disorders. Sensitive and robust detection and quantification of chemical modifications are critical to discovering functionally relevant and regulatory tRNA chemical modifications. Here we report a method “MapID-tRNA-seq” deploying a recently evolved processive reverse transcriptase to map modifications in human tRNAs and MapID-based data processing pipeline for de novo modification identification and tRNA expression quantification. MapIDs refer to consolidated sequences of human tRNA genes with reduced redundancy and annotations of genetic variation sites. MapID-based data processing largely improved the accuracy of modification detection and expression quantification by tRNA-seq, which otherwise got compromised from reads mis- and multi-alignment to the highly redundant human tRNA genome. “MapID-tRNA-seq” robustly detected the occurrence and stoichiometries of N1-methyladenosines, providing insights into the function and biosynthesis of N1-methyladenosine in human tRNAs. Our data revealed unique signatures of the evolved reverse transcriptase against N1-methyladenosine and four other types of chemical modifications. “MapID-tRNA-seq” provides a generalizable platform for de novo identification and quantitation of chemical modifications in human tRNAs to elucidate their functions in biology and diseases.

overall_design:
Mapping of chemical modifications in tRNAs extracted from HEK-293T cells.

Mapping of chemical modifications in tRNAs extracted from MCF10A, MCF7 and MDA-MB-231 cells

first: Mtichel

last: Tepe

first: Yitan

last: Chen

last: Carso


title: Single-cell Transcriptional Analysis Reveals Allergen-specific Signatures in Human γδT Cells

status: Public on Apr 10 2025

city: La Jolla

first: Kendall

last: Kearns

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

summary: The role of gamma-delta T (γδT) cells in immune responses to common allergens is poorly understood. Here, we utilized single-cell (sc) transcriptomic analysis of allergen-reactive γδT cells in humans to characterize the transcriptional landscapes and TCR repertoires in response to cockroach (CR) and mouse (MO) allergens. Using a novel Activation-Induced Marker (AIM) assay that allows detection of γδT cells combined with scRNA sequencing and TCR repertoire analysis, we identified both shared and allergen-specific γδT cell activation patterns and gene expression profiles. While CR extract activated both Vδ1 and Vδ2 subsets, MO extract primarily stimulated Vδ2 cells. Our analysis revealed allergen-specific clusters with distinct functional signatures, including enhanced inflammatory responses and cytotoxic effector functions in MO-specific γδT cells and natural killer cell-mediated immunity and IFNγ signaling in CR-specific populations. Comparison of allergic and non-allergic individuals highlighted differences in gene expression and TCR repertoires, including a higher IFNG expression in the CR-allergic compared to non-allergic cohorts, suggesting that phenotypic and functional differences are associated with γδT allergen responses. This study provides insights into the cellular and molecular heterogeneity and functionality of allergen-reactive γδT cells, offering a foundation for understanding their role in allergic diseases and potential therapeutic interventions.

overall_design: PBMCs were isolated from 53 donors, of which 37 were sensitized to either mouse (MO, n=17) or cockroach (CR, n=20), 1 donor was sensitized to both MO and CR, and 15 were non-allergic healthy control subjects with undetectable IgE titers for both MO and CR allergens. Briefly, after overnight resting PBMCs were stimulated with extracts (10 µg/ml) or HDMAPP (10 µg/ml), or medium alone as negative control, and incubated for 24h at 37ºC. AIM+ (CD69+CD137+) Vδ1 and Vδ2 cells were captured by fluorescence-activated cell sorting and underwent 10x single-cell RNA sequencing.

first: Sloan

middle: A

last: Davis

first: Esther Dawen

last: Yu

first: Adam

last: Abawi

first: Eric

last: Wang

first: Synaida

last: Maiche

first: Monalisa

last: Mondal

first: Pandurangan

last: Vijayanand

first: Grégory

last: Seumois

first: Bjoern

last: Peters

first: Alessando

last: Sette

first: Ricardo

last: da Silva Antunes


title: Next-Generation Mapping of the ACINUS-Mediated Alternative Splicing Machinery and Its Regulation by O-glycosylation in Arabidopsis

city: Palo Alto

first: Shouling

last: Xu

state: CA

address: 260 Panama St

department: Department of Plant Biology

institute: Carnegie Institution at Stanford

summary: Alternative splicing (AS) is a key mechanism of gene regulation, but the full repertoire of proteins involved and the regulatory mechanisms governing this process remains poorly understood. Using TurboID-based proximity labeling coupled with mass spectrometry (PL-MS), we comprehensively mapped the Arabidopsis AS machinery, focusing on the evolutionarily conserved splicing factor ACINUS, its paralog PININ, and the stable interactor SR45. Our analysis identified a high-confidence list of 315 components, including both established and novel interactors, providing strong evidence that alternative splicing is coupled to transcription and that multiple RNA processing steps occur simultaneously in plants. Selected interactors were validated through AS readouts and phenotypic analysis. Furthermore, a systematic evaluation of O-glycosylation double mutants revealed that SECRET AGENT (O-GlcNAc transferase) and SPINDLY (O-fucose transferase) modulate AS through both ACINUS-dependent and -independent pathways.

