first: Ali

last: Abdallah

address: Joseph Stelzmann Str. 26

department: Medical Faculty

institute: University of Cologne

summary: Mimicry of neuronal features are emerging as malignant regulators of cancer growth and metastasis. Neuroendocrine (NE) cancers and small cell lung cancers (SCLC) in particular have been shown to share expression profiles marking various stages of neuronal differentiation. Yet, how these state changes are caused and malignant consequences thereof have remained unexplored.  Here, we devise a novel mouse model of SCLC recapitulating low expression of caspase 8 as seen in humans and uncover that this allows for epigenetic reprogramming towards a more aggressive and metastasising stem-cell like neuronal state. Notably, transcriptional signatures of this neuroendocrine cellular state are enriched in relapsed and metastatic human SCLC. Mechanistically, caspase 8 loss within the pre-tumoral niche promoted immunosuppression and metastasis via induction of immunogenic cell death. Inactivation of the necroptosis executioner Mixed lineage kinase domain-like protein (MLKL) neutralised caspase 8 loss-induced immunosuppression, metastasis and diminished the stem-cell like state providing genetic evidence for a role of necroptosis in promoting these effects. Collectively our data uncover an unexpected role for low expression of caspase 8 in directing neuronal-like reprogramming towards a highly metastatic stem cell-like state in SCLC.

overall_design: In order to investigate the role of low Caspase 8 in SCLC development we generated RP mice with conditional deletion of Caspase 8 (RPC mice) and inuced tumor by adeno cre inahlation. Next, from endpoint SCLC tumors of RP and RPC mice we generated cell lines  (four of each genotype) and perfomed RNA seq analysis in order to identify the effect of Caspase 8 deletion in RP tumor  cells

first: Christina

last: Bebber


title: Sensitive and unbiased genome-wide profiling of base-editor-induced off-target activity with CHANGE-seq-BE [CHANGE-seq-BE for CD40L target]

status: Public on Nov 05 2025

city: Memphis

first: Shengdar

last: Tsai

state: TN

address: 262 Danny Thomas Pl

department: Department of Hematology

country: USA

institute: St Jude Children's Research Hospital

summary: By CHANGE-seq-BE, we identified a total of 81 potential off-targets and confirmed 95.4% frequencies of on-target editing with no evident off-targets above the detection threshold compared to controls (rhAmp-seq, IDT).

overall_design: CHANGE-seq-BE applied as an IND-enabling assay to support an emergency FDA-cleared IND study to treat a patient with X-linked Hyper IgM syndrome due to CD40L mutation.

first: Garret

last: Manquen

first: Varun

last: Katta

first: Yichao

last: Li


title: RNA-seq analysis of Wild Type (WT) and Mettl3-/- (KO) BMDMs (bone-marrow-derived macrophages) Transcriptomes

status: Public on Nov 04 2025

city: Xi’an

first: Huilong

last: Yin

state: Shaanxi

address: No.169, Changle West Road

country: China

institute: Fourth Military Medical University

type: Expression profiling by high throughput sequencing

summary:
To investigate the role of METTL3-mediated m6A modification in macrophage, we performed RNA-sequencing in bone-marrow-derived macrophages (BMDMs) in wild type (WT) and Mettl3-/- (KO) mice
We then performed gene expression profiling analysis using data obtained from RNA-seq of WT and KO BMDMs

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and KO BMDMs

first: Rui

last: Zhang


title: Lack of Caspase 8 Directs Neuronal Progenitor-like reprogramming and Small Cell Lung Cancer Progression

city: Cologne

last: Grimm

address: Weyertal 115b

department: Translational Epigenetics

country: Germany

institute: University of Cologne, Medical Faculty and University Clinic Cologne

type: Methylation profiling by high throughput sequencing

summary: Mimicry of neuronal features is emerging as malignant regulator of cancer growth and metastasis. Neuroendocrine (NE) cancers including small cell lung cancers (SCLC) have been shown to share expression profiles marking various stages of neuronal differentiation. Yet, how these state changes are caused and malignant consequences thereof have remained unexplored.Here, we devise a novel mouse model of SCLC recapitulating low expression of caspase 8 as seen in humans and uncover that this allows for epigenetic reprogramming towards a more aggressive and metastasising stem-cell like neuronal state, resembling neuronal intermediate progenitor cells (nIPCs). Notably, transcriptional signatures of this cellular state are enriched in relapsed and metastatic human SCLC. Mechanistically, caspase 8 loss within the pre-tumoral niche promoted immunosuppression and metastasis via induction of immunogenic cell death. Inactivation of the necroptosis executioner Mixed lineage kinase domain-like protein (MLKL) neutralised caspase 8 loss-induced immunosuppression, metastasis and diminished the stem-cell like state providing genetic evidence for a role of necroptosis in promoting these effects. Collectively our data uncover an unexpected role for low expression of caspase 8 in directing neuronal-like reprogramming towards an immunosuppressive and highly metastatic state in SCLC.

overall_design: In order to investigate the role of low Caspase 8 in SCLC development we generated RP mice with conditional deletion of Caspase 8 (RPC mice) and inuced tumor by adeno cre inhalation. Next, from endpoint SCLC tumors of RP and RPC mice we generated cell lines (four of each genotype) and perfomed Methyl-seq analysis in order to identify the effect of Caspase 8 deletion in RP tumor cells

first: Alicja

last: Pacholewska

first: Michal

middle: R

last: Schweiger

first: Ariadne

last: Androulidaki

first: Silvia

last: von Karstedt


title: Molecular and epistatic interactions between pioneer transcription factors shape nucleosome dynamics and cell differentiation

status: Public on Nov 03 2025

city: paris

first: Pablo

last: Navarro

address: 25 rue du Docteur Roux

country: France

institute: Institut Pasteur

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

first: Rémi-Xavier

last: Coux


title: Single-cell RNA-seq of patient-derived cancer-associated fibroblast in vitro cell line models from pancreatic ductal adenocarcinoma

status: Public on Nov 01 2025

city: South San Francisco

first: Elysia

middle: Cecilia

last: Saputra

state: CA

address: 213 E Grand Ave

department: Data, AI, and Genome Sciences

institute: Merck & Co., Inc.

summary: Cancer-associated fibroblasts (CAFs) are sought after as potential therapeutic targets due to their plethora of pro- and antitumorigenic functions. Recent findings attributed this functional heterogeneity to specializations in CAF subtypes. A precise targeting of specific subtypes would thus be required to design therapies that effectively modulate CAF phenotypes, but our knowledge of CAF heterogeneity in solid tumors, particularly pancreatic ductal adenocarcinoma (PDAC), is still lacking. Here, we use single-cell transcriptomics to characterize CAF subtype heterogeneity in in vitro CAF cell lines isolated from PDAC patients and investigate subtype-resolution modulations arising from perturbing potential stromal genes. We demonstrate that co-culturing CAFs with tumor cells can produce primary cell line models that can reliably represent CAF phenotypes observed in tumors, with correlations to immuno-resistant and immuno-modulatory phenotypes. With trajectory analysis, we infer the continuum of state changes that underlie the interconvertibility of CAF subtypes. Finally, we use the immortalized CAF cell lines to perform single-cell CRISPR perturbations of candidate stromal targets, revealing not only the subtype-specific effects of the perturbations, but also the impact of model-type selection on the translatability of insights.

overall_design: Patient-derived CAFs were cultured in vitro and subjected to one of three experimental conditions: Untreated, treatment with TGFb1, or co-culturing with BxPC3 cell line. The BxPC3-CAF co-cultures were then hTERT-immortalized.

first: Shamsudheen

middle: K

last: Vellarikkal

first: Lixia

first: Hong

last: Sun

first: Suchitra

last: Natarajan

first: Federica

last: Piccioni

first: Alex

middle: M

last: Tamburino

first: Xin

last: Yu

first: Aleksandra

last: Olow


title: Western Diet-induced Visceral Adipose Tissue Inflammation Promotes Alzheimer's Disease Pathology via Microglial Activation in a Mouse Model

status: Public on Oct 31 2025

city: DAEGU

first: Soyoung

last: Kwak

address: Myeongdeok-ro 16-gil

department: Nuclear Medicine

country: South Korea

institute: Keimyung University Dongsan Hospital

summary: Introduction: Western diet (WD)-induced visceral adipose tissue (VAT) inflammation is characterized by adipocyte hypertrophy, hypoxia, and apoptosis. Epididymal white adipose tissue (eWAT), a representative VAT depot in rodents, plays a central role in WD-induced inflammation by secreting pro-inflammatory cytokines that contribute to systemic and neuroinflammation. However, the mechanistic link between WD-driven eWAT inflammation and Alzheimer’s disease (AD) pathology remains unclear. Methods: WD feeding for 20 weeks was conducted to evaluate its effects on AD-related neuroinflammation and pathology in mice. Cerebral glucose metabolism was assessed using F-18 FDG-PET. RNA sequencing of eWAT and plasma cytokine profiling identified inflammation-associated factors. In vitro assays were performed to examine the effects of these cytokines on microglial activation, neuronal viability, and IL-6/STAT3 signaling. Results: WD group exhibited significantly increased levels of neuroinflammatory markers and increased hippocampal levels of AD-related proteins including amyloid-beta oligomers, amyloid precursor protein, and phosphorylated tau. Additionally, F-18 FDG PET imaging revealed reduced glucose metabolism in the thalamus and hippocampus of WD group compared to controls. RNA sequencing of eWAT and cytokine profiling of plasma identified CCL8, CCL9, CXCL13, and IL-18 as significantly elevated pro-inflammatory cytokines. In vitro analyses demonstrated that these eWAT-associated cytokines directly activate microglial cells via the IL-6/STAT3 signaling pathway, promoting hippocampal neuronal death. Discussion: These findings elucidate a critical pathway through which WD-induced eWAT inflammation exacerbates AD pathology through a systemic–to–neuroinflammation axis, highlighting the therapeutic potential of targeting eWAT-associated cytokines to mitigate diet-associated AD progression.

overall_design: Eighteen male C57BL/6J mice were randomly assigned to either the normal diet group (control) or WD group (n = 9, Western diet for 20 weeks) to assess the impact of eWAT inflammation on AD-related pathology. Body weight, food intake, and fasting glucose were monitored, followed by behavioral tests and F-18 fluorodeoxyglucose (FDG) brain positron emission tomography (PET) imaging to evaluate cognitive function and cerebral glucose metabolism, respectively. Following the intervention, epididymal fat (as a representative of eWAT), plasma, and brain tissues were collected for analysis. eWAT inflammation, systemic cytokine levels, neuroinflammatory responses, hippocampal neuronal damage, and AD-related protein expression were comprehensively evaluated using molecular and histological techniques. eWAT-associated proinflammatory cytokines were identified through transcriptomic and proteomic analyses and validated across tissues. To confirm their eWAT origin, eWAT-removal surgery was performed in a subset of WD group, resulting in a marked reduction of these cytokines in plasma. In vitro experiments further demonstrated that eWAT-associated cytokines promoted neurotoxicity via microglial activation. Specifically, the interleukin-6/signal transducer and activator of transcription 3 (IL-6/STAT3) pathway was implicated in mediating this effect, as pharmacological inhibition of STAT3 attenuated microglia-induced neuronal damage.

