Transcriptional Profiling Research Articles

YAP1 and WWTR1 are required for murine pregnancy initiation.

Endometrial stromal cell decidualization is required for pregnancy success. Although this process is integral to fertility, many of the intricate molecular mechanisms contributing to decidualization remain undefined. One pathway that has been implicated in endometrial stromal cell decidualization in humans in vitro, is the Hippo signaling pathway. Two previously conducted studies showed that the effectors of the Hippo signaling pathway, YAP1 and WWTR1, are required for decidualization of primary endometrial stromal cells in vitro. To investigate the in vivo role of YAP1 and WWTR1 in decidualization and pregnancy initiation, we generated Progesterone receptor Cre mediated mutation of a combination of Yap1 and Wwtr1 alleles. Female Yap1 and Wwtr1 triple allele mutants exhibited subfertility, a compromised decidualization response, decreased endometrial receptivity, delayed embryonic development, and a unique transcriptional profile at 7.5 days post coitus. Bulk mRNA sequencing revealed aberrant maternal remodeling evidenced by significant alterations in extracellular matrix encoding genes at 7.5 days post-coitus in mutant dams and enrichment for terms associated with fertility-compromising diseases like pre-eclampsia and endometriosis. In addition, differentially expressed genes overlapped directionally with Estrogen receptor and Epidermal growth factor receptor regulated genes as identified by microarray. Our results indicate that Yap1 and Wwtr1 are necessary for successful mammalian pregnancy initiation.

Transcriptional evidence of HPA axis dysregulation in adolescent females: Unique contributions of chronic early-life stressor exposure and maternal depression history

BackgroundDepression risk increases dramatically for adolescent females following the pubertal transition. Although chronic early-life stressor exposure and a maternal history of depression are established risk factors for depression onset in this population, we know little about the biological mechanisms underlying these associations. MethodTo investigate, we examined how chronic early-life stressor exposure and maternal depression history were associated with stress-related gene expression patterns, using a high-risk family design in 48 psychiatrically healthy adolescent females, 20 of whom had a mother with a lifetime history of depression. Lifetime chronic stressor exposure was assessed using the STRAIN and gene expression patterns were estimated using transcriptional profiling of whole blood. ResultsConsistent with hypotheses, we found that adolescent females with greater chronic stressor exposure had higher NR3C1 expression levels compared to those with less chronic stressor exposure. Additionally, youth with a depressed mother had lower levels of FKBP5 expression compared to those without a depressed mother. Levels of FKBP5 expression, in turn, interacted with chronic stressor exposure to predict NR3C1 expression. Specifically, for those with low chronic stressor exposure, levels of FKBP5 and NR3C1 expression were strongly interrelated, whereas for those with high chronic stressor exposure, NR3C1 expression was high regardless of levels of FKBP5 expression. LimitationsThis study was correlational, the sample size was limited, and additional research is needed to elucidate the underlying mechanisms and predict who subsequently develops depression. ConclusionsNotwithstanding these limitations, these data indicate that having low FKBP5 expression, alongside high NR3C1 expression, may be a potential preclinical marker of depression risk in adolescent females that warrants additional investigation.

Differential contributions of fetal mononuclear phagocytes to Zika virus neuroinvasion versus neuroprotection during congenital infection.

Fetal immune cell functions during congenital infections are poorly understood. Zika virus (ZIKV) can vertically transmit from mother to fetus, causing nervous system infection and congenital ZIKV syndrome (CZS). We identified differential functional roles for fetal monocyte/macrophage cell types and microglia in ZIKV dissemination versus clearance using mouse models. Trafficking of ZIKV-infected primitive macrophages from the yolk sac allowed initial fetal virus inoculation, while recruited monocytes promoted non-productive neuroinflammation. Conversely, brain-resident differentiated microglia were protective, limiting infection and neuronal death. Single-cell RNA sequencing identified transcriptional profiles linked to the protective versus detrimental contributions of mononuclear phagocyte subsets. In human brain organoids, microglia also promoted neuroprotective transcriptional changes and infection clearance. Thus, microglia are protective before birth, contrasting with the disease-enhancing roles of primitive macrophages and monocytes. Differential modulation of myeloid cell phenotypes by genetically divergent ZIKVs underscores the potential of immune cells to regulate diverse outcomes during fetal infections.