overall_design: We used whole seedlings of Arabidopsis thaliana  to explore the transcriptomic and alternative splicing changes between WT, acinus pinin, spy-4, Dex inducible SEC RNAi spy-4 lines ( mock- and Dex-treated). Four biological replicates were included for each sample type.

first: Andres V

last: Reyes

first: Shane

last: Carey

first: Sumudu S

last: Karunadasa

first: Wen-Dar

last: Lin


title: Single nucleus RNA-seq of subcortical white matter from lysophosphatidylcholine (LPC) and cuprizone toxicity mouse models

status: Public on Apr 09 2025

city: Notre Dame

first: Katrina

last: Adams

state: Indiana

address: 100 Galvin Life Science Center

department: Biology

institute: University of Notre Dame

summary: We compared the transcriptional changes in the cells of the corpus callosum, focusing on the oligodendrocyte and microglia, between LPC and cuprizone mediate demyelination. We further compared the transcriptional phenotypes to human MS patient samples. We identified distinct disease-associated oligodendrocyte states with shared pathological changes to MS, and observed a common but altered remyelination state between the models. Microglia response to demyelination is highly conserved, but human MS-associated microglia exhibit significantly more heterogeneity than we found in the mouse models. (doi: https://doi.org/10.1101/2025.03.24.645058)

overall_design: LPC: Adult (8-12wk) C57BL6 mice were injected with 1% LPC into the corpus callosum of one brain hemisphere. Saline was injected on the contralateral side. 7 days later, mice were injected with Neutral Red dye by IP 2 hours prior to sacrifice. Mice were anesthetized, perfused with cold PBS for 5mins, and the brain was dissected out into cold PBS. Coronal slices of the brain were made and corpus callosum lesions were identified by the presence of Neutral red stain. The corpus callosum lesion was dissected out and the corresponding region on the contralateral side was also collected. Tissue was placed in Eppendorf tubes, excess liquid was removed as much as possible, and tissue was flash frozen in liquid nitrogen and stored at -80 until single nuclei processing. Cuprizone: Adult (8-12wk) C57BL6 mice were fed 0.2% cuprizone chow for 5 consecutive weeks. Control mice were fed normal chow. Mice were anesthetized, perfused with cold PBS for 5mins, and the brain was dissected out into cold PBS. Coronal slices of the brain were made. The corpus callosum was dissected out for cuprizone-fed mice and normal chow-fed mice. Tissue was frozen as above, and stored at -80 until processing.

first: Erin

last: Aboelnour


title: Tubular-specific ablation of Tiki2 exacerbates inflammation in ischemia/reperfusion-induced acute kidney injury by derepressing Wnt5a/Ror signaling

status: Public on Apr 08 2025

city: Wuhan

first: Cui

last: Yang

state: hubei

address: Luoyu Road 1037

department: College of Life Science and Technology

institute: Huazhong University of Science and Technology

summary: Ischemia/reperfusion-induced acute kidney injury (AKI) occurs in several clinical conditions accompanied by inflammation, but the underlying mechanisms remain elusive. The Wnt inhibitor Tiki2 is highly expressed in the kidney with unknown function. Here, we demonstrated that Tiki2 is highly expressed in proximal tubular epithelial cells (PTECs) and is dynamically regulated in AKI. Tubular epithelial cell-specific ablation of Tiki2 aggravated immune cell infiltration and tubular injury in IR-induced AKI. Mechanistically, Tiki2 ablation increased the activity of Wnt5a/Ror signaling, which is activated in PTECs in IR-induced AKI, leading to increased active JNK/ERK signaling and the secretion of chemokines and cytokines to promote the infiltration of immune cells. Furthermore, the increased severity of injury and inflammation caused by Tiki2 ablation could be relieved by knocking down Ror2 in PTECs. Our study reveals the critical roles of Wnt5a/Ror signaling and its negative regulator Tiki2 in IR-induced AKI, which are potential therapeutic targets for treating AKI

overall_design: RNA-seq profiling of Tiki2 tubular specific knockout mice and littermate control mice kidney suffering ischemical reperfusion injury on day 7.