first: Hae Won

last: Kim

first: Ji Sun

last: Lim

first: Jeong-Ho

last: Hong

first: Mi-Hee

first: Mee-Na

last: Park

first: Junho

last: Kang


title: Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs

city: Kansas City

first: Melanie

last: Weilert

state: MO

institute: Stowers Institute for Medical Research


title: Retinoic Acid Inhibition Alters Intestinal Composition in Zebrafish: a non-genetic model to study Hirschsprung Disease

city: Rotterdam

first: Wei

last: Zhang

address: Dr. Molewaterplein 40, 3015 GD Rotterdam

department: Clinical Genetics

country: Netherlands

institute: Erasmus MC

summary: In this study, zebrafish larvae were treated with diethylaminobenzaldehyde (DEAB), an inhibitor of RA synthesis, to induce phenotypes resembling total colonic aganglionosis. Single-cell RNA sequencing was performed on the intestinal tissue of DEAB-treated zebrafish.

overall_design: Tg(phox2bb:GFP) zebrafish embryos were treated with 20 μM DEAB  from 24 hpf until 5 dpf. At 5 dpf, zebrafish larvae were euthanized using tricaine methanesulfonate (MS-222) and the intestines were carefully dissected under a stereomicroscope. Dissected intestines were enzymatically dissociated into a single-cell suspension for single-cell RNA sequencing.

first: Naomi

last: J.M. Kakiailatu

first: Laura

last: E. Kuil

first: Eric

last: Bindels

first: Joke

last: T.M. Zink

first: Michael

last: Vermeulen

first: Emma

last: de Pater

first: Veerle

last: Melotte

first: Maria

last: M. Alves


title: Transcriptomic Profiling of Bronchial Epithelium Reveals Dysregulated Interferon and Inflammatory Responses to Rhinovirus in Exacerbation-Prone Pediatric Asthma

status: Public on Oct 30 2025

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute


title: Tumor intrinsic METTL5 induces immune resistance in ovarian cancer by suppressing ferroptosis

city: Cleveland

first: Daniel

last: McGrail

state: Ohio

address: 9500 Euclid Avenue

department: Center for Immunotherapy and Precision Immuno-Oncology

institute: Cleveland Clinic

summary: Despite approval of immunotherapy for the treatment of ovarian cancer patients, the majority of patients fail to respond to immunotherapy or relapse following initial response. These failures may be attributed to immunosuppressive mechanisms co-opted by tumor cells. However, it is challenging to use conventional methods to systematically evaluate the potential of tumor intrinsic factors to act as immune regulators in patients with cancer. To identify immunosuppressive mechanisms in non-responders to cancer immunotherapy in ovarian cancer , we firstly performed an unbiased genome-wide CRISPR immune screens to explore tumor intrinsic factors which regulates ovarian cancer cell lines response to T cell mediated killing. Then we integrated the in vitro CRISPR screen results with multi-omics clinical data to generate a sub-library including top candidates for in vivo CRISPR screen to further evaluate the role of potential tumor intrinsic factors in regulating ovarian cancer cell response to immunotherapy with using the immune checkpoint blocker. Collectively, the data provide a rich resource of novel targets for rational immuno-oncology combinations.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: For the transcriptome analysis of Mettl5-KO and negative control gRNA-transduced ID8/GC and SKOV3-Cas9 cell lines, RNAs were extracted from cells in triplicate using a Direct-zol RNA Miniprep Plus kit. RNA-seq libraries were prepared and subjected to paired-end sequencing by the Novogene.


title: Transcriptomic Profiling of Bronchial Epithelium Reveals Dysregulated Interferon and Inflammatory Responses to Rhinovirus in Exacerbation-Prone Pediatric Asthma [RNA-Seq]

summary: Host factors influencing susceptibility to rhinovirus-induced asthma exacerbations remain poorly characterized. Using organotypic bronchial epithelial cultures from well-characterized children with asthma and healthy children, this study investigated viral load kinetics and resultant host responses by bulk and single-cell transcriptomics and targeted protein analyses. Bronchial epithelium from exacerbation-prone children exhibited greater rhinovirus replication and a cascade of exaggerated downstream interferon (IFN), inflammatory, epithelial stress, and remodeling responses. These transcriptional patterns were confirmed and further refined using single-cell transcriptomics, revealing cell type-specific contributions—particularly from non-ciliated cell populations including secretory immune response, tuft, and basal cells. We observed that these post-infection differences were associated with lower pre-infection IFN-stimulated gene (ISG) expression and protein levels of the ISG CXCL10. Prophylactic IFN-β treatment reduced viral replication and normalized downstream responses, supporting low baseline (pre-infection) IFN tone as a modifiable causal determinant of host susceptibility to adverse rhinovirus-induced responses in exacerbation-prone children with asthma.

overall_design: Bronchial epithelial cells (BECs) from children with asthma (n=37) and healthy children (n=3) ages 6-18 years of age were obtained from subjects while under general anesthesia for an elective surgery using 4-mm Harrell unsheathed bronchoscope cytology brushes (CONMED®) inserted through an endotracheal tube as we have previously described (8, 42). RNA was collected from BEC cultures pre-infection and at 2d, 4d, 7d, and 10d post RV infection.

first: Basilin

last: Benson

first: Jason

last: S. Debley

first: Matthew

last: C. Altman


title: Sensitive and unbiased genome-wide profiling of base-editor-induced off-target activity with CHANGE-seq-BE [Hybrid Capture Sequencing for Cas9]

first: Shengdar

last: Tsai

summary: To assess genome-wide off-target activity of base editors and Cas9 nucleases identified by CHANGE-seq-BE, Digenome-seq, and CHANGE-seq, we performed hybrid capture sequencing for five therupatic loci (B2M, CBLB, CD7, CIITA, PDCD1) in human primary T-cells and PCSK9 in human hepatocytes. We observed high on-target editing for ABE, CBE, Cas9 mRNA edited cells and potential off-targets confirmed by hybrid capture sequencing. Our results demonstrate that CHANGE-seq-BE is highly sensitive than Digenome-seq to detect more bona fide off-targets with cellular activity ranging from 0.5% to 92.2%. Moreover, ABE exhibit more off-targets than Cas9 under same delivery conditions.

overall_design: Hybrid capture sequencing to validate bona fide off-targets sites nominated by CHANGE-seq-BE, CHANGE-seq, and Digenome-seq in primary human T-cells and hepatocytes.

first: Varun

last: Katta

first: Yichao

last: Li

first: Garret

last: Manquen


title: Imaginal discs produce neuropeptide-like precursor 1 to alleviate ER stress in response to warm temperatures

status: Public on Oct 29 2025

city: Gwangju

first: Il-Ju

last: Kim

address: 123, Cheomdangwagi-ro, Buk-gu, Gwangju, Republic of Korea

institute: GIST

summary: In mammals, prolonged heat stress induces an endoplasmic reticulum (ER) stress response that can damage internal organs. In Drosophila, larvae grow and develop into adults faster at warmer temperatures (e.g., 30°C) than at lower temperatures, but with reduced body size and fertility. In this study, we show that the neuropeptide gene neuropeptide-like precursor 1 (Nplp1) alleviates temperature-induced ER stress in imaginal discs. Warm temperatures increase production of a specific Nplp1 splice variant that inhibits PKR-like endoplasmic reticulum kinase (PERK) activation and cell death. Nplp1 inhibits Dilp8 expression through the PERK/ATF4/Yki pathway, thereby enabling imaginal disc growth and ecdysone homeostasis under warm temperature conditions. These findings provide valuable insights into how animals cope with elevated temperatures.

overall_design: For each sample, total RNA was extracted from thirty sets of larval brains and associated tissues, including salivary glands, imaginal discs, and fat bodies, dissected at 90 or 108 hours after egg laying (AEL). Dissections were performed in PBS. Total RNA was isolated using TRIzol reagent (Takara) according to the manufacturer's protocol. RNA (1 μg) was reverse transcribed using oligo(dT) primers (Promega) and Accupower RT premix (Bioneer). Sequencing libraries were generated using a poly(A)-based enrichment protocol and sequenced on the Illumina NextSeq 500 platform (single-end). Transcript-level abundance was quantified using Kallisto (v0.48.0) with the Drosophila melanogaster transcriptome index (FlyBase release r6.54)


title: T cell help awakens embryonic stem-like programs in germinal center B-cells

city: New York

first: Prokopios Alexandros

last: Polyzos

address: 413 E 69th St

institute: Weill Cornell Medicine

summary: True stem-like phenotypic plasticity is gradually lost during cellular differentiation due to the strengthening of epigenetic barriers. Here, we describe an unprecedented physiological gain of stem-like plasticity in germinal center B cells, that we termed “anaplasis”. Anaplasis was strictly dependent on help from T follicular helper cells and restricted to germinal center (GC) but not activated B cells, indicating both non- and cell-autonomous contributions to this phenotype. Anaplasis involved the transient reactivation of embryonic stem cell programs by T cell-responsive germinal center B cell transcription factors, suggesting an immunological functional checkpoint, that we show can be hijacked and even bypassed by specific lymphoma mutations. Anaplasis signatures were associated with unfavorable outcomes in B cell lymphomas, suggesting their contribution to tumor fitness. Altogether, we document a physiological re-acquisition of stem-like plasticity in germinal center B cells, which co-evolved with non cell-autonomous checkpoints linked to immune selection processes.

overall_design: Splenic B cells from mice immunized with SRBC for 9 days were pre-enriched for B220pos cells by negative magnetic enrichment and stained for Naïve (B220+ IgD+) and GC (B220+ GL7+ Fas+) B markers pooled from 2 individual male mice, before processing for scRNA-seq using Chromium Next GEM Single Cell 3' Reagent Kits v2 (10X Genomics #N-120267) according to the provider specifications. cDNA Indexed libraries were quantified using Qubit and QC using Agilent Bioanalyzer 2100. Libraries were diluted to 2 nM and clustered on an Illumina Hiseq4000. Additionally, GC and post-GC (YFP+ IgD−) from 3 individual mice were isolated similarly before processing for Single Cell 5' gene expression + B Cell Repertoire.

first: Laurianne

last: Scourzic

first: Leandro

last: Venturutti

first: Franco

last: Izzo

first: Alexander

first: Christopher

last: Chin

first: Ari

last: Melnick

first: Effie

last: Apostolou


title: A Y-linked duplication of anti-Mullerian hormone is the sex determination gene in threespine stickleback

city: Athens

last: Treaster

state: GA

address: 120 E Green St

department: Genetics

institute: University of Georgia

summary: Many taxa have independently evolved genetic sex determination where a single gene located on a sex chromosome controls gonadal differentiation. The gene anti-Mullerian hormone (amh) has convergently evolved as a sex determination gene in numerous vertebrate species, but how this gene has repeatedly evolved this novel function is not well understood. In the threespine stickleback (Gasterosteus aculeatus), amh was duplicated onto the Y chromosome (amhy) ~22 million years ago. To determine whether amhy is the primary sex determination gene, we used CRISPR/Cas9 and transgenesis to show that amhy is necessary and sufficient for male sex determination, consistent with the function of a primary sex determination gene. We find that amhy contributes to a higher total dosage of amh early in development and likely contributes to differential germ cell proliferation key to sex determination. The creation of sex reversed lines also allowed us to investigate the genetic basis of secondary sex characteristics. Threespine stickleback have striking differences in behavior and morphology between sexes. Here we show one of the classic traits important for reproductive success, blue male nuptial coloration, is controlled by both sex-linked genetic factors as well as hormonal factors independent of sex chromosome genotype. This research establishes stickleback as a model to investigate how amh regulates gonadal development and how this gene repeatedly evolves novel function in sex determination. Analogous to the “four core genotypes” model in house mice, sex-reversed threespine stickleback offer a new vertebrate model for investigating the separate contributions of gonadal sex and sex chromosomes to sexual dimorphism.