Molecular characterization, spatio-temporal expression patterns of crtc2 gene and its immune roles in yellow catfish (Pelteobagrus fulvidraco)

cAMP response element binding (CREB) protein 2 (CRTC2) is a transcriptional coactivator of CREB and plays an important role in the immune system. Thus far, the physiological roles of Crtc2 in teleost are still poorly understood. In this study, the crtc2 gene was identified and characterized from yellow catfish (Pelteobagrus fulvidraco; therefore, the gene is termed as pfcrtc2), and its evolutionary and molecular characteristics as well as potential immunity-related roles were investigated. Our results showed that the open reading frame of pfcrtc2 was 2,346 bp in length, encoding a protein with 781 amino acids. Gene structure analysis revealed its existence of 14 exons and 13 introns. A phylogenetic analysis proved that the tree of crtc2 was clustered into five groups, exhibiting a similar evolutionary topology with species evolution. Multiple protein sequence alignment demonstrated high conservation of the crtc2 in various vertebrates with similar structure. Syntenic and gene structural comparisons further established that crtc2 was highly conserved, implying its similar roles in diverse vertebrates. Tissue distribution pattern detected by quantitative real-time PCR showed that the pfcrtc2 gene was almost expressed in all detected tissues except for eyes, with the highest expression levels in the gonad, indicating that Crtc2 may play important roles in various tissues. In addition, pfcrtc2 was transcribed at all developmental stages in yellow catfish, showing the highest expression levels at 12 h after fertilization. Finally, the transcriptional profiles of crtc2 were significantly increased in yellow catfishes injected with Aeromonas hydrophila or Poly I:C, which shared a consistent change pattern with four immune-related genes including IL-17A, IL-10, MAPKp38, and NF-κBp65, suggesting pfCrtc2 may play critical roles in preventing both exogenous bacteria and virus invasion. Anyway, our findings lay a solid foundation for further studies on the functions of pfcrtc2, and provide novel genetic loci for developing new strategies to control disease outbreak in teleost.

Compatibility of dry incubator on in vitro production of bovine embryos

Embryo culture is crucial to achieve successful outcomes in in vitro production-embryo transfer for cattle. This study explored the innovative use of dry incubators for bovine embryo culture, building on their advantages in human medicine, such as reduced contamination risk, stable temperature control, and lower gas consumption. In this study, we examined changes in osmotic pressure, the in vitro developmental potential of IVP embryos including the cleavage rate, blastocyst development rate, blastocyst diameter, and blastocyst cell number, morphokinetics, and the transcriptional profile of the blastocysts between humidified and dry incubators. Our research demonstrates the feasibility of this approach, showing that although the osmotic pressure gradually increases over the culture period (on day 8: 271.7 vs. 299.0, respectively; P < 0.09), it did not negatively affect the blastocyst formation rate (62.4% vs. 69.8%) and the morphological quality of blastocysts (diameter: 237.4 vs. 242.8, total cell number: 189.2 vs. 242.8). Embryos cultured in dry incubators exhibited morphokinetics comparable to those cultured in conventional humidified incubators. Furthermore, RNA-seq revealed that while a few genes showed changes, the transcriptomic profiles of blastocysts cultured in dry incubators were largely similar to those of blastocysts cultured in humidified incubators. These findings highlight the considerable potential of dry incubators for the in vitro production of bovine embryos.

Single-cell analysis of bone marrow CD8+ T cells in Myeloid Neoplasms reveals pathways associated with disease progression and response to treatment with Azacitidine.