first: Xinjun

last: Zhang


title: Two-Stage CAR T-Cell Differentiation in Patients with Large B-Cell Lymphoma

status: Public on Apr 03 2025

city: Chicago

first: Jun

last: Huang

state: IL

address: Eckhardt, 5640 S Ellis Ave

department: Institute for Molecular Engineering

institute: University of Chicago

summary: To investigate the CAR T-cell differentiation in vivo, we performed single-cell, multi-omics analyses of CD28-costimulated CAR T cells from patients with DLBCL who were successfully treated with axicabtagene ciloleucel. Our data shows that CAR T cells undergo two distinct stages of post-infusion clonal expansion.

overall_design: Data includes CAR T cells from infusion products and peripheral blood mononuclear cells from three patients with diffuse large B-cell lymphoma who achieved a complete response to axicabtagene ciloleucel. CAR T cells were sorted from peripheral blood using CD19-tetramers. Peripheral blood CAR T cells were analyzed at multiple timepoints within 90 days following administration of the infusion product to capture the CAR T-cell expansion, peak, and contraction phases.

first: Justin

last: Kline

first: Guoshuai

last: Cao

first: Yifei

last: Hu

first: Tony

last: Pan


title: Formyl peptide receptor 2 contributes to intestinal epithelium homeostasis by regulating intestinal stem cell proliferation and differentiation [scRNA-seq]

status: Public on Mar 31 2025

first: shuting

last: Yu

address: 320 Yueyang Road, Xuhui District

institute: Shanghai Institute of Nutrition and Health

summary: To investigate the contribution of formyl peptide receptor 2 (FPR2) to intestinal epithelium homeostasis and the underlying mechanisms, we isolated small intestinal crypts from intestinal epithelial-specific knockout (Fpr2VKO) and control (Fpr2f/f) mice, isolated epithelial cells from the crypts and performed single-cell RNA sequencing (scRNA-Seq). The transcriptome profiles of Fpr2VKO and Fpr2f/f mice were compared.

overall_design: Epithelial cells were isolated from small intestinal crypts of Fpr2f/f and Fpr2VKO mice and gene expression was analyzed by single-cell RNA sequencing (scRNA-seq).

first: Shuting

first: Yingying

last: Le


title: Exonic enhancers are a widespread class of dual-function regulatory elements

city: Marseille

first: Benoit

last: Ballester

address: 162 Avenue de Luminy

country: France

institute: INSERM

summary: This study aimed to interrogate enhancer activity within a custom library of 11,999 exons enhancers candidate regulatory sequences in the K-562 cell line using the STARR-seq approach.

overall_design: A library of 11,999 candidate enhancer sequences was cloned into a STARR-seq vector and transfected into K-562 cells in five replicates, with an empty-vector control. After 24 hours, total RNA and corresponding gDNA were isolated. Libraries were constructed from mRNA-derived cDNA and from gDNA, then sequenced to identify and quantify active regulatory sequences.

first: Jean-Christophe

last: Mouren

first: Magali

last: Torres

first: Antoinette

last: Van Ouwerkerk

first: Iris

last: Manosalva

first: Frederic

last: Gallardo

first: Salvatore

last: Spicuglia


title: Transcriptome of human dermal endothelial cells treated with control or RAPTOR siRNA

status: Public on Apr 01 2025

city: Houston

first: Tu N

last: Tran

state: Texas

address: 6670 Bertner Ave,

department: Cardiovascular

institute: Houston Methodist Research Institute

summary: Cultured human dermal endothelial cells were transfected with control or RAPTOR siRNA. RNA was exacted and assessed by RNA-seq.

overall_design: We have two experimental groups: control siRNA and RAPTOR siRNA. We prepared three replicates in each group.

first: Fei

last: Han

first: Weiqing

last: Chen

first: Guangyu

last: Wang

first: Pengchun


title: Differentiation in the human urothelia is defined by distinct alternative transcript polyadenylation

first: Angela

middle: H

last: Ting

state: Tx

address: 1881 East Road

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

summary: Tissue epithelia comprise distinct cell states, yet the mechanisms that diversify their transcriptomes remain incompletely understood. The human ureter urothelium contains basal progenitors, intermediate cells, and terminally differentiated umbrella cells that maintain urinary tract barrier integrity. Although transcriptional differences are widely assumed to define these states, prior single-cell RNA sequencing (scRNA-seq) revealed highly similar global gene expression profiles. Here, we show that alternative cleavage and polyadenylation (APA) introduces a major layer of transcriptomic diversity during urothelial differentiation, largely independent of changes in total mRNA abundance. Analysis of 13,544 urothelial cells identified hundreds of differentiation-associated APA events. By single-cell imaging, we visualized APA events in the tissue, revealing their spatial specificity within the adult human ureter. Using a reporter assay, we demonstrated that the alternative 3′ UTRs in these differentiation-associated APA genes directly impacted protein expression levels. We discovered that key APA genes share conserved motifs in their 3′ UTRs, including transcription factor binding sites and Alu elements, suggesting a potential mechanism regulating poly(A) site selection. Our study establishes APA as a major source of urothelial transcriptome diversity.