overall_design: Threespine stickleback fish embryos were sequenced for bulk gene expression on the Illumina platform. This gene expression data was used to investigate differential gene expression between males and females across early development.


title: Exposure to the organochlorine pesticide cis-chlordane induces ALS-like mitochondrial perturbations in stem cell-derived motor neurons

city: Middletown

first: Alison

middle: Linsley

last: ONeil

state: CT

address: 52 Lawn Ave

department: Chemistry

institute: Wesleyan University

summary: Amyotrophic Lateral Sclerosis (ALS) is a debilitating and incurable neurodegenerative dis-ease with unsolved etiology. Due to the large proportion of patients lacking direct disease inher-itance, understanding the environmental factors that contribute to ALS development is of high priority. Epidemiological studies have implicated pesticides and other environmental exposures as possible contributors to ALS pathogenesis. Recently, our group determined that the organo-chlorine pesticide cis-chlordane is toxic to human motor neurons in a dose-dependent manner, causing an ALS-like phenotype in culture and animals with a mode of action independent of its known GABAA antagonism. Here, we aimed to characterize downstream motor neuron pheno-types associated with cis-chlordane treatment. We performed bulk RNA sequencing, live imaging, immunofluorescent labeling, and real-time metabolic assays on stem cell-derived motor neurons to assess chlordane-associated phenotypes in vitro. We demonstrate that cis-chlordane treatment causes a highly altered mitochondrial phenotype in motor neurons, including increased produc-tion of reactive oxygen species, decreased oxygen consumption rate and ATP production, and loss of mitochondrial membrane potential. We further implicate cis-chlordane as a possible medi-ator of potent motor neuron damage, with exposure to the pesticide inducing mitochondrial phe-notypes akin to those seen in ALS. We suggest that future studies investigating the role of pesti-cides in ALS development center upon the organochlorine molecules.

overall_design: Wild type human embryonic stem cell derived motor neruons, which express GFP when mature (WA09-Islet1-GFP), were treated with either solvent (control)  or the pesticide cis-chlordane (Treated) for 16 hours and then FACS purified (GFP pos and GFP neg). The 12 samples, 3 treated GFP pos/neg, and 3 control GFP pos/neg, were then subjected to bulk RNA sequencing.

first: Daniel

last: Kulick

middle: L

last: O'Neil


title: T follicular helper cells transiently unlock a plasticity state in germinal centre B cells during the humoral immune response

summary: During the germinal centre (GC) reaction, mature B cells undergo rapid and reversible phenotypic shifts that are essential for adaptive immunity. Here we report that GC B cells, unlike other mature B cells, transiently acquire a unique epigenetic plasticity, demonstrated by their enhanced capacity to reprogram to induced pluripotent stem cells. This plasticity depends on T follicular helper (TFH) cells and is not due to increased proliferation or MYC activation. Instead, it involves weakening of B-cell identity and derepression of stem and progenitor programs driven by NF-κB and other TFH-derived signals. Thus, physiological GC plasticity is tightly constrained by the affinity maturation process of positive selection. Loss of histone 1, a chromatin compaction regulator restricting the accessibility of embryonic stem cell programs, further enhances GC plasticity by bypassing this gatekeeping mechanism. Importantly, patients with B-cell lymphoma enriched for GC plasticity signatures had worse outcomes, suggesting that this mechanism may also contribute to lymphoma aggressiveness.


title: Cas9 senses CRISPR RNA abundance to regulate CRISPR spacer acquisition

city: Ann Arbor

first: P. Lydia

last: Freddolino

state: MI

address: 1150 W. Medical Center Dr.

department: Biological Chemistry

institute: University of Michigan

summary: Prokaryotes adapt to viral challenges by acquiring CRISPR memories from invaders through a process called adaptation. Previous study showed that this process requires Cas9 complexed with its RNA partners in type II-A system. How Cas9 functions in adaptation in other type II systems is poorly understood. Here using type II-C system of N. meningitidis and meningococcal disease associated filamentous phage MDAΦ as model, we show that RNA free apoCas9 dramatically enhances adaptation efficiency and that tracrRNA and crRNA together repress rather than enhance adaptation through interacting with Cas9. We also discovered that a Cas9 lacking the recognition lobe can no longer be suppressed by its RNA partners. We demonstrate how this interplay between Cas9 and its RNA partners benefit the host bacteria by regulating adaptation during CRISPR neo-genesis and CRISPR array collapse. We further show that this regulation is a conserved process in type II-C systems. Our results uncover a brand-new adaptation regulation mechanism and demonstrate the first biological function of RNA-free apoCas9.

overall_design: MDA phage treated Neisseria meningitidis strains with genetic manipulation of CRISPR-Cas system components.

first: Xufei

last: Zhou

first: Rucheng

last: Diao

first: Christine

middle: A

last: Ziegler

first: Max

middle: J

last: Gramelspacher

first: Xin

first: P

first: Zhonggang

last: Hou

first: Yan

last: Zhang


title: A small cationic probe highly selective for RNA tertiary structure

city: Chapel Hill

first: David

last: Qiu

state: NC

address: 104 Airport Dr

institute: UNC Chapel Hill

summary: RNA is unique among the large biomolecules due to the intersection of its distinctive electrostatic properties, created by the permanent charge at each phosphate group, coupled with its ability to form diverse three-dimensional tertiary structures. We demonstrate that at rare, but distinctive, sites tertiary folding creates electronegative pockets that preferentially react with a small positively-charged chemical probe, trimethyloxonium (TMO), which alkylates RNA. TMO performs the same chemistry with RNA as the classical uncharged probe, dimethyl sulfate (DMS). Sites preferentially reactive with the TMO cation, relative to the uncharged DMS, are detected efficiently by massively parallel sequencing, at low read depths. These motifs, which we call T-sites, reflect preferential interaction of TMO at an electronegative pocket created by juxtaposition of a reactive nucleobase with non-bridging oxygen atoms, and specifically map to the centers of higher-order structural interactions and functional cores in model RNAs. T-site probing is a facile robust strategy, poised to create broad opportunities to detect and analyze RNA tertiary structures transcriptome-wide.

sample_organism:
Escherichia coli
Geobacillus stearothermophilus
Oceanobacillus iheyensis
Orthoflavivirus denguei

overall_design: In-vitro transcribed TPP riboswitch aptamer domain, Group II intron catalytic domain, and RNase P catalytic domain constructs with structure cassettes, either native sequence or various mutants, were refolded and structure was probed with TMO, DMS, or a non-reactive control. Naked RNA extracted from dengue virions was also chemically probed. Modified RNA was reverse transcribed under MaP conditions using SuperScript II. cDNA sequencing libraries were prepared and sequenced on an Illumina MiSeq instrument.

first: Jeffrey

middle: E

last: Ehrhardt

middle: Y

first: Shouhong

last: Jin

first: Caroline

last: Aufgebauer

first: Mark

last: Boerneke

first: Stacy

last: Horner

first: Kevin

last: Weeks


title: Docosahexaenoic Acid Enhances Dexamethasone-Mediated Suppression of Interferon-Regulated Genes in NZBWF1 Macrophages: Implications for Steroid-Sparing Lupus Treatment

status: Public on Oct 28 2025

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

institute: Michigan State University

summary: Introduction: Glucocorticoids (GC) are one of the most common anti-inflammatory treatments for autoimmune diseases such as systemic lupus erythematosus (lupus). Chronic use of GCs leads to several deleterious side-effects and diminished quality of life, inciting a need for steroid-sparing therapeutics. Polyunsaturated fatty acids (PUFA), such as docosahexaenoic acid (DHA), have been shown to inhibit proinflammatory and Type I Interferon (IFN) gene signatures in macrophages, which are central to initiation of autoimmunity triggered by inhaled environmental toxicants such as bacterial lipopolysaccharide (LPS). The goal of the present study was to determine whether combination treatment with suboptimal concentrations of DHA and GC in LPS-primed alveolar-like macrophages could potentiate the anti-inflammatory effects of DHA and GC individual treatment. Methods: RNAseq was used to evaluate whether DHA could potentiate the anti-inflammatory effects of the GC dexamethasone (DEX) in LPS-stimulated fetal liver-derived alveolar-like macrophages (FLAMs) isolated from NZBWF1 lupus-prone mice. FLAMs were treated were treated with suboptimal concentrations of either DHA alone, DEX alone, or DHA+DEX in combination prior to LPS stimulation (20 ng/mL) for 4 or 8 hr. Results: LPS stimulation resulted in significant enrichment of innate immunity and Type I/II IFN pathways with corresponding upregulation of gene sets falling under these pathways at both timepoints. LPS-primed FLAMs treated in combination with suboptimal concentrations of DHA and DEX exhibited combinatorial affects greater than DHA and DEX treatment alone. DHA+DEX co-treatment resulted in downregulation of innate immunity and Type I/II IFN pathways initially altered by LPS treatment. Lastly, DHA+DEX co-treatment exhibited superior downregulation of individual Type I/II IFN genes compared to DHA and DEX treatment alone. Discussion: Our findings demonstrate that while DHA and DEX can significantly alter LPS-stimulated gene expression in alveolar-like macrophages when used in high enough concentrations alone, DHA can be used to potentiate the anti-inflammatory effects of DEX when both are used at lower concentrations. This study provides promising evidence that DHA can potentially be used to lower requisite amounts GCs required to reduce inflammation.

overall_design: RNA-seq profiling of fetal liver-derived alveolar-like macrophages pre-treated with dexamethasone (DEX), docosahexaenoic acid (DHA), DHA+DEX, or vehicle, then stimulated with lipopolysaccharide (LPS) for 4 and 8 hours.

first: Lauren

last: Heine

first: Andrew

last: Thompson

first: Ingo

last: Braasch

first: Jalen

last: Jackson

first: Ashley

middle: N

last: Anderson

first: Jack

last: Harkema

last: Olive

first: James

last: Pestka

first: Olivia

middle: F

last: McDonald


title: Transcriptional profiling of sensory cells of the murine gut and vagus nerve

status: Public on Oct 27 2025

first: Robert

last: Lovelett

state: New York

address: 430 E 29th Street, 10th Floor

institute: Kallyope

summary: Sensory cells of the gut epithelium and vagus nerve are key regulators of various physiological processes including satiety and metabolism. In this study, we profile sensory cells of the gut (enteroendocrine cells, EECs) and vagus nerve (neurons) using 10X Genomics single cell sequencing.

overall_design: Mouse gut and nodose ganglion of the vagus nerve tissue were digested to single cell suspensions. FACS sorting was used to enrich transgenic mouse gut tissue for EECs. GPR41, Ngn3, NeuroD1, Tph1, Chga, Epcam, and Cldn were used to sort for different populations of EECs. 12 EEC libraries and 4 nodose libraries were generated.