CD8+ T cells are crucial for antitumor immunity. In higher-risk myelodysplastic neoplasms (HR-MDS) and acute myeloid leukemia (AML), CD8+ T cells exhibit altered functionality. To address their role in the course of the disease, we performed in-depth immunophenotypic analysis of 104 pre-treatment bone marrow (BM) samples using mass and flow cytometry and observed an increased frequency of the CD57+CXCR3+ subset of CD8+ T cells in patients who failed azacitidine (AZA) therapy. Furthermore, an increased baseline frequency (>29%) of the CD57+CXCR3+CD8+ T cell subset was correlated with poor overall survival. We performed scRNA-seq to assess the transcriptional profile of BM CD8+ T cells from treatment-naive patients. The response to AZA was positively associated with the enrichment of IFN-mediated pathways, whereas an enhanced TGF-β signaling signature was observed in non-responders. Our results suggest that targeting CD8+ T cells with inhibitors of TGF-β signaling in combination with AZA is a potential therapeutic strategy for HR-MDS and AML.

A ferroptosis-associated prognostic model correlated with immune landscape and radiotherapy response in low-grade gliomas (LGGs)

Despite receiving comprehensive treatment, the prognosis for low-grade gliomas (LGGs) patients varies considerably. Recent studies have focused extensively on ferroptosis, across a range of tumor types. Nevertheless, methodologies to evaluate the efficacy of radiotherapy for LGGs, from the perspective of ferroptosis-related genes (FRGs), remain strikingly rare. In this study, we conducted a retrospective study on the transcriptional profiles of LGG patients from the public databases and a local cohort. An FRG model was developed and validated, exhibits heightened robustness when contrasted with the traditional ssGSEA model. Patients demonstrating higher FRG scores were identified as a high-risk group, displaying a worse prognosis. By incorporating the FRG score alongside other prognosis-associated clinical indicators, we formulated an enhanced nomogram to achieve a higher level of prediction performance. Additionally, among LGG patients receiving radiotherapy, a poorer prognosis was observed in the high-risk group. Further investigation revealed that samples from the high-risk group generally exhibit a TME in an immuno-suppressive state. Collectively, we developed an FRG model and a robust nomogram for LGG prognostication. This study suggests that a high FRG score, indicative of an immunosuppressive TME, could potentially lead to a less favorable prognosis for certain LGG patients receiving radiotherapy.

Maintenance and functional regulation of immune memory to COVID-19 vaccines in tissues.

Memory T and B cells in tissues are essential for protective immunity. Here, we performed a comprehensive analysis of the tissue distribution, phenotype, durability, and transcriptional profile of COVID-19 mRNA vaccine-induced immune memory across blood, lymphoid organs, and lungs obtained from 63 vaccinated organ donors aged 23-86, some of whom experienced SARS-CoV-2 infection. Spike (S)-reactive memory Tcells were detected in lymphoid organs and lungs and variably expressed tissue-resident markers based on infection history, and S-reactive B cells comprised class-switched memory cells resident in lymphoid organs. Compared with blood, S-reactive tissue memory Tcells persisted for longer times post-vaccination and were more prevalent with age. S-reactive Tcells displayed site-specific subset compositions and functions: regulatory cell profiles were enriched in tissues, while effector and cytolytic profiles were more abundant in circulation. Our findings reveal functional compartmentalization of vaccine-induced Tcell memory where surveilling effectors and in situ regulatory responses confer protection with minimal tissue damage.

RNA-Seq Reveals Transcriptome Changes Following Zika Virus Infection in Fetal Brains in c-Flip Knockdown Mice