overall_design: We reanalyzed previously generated 10x 3' scRNA-seq data on 10 normal human ureters (GSE184111) to identify and quantify polyadenylation site usage information in basal, intermediate, and umbrella cells of the urothelium.

first: Ninh

middle: B

first: Surbhi

last: Sona

first: Byron

last: Lee


title: RIPK2-Regulated Gene Signature Associated with Poor Prognosis in Prostate Cancer

city: Stony Brook

first: Wei

last: Yang

address: Lauterbur Drive, MART 8M-0832

institute: Stony Brook University

summary: Receptor-interacting protein kinase 2 (RIPK2) has emerged as a promising drug target in various cancers, including prostate cancer (PC). However, the absence of reliable biomarkers to assess RIPK2 activity limits patient selection for anti-RIPK2 therapies and treatment monitoring. To address this gap, we performed RNA-Seq analysis on PC cancer cell lines (22Rv1, DU145, and PC3) with CRISPR/Cas9-mediated RIPK2 knockout (RIPK2-KO) using two independent guide RNAs. This analysis identified 13 candidate RIPK2-regulated genes. Reverse transcription quantitative PCR (RT-qPCR) validated eight of these genes. Furthermore, treatment with two distinct RIPK2 inhibitors significantly reduced RIPK2 signature scores in four independent PC cell lines in a dose- and time-dependent manner. Clinical association analyses revealed that high RIPK2 signature scores correlate with metastasis and worse biochemical recurrence-free, progression-free, disease-free, and overall survival, outperforming RIPK2 mRNA levels as a prognostic biomarker. This study establishes, for the first time, a RIPK2-regulated gene signature as a potential biomarker for RIPK2 activity and PC prognosis, warranting further validation in clinical specimens to provide a much-needed tool for patient stratification and response monitoring in RIPK2-targeted therapies.

overall_design: RNA-Seq analysis of control and RIPK2-knockout 22Rv1, DU145, and PC3 cells

first: Qian

first: Sungyong

last: You


title: Revealing RNA poly(A) tail dynamics during spermiogenesis and its function to support male fertility [dRNA-seq_wildtype]

status: Public on Mar 20 2025

city: Durham

first: Marcos

last: Morgan

address: 111 TW Alexander Dr

institute: NIEHS

summary: Poly(A) tail processing of mRNAs have been shown to dictate mRNAs metabolism of a few transcripts critical for fertility, but the extent of poly(A) tail-mediated regulation at the transcriptome level remains poorly characterized. Here, we performed whole transcriptome poly(A) tail profiling of purified late spermatocytes and round spermatids using direct RNA sequencing. As the germ cells enter spermiogenesis, we show a global increase in poly(A) tail length up to ~150-nts associated with transcript stabilization.

overall_design:
Pachytene spermatocytes and round spermatids were isolated from adult mice testis using Hoescht/PI staining and FACS sorting.
Cells were isolated from C57BL/6J/B6 male mice. Each replicate is representative of a pool of 3 individual mice - 3 replicates per condition were considered for analysis.
Nanopore technologies were used to sequence the testicular transcriptome and determine mRNA poly(A) tail length.

first: Marine

last: Baptissart

first: Ankit

last: Gupta

first: Brian

middle: N

last: Papas


title: FADS2 Mediated Nrf2-SLC7A11 Axis Activation Promotes Breast Ductal Carcinoma in Situ Progression via Glutamate Efflux

status: Public on Mar 26 2025

city: Chengdu

first: Hong

state: Sichuan

address: Keyuan South Road

institute: West China Hospital, Sichuan University

summary: Elucidating the progression mechanism from ductal carcinoma in situ (DCIS), a non-obligate precursor of invasive ductal carcinoma (IDC), remains a critical challenge in oncology. Metabolic profiling of lesions with differential invasiveness may help reveal key drivers underlying DCIS progression. This study employed mass spectrometry imaging to delineate the small-molecule metabolic profiles of DCIS, DCIS with synchronous IDC, and IDC lesions. Key metabolic alterations driving DCIS-to-IDC progression were identified, including elevated fatty acid biosynthesis in tumor tissues. Comparative analyses revealed that IDC exhibited significantly higher accumulation of polyunsaturated fatty acids (PUFAs) than DCIS (P<0.05), consistent with immunohistochemical validation showing upregulated fatty acid desaturase 2 expression in IDC. DCIS lesions predominantly accumulated phosphatidylinositols with saturated/monounsaturated acyl chains, while IDC exhibited a marked enrichment of phosphatidylinositols with PUFA (P<0.01). Furthermore, IDC showed significantly reduced levels of antioxidant molecules (taurine, ascorbic acid, glutathione) and the detoxification enzyme glutathione S-transferase mu 2 compared to DCIS (P<0.05), indicating dysregulation of redox homeostasis. Strikingly, DCIS with synchronous IDC displayed metabolic signatures closely aligned with IDC, suggesting its role as a transitional state during malignant progression. These findings indicate that DCIS malignant progression exhibits metabolic dependency on PUFAs/phosphatidylinositols with PUFA and depletion of antioxidants. Therapeutic targeting of PUFA biosynthesis or redox homeostasis regulators may offer novel translational approaches for tracking and intercepting DCIS progression.