first: Maja

last: Engelstoft

first: John

last: Whang

first: Maximilian

middle: G

last: Lombardo

first: Adrian

last: Heilbut

first: Shirly

last: Pinto


title: Establishment of sex-specific liver transcriptomes and H3K9me3 profiles during sexual maturity: the impact of maternal obesity [ChIP-seq]

city: Indianapolis

first: Núria

last: Morral

state: IN

address: 975 West Walnut, IB130

department: Medical and Molecular Genetics

institute: Indiana University School of Medicine

summary: The escalating prevalence of metabolic dysfunction-associated steatotic liver disease (MASLD) is strongly linked to rising obesity rates. Maternal obesity (MO) increases offspring susceptibility to metabolic disorders, including MASLD. This elevated risk could be a consequence of epigenetic modifications established during fetal development, a period highly sensitive to the maternal diet. H3K9me3, a heterochromatin hallmark, silences gene programs dispensable for differentiated cell types. This study investigated how MO influences sex-specific gene expression and chromatin architecture in offspring liver. Female mice consumed a Western-style or control diet pre-pregnancy and throughout gestation/lactation. Offspring were weaned at 3 weeks and transitioned to chow for five weeks. At 3 weeks, liver transcriptomes of control offspring were similar between sexes. However, MO significantly disrupted hepatic gene expression in both sexes, dysregulating hundreds of genes and altering H3K9me3 binding. By 8 weeks, with sexual maturity, control offspring showed substantial sex-based gene expression divergence, predominantly genes involved in immune response, cell adhesion, xenobiotic detoxification, cholesterol metabolism, and lipid partitioning. Thousands of differentially bound H3K9me3 peaks were also observed between 3 and 8 weeks, with many on the female X chromosome. Remarkably, by 8 weeks, MO offspring showed incomplete normalization of gene expression, H3K9me3 profiles, and hepatic lipid classes, emphasizing the persistent impact of maternal diet on the genomic and metabolic landscape. This study highlights inherent sex differences in liver gene expression and suggests H3K9me3's role in establishing sex-specific liver function during sexual maturation. Moreover, MO disrupts these patterns, which are not fully corrected by postnatal dietary normalization.

overall_design: Female mice consumed a Western-style or control diet pre-pregnancy and throughout gestation/lactation. Offspring were weaned at 3 weeks and transitioned to chow for five weeks. H3K9me3 ChIPseq was conducted from liver tissue.


title: HSC-derived exosomal miR-122- 5p inhibits EMT and fibrosis of intrahepatic biliary epithelial cells to alleviate primary biliary cholangitis

city: Hefei

first: Yaqin

last: Zhang

state: China

institute: The First Affiliated Hospital of Anhui Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Objective: The objective was to study the expression profile of serum exosomal ncRNAs in patients with PBC and to explore their potential molecular mechanisms.
Methods: The expression profile of ncRNAs in serum exosomes of PBC patients was analyzed by RNA-sequence. Bioinformatics analysis predicted target genes and related signaling pathways. Spearson correlation analysis and receiver operating characteristic (ROC) curve were used to explore the relationship between ncRNAs and PBC clinical indicators and application value. Primary human intrahepatic biliary epithelial cells (HIBECs) were cultured in vitro and lipopolysaccharide (LPS) induced HIBECs inflammatory injury model. The expression of miR-122-5p is regulated by miR-122-5p mimics and inhibitors. Enzyme linked immunosorbent assay (Elisa) measured levels of inflammatory cytokines. HIBECs cycle and apoptosis were detected by flow cytometry and HIBECs activity was detected by CCK8. The biomarkers of epithelium-mesenchymal transition (EMT), fibrogenesis, and p38 mitogen-activated protein kinase (MAPK) pathway were detected by real time quantitative polymerase chain reaction (RT-qPCR) and Western blot (WB). Dual luciferase reporter assay to confirm the binding of miR-122-5p.
Results: 8531 differential expressed (DE) lncRNAs and 263 DE miRNAs were identified in serum exosomes of PBC patients. RNA-sequence and verification results showed that miR-122-5p was increased in serum exosomes of PBC patients, and was positively correlated with liver injury and cholestasis indexes. Exosomal miR-122-5p combined with gp210 and sp100 could improve the sensitivity of PBC diagnosis. In vitro experiments showed that the high expression of miR-122-5p promoted the proliferation of HIBECs, and inhibited the apoptosis, EMT and fibrosis of HIBEC. TNFRSF19, p38, p-p38, and inflammatory cytokines interleukin (IL)-1β, IL-6, IL-8, IL-12, IL-17, tumor necrosis factor (TNF)-α, transforming growth factor (TGF)-β1, and interferon (IFN)-γ were down-regulated and the effect was largely reversed after blocking p38 MAPK pathway. In addition, TNFRSF19 has binding site with miR-122-5p, which is the target gene of miR-122-5p, and could regulate the level of apoptosis signal-regulated kinase 1 (ASK1). Then ASK1 further regulate the downstream p38 MAPK signaling pathway.
Conclusion: MiR-122-5p regulates ASK1 by targeting TNFRSF19 and plays an important role in EMT and fibrosis of PBC through p38 MAPK signaling pathway. MiR-122-5p may be a new marker for the diagnosis of PBC and a potential therapeutic target.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PBC and normal control serum exosomal.

first: Xiangzhi

first: Ruofei

last: Chen

first: Bing

last: Shen

first: Zongwen

last: Shuai

first: Xueqing

last: Yang


title: Establishment of sex-specific liver transcriptomes and H3K9me3 profiles during sexual maturity: the impact of maternal obesity [RNA-seq]

overall_design: Female mice consumed a Western-style or control diet pre-pregnancy and throughout gestation/lactation. Offspring were weaned at 3 weeks and transitioned to chow for five weeks. RNAseq was conducted using liver tissue


title: Combining p53 mRNA nanotherapy with immune checkpoint blockade reprograms the immune microenvironment for effective cancer therapy

status: Public on Oct 26 2025

city: Boston

first: Dan

last: Duda

state: MA

address: 55 Fruit St

department: Radiation Oncology

institute: Massachusetts General Hospital

summary: Immunotherapy with immune checkpoint blockade (ICB) has shown limited benefits in hepatocellular carcinoma (HCC) and other cancers, mediated in part by the immunosuppressive tumor microenvironment (TME). As p53 loss of function may play a role in immunosuppression, we herein examine the effects of restoring p53 expression on the immune TME and ICB efficacy. We develop and optimize a CXCR4-targeted mRNA nanoparticle platform to effectively induce p53 expression in HCC models. Using p53-null orthotopic and ectopic models of murine HCC, we find that combining CXCR4-targeted p53 mRNA nanoparticles with anti-PD-1 therapy effectively induces global reprogramming of cellular and molecular components of the immune TME. This effect results in improved anti-tumor effects compared to anti-PD-1 therapy or therapeutic p53 expression alone. Thus, our findings demonstrate the reversal of immunosuppression in HCC by a p53 mRNA nanomedicine when combined with ICB and support the implementation of this strategy for cancer treatment.

overall_design: Using murine tumor tissues collected in a time-matched manner, we employed RNA-seq to evaluate the transcriptional changes in murine RIL-175 hepatocellular carcinoma (HCC) tissues after the treatment with p53 mRNA nanotherapy or immune checkpoint blockade or the combination.

first: Xin

last: Liu

first: Jiang


title: Regorafenib combined with PD1 blockade increases CD8 T-cell infiltration by inducing CXCL10 expression in hepatocellular carcinoma

summary: Background and purpose: Combining inhibitors of vascular endothelial growth factor and the programmed cell death protein 1 (PD1) pathway has shown efficacy in multiple cancers, but the disease-specific and agent-specific mechanisms of benefit remain unclear. We examined the efficacy and defined the mechanisms of benefit when combining regorafenib (a multikinase antivascular endothelial growth factor receptor inhibitor) with PD1 blockade in murine hepatocellular carcinoma (HCC) models. Basic procedures: We used orthotopic models of HCC in mice with liver damage to test the effects of regorafenib-dosed orally at 5, 10 or 20 mg/kg daily-combined with anti-PD1 antibodies (10 mg/kg intraperitoneally thrice weekly). We evaluated the effects of therapy on tumor vasculature and immune microenvironment using immunofluorescence, flow cytometry, RNA-sequencing, ELISA and pharmacokinetic/pharmacodynamic studies in mice and in tissue and blood samples from patients with cancer. Main findings: Regorafenib/anti-PD1 combination therapy increased survival compared with regofarenib or anti-PD1 alone in a regorafenib dose-dependent manner. Combination therapy increased regorafenib uptake into the tumor tissues by normalizing the HCC vasculature and increasing CD8 T-cell infiltration and activation at an intermediate regorafenib dose. The efficacy of regorafenib/anti-PD1 therapy was compromised in mice lacking functional T cells (Rag1-deficient mice). Regorafenib treatment increased the transcription and protein expression of CXCL10-a ligand for CXCR3 expressed on tumor-infiltrating lymphocytes-in murine HCC and in blood of patients with HCC. Using Cxcr3-deficient mice, we demonstrate that CXCR3 mediated the increased intratumoral CD8 T-cell infiltration and the added survival benefit when regorafenib was combined with anti-PD1 therapy. Principal conclusions: Judicious regorafenib/anti-PD1 combination therapy can inhibit tumor growth and increase survival by normalizing tumor vasculature and increasing intratumoral CXCR3+CD8 T-cell infiltration through elevated CXCL10 expression in HCC cells.

overall_design: Using murine tumor tissues collected in a time-matched manner, we employed RNA-seq to evaluate the transcriptional changes in murine RIL-175 hepatocellular carcinoma (HCC) tissues after the treatment with immune checkpoint blockade with or without regorafenib.

first: Kohei

last: Shigeta


title: Histone 2B Monoubiquitylation regulates elongation-to-termination transition in RNA Polymerase II transcription

status: Public on Nov 02 2025

city: Bronx

first: Pabitra

middle: Kumar

last: Parua

state: NY

address: 1300 Morris Park Avenue, Forchheimer/236

department: Molecular Pharmacology

institute: Albert Einstein College of Medicine

summary: RNA Polymerase II (Pol II)-dependent transcription is meticulously regulated during initiation, elongation, termination, and two pivotal transitions: from initiation to elongation and from elongation to termination 1. The successful transition from elongation to termination is vital for accurate transcription termination 2,3. While elongation and termination have been extensively studied, the regulatory mechanisms governing the transition between these stages are not fully understood. Here we report that, in fission yeast Schizosaccharomyces pombe (S. pombe) and human cells, Cdk9 and its cyclin partner (Cyclin T in humans, and Pch1 in S. pombe) disengage from the elongation machinery near gene 3'-ends, as Pol II crosses the cleavage and polyadenylation signal (CPS). Concurrently, chromatin immunoprecipitation (ChIP) data shows an increased association of Dis2 (the PP1 ortholog in S. pombe)4 beyond the CPS. Additionally, ChIP-seq indicates that histone 2B monoubiquitylation (H2Bub1) is pivotal for Cdk9 occupancy but serves differential roles along the gene. H2Bub1 facilitates Cdk9 chromatin recruitment during elongation but prompts Cdk9 dissociation from the elongation complex as Pol II traverses the CPS. Furthermore, in S. pombe, disruptions of H2Bub1 in htb1-K119R 5 and sustained levels in ubp8D 6 inversely affect the chromatin occupancy of Pol II, Pol II CTD phosphorylation within the heptad repeats, Spt5, phosphorylated Spt5 (pSpt5), Dis2, components of the mRNA 3’-end processing complex (Pfs2 and Pla1), and termination factors Rhn1 (Rtt103) and Pcf1 around the CPS—diminishing with H2Bub1 loss and increasing with H2Bub1 stabilization. In essence, our data indicates that the H2Bub1-mediated eviction of Cdk9 as Pol II navigates the CPS precipitates a rise in PP1 binding, which, in turn, dephosphorylates pSpt5, slowing Pol II to facilitate efficient termination. The unique modulation of Cdk9 occupancy by H2Bub1 during transcription progression presents a compelling, novel concept requiring further exploration.