The FADD-like interleukin-1β converting enzyme (FLICE)-inhibitory protein (c-FLIP) plays a crucial role in various biological processes, including apoptosis and inflammation. However, the complete transcriptional profile altered by the c-FLIP is not fully understood. Furthermore, the impact of the c-FLIP deficiency on the transcriptome during a Zika virus (ZIKV) infection, which induces apoptosis and inflammation in the central nervous system (CNS), has not yet been elucidated. In this study, we compared transcriptome profiles between wild-type (WT) and the c-Flip heterozygous knockout mice (c-Flip+/−) fetal heads at embryonic day 13.5 from control and PBS-infected WT dams mated with c-Flip+/− sires. In the non-infected group, we observed differentially expressed genes (DEGs) mainly involved in embryonic development and neuron development. However, the ZIKV infection significantly altered the transcriptional profile between WT and the c-Flip+/− fetal heads. DEGs in pattern recognition receptor (PRR)-related signaling pathways, such as the RIG-I-like receptor signaling pathway and Toll-like receptor signaling pathway, were enriched. Moreover, the DEGs were also enriched in T cells, indicating that the c-FLIP participates in both innate and adaptive immune responses upon viral infection. Furthermore, our observations indicate that DEGs are associated with sensory organ development and eye development, suggesting a potential role for the c-FLIP in ZIKV-induced organ development defects. Overall, we have provided a comprehensive transcriptional profile for the c-FLIP and its modulation during a ZIKV infection.

Local translatome sustains synaptic function in impaired Wallerian degeneration.

After injury, severed axons separated from their somas activate programmed axon degeneration, a conserved pathway to initiate their degeneration within a day. Conversely, severed projections deficient in programmed axon degeneration remain morphologically preserved with functional synapses for weeks to months after axotomy. How this synaptic function is sustained remains currently unknown. Here, we show that dNmnat overexpression attenuates programmed axon degeneration in distinct neuronal populations. Severed projections remain morphologically preserved for weeks. When evoked, they elicit a postsynaptic behavior, a readout for preserved synaptic function. We used ribosomal pulldown to isolate the translatome from these projections 1 week after axotomy. Translatome candidates of enriched biological classes identified by transcriptional profiling are validated in a screen using a novel automated system to detect evoked antennal grooming as a proxy for preserved synaptic function. RNAi-mediated knockdown reveals that transcripts of themTORC1 pathway, a mediator of protein synthesis, and of candidate genes involved in protein ubiquitination and Ca2+ homeostasis are required for preserved synaptic function. Our translatome dataset also uncovers several uncharacterized Drosophila genes associated with human disease. It may offer insights into novel avenues for therapeutic treatments.

A modified multiple-criteria decision-making approach based on a protein-protein interaction network to diagnose latent tuberculosis

BackgroundDNA microarrays provide informative data for transcriptional profiling and identifying gene expression signatures to help prevent progression of latent tuberculosis infection (LTBI) to active disease. However, constructing a prognostic model for distinguishing LTBI from active tuberculosis (ATB) is very challenging due to the noisy nature of data and lack of a generally stable analysis approach.MethodsIn the present study, we proposed an accurate predictive model with the help of data fusion at the decision level. In this regard, results of filter feature selection and wrapper feature selection techniques were combined with multiple-criteria decision-making (MCDM) methods to select 10 genes from six microarray datasets that can be the most discriminative genes for diagnosing tuberculosis cases. As the main contribution of this study, the final ranking function was constructed by combining protein-protein interaction (PPI) network with an MCDM method (called Decision-making Trial and Evaluation Laboratory or DEMATEL) to improve the feature ranking approach.ResultsBy applying data fusion at the decision level on the 10 introduced genes in terms of fusion of classifiers of random forests (RF) and k-nearest neighbors (KNN) regarding Yager’s theory, the proposed algorithm reached a sensitivity of 0.97, specificity of 0.90, and accuracy of 0.95. Finally, with the help of cumulative clustering, the genes involved in the diagnosis of latent and activated tuberculosis have been introduced.ConclusionsThe combination of MCDM methods and PPI networks can significantly improve the diagnosis different states of tuberculosis.Clinical trial numberNot applicable.