overall_design:
This study included 5 IDC, 5 DCIS, 5 DCIS with coexisting IDC, 5 DCIS with microinvasion, and 5 distant surrounding tissues (DSTs; >5 cm from tumor bed). These samples were collected from West China Hospital, Sichuan University between November 2020 to December 2021. All patients had no evidence of distant metastasis and did not receive neoadjuvant therapy.

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


title: A Deep Dive into the Functional and Spatial Heterogeneity of Lung Interstitial Macrophages [Xenium]

status: Public on Mar 28 2025

city: Lebanon

first: Claudia

last: Jakubzick

state: NH

address: 1 Medical Center Drive, Rm 626 W Borwell, PO#1250960

department: Microbiology and Immunology

institute: Dartmouth College

summary: Interstitial macrophages (IMs) are increasingly recognized for their vital roles in maintaining tissue homeostasis and orchestrating immune responses. Here, we present a comprehensive transcriptomic analysis of murine lung IMs that highlights their diverse functional roles, specialized divisions of labor, and distinct spatial organization within the lung microenvironment. Building on earlier work showing that two overarching IM subsets—CD206hi and CD206lo—encompass ten unique chemokine-expressing subpopulations that regulate immune cell recruitment and tertiary lymphoid structures, we now demonstrate that these IM subsets also exhibit distinct cytokine and receptor gene profiles, along with an extensive autocrine network that influences their migration and cytokine-driven functions. Furthermore, we identify distinct innate immune signatures, including complement components, scavenger receptors, and pattern recognition pathways (e.g., Toll-like receptors and C-type lectins), underlining their broad contributions to innate immunity. Using Xenium spatial transcriptomics, we show that IMs predominantly localize to three lung regions: bronchovascular bundles, interstitium, and periphery. CD206hi and CD206lo IMs preferentially occupy specific sub-tissular niches, likely driven by differential integrin and metallopeptidase gene expression. Additionally, chemokine expression within IMs exhibits distinct spatial localization patterns, directing the recruitment of T cells and B cells. Two summary tables were provided to outline the differential gene expression across IM subsets in the dataset. Overall, our findings advance the understanding of IM heterogeneity and their multifaceted roles in chemoattraction, inflammation regulation, innate immune defense, and tissue maintenance, while providing a high-resolution framework for investigating their localization, interactions, and contributions to lung immunity and disease.

overall_design: Two groups of C57BL/6 mice (n = 2 per group) were used for analysis: Group 1 (Naive), which received no treatment and was expected to contain steady-state interstitial macrophages (IMs); and Group 2 (LPS), treated with lipopolysaccharide (LPS; Sigma-Aldrich) administered intranasally at 10 μg in 50 μl sterile PBS (Corning) 24 hours before collection, expected to contain stimulated IMs and recruited monocytes. The samples were analyzed using Xenium spatial transcriptomics with a 100-gene panel.

first: Xin

last: Li


title: Revealing RNA poly(A) tail dynamics during spermiogenesis and its function to support male fertility [dRNA-seq_mutants]

summary: TENT5C is a terminal nucleotidyltransferase with mRNA polyadenylation activity, required for the fastening of the flagella and the head of the sperm. However, TENT5C’s role in shaping the poly(A) tail of the elongating spermatid transcriptome remains limited. Here we show that the poly(A) polymerase activity of TENT5C is required for fertility and spermiogenesis: male mice expressing catalytically inactive TENT5C (Tent5cdCat/dCat) are sterile and produce headless spermatozoa phenocopying TENT5C-deficient animals. We found that the transcript encoding for the structural proteins SMCP and ODF1 are directly targeted by TENT5C. We propose a model in which TENT5C secures the fastening of the flagella to the head of the sperm by targeting ODF1 in elongating spermatids.

overall_design:
Round (RS) and elongated (ES) spermatids were isolated from adult mice testis using Hoescht/PI staining and FACS sorting.
Cells were isolated from wt/wt male mice or mice expressing a catalytically inactive TENT5C (Tent5cdcat/dcat). Each replicate is representative of a pool of 3 individual mice - 3 replicates per condition were considered for analysis.
Nanopore technologies were used to sequence the transcriptome of round and elongated spermatids. Data were processed to measure the poly(A) tail length and the presence of 3'-end addition to mRNAs.