sample_organism:
Schizosaccharomyces pombe
Homo sapiens

platform_organism:
Schizosaccharomyces pombe
Homo sapiens

overall_design: ChIP-seq and RNA-seq: Data represent thirteen different ChIP-seq and 3 different RNA-seq experiments in S. pombe and human colon carcinoma (HCT116) cells, performed in biological replicates. There are raw and processed files (bigWig) for all biological replicates.

first: Tirthankar

last: Bandyopadhyay

first: Baidehi

last: Basu

first: Nayem

last: Haque


title: Single-Cell Atlas of the Tumor Immune Microenvironment Across Syngeneic Murine Models

city: Beijing

first: Jia

last: Wang

address: No.30 Science Park Road, Zhong-Guan-Cun Life Science Park, Changping District

institute: BeOne Medicines

summary: The tumor immune microenvironment plays a critical role in tumor progression and responses to immunotherapy. Nevertheless, its cellular complexity and heterogeneity remain incompletely understood. In this study, we employed high-resolution single-cell RNA sequencing on CD45+ immune cells isolated from ten syngeneic murine tumor models, representing seven distinct cancer types under treatment-naïve conditions, thereby enabling a comprehensive profiling of tumor-infiltrating immune cells. We classified seven principal immune cell populations and provided an in-depth characterization of T cells, NK/innate lymphoid cells, dendritic cells, monocytes/macrophages, and neutrophils.

overall_design: Single-cell RNA sequencing (scRNA-seq) was performed on CD45+ immune cells isolated from ten treatment-naïve murine models. These models encompassed seven prevalent cancer types: breast mammary carcinoma (4T1, EMT6, MMTV-PyMT), colon carcinoma (CT26.WT, MC38), glioma (GL261), renal adenocarcinoma (Renca), lung carcinoma (LL2), melanoma (B16F10), and pancreatic adenocarcinoma (Pan02).

first: Bin

last: Jiang

first: Minjuan

last: Deng

first: Han

last: Yan


title: Single-cell transcriptomics reveals probiotic reversal of neonatal morphine-induced gene disruptions underlying adolescent pain hypersensitivity.

status: Public on Oct 24 2025

city: MIAMI

first: JUNYI

last: TAO

address: 501 NW 10th Ave

institute: University of Miami

summary: Neonatal morphine is commonly administered in the Neonatal Intensive Care Unit (NICU) to manage pain. However, its long-term effects on neurodevelopment of pain pathways, remain a significant concern. The midbrain is a core region that plays a central role in pain processing and opioid-mediated analgesia. Here, we performed single-cell RNA sequencing to study gene expression in 107,427 midbrain single cells from adolescent mice neonatally exposed to either saline, morphine, or morphine with the probiotic Bifidobacterium infantis (B. infantis). We found broad alterations in transcriptomics within neurons, astrocytes, oligodendrocytes, and microglial cells. Analysis of differentially regulated genes revealed down regulation of HOX genes and upregulation of pathways related to neurotransmitter signaling and pain in adolescence that were neonatally treated with morphine. Interestingly, neonatal probiotic supplementation mitigated these morphine-induced alterations on the transcriptome. This study presents the first single-cell RNA sequencing dataset of the adolescent midbrain following neonatal morphine exposure and probiotic intervention. These findings offer new insights into the neurodevelopmental impact of early opioid exposure and highlight the therapeutic potential of microbiome-targeted interventions.

overall_design: Chromium Fixed RNA Profiling by probe

first: Junyi

last: Tao

first: Danielle

last: Antoine

first: Sabita

last: Roy


title: Diel expression dynamics in filamentous cyanobacteria

city: Woods Hole

first: Blair

last: Paul

address: 7 MBL St

institute: Marine Biological Laboratory

summary: Filamentous cyanobacteria of the Nostocaceae family are able to differentiate into multicellular forms to adapt to environmental stresses, and members can establish symbiosis with various embryophytes. Representative laboratory strains are typically grown under continuous light to maintain stable metabolic conditions, however, this departure from a natural diel cycle can result in extended stress. Early genomic examination of Nostoc punctiforme suggests the genetic potential for a circadian clock, but we lack insight into global cellular dynamics through the natural diel cycle for this model organism. Here, we comprehensively assess changes in expression of core cellular processes and the mobilome of accessory genetic elements during diel growth of N. punctiforme PCC 73102. The primary transcriptome confirmed that multicellular cyanobacteria precisely coordinate photosynthesis and carbon assimilation for cell division during the day, while control of DNA recombination and repair appeared to be sequestered to darkness. Moreover, we expanded the known repertoire of light sensing proteins to uncover a putative regulator of circadian rhythm that itself exhibits striking oscillation between day-night expression. This was in sharp contrast to the arrhythmic pattern observed for a homolog of the canonical circadian regulator in unicellular cyanobacteria.  Looking beyond cellular coordination of diel growth, we uncovered dynamic mobile elements, and notably, targeted hypermutation by retroelements that are likely maintained to ensure conflict mitigation, which is crucial to a multicellular lifestyle.

overall_design: To investigate global diel expression dynamics, we grew Nostoc punctiforme PCC 73102 / ATCC 29133 on a 12-hour light and 12-hour dark growth cycle for 9 days. Time points were chosen at transition stages (Pre-Dawn, Pre-Dusk), steady-state stages (MidLight, MidDark) for the first 8 days. At day 9, the cycle was disrupted and samples were maintained at either 24-hours of light (Light24) or 24-hours of dark (Dark24). Samples were collected in biological triplicate for all 12 time points.

first: Sarah

last: Kennedy

first: Douglas

last: Risser


title: Winter temperature affects fatty acid composition and gene expression, but not fat content and survival in a northern population of a range-expanding spider

city: Greifswald

first: Carolina

last: Ortiz Movliav

state: Mecklenburg-Vorpommern

address: Loitzer Straße 26

department: Zoological Institute and Museum

institute: University of Greifswald

summary: Species expand their geographic distribution when environmental conditions are favorable or when mutations arise that allow them to live in previously unfavorable conditions. The European wasp spider, Argiope bruennichi, has expanded its range poleward, and populations at the northern edge show higher tolerance to cold and are genetically differentiated from the core populations. We aimed to investigate the degree and limits of plasticity in a recently cold-adapted Estonian population by exposing overwintering juveniles (spiderlings) to three fixed winter regimes over the course of three months. These regimes differed in absolute and relative day and night temperature: cold (5°C day, −15°C night), moderate (5°C day, −5°C night), and warm (15°C day, −5°C night). We expected a differential response to the winter regimes in survival, lipid content, metabolites, and gene expression patterns. The survival probability of the spiderlings decreased over winter by approximately 20% and their lipid content by 28%, with no significant differences between groups. Spiderlings also did not differ in content of saturated and monounsaturated fatty acids per dry weight. However, in spiderlings exposed to the warm winter regime, short-chain omega-3 PUFAs were less abundant (~57%) and long-chain omega-3 PUFAs more abundant (~66%) compared to the other regimes. The gene expression response was low under the cold regime and much higher under the warm regime, as compared to the moderate regime. The affected pathways suggest a more pronounced stress response under warmer winter temperatures. Taken together, our findings demonstrate that A. bruennichi spiderlings from a northern population can endure very different winter regimes. However, the observed physiological responses to the warmer regime suggest metabolic costs that may reduce spiderling survival probability after emergence from the egg sac. We conclude that, despite remarkable tolerance to different winter regimes, warmer winters have nuanced effects on spiderling physiology beyond survival probability.

overall_design: RNAseq of winter treatments cold (5°C day, -15°C night), moderate (5°C day, -5°C night), and warm (15°C day, -5°C night) after three months of exposure.

last: Ortiz-Movliav

first: Andreas W.

last: Kuss

first: Lars R.

last: Jensen

first: Corinna

first: Alexander

last: Wacker

first: Gabriele

last: Uhl


title: Inhibiting B-cell-mediated Immunosuppression to Enhance the Immunotherapy Efficacy in Hepatocellular Carcinoma

first: Dan

last: Duda

summary: Immunotherapy benefits only a minority of hepatocellular carcinoma (HCC) patients due to immune checkpoint blockade (ICB) resistance, and agonists of the stimulator of interferon genes (STING) also showed limited efficacy despite their immune-stimulating properties. Here we show that increased intratumoral B cells mediate the resistance to ICB and STING agonism. In the preclinical models with liver fibrosis that mimic human HCCs, tumors treated by anti-PD-1 ICB or a STING agonist (BMS-986301) showed more B-cell infiltration. STING agonism increased circulating IL-10 and intratumoral infiltration by B cells, including B cells expressing T-cell immunoglobulin and mucin domain 1 (TIM-1), and promoted the formation of tertiary lymphoid structure (TLS)-like structures, especially in the peritumoral areas. Strikingly, adding B cell depletion to ICB or STING agonism treatment significantly increased survival. Unlike ICB, STING agonism also had a pronounced anti-metastatic activity. In addition, the combination of STING agonism and TIM-1 blockade augmented B cell differentiation and antigen presentation in vitro and improved the anti-tumor effects in murine HCC in vivo. This approach decreased TIM-1+ B cells in the tumor and shifted B cells to higher expression of CD86 and MHC class II, enhancing their antigen presentation capability and further boosting the antitumor efficacy of CD8+ cytotoxic T cells. Our findings demonstrate that B cells are associated with ICB- and STING-mediated therapy resistance, and that depleting B cells or targeting TIM-1 enhances both innate and acquired therapeutic efficacy in HCC.

overall_design: Using murine tumor tissues and cultured B cells collected in a time-matched manner, we employed RNA-seq to evaluate the transcriptional changes in murine RIL-175 and HCA-1 hepatocellular carcinoma (HCC) tissues as well as in vitro cultured B cells isolated from spleen tissues after the treatment with STING agonist or immune checkpoint inhibitors or the combination.

first: Xin

last: Liu

first: Zelong


title: Establishing competence for trophectoderm specification in mouse embryos before the first lineage bifurcation [ChIP-seq]

city: Barcelona

first: Thomas

last: Graf

address: Carrer del Dr. Aiguader, 88

country: Spain

institute: Center for Genomic Regulation

summary: How embryonic blastomeres transition from totipotency to differentiation remains a fundamental question in developmental biology. Here, we uncover the transcription factor CEBPa as an orchestrator of this process. CEBPa expression is first activated by NR5A2 at the 2-cell to 4-cell transition and in a second wave peaks in the trophectoderm of blastocysts. Loss of CEBPa disrupts timely blastocyst formation and impairs trophectoderm development, while its forced expression in embryonic stem cells drives differentiation into trophectoderm-like cells. Mechanistically, CEBPa sequentially activates key trophectoderm enhancers in a dose-dependent manner. At the 4-cell stage, some of these trophectoderm enhancers are already active while others are primed or still closed, placing blastomeres in a state of alert. These findings establish CEBPa as a molecular switch that equips 4-cell blastomeres with the competence for trophectoderm differentiation, defining the earliest steps in cell fate bifurcation and shedding new light on the mechanisms driving embryonic lineage specification.

overall_design: Temporal study of CEBPa binfding after CEBPa induction in mouse embryonic stem cells.

first: Xiao

last: Wei

first: Irepan

last: Salvador-Martinez

first: Maciej

last: Meglicki

first: Marcos

last: Plana-Carmona

first: Antonios

last: Klonizakis

first: Barbara

last: Pernaute

first: Manuel

last: Irimia

first: Gregoire

last: Stik

first: Mina

last: Popovic

first: Guillem

last: Torcal Garcia

first: Holger

last: Heyn

first: Magdalena

last: Zernicka-Goetz


title: Establishing competence for trophectoderm specification in mouse embryos before the first lineage bifurcation [ATAC-seq]

overall_design: Temporal study of chromatin accessibility changes after CEBPa induction in mouse embryonic stem cells.