The Influence of Aspergillus fumigatus Fatty Acid Oxygenases PpoA and PpoC on Caspofungin Susceptibility

Aspergillus fumigatus can cause invasive pulmonary aspergillosis (IPA). Fungicidal azoles and fungistatic caspofungin (CAS) are the first- and second-line therapies, respectively, used to treat IPA. Treatment of A. fumigatus with CAS or micafungin induces the production of the oxylipin 5,8-diHODE by the fungal oxygenase PpoA. For this article, we investigated the influence of ppo genes, which encode the fatty acid oxygenases responsible for oxylipin biosynthesis, on CAS tolerance. The influence of PpoA and PpoC on CAS tolerance is mediated by MpkA phosphorylation and protein kinase A (PKA) activity. RNAseq transcriptional profiling and the label-free quantitative proteomics of the ppoA and ppoC mutants showed that differentially expressed genes and proteins are related to secondary metabolites and carbohydrate metabolism. We also characterized two clinical isolates, CM7555 and IFM61407, which decrease and increase susceptibility to CAS, respectively. CM7555 does not exhibit increased oxylipin production in the presence of CAS but oxylipin induction upon CAS exposure is increased in IFM61407, suggesting that oxylipins are not the only mechanism involved in CAS tolerance in these isolates. Upon CAS exposure, CM7555 has higher MpkA phosphorylation and PKA activity than IFM61407. Our results reveal the different aspects and genetic determinants involved in A. fumigatus CAS tolerance.

Cariogenic potential of the Streptococcus mutans Cid/Lrg system: an in vivo animal case study.

In our prior study using a dual-species (Streptococcus mutans/Streptococcus gordonii) competitive mouse caries model to investigate the contribution of S. mutans LrgAB to in vivo fitness, S. mutans wild-type and ΔlrgAB mutants consistently outnumbered S. gordonii and had high caries scores, even though the ΔlrgAB mutant is highly sensitive to oxidative stress. To determine whether the highly cariogenic sucrose diet used in the previous study masked the contribution of LrgAB to competitive fitness of S. mutans against S. gordonii, we recapitulated our previous mouse caries experiment with a modification in which 4% sucrose drinking water was replaced with sterile water, hypothesized to decrease the frequency of exposure of mice to sucrose, a determinant in the cariogenicity of S. mutans. Given that both S. mutans ΔlrgAB and ΔcidB mutants are sensitive to oxidative stress and share similar transcriptional profiles, these strains, as well as wild-type UA159, were tested in this modified dual-species mouse caries model. When comparing between groups the colonization within molar dental biofilms of S. mutans strains, ΔlrgAB mutant was at a level similar to the wild type, whereas S. mutans ΔcidB was modestly lower than both wild-type and S. mutans ΔlrgAB. The severity of total sulcal caries in both the ∆cidB and ∆lrgAB mutant infections was significantly lower than that of wild type. These results demonstrate that the Cid/Lrg system aids in S. mutans fitness against S. gordonii and caries potential in vivo, a phenotype likely masked in our previous study by more frequent exposure to sucrose.IMPORTANCEThe development of a mature biofilm on the tooth surface is the central event in the pathogenesis of dental caries, which primarily requires that cariogenic organisms withstand the limited resources or environmental fluctuations experienced in the oral cavity. The sensitive and heterogeneous response of the cid and lrg operons to complex external signals has been hypothesized to trigger differentiation of the Streptococcus mutans biofilm community into distinct functional subpopulations to promote survival and persistence of the S. mutans community when challenged by an unfavorable environment. The study described herein enlightens our understanding of how Cid/Lrg contributes to S. mutans pathogenic potential in vivo (caries development), warranting further research regarding the adaptive role of Cid/Lrg system in human oral biofilms toward the development of anti-caries strategies directed at the Cid/Lrg system.

How do Large Language Models understand Genes and Cells

Researching genes and their interactions is crucial for deciphering the fundamental laws of cellular activity, advancing disease treatment, drug discovery, and more. Large language Models (LLMs), with their profound text comprehension and generation capabilities, have made significant strides across various natural science fields. However, their application in cell biology remains limited and a systematic evaluation of their performance is lacking. To address this gap, in this paper, we select seven mainstream LLMs and evaluate their performance across nine gene-related problem scenarios. Our findings indicate that LLMs possess a certain level of understanding of genes and cells, but still lag behind domain-specific models in comprehending transcriptional expression profiles. Moreover, we have improved the current method of textual representation of cells, enhancing the LLMs’ ability to tackle cell annotation tasks. We encourage cell biology researchers to leverage LLMs for problem-solving while being mindful of the associated challenges. We release our code and data at https://github.com/epang-ucas/Evaluate_LLMs_to_Genes .