title: Revealing RNA poly(A) tail dynamics during spermiogenesis and its function to support male fertility [dRNA-seq_busulfan]

summary: To investigate the poly(A) polymerase activity of TENT5C in testicular somatic cells, we enriched the testis of wild-type and TENT5cdcat/dcat mice with interstitial cells by depleting germ cells with busulfan. Sequencing of busulfan treated testis revealed Insl3 transcripts with poly(A) tails almost exclusively accumulating at ~180-nts in wild-type samples. In Tent5c mutants, Insl3 transcript show gradual deadenylation down to ~60-nt with a significant depletion of the ~180-nt long tails. A significant decrease in Insl3 transcripts was also observed in TENT5cdcat/dcat busulfan treated testis compared to wild-type. These results indicate that TENT5C poly(A) polymerase is required to maintain or readenylate Insl3 poly(A) tails up to ~180-nts in interstitial cells. The shortening of the poly(A) tail may lead to transcripts decay.

overall_design:
Tent5c wt/wt or Tent5c dcat/dcat adult male mice were injected with a single dose of busulfan 20mg/kg or the corresponding vehicle. Testis were harvested 4-weeks after injection to allow for an adequate depletion of germ cells.
RNA was isolated from total testis. Each sample is representative of individual mice - 2 replicates per condition were considered for analysis.
Nanopore technologies were used to sequence the testicular transcriptome and determine mRNA poly(A) tail length.


title: The GPCR Latrophilin2 Signals via Gα13 to Regulate Epidermal Differentiation

status: Public on Mar 19 2025

city: Stanford

first: Douglas

last: Porter

address: 269 Campus Drive

department: Dermatology

institute: Stanford

summary: Latrophilin 2 (ADGRL2), an adhesion GPCR, mediates signaling through its intracellular loop 3 via a unique QQQ binding patch within the Gα13 GTPase domain, playing a critical role in the regulation of normal epidermal differentiation.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Cas9 CRISPR libraries targeting GPCRs and controls were infected via lentivirus to primary keratinocytes (two biological replicates), which were then seeded for differentiation. Differentiating cells were sorted by FACS for the differentiation marker KRT10, splitting high, medium and low KRT10 populations. The fastq files are Cas9 guide sequences either from cells infected with lentivirus or plasmid DNA. In addition, libraries were generated from progenitor and differentiated cells without sorting, leading to five samples per biological replicate and a total of ten samples. The plasmid library used to generate the lentivirus was also sequenced.

first: Xue

first: Feng

last: He

first: Georgios

last: Skiniotis

first: Paul

last: Khavari


title: Impact of ATEVs and EV-DNA on transcriptional profile of dendritic cells in lymph nodes

status: Public on Mar 06 2025

city: New Ypok

first: Mengying

last: Hu

state: New York

address: 413 E 69th St, New York, NY 10021

institute: Weill Cornell Medical College

summary: Antigen processing and presentation (APP) is essential for adaptive immunosurveillance in all nucleated cells. Here we describe a novel mechanism through which secreted factors other than cytokines, specifically extracellular vesicles (EVs) released from activated T cells (ATEVs) drive a positive feedback loop that enhances antigen presentation and immune responses in normal physiology and cancer. ATEV-induced immunogenicity relies on extravesicular double-stranded DNA (EVDNA) and granzyme B (Gzmb). ATEV-DNA is notably abundant, primarily consisting of genomic DNA enriched in copies of specific genes, including numerous APP machinery genes. Mechanistically, ATEV transfer of APP machinery genes to recipient dendritic or tumor cells is facilitated by Gzmb disruption of recipient cell nuclear integrity. DNAse treatment of ATEVs removed the majority of EVDNA, preventing APP machinery upregulation in recipient cells, which in turn failed to recruit T lymphocytes into tumors. Notably, ATEVs hold promise as an immune-boosting therapeutic, particularly in restoring MHC-I antigen processing and presentation, and synergize with checkpoint blockade therapy in several immunotherapy-refractory tumors. Collectively, our findings uncover a novel mechanism through which ATEVs boost APP and anti-tumor immunity. Gzmb-mediated nuclear transfer opens new avenues for non-viral gene delivery, offering potential for enhanced intranuclear gene transport and expression efficiency.