title: Establishing competence for trophectoderm specification in mouse embryos before the first lineage bifurcation [RNA-seq]

overall_design: Temporal study of gene expression changes after CEBPa induction in mouse embryonic stem cells.


title: RNA-seq identifies the gene differential expression after Cisatracurium besylate (CIS) treatment in bone marrow-derived macrophages during Mycobacterium tuberculosis (Mtb) infection

city: Guangzhou

first: Zhang

last: Jing

address: Southern Medical University

institute: Institute of Molecular Immunology, School of Laboratory Medicine and Biotechnology

summary: To figure out the role of Cisatracurium besylate (CIS) treatment in Mycobacterium tuberculosis (Mtb) and the underlying mechanism, we performed RNA-seq analysis after CIS treatment in bone marrow-derived macrophages during Mtb infection.

overall_design: Performed Cisatracurium besylate (CIS) treatment bone marrow-derived macrophages during Mtb infection to identify the gene differential expression.

first: Qian

last: Wen

first: Jing

last: Zhang

first: Li

last: Ma


title: High-Yield Extruded Nanovesicles from Adipose Stem Cells Promote High-quality Healing of Diabetic Wound through WNT/beta-Catenin Pathway Activation.

status: Public on Oct 23 2025

city: Harbin

first: Tonghao

last: Yao

state: Heilongjiang

address: No. 246 Xuefu Road

department: Second Affiliated Hospital of Harbin Medical University

institute: Harbin Medical University

summary: Diabetes is a significant global chronic disease characterized by elevated mortality and disability rates due to persistent infections resulting from refractory wounds. Currently, effective treatment strategies are lacking. Adipose-derived stem cell extracellular vesicles (ADSC-EVs) have been shown to promote skin wound healing; however, their clinical application is impeded by low yield and heterogeneity. We successfully isolated high-yield extruded nanovesicles from adipose stem cells (ADSC-NVs), achieving yields over 30 times greater than those of ADSC-EVs while maintaining similar morphological characteristics. Our findings indicate that ADSC-NVs exhibit a dose-dependent enhancement of proliferation and migration in primary human dermal fibroblasts (HDF) in vitro. Notably, the expression levels of proliferating cell nuclear antigen (PCNA), collagen type I (COL-I), and collagen type III (COL-III) were significantly upregulated in HDF following treatment with ADSC-NVs. RNA-seq analysis further revealed that the differentially expressed genes (DEGs) shared between the ADSC-NVs group and control group were predominantly enriched in the Wnt signaling pathway. Consistently, ADSC-NVs facilitate efficient diabetic wound healing while promoting proliferation and inhibiting inflammation via the Wnt/beta-catenin signaling pathway. In summary, high-yield ADSC-NVs represent a promising alternative to ADSC-EVs for enhancing diabetic wound healing, providing novel insights and methodologies for improving therapeutic outcomes.

overall_design: Control rep1, rep2, rep3, rep4;Fibroblasts treated with ADSC NVs rep1,rep2,rep3, rep4


title: Epigenomic analysis of human advanced heart failure

status: Public on Oct 22 2025

city: Valencia

first: Estefanía

last: Tarazón

address: Avenida Fernando Abril Martorell 106

institute: Instituto de investigación Sanitaria La Fe

summary: The goal of this study is to compare the epigenome of advanced heart failure patients (with idiopathic dilated cardiomyopathy) undergoing heart transplantation compared with healthy controls.

overall_design: We analyzed 15 human samples: 6 from idiopathic dilated cardiomyopathy compared to 9 helathy control donors.

first: Esther

last: Roselló-Lletí


title: RAS(ON) multi-selective inhibition drives anti-tumor immunity in preclinical models of NRAS-mutant melanoma

city: Tampa

first: Keiran

last: Smalley

state: FL

address: 12902 Magnolia Drive

institute: Moffitt Cancer Center

summary: Targeted therapies for NRAS-mutant melanoma remain an unmet clinical need. Here, we demonstrate that RMC-7977, a preclinical RAS(ON) multi-selective inhibitor respresentative of the investigational agent daraxonrasib (RMC-6236), elicits potent anti-tumor immune responses across several NRAS-mutant melanoma models. Treatment with RMC-7977 led to rapid tumor regressions driven by inhibition of MAPK signaling, upregulation of MHC and PD-L1 proteins, and enhanced infiltration of CD4⁺ and CD8⁺ T cells. Complete responses was dependent on adaptive immunity, as both CD4⁺ and CD8⁺ T cells were essential for extended survival. Resistance to treatment was marked by reduced T cell infiltration, loss of MHCI expression, and expansion of MDSCs. Combining RMC-7977 with anti-PD-1 boosted T cytotoxic cell infiltration, reprogrammed myeloid cells toward an antigen-presenting phenotype, and improved survival in models resistant to PD-1 blockade. Notably, objective clinical responses were observed in two NRAS-mutant melanoma patients treated with daraxonrasib (RMC-6236) in an ongoing phase I/Ib clinical trial.

overall_design: Female, 6-week-old immunocompetent C57BL/6J mice were subcutaneously injected with 1e6 OSUMMER.13 cells into the right flank. The treatment started when tumors reached approximately 100 mm3. Mice were randomized and assigned into 4 groups of 3: IgG2a control, anti-PD-1, RMC-7977, and combination of anti-PD-1 and RMC-7977. The tumors were collected at the desired timepoint, weighed, and processed for single cell RNA sequencing (scRNA-seq).

first: Larissa

last: Da Costa Carvalho

first: Nataliya

middle: T

last: Shifrin

first: Michael

last: Emmons

first: Ximo

last: Pechuan-Jorge

first: Felix

last: Mbuga

first: Oscar

last: Espinosa

first: Christopher

last: Chow

first: Lillian

last: Seu

first: Manali

middle: S

last: Phadke

first: Olivia

last: Rose

first: Aparna

last: Hegde

first: Nikhil

middle: I

last: Khushalani

first: Elsa

last: Quintana


title: Single-cell transcriptomic analysis of HPV-related multiphenotypic sinonasal carcinoma uncovers MYB-HPV association

city: Jerusalem

first: Avishai

last: Wizel

address: Faculty of Medicine, The Hebrew University, Ein Kerem

country: Israel

institute: The Hebrew University of Jerusalem

summary: Human papillomavirus (HPV)-related multiphenotypic sinonasal carcinoma (HMSC) is a recently described rare tumor that is morphologically similar to high grade adenoid cystic carcinoma (ACC), but clinically distinct. We utilized single-cell RNA sequencing (scRNA-seq) to characterize transcriptional heterogeneity in a human HMSC tumor and compared it to published ACC and oropharyngeal squamous cell carcinoma (OPSCC) scRNA-seq datasets.

overall_design:
A fresh tumor biopsy was collected during the surgery from a 56-year-old woman who underwent a left partial maxillectomy for recurrent poorly differentiated basaloid carcinoma. Pathology confirmed the diagnosis of HMSC. The freshly resected specimen was dissociated into a single-cell suspension, flow-sorted to deplete nonviable and CD45-positive cells, and profiled by the SMART-seq2 protocol, which provided full-length transcripts for sequencing. Sequencing was conducted as paired-end 38-base reads on a NextSeq 500 (Illumina).

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

first: Yotam

last: Drier

first: Anuraag

last: Parikh

first: Sidharth

middle: V

last: Puram

first: Spence

last: Matthew

first: Wizel

last: Avishai


title: Trophectoderm-like cells from EPS cells enable generating EPS cell-derived post-implantation embryoids that complete gastrulation [bulk RNA-seq]

status: Public on Oct 21 2025

first: Ruoqi

last: Cheng

state: Beijing

address: NO.5, Yiheyuan Road, Haidian District

department: School of Life Sciences

institute: Peking University

summary: Mouse extended pluripotent stem (EPS) cells have demonstrated significant potential for generating embryo models in vitro. However, their limited capacity for extraembryonic trophoblast development has hindered their use in constructing whole embryo models, particularly post-implantation embryoids. Here, we establish a stepwise induction protocol to generate trophectoderm-like cells from mouse EPS cells. These cells retain trophectoderm-specific transcriptomic features and can differentiate into trophoblast lineages in vivo. Moreover, combining these trophectoderm-like cells with EPS cell-derived primitive endoderm/epiblast bilineage structures enabled the robust generation of post-implantation embryoids in a transgene-free manner. EPS-derived embryoids recapitulate key developmental events of post-implantation mouse embryos, including the formation of the pro-amniotic cavity, anterior-posterior axis, primitive streak, gastrulation, and complex extraembryonic tissues. Notably, single-cell transcriptomic analysis revealed a high degree of transcriptional similarity between EPS-derived embryoids at day 6 and natural E7.5 mouse embryos. Our study presents a novel platform for modeling post-implantation mouse embryogenesis in vitro.

overall_design: Gene expression profiling analysis of RNA-seq data for EPS,  EPS-N, EPS-C3, EPS-C6, EPS-C10, EPS-C20, FAXY-TS, FBS-TS, OG-BLES, OG-EPS, OG-PE, TES1 and TES2 (P1, P3, P6, P21) cells.

first: Xuyang

last: Wang

first: Chenyang

last: Wu

first: Haiyin

last: Liu

first: Dongyu

last: Zhao

first: Cheng

last: Li

first: Hongkui

last: Deng

first: Jun

last: Xu


title: Single-Cell RNA-Seq Reveals Adventitial Fibroblast Alterations during Mouse Atherosclerosis

city: New York

first: Lauren

last: Fries

department: Medicine

institute: Columbia University

summary: Background: Atherosclerotic cardiovascular disease (ASCVD) remains the leading cause of mortality in the western world despite the success of lipid lowering therapies, highlighting the need for novel lipid-independent therapeutic strategies. Genome-wide association studies (GWAS) have identified numerous genes associated with ASCVD that appear to predominantly function in the vessel wall, suggesting both that vascular cells mediate ASCVD, and that the genes and pathways essential for this vascular cell function may be novel therapeutic targets for the treatment of ASCVD. Furthermore, some of these implicated genes appear to function in the adventitial layer of the vasculature, suggesting these cells are able to potentiate ASCVD. Methods: To investigate the contribution of adventitial cells in atherosclerosis, we conducted single-cell RNA sequencing (scRNA-seq) of the aortic adventitia during atherogenesis in male Ldlr-/- mice via pools of three mice, two samples per condition. We cross-referenced the scRNA-seq data with human ASCVD GWAS to identify regulators of adventitial responses in ASCVD. These regulators were then validated in vitro in human adventitial fibroblasts. Results: We identified four adventitial fibroblast populations, all of which displayed shifts in population size and gene expression over the course of atherogenesis. SERPINH1, an ASCVD-linked GWAS gene, was differentially expressed in adventitial fibroblasts during atherogenesis. Knockdown of SERPINH1 in vitro reduced fibroblast migration and altered subcluster marker gene expression. Conclusions: These findings reveal dynamic changes in adventitial fibroblasts during atherosclerosis and suggest that reduced SERPINH1 expression disrupts adventitial fibroblast function, contributing to ASCVD progression.