Transcriptional responses to direct and indirect TGFB1 stimulation in cancerous and noncancerous mammary epithelial cells

BackgroundTransforming growth factor beta (TGFβ) is important for the morphogenesis and secretory function of the mammary gland. It is one of the main activators of the epithelial–mesenchymal transition (EMT), a process important for tissue remodeling and regeneration. It also provides cells with the plasticity to form metastases during tumor progression. Noncancerous and cancer cells respond differently to TGFβ. However, knowledge of the cellular signaling cascades triggered by TGFβ in various cell types is still limited.MethodsMCF10A (noncancerous, originating from fibrotic breast tissue) and MCF7 (cancer, estrogen receptor-positive) breast epithelial cells were treated with TGFB1 directly or through conditioned media from stimulated cells. Transcriptional changes (via RNA-seq) were assessed in untreated cells and after 1–6 days of treatment. Differentially expressed genes were detected with DESeq2 and the hallmark collection was selected for gene set enrichment analysis.ResultsTGFB1 induces EMT in both the MCF10A and MCF7 cell lines but via slightly different mechanisms (signaling through SMAD3 is more active in MCF7 cells). Many EMT-related genes are expressed in MCF10A cells at baseline. Both cell lines respond to TGFB1 by decreasing the expression of genes involved in cell proliferation: through the repression of MYC (and the protein targets) in MCF10A cells and the activation of p63-dependent signaling in MCF7 cells (CDKN1A and CDKN2B, which are responsible for the inhibition of cyclin-dependent kinases, are upregulated). In addition, estrogen receptor signaling is inhibited and caspase-dependent cell death is induced only in MCF7 cells. Direct incubation with TGFB1 and treatment of cells with conditioned media similarly affected transcriptional profiles. However, TGFB1-induced protein secretion is more pronounced in MCF10A cells; therefore, the signaling is propagated through conditioned media (bystander effect) more effectively in MCF10A cells than in MCF7 cells.ConclusionsEstrogen receptor-positive breast cancer patients may benefit from high levels of TGFB1 expression due to the repression of estrogen receptor signaling, inhibition of proliferation, and induction of apoptosis in cancer cells. However, some TGFB1-stimulated cells may undergo EMT, which increases the risk of metastasis.

Sex-specific immune responses to COVID-19 vaccination in end-stage renal disease patients

Abstract Background End-stage renal disease (ESRD) patients have muted memory B cell formation and reduced humoral responses to COVID-19 vaccination; however, early innate immune responses have yet to be characterized. Sex-stratification is also limited in COVID-19 vaccination research. Methods We collected blood before (BD1) and 1-4 days post-dose 1 (PD1) of BNT162b2 vaccination for RNA-sequencing in ESRD patients (n = 35 BD1; 18 PD1) and healthy controls (HC) (n = 31 BD1; 30 PD1). Additionally, 20 plasma cytokines were quantified in ESRD patients (n = 39 BD1, 35 PD1) and HC (34 BD1, 15 PD1). Results Transcriptional profiling of vaccine responses identified 125 significantly differentially expressed genes (DEG) (padj&amp;lt;0.04) in ESRD patients and 107 DEGs (padj&amp;lt;0.05) in HC. 71 DEGs were shared, 54 unique to ESRD, and 36 unique to HC. DEG, pathway analyses, and cytokine responses in the combined dataset showed ESRD patients were more inflamed than HC at baseline, with an elevated inflammatory cytokine profile compared to HC. These results were driven by female ESRD patients where IL-2, IL-10, and IP-10 were more significant in females (p &amp;lt; 0.001) compared to males (p &amp;lt; 0.01). While IL-6, IFN-γ, IL-13, eotaxin, were exclusively associated in females (p &amp;lt; 0.05). Healthy females also had a stronger immunological response to vaccination compared to healthy males. Conclusions Despite baseline inflammation, ESRD patients were able to mount similar early immune responses to vaccination as HC, with females in both populations more reactogenic than males. Sex-stratification is recommended for ongoing immunological research to better understand unique responses to COVID-19 vaccination. Key messages • End-stage renal disease patients have similar early innate immune responses to COVID-19 vaccination as healthy controls. • Sex-stratification is important to identify unique immunological responses that may be leveraged for sex-specific vaccination strategies.