overall_design: Naïve C57BL/6 mice received i.v. injections retro-orbitally of PBS, 50 µg of NTEVs or 25 µg of ATEVs (containing 10 µg of EV-DNA), or 25 µg of Baseline-ZERO DNase-pretreated ATEVs every other day for in total 3 doses. Subsequently, cervical lymph nodes were subjected to FACS sorting of CD45+CD11b-CD11c+ dendritic cells (DCs) for RNAseq profiling


title: Breaking Rules: The complex relationship between DNA methylation and X-chromosome inactivation in the human placenta

status: Public on Mar 12 2025

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

country: Canada

institute: University of British Columbia

type: Methylation profiling by genome tiling array

summary:
Background: The human placenta is distinct from most organs due to its uniquely low-methylated genome. Previous research has shown that DNA methylation (DNAme) is particularly depleted in the placenta at partially methylated domains and on the inactive X chromosome (Xi) in XX samples. While Xi DNAme is known to be critical for X-chromosome inactivation (XCI) in other tissues, its role in the placenta remains unclear. Understanding X-linked DNAme variation in the placenta may provide insights into XCI and implications for prenatal development and phenotypic sex differences.
Methods: DNAme data were analyzed from over 350 human placental (chorionic villus) samples, along with samples from cord blood, amnion, chorion, and fetal somatic tissues. We characterized X chromosome DNAme variation in the placenta relative to sample variables including cell composition, maternal age, placental weight, and fetal birth weight, and compared these patterns to other tissues. We also evaluated the relationship between X-linked DNAme and previously reported XCI gene expression status in placenta.
Results: Our findings confirm that the placenta exhibits significant depletion of DNAme on the Xi compared to other tissues. Additionally, we observe that X chromosome DNAme profiles in the placenta are influenced by cell composition, particularly trophoblast proportions, with minimal variation across gestation. Notably, low promoter DNAme is observed at most genes on the Xi, regardless of XCI status, challenging known associations in somatic tissues between low promoter DNAme and XCI escape.
Conclusions: This study provides evidence that the human placenta has a distinct Xi DNAme landscape, which may inform our understanding of sex differences during prenatal development. Future research should explore the mechanisms underlying the placenta's unique X-linked DNAme profile and the factors involved in XCI maintenance.

overall_design:
DNAme data for 28 chorionic villous (placental) samples, taken from the fetal-facing side of the placenta and combined before running on either of the Illumina Infinium HumanMethylation450 or MethylationEPIC arrays in Vancouver, Canada. DNAme data from raw IDAT files were read into R, and betas were extracted using the preprocessRaw function from minfi. Methylated intensity, unmethylated intensity, and detection p values were calculated for all probes, separately in the samples run on the 450K array (n=3) and the EPIC array (n=28). The raw data (meth/unmeth/detp) is available, as ae the full beta value matrices after using preprocessRaw for both 450K and EPIC samples.

***************************************************************
IDAT files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable SNP genotyping data for open access.
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first: Amy

middle: M

last: Inkster

first: Allison

last: Matthews

first: Tanya

last: Phung

first: Seema

last: Plaisier

first: Melissa

last: Wilson

first: Carolyn

middle: J

last: Brown


title: microRNA sequencing of MSC-derived Extracellular vesicles

city: Toronto

middle: Chimisso

last: dos Santos

state: ON

address: 30, Bond Street, room 4-011

department: University of Toronto

institute: Saint Michaels Hospital

summary: Human bone marrow-derived MSCs were stimulated with Bronchoalveolar lavage fluid (BALF) from healthy individuals or patients with ARDS, Cystic Fibrosis, Cystic Fibrosis positive for Aspergillus or untreated untreated MSC. Extracellular vesicles were isolated from MSC conditioned medium following minimal experimental requirements for definition of extracellular vesicles and their functions: a position statement from the International Society for Extracellular Vesicles (J Extracell Vesicles. 2014 Dec 22:3:26913. doi: 10.3402/jev.v3.26913. eCollection 2014). In Phase 1 of this study, differential expression as well as discriminant analysis was used to identify 14 microRNAs that were differentially expressed in MSC-derived EVs from MSCs exposed to BALF from ARDS patients compared to healthy controls. The effect of EVs on cellular physiology and was demonstrated in vitro by demonstration that wwo miRNAs involved in regulation of the cystic fibrosis transmembrane conductance regulator (CFTR), miRNA-145-5p and miRNA-138-5p, were also significantly increased in ARDS BALF-exposed hMSCs EVs. Functionally, EVs from hMSCs exposed to either ARDS or HV BALF had differential on CFTR Cl- secretion by cultured primary human bronchial epithelial cells, an effect predicted to reduce mucociliary clearance.