overall_design: Ldlr-/- mice were initiated on a western diet for 0, 9, or 16 weeks. The aortic adventitia was collected from 3 mice per sample, and all samples were run for scRNA-seq

first: Allen

last: Chung

first: Hyun

last: Chang

first: Timothy

last: Yuan

first: Robert

middle: C

last: Bauer


title: Collision-induced ribosome degradation driven by ribosome competition and translational perturbations

status: Public on Oct 20 2025

city: Tokyo

first: Sihan

address: Shirokanedai 4-6-1, Minato-ku

department: The Institute of Medical Science

country: Japan

institute: The University of Tokyo

summary: Individual stalling of catalytically inactive ribosomes at the start codon triggers ubiquitination of ribosomal protein uS3 and subsequent 18S rRNA decay. While collisions between ribosomes during translation elongation represent a more widespread form of translation perturbation, their impact on ribosome stability remains unknown. Here, we clarify a bifurcation in ubiquitination-mediated ribosome turnover, identifying a collision-induced branch of uS3 ubiquitination and small subunit destabilization in yeast. This pathway eliminates not only non-functional ribosomes but also translationally active ones with a prokaryotic-like decoding center, driven by competition with wild-type ribosomes due to differing translation rates. We further show that endogenous ribosomal subunit stoichiometry shifts toward a small-subunit-shortage state via ubiquitination upon perturbed translation triggered by the anti-cancer drug cisplatin and the growth phase transition. These findings reveal a mechanism by which ribosome dynamics generally affects ribosome stability, implicating ribosome dysfunction, heterogeneity, and stress-related translational disturbances in small subunit degradation.

overall_design: Two ribosome profiling datasets: one from purified MS2-tagged ribosomes carrying either 18S: WT or 18S: G1645A/A1754G (GA/AG); another from W303 cells treated with either cisplatin or the vehicle control (DMSO).

first: Okuto

last: Shounai

first: Misaki

last: Kato

first: Ken

last: Ikeuchi

first: Toshifumi

last: Inada


title: Human oligodendrocyte progenitor cells mediate synapse elimination through TAM receptor activation

city: Stockholm

first: Carl

last: Sellgren

address: Solnavagen 1

country: Sweden

institute: Karolinska Institute

summary: Recent work in animal models suggests that oligodendrocyte progenitor cells (OPCs) contribute to elimination of synapses in the developing brain. However, a mechanistic understanding of this process is still missing, and it remains uncertain whether human OPCs also display this feature. In this study, we develop a human multi-lineage forebrain organoid model in which OPCs, alongside microglia, exhibit close interactions with synapses and spontaneously internalize synaptic material. Unbiased cell-cell communication analysis based on single-nucleus transcriptomic profiling predicted GAS6-TAM receptor interaction as a major signaling pathway, with neurons and microglia expressing GAS6 ligand and certain OPCs expressing the TAM receptor AXL. Dose-dependent pharmacological inhibition of TAM receptors then demonstrated the importance of AXL receptor activation, and specific knockdown of AXL in OPCs resulted in impaired uptake of synaptic material. In summary, these data define a role of GAS6-AXL signaling in promoting OPC-mediated internalization of synaptic structures during early brain development.

overall_design: Four forebrain organoids per subject (n=2 subjects) were pooled and dissociated to isolate nuclei. High qulaity nuclei were processed for single-nuclei RNA sequencing using 10X Genomics 3' Chromium platform (dual index). The barcoded library was sequenced on Illumina Novaseq. S1-100.

first: Susmita

last: Malwade

first: S

last: Samudyata


title: Sensitive and unbiased genome-wide profiling of base-editor-induced off-target activity with CHANGE-seq-BE

city: Memphis

first: Shengdar

last: Tsai

state: TN

address: 262 Danny Thomas Pl

department: Department of Hematology

institute: St Jude Children's Research Hospital

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

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: GABA produced by multiple bone marrow niche cell types regulate hematopoietic stem and progenitor cells

status: Public on Oct 16 2025

city: Madison

first: Owen

middle: James

last: Tamplin

state: WI

address: 1111 Highland Ave

department: Cell and Regenerative Biology

institute: University of Wisconsin-Madison

summary: Hematopoietic stem and progenitor cells (HSPCs) maintain homeostasis of the blood system by balancing proliferation and differentiation. Many extrinsic signals in the bone marrow (BM) microenvironment that regulate this balance are still unknown. We report gamma aminobutyric acid (GABA) metabolite produced in the BM as a  regulator of HSPCs . Deletion of the glutamate decarboxylase enzymes (Gad1/2) that produce GABA in either B lineages or BM endothelial cells (BMECs) leads to a moderate reduction in BM GABA levels and HSPC number, suggesting both cell types are GABA sources. However, simultaneous blockade of GABA production from both hematopoietic cells and BMECs resulted in a greater reduction of both GABA levels and HSPC numbers. Lower GABA levels in the BM altered the gene expression profile of HSPCs, with expression reduced for proliferation-associated genes and increased for B lineage genes . Our findings suggest GABA from multiple sources coordinates to regulate HSPC activity.

overall_design: RNA-seq profiling of HSPCs from 8-12 week-old wild-type or Cd19-cre+;Gad1/2fl/fl mice, Cdh5-creERT2+;Gad1/2fl/fl mice and Tie2-cre+;Gad1/2fl/fl mice (triplicates for each group) .

first: Cesi


title: Multi-kinase inhibition of STE20 kinases is neuroprotective against chemotherapy-induced axon degeneration

status: Public on Oct 17 2025

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

summary: Chemotherapy-induced peripheral neuropathy (CIPN) is a debilitating condition resulting from the toxic action of cancer therapies on peripheral neurons. CIPN features axon terminal retraction from target organs leading to a myriad of sensory symptoms such as mechanical and thermal insensitivity, tingling, numbness and burning pain. There are currently no preventative or curative treatments, mostly because the mechanisms leading to axon degeneration upon chemotherapy treatment in humans remain largely unknown. We developed a model of CIPN suitable for high-throughput screening that involves progressive axon degeneration culminating in the death of human iPSC-derived sensory neurons exposed to paclitaxel. Using this model, we screened a library of 192 kinase inhibitors and identified 19 neuroprotective compounds. The top neuroprotective compounds all inhibited members of the STE20 family of kinases; MAP4K4, MAP4K6, and MAP4K7. Genetic and pharmacological inhibition confirmed that simultaneous, but not individual, inhibition of these three kinases is necessary for protection against paclitaxel-induced axonal toxicity in our model, and also in human primary DRG neurons. Importantly, pharmacological inhibitors specific to the STE20 family of kinases did not prevent paclitaxel-mediated killing of three breast cancer cell lines. Transcriptomic studies revealed that it was inhibition of the JNK-c-Jun pathway that prevented cell death and inhibition of the MAP4K-p38 axis that rescued axon degeneration. STE20 kinases are, therefore, a potential therapeutic target for mitigating paclitaxel-induced axon degeneration in sensory neurons while maintaining the therapeutic effects of chemotherapy in cancer patients.

overall_design:
28DIV iPSC-derived sensory neurons are treated for 24hrs with paclitaxel in the presence of STE20 inhibitor (GNE-495) to prevent axon degeneration or in the presence of JNK inhibitor (JNK-IN-8) to prevent cell death
GSE298389_ProcessedData.xlsx has data for samples GSM9013321-GSM9013356
GSE298389_ProcessedData2.xlsx has data for samples GSM9345116-GSM9345163

first: Veselina

last: Petrova

first: Qing

last: Wang

first: Clifford

last: Woolf


title: Fasting boosts breast cancer therapy efficacy via glucocorticoid activation

status: Public on Oct 14 2025

city: Amsterdam

first: Wilbert

last: Zwart

state: Noord-Holland

address: Plesmanlaan 121

department: Oncogenomics

institute: Netherlands Cancer Institute


title: Effect of depletion of CNOT4 on gene expression in human cells

city: Dallas

first: Yi

last: Liu

state: TX

address: 5323 HARRY HINES BLVD

department: Physiology

institute: UT Southwestern Medical Center

summary: Codon usage bias of an organism plays an important role in determining its gene expression levels. Here, we have identified that a subunit of CCR4-NOT complex, CNOT4, plays a significant role in mediating codon usage effect on gene expression in human cells by affecting mRNA levels in a codon usage dependent manner.

overall_design: To investigate a role of CNOT4 in the regulation of codon-usage effect on gene expression, we depleted CNOT4 in HEK293 cells using siRNA for 72 h. RNA-seq analysis was performed using total RNA of control (treated with negative control siRNA for 72 h) and knockdown cells.

first: Renu

last: Garg


title: Effect of depletion of ZFC3H1, PABPN1 and CNOT4 on gene expression in human cells.

summary: Codon usage bias of an organism has been reported to affect the level of gene expression by influencing this process at multiple steps. Here, we have identified a role of poly-A exosome targeting complex (PAXT), which is a substrate adaptor of nuclear RNA exosome, in regulating codon usage effect on gene expression. PAXT complex subunits, ZFC3H1 and PABPN1, regulate stability and subcellular localization of mRNA in a codon usage dependent manner. This suggests that codon usage dependent mRNA stability and nuclear export are important factors of codon usage effect on gene expression in human cells. Also, a subunit of CCR4-NOT complex, CNOT4, was found to play a significant role in this regulation by affecting the nuclear mRNA levels and their subcellular localization in codon usage dependent manner.

overall_design: To investigate a role of nuclear exosome PAXT complex and CCR4-NOT complex subunit, CNOT4, in the regulation of codon-usage effect on gene expression, we depleted ZFC3H1, PABPN1 and CNOT4 in HEK293 cells using siRNA for 72 h. Control (treated with negative control siRNA for 72 h) and knockdown cells were harvested and total, cytosolic and nuclear RNA fractions were isolated. RNA-seq analysis was performed using total, cytosolic and nuclear RNA of control and knockdown cells.


title: Trophectoderm-like cells from EPS cells enable generating EPS cell-derived post-implantation embryoids that complete gastrulation [scRNA-seq]

city: Beijing

first: Ruoqi

last: Cheng

overall_design: A total of 2 scRNAseq samples of day 6 EPS-derived embryoids were analyzed, similar to E7.5 stage in vivo

first: Xuyang

first: Chenyang

last: Wu

first: Haiyin

first: Dongyu

last: Zhao

first: Cheng

last: Li

first: Hongkui

last: Deng

first: Jun

last: Xu


title: Fasting boosts breast cancer therapy efficacy via glucocorticoid activation (RNA-Seq)

summary: The vast majority of all breast cancers are driven by oestrogen receptor alpha (ERα) activation, and endocrine therapy represents the mainstay treatment for these patients. However, resistance is common and tumours progress despite years of systemic endocrine suppression. Periodic fasting enhances the efficacy of standard endocrine drugs and delay acquired resistance to them, although the underlying mechanisms remain unclear. Here, we show that fasting, in combination with endocrine therapy, induces extensive epigenetic reprogramming in hormone receptor-positive (HR+) breast cancer xenografts, with large-scale activation of glucocorticoid receptor (GR) and progesterone receptor (PR) signalling, and impairment of activator protein-1 (AP-1) family activity. GR-driven gene programs were selectively activated after fasting, and GR knockout perturbed the beneficial effects of fasting in combination with tamoxifen, in vivo. Exogenous administration of GR-ligands fully recapitulated the observed fasting-enhanced anti-oestrogen action, resulting in tumour regression. Finally, elevated progesterone and cortisol levels were detected in the blood of breast cancer patients after fasting, thus providing clinical validation of our animal findings. Our results indicate GR activation to play a pivotal role in fasting’s ability to enhance endocrine drug activity against hormone-receptor positive breast cancer and suggest that corticosteroid administration should be evaluated as an adjuvant to endocrine therapy in this condition.