Complement factor D deficiency ameliorates adverse cardiac remodelling by inhibiting C5a-C5aR mediated ISGs+ neutrophil activation post myocardial infarction

Abstract Background Exaggerated inflammatory response after myocardial infarction (MI) exacerbates myocardial injury and adverse cardiac remodeling, leading to heart failure. Current management of MI involves myocardial protection and antifibrotic therapy but do not target the inflammatory response per se. Complement factor D (CFD) is an upstream rate-limiting enzyme of complement system activation, which is the early event of inflammatory response post MI. We hypothesize that CFD can be an important modulator of the inflammation-remodeling cascade post MI, but the specific mechanism remains elusive. Purpose To investigate the role and mechanism of CFD in regulating inflammatory expansion and adverse remodeling post MI. Methods We generated Cfd-AKO (Cfdfl/fl Adipoq-cre) mice using the Cre-LoxP recombination system, as CFD is mainly secreted by adipocytes. Immune status and cardiac remodeling progress were assessed by cardiovascular magnetic resonance (CMR), histology, flow cytometry, immunofluorescence, and ELISA. Single cell RNA sequencing (scRNA-seq) analyzed non­cardiomyocytes isolated from Cfd-AKO and WT mice post MI or sham operation. Genetic ablation and co-culture experiments dissected the functional molecular properties and intercellular communication. An CFD inhibitor ACH-4471 was used to explore the role of CFD in ischemia-reperfusion (IR) injury. Results The survival of Cfd-AKO mice was strongly improved, while ventricular arrhythmia induction rates and number of episodes were significantly reduced compared with those of WT mice. CMR imaging showed that Cfd-AKO mice had higher ejection fraction and reduced left ventricular dilation than WTs. Masson trichrome and picrosirius red staining revealed that besides smaller infarct size, the extent of fibrosis in the border and distal remote area decreased in Cfd-AKO mice. Cfd loss reduced myocardial injury, inhibited the release of inflammatory factors, and limits the amplification of complement components C3a and C5a post MI. ScRNA-seq revealed that CFD modulated neutrophil chemotactic ability and pro-inflammatory function by inducing interferon-stimulated genes expressing (ISG+) neutrophil CXCL10 expression. Mechanistically, CFD activates the ISG transcriptional profile via the C5a/C5aR dependent STAT1/2-IRF9 pathway. Activated neutrophils promote myofibroblast transformation through IL1β/IL1R dependent intercellular communication, thus facilitating pathological fibrosis. Early pharmacological blocking of CFD in mice IR injury models inhibited inflammation, reduced infarct size and ameliorated cardiac dysfunction. Conclusions We demonstrate the crucial role of CFD in cardiac remodeling post MI. This process is critically regulated by C5a-C5aR, an important component of complement-inflammation cascade. This CFD-C5a mediated neutrophil pro-inflammatory and pro-fibrotic dual activity represents a novel pathway and an attractive therapeutic window for heart failure post MI.CFD in cardiac remodelling post MI

SARS-CoV-2 variants induce increased inflammatory gene expression but reduced interferon responses and heme synthesis as compared with wild type strains