overall_design: Translational study to demonstrate the acute respiratory distress syndrome (ARDS) inflammatory environment alters mesenchymal stromal cell (MSC) gene and protein expression as well as the microRNA (miRNA) content of MSC-extracellular vesicle (EVs). RNA was isolated from each EV preparation as described in the manuscript submitted and only samples that passed quality control with an A260/A280 above 1.80 were used for RNA sequencing (control=16; ARDS=12; HV=14). A total of 35 ul (35 ng/µl) of eRNA (EV preparation-derived RNA) was used for miRNA sequencing performed using the HTG EdgeSeq miRNA Whole Transcriptome Assay (miRNA WTA, as per manufacturer’s instructions as published). The miRNA library was sequenced on a NextSeq (Illumina, Inc., San Diego, CA) using a V3 150-cycle kit with two index reads. PhiX (Roche, Mississauga, ON, CAN). Data were returned from the sequencer in the form of demultiplexed FASTQ files, with one file per original well of the assay. The HTG EdgeSeq Parser (v. 5.0.535.3181, HTG Molecular, Tucson, AZ, USA) was used to align the FASTQ files to the probe list to collate the data. Raw read counts for the 42 samples were imported into R to perform differential expression analyses with the R package DESeq2 28. Variance stabilization transformation was used to prepare data for analyses. Significance analyses of microarrays (SAM) was run using one class analysis approach to identify miRNAs over-represented in EVs derived from control hMSCs 29 based on the normalized data using variance stabilization transformation. The delta value was set to 7 (the best delta parameter value selected by the software with the lowest False Discovery Rate (FDR]) using 1000 permutations, FDR cut-off was 0.001 (%).

first: C

first: S

last: Enes

first: D

last: Weiss


title: Unique B Cell and Germinal Center Responses in Mice with Severe versus Mild Orientia tsutsugamushi Infection

status: Public on Mar 02 2025

city: Galveston

first: Lynn

last: Soong

state: TX

address: 301 University Blvd MRB 3.132

institute: University of Texas Medical Branch

summary: We performed RNAseq on total RNA extracted from spleens isolated from mice infected with Orientia tsutsugamushi Karp or Gilliam strains, as well as mock-infected mice to investigate the unique transcriptomic environments elicited by two different Orientia tsutsugamushi strains.

overall_design: We then performed differential expression analysis and gene set enrichment anaylsis using data obtained by RNA-seq of mock infected and O. tsutsugamushi Karp- and Gilliam-infected mice (D4, D8, and D12).

first: Casey

last: Gonzales

first: Yuejin

last: Liang


title: Hepatic stellate cells regulate liver fatty acid utilization via plasmalemma vesicle-associated protein [snRNA-seq]

status: Public on Mar 04 2025

city: Odense M

first: Daniel

last: Hansen

address: Campusvej 55

country: Denmark

institute: University of Southern Denmark

summary: The liver is essential for normal fatty acid utilization during fasting. Circulating fatty acids are taken up by hepatocytes and esterified as triacylglycerols for either oxidative metabolization and ketogenesis or export. Whereas the regulation of fatty acid oxidation in hepatocytes is well understood, the uptake and retention of non-esterified fatty acids by hepatocytes is not. Here, we show that murine hepatic stellate cells (HSCs) and their abundantly expressed plasmalemma vesicle-associated protein (PLVAP) control hepatic substrate preference for fasting energy metabolism. HSC-specific ablation of PLVAP in mice elevated hepatic insulin signaling and improved glucose tolerance. Fasted HSC PLVAP knockout mice showed suppressed hepatic fatty acid esterification to di- and triacylglycerols shifting fasting metabolism from fatty acid oxidation to reliance on carbohydrates. By super-resolution microscopy we localized HSC PLVAP to caveolae residing along the sinusoidal lumen supporting a role for HSCs and PLVAP-diaphragmed caveolae in normal fasting metabolism of the liver.

overall_design: 10x Genomics single-nucleus RNA-sequencing of fasted littermate control and HSC-Plvap knockout mice

first: Kim

last: Ravnskjaer


title: Recognition of ubiquitinated histone H2A constitutes a treatment target for RSF1-driven ovarian cancer [RNA-seq]

status: Public on Mar 01 2025

city: RICHMOND

first: Hengbin

last: Wang

state: VA

address: 401 college st

institute: Virginia Commonwealth University

summary: RNA-seq results revealed that overexpression of RSF1, but not RSF1ΔUAB, induced a gene expression program enriched for cancer stem cell markers. Conversely, overexpression of a UAB domain decoy peptide reduced cell proliferation and blocked the cancer stem cell gene expression programs in OVCAR3 cells. Together, these studies reveal the critical role of recognizing H2Aub in RSF1-driven ovarian cancer and demonstrate that the interaction between RSF1 and H2Aub constitutes a druggable target for treating ovarian cancers with high levels of RSF1.

overall_design: Expression profiling by high throughput sequencing

first: Chunxu

last: Chen

first: Christiane

last: Morecock

first: Mikail

last: Bala