overall_design: RNA-seq from MCF7 xenografts in mice treated with Control (ad libitum diet), tamoxifen (30mg/Kg; TMX), fasting (48h water only) and combination of TMX+Fasting .

first: Nuno

last: Padrão

first: Tesa

middle: M

last: Severson

first: Sebastian

last: Gregoricchio

first: Ana

last: Guijarro

first: Angelica

last: Persia

first: Francesa

last: Ligorio

first: Merel

last: Roest

first: Joyce

last: Sanders

first: Maria

last: Donaldson Collier

first: Claudio

last: Vernieri

first: Filippo

last: de Braud

first: Livia

last: Pisciotta

first: Alessio

last: Nencioni

first: Irene

last: Caffa


title: Dual Programmed Death Receptor-1 and Vascular Endothelial Growth Factor Receptor-2 Blockade Promotes Vascular Normalization and Enhances Antitumor Immune Responses in Hepatocellular Carcinoma

city: Boston

first: Dan

last: Duda

address: 55 Fruit St

institute: Massachusetts General Hospital

summary: Background and aims: Activation of the antitumor immune response using programmed death receptor-1 (PD-1) blockade showed benefit only in a fraction of patients with hepatocellular carcinoma (HCC). Combining PD-1 blockade with antiangiogenesis has shown promise in substantially increasing the fraction of patients with HCC who respond to treatment, but the mechanism of this interaction is unknown. Approach and results: We recapitulated these clinical outcomes using orthotopic-grafted or induced-murine models of HCC. Specific blockade of vascular endothelial receptor 2 (VEGFR-2) using a murine antibody significantly delayed primary tumor growth but failed to prolong survival, while anti-PD-1 antibody treatment alone conferred a minor survival advantage in one model. However, dual anti-PD-1/VEGFR-2 therapy significantly inhibited primary tumor growth and doubled survival in both models. Combination therapy reprogrammed the immune microenvironment by increasing cluster of differentiation 8-positive (CD8+ ) cytotoxic T cell infiltration and activation, shifting the M1/M2 ratio of tumor-associated macrophages and reducing T regulatory cell (Treg) and chemokine (C-C motif) receptor 2-positive monocyte infiltration in HCC tissue. In these models, VEGFR-2 was selectively expressed in tumor endothelial cells. Using spheroid cultures of HCC tissue, we found that PD-ligand 1 expression in HCC cells was induced in a paracrine manner upon anti-VEGFR-2 blockade in endothelial cells in part through interferon-gamma expression. Moreover, we found that VEGFR-2 blockade increased PD-1 expression in tumor-infiltrating CD4+ cells. We also found that under anti-PD-1 therapy, CD4+ cells promote normalized vessel formation in the face of antiangiogenic therapy with anti-VEGFR-2 antibody. Conclusions: We show that dual anti-PD-1/VEGFR-2 therapy has a durable vessel fortification effect in HCC and can overcome treatment resistance to either treatment alone and increase overall survival in both anti-PD-1 therapy-resistant and anti-PD-1 therapy-responsive HCC models.

overall_design: Using murine tumor tissues collected in a time-matched manner, we employed RNA-seq to evaluate the transcriptional changes in murine RIL-175 hepatocellular carcinoma (HCC) tissues after the treatment with anti-PD-1 or dual anti-PD-1/VEGFR-2 therapy with or without anti-CD4.

first: Xin

last: Liu

first: Kohei

last: Shigeta


title: Comparative analysis of mouse and human ovaries across age [mouse data]

status: Public on Oct 09 2025

city: San Francisco

first: Diana

middle: Matthew

last: Laird

address: 35 Medical Center Way RM913D

institute: University of California

summary: A combination of droplet based and plate based single cell sequencing was used to profile and compare all cell types in the mouse and human ovaries throughout the reproductive span.

overall_design: For each sample, the ovary was dissociated and cells were size filtered to separate large oocytes from small oocytes and somatic cells. Large oocytes were sequenced using SmartSeq2 while the suspension of small cells was sequenced using 10X Genomics.

first: Ryan

last: Samuel

first: Eliza

last: Gaylord

first: Mariko

last: Foecke


title: Actin Dysregulation Induces Neuroendocrine 1 Plasticity and 2 Immune Evasion: A Vulnerability of Small Cell Lung Cancer

city: Houston

first: Jinho

last: Jang

state: Texas

address: 1755 Wyndale Street

institute: MD Anderson Cancer Center

summary: Small cell lung cancer (SCLC) is aggressive with limited therapeutic options. Despite recent advances in targeted therapies and immunotherapies, therapy resistance is a recurring issue, which might be partly due to tumor cell plasticity, a change in cell fate. Nonetheless, the mechanisms underlying tumor cell plasticity and immune evasion in SCLC remain elusive. CRACD, a capping protein inhibitor that promotes actin polymerization, is frequently inactivated in SCLC. Cracd knockout (KO) transforms preneoplastic cells into SCLC tumor-like cells and promotes in vivo SCLC development driven by Rb1, Trp53, and Rbl2 triple KO. Cracd KO induces neuroendocrine (NE) plasticity and increases tumor cell heterogeneity of SCLC tumor cells via regulated NOTCH1 signaling by actin cytoskeleton disruption. CRACD depletion also reduces nuclear actin and induces EZH2-mediated H3K27 methylation. This nuclear event suppresses the MHC-I genes and thereby depletes intratumoral CD8+ T cells for accelerated SCLC tumorigenesis. Pharmacological blockade of EZH2 inhibits CRACD-negative SCLC tumorigenesis by restoring MHC-I expression and immune surveillance. Unsupervised single-cell transcriptomics identifies SCLC patient tumors with concomitant inactivation of CRACD and downregulated MHC-I pathway. This study defines CRACD, an actin regulator, as a tumor suppressor that limits cell plasticity and immune evasion and proposes EZH2 blockade as a viable therapeutic option for CRACD-negative SCLC.

overall_design: CUT&RUN assays for 2 cell lines

first: Yoojeong

last: Seo

first: Shengzhe

last: Zhang

first: Kyung-Pil

last: Ko

first: Kyung-Pil Ko

last: Kim

first: Yuanjian

last: Huang

first: Dong-Wook

first: Bongjun

first: Gengyi

last: Zou

first: Jie

first: Sohee

last: Jun

first: Wonhong

last: Chu

first: Nicole

last: Kirk

first: Ye Eun

last: Hwang

first: Young Ho

last: Ban

first: Shilpa

last: Dhar

first: Joseph

last: Chan

first: Min Gyu

last: Lee

first: Charles

last: Rudin

first: Kwon-Sik

last: Park

first: Jae-Il


title: Improved Prediction of Venetoclax and Azacitidine Efficacy in Acute Myeloid Leukemia through Machine Learning [AML patients]

city: Shanghai

first: Peng

last: Jin

address: Ruijin Rd. II

department: Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics

institute: Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: Despite the transformative impact of venetoclax-azacitidine in treating acute myeloid leukemia (AML), reliable markers for accurately predicting patient responses remain urgently needed. To address this challenge, we employed a multidisciplinary approach that combined transcriptomic profiling, ex vivo drug sensitivity testing, functional assays, and clinical data to identify robust predictors of venetoclax-azacitidine response. We pinpointed a set of core genes linked to both ex vivo and in vivo drug responsiveness, validated through CRISPR-Cas9 screens in the setting of both venetoclax and azacitidine therapies. In particular, silencing BCL2L1 and PINK1 preferentially enhanced response to the venetoclax-azacitidine treatment. Building on these insights, we further developed and validated an 8-gene random forest model (RF8) that demonstrated high specificity and sensitivity in four independent cohorts comprising 498 patients. This model was capable of distilling downstream effects of genetic alterations to assist in predicting treatment response and outperformed existing genetic mutation-based signatures. Furthermore, the RF8 score demonstrated a nearly monotonic relationship with venetoclax-azacitidine response probabilities and patient outcomes, enabling precise stratification of patients. These findings illustrated the feasibility of translating integrated transcriptomic and drug-response profiling data into more refined risk stratification approaches, offering a new avenue for optimizing clinical decision-making in AML.

overall_design:
Comprehensive transcriptome profiling on a total of 142 AML patients (cohort1 and cohort2) treated with Aza-Ven.

***************************************************************
Law restrictions prohibit us from publicly sharing raw sequencing data, which however can be made available upon reasonable request and permission of the local ethics committee.
***************************************************************

Please note that the previous/incomplete processed data file has been replaced on Dec 22, 2025.

first: Dan

last: Wang

first: Kankan


title: Single-nucleus transcriptome of the hippocampus from Stra8-cKO (Stra8L/-; Nestin-Cre) mice

status: Public on Oct 03 2025

city: Kansas City

first: Ning

state: KS

address: 3901 Rainbow Boulevard, Kansas City, KS

department: Cell Biology and Physiology

institute: UNIVERSITY OF KANSAS MEDICAL CENT

summary: We performed single-nucleus RNA sequencing (snRNA-seq) of the hippocampus from Stra8-cKO mice using the 10x Genomics Chromium platform to investigate the effects of Stra8 loss.

overall_design: Single-nucleus RNA sequencing data from the hippocampus of Stra8-cKO mice were generated using the 10x Genomics platform and deep sequencing.

first: Ming

first: Xiaoyu

last: Zhang


title: SIRT6 regulates Tryptophan catabolism preventing metabolite imbalance and neurodegeneration

status: Public on Oct 01 2025

city: Beer Sheva

first: Debra

last: Toiber

state: Israel

address: Ben Gurion Road #1, Building 40, room 205

institute: Ben Gurion University of the Negev

summary: In the brain, tryptophan byproducts are involved in the biosynthesis of proteins, energy-rich molecules (e.g., NAD+), and neurotransmitters (serotonin and melatonin). Impaired tryptophan catabolism, seen in aging, neurodegeneration and psychiatric diseases affects mood, learning, and sleep; however, the reasons for those impairments in elder and these ailments remain unknown. Our results from cellular, Drosophila melanogaster, and mouse models indicate that SIRT6 regulates tryptophan catabolism by balancing its usage. Mechanistically, SIRT6 regulates tryptophan and sleep quality through changes in gene expression of key genes (e.g., TDO2, AANAT), which results in elevated concentration of neurotoxic metabolites from the kynurenic pathway at the expense of serotonin and melatonin production. Such neurotoxic metabolites can affect various processes in the brain. However, by redirecting tryptophan through TDO2 inhibition in our new SIRT6-KO Drosophila model, the impairments in neuromotor behavior and vacuolar formation a parameters of neurodegeneration could be significantly reversed.

overall_design: RNA was extracted from single head of 21 days old verging female w1118 / SIRT6 KO Drosophila fed with 100µM TDO2 inhibitor/ DMSO for 21 days.

first: Shai

last: Kaluski-Kopatch

first: Daniel

last: Stein

first: Alfredo

last: Garcia-Venzor

first: Ana Margarida

last: Ferreira Campos

first: Melanie

last: Planque

first: Bareket

last: Goldstein

first: Estefanía

last: De Allende-Becerra

first: Dmitrii

last: Smirnov

first: Adam

last: Zaretsky

first: Ekaterina

last: Eremenko

first: Miguel

last: Portillo

first: Monica

last: Einav

first: Alena

last: Bruce Krejci

first: Uri

last: Abdu

last: Khrameeva

last: Gitler

first: Sarah-Maria

last: Fendt