SARS-CoV-2 variants of concern (VOC) have been associated with increased viral transmission and disease severity. We investigated the mechanisms of pathogenesis caused by variants using a host blood transcriptome profiling approach. We analysed transcriptional signatures of COVID-19 patients comparing those infected with wildtype (wt), alpha, delta or omicron strains seeking insights into infection in Asymptomatic cases.Comparison of transcriptional profiles of Symptomatic and Asymptomatic COVID-19 cases showed increased differentially regulated gene (DEGs) of inflammatory, apoptosis and blood coagulation pathways, with decreased T cell and Interferon stimulated genes (ISG) activation. Between SARS-CoV-2 strains, an increasing number of DEGs occurred in comparisons between wt and alpha (196), delta (1425) or, omicron (2313) infections. COVID-19 cases with alpha or, delta variants demonstrated suppression transcripts of innate immune pathways. EGR1 and CXCL8 were highly upregulated in those infected with VOC; heme biosynthetic pathway genes (ALAS2, HBB, HBG1, HBD9) and ISGs were downregulated. Delta and omicron infections upregulated ribosomal pathways, reflecting increased viral RNA translation. Asymptomatic COVID-19 cases infected with delta infections showed increased cytokines and ISGs expression. Overall, increased inflammation, with reduced host heme synthesis was associated with infections caused by VOC infections, with raised type I interferon in cases with less severe disease.

Transcriptional Analysis of Cancer Cachexia: Conserved and Unique Features Across Pre-Clinical Models and Biological Sex.

Studies suggest heterogeneity in cancer cachexia (CC) among models and biological sexes, yet examinations comparing models and sexes are scarce. We compared the transcriptional landscape of skeletal muscle across murine CC models and biological sexes during early and late CC. Global gene expression analyses were performed on gastrocnemius (LLC-Lewis Lung Carcinoma), quadriceps (KPC-pancreatic), and tibialis anterior (C26-colorectal and ApcMin/+) muscles across biological sexes. Differentially expressed genes (DEGs) were identified using an adj-p-value of <0.05, followed by pathway and computational cistrome analyses. Integrating all controls, early, and late-stage of all models and sexes revealed up to 68% of DEGs and pathways were enriched at early and late CC, indicating a conserved transcriptional profile during CC development. Comparing DEGs and pathways within sexes and across models, in early-CC, the transcriptional response was highly heterogeneous. At late-stage, 11.5% of upregulated and 10% of downregulated genes were shared between models in males, while 18.9% of upregulated and 7% of downregulated DEGs were shared in females. Shared DEGs were enriched in proteasome and mitophagy/autophagy pathways (upregulated), and downregulation of energy metabolism pathways in males only. Between sexes, though proportion of shared DEGs was low (<16%), similar pathway enrichment was observed, including proteasome and mitophagy at late-stage CC. In early-CC, Osmr upregulation was the only commonality across all models and sexes, while CLOCK and ARNTL/BMAL1 were predicted transcriptional factors associated with dysregulations in all three male models. This study highlights sex and model differences in CC progression and suggests conserved transcriptional changes as potential therapeutic targets.

Cannabidiol (CBD) modulates the transcriptional profile of ethanol-exposed human dermal fibroblast cells.

Cannabidiol (CBD) is abundant in the Cannabis sativa plant and exhibits complex immunomodulatory, anxiolytic, antioxidant, and antiepileptic properties. Several studies suggest that CBD could be used for different purposes in alcohol use disorder (AUD) and alcohol-related injuries to the brain and the liver. In this study, we focused on analyzing transcriptional alterations in human dermal fibroblasts (HDFs) cell line challenged simultaneously with ethanol and CBD as an ethanol-protective agent. We aimed to expose the genes and pathways responsible for at least some of the CBD effects in those cells that can be related to the AUD. Transcriptome analysis was performed using HDFs cell line that expresses both cannabinoid receptors and can metabolize ethanol through alcohol dehydrogenase activity. Fibroblasts are also responsible for the progression of liver fibrosis, a common comorbidity in AUD. With the use of a cellular test, we found that CBD at the lowest applied concentration (0.75μM) was able to stimulate depressed metabolism and reduce the level of apoptosis of cells treated with different concentrations of ethanol to the level observed in the control cells. Similar observations were made at the transcriptome level, in which cells treated with ethanol and CBD had similar expression profiles to the control cells. CBD also affects several genes connected with extracellular matrix formation (especially its collagen constituent), which can have potential implications for, e.g., fibrosis process.