Biophys J. 2024 Dec 4:S0006-3495(24)04064-5. doi: 10.1016/j.bpj.2024.12.003. Online ahead of print.

ABSTRACT

We review empirical methods that can be used to provide physical descriptions of dynamic cellular processes during development and disease. Our focus will be non-spatial descriptions and the inference of underlying interaction networks including cell state lineages, gene regulatory networks, and molecular interactions in living cells. Our overarching questions are: How much can we learn from just observing? To what degree is it possible to infer causal and/or precise mathematical relationships from observations? We restrict ourselves to datasets arising from only observations, or experiments in which minimal perturbations have taken place to facilitate observation of the systems as they naturally occur. We discuss analysis perspectives in order from those offering the least descriptive power but requiring the least assumptions such as statistical associations. We end with those which are most descriptive, but require stricter assumptions and more prior knowledge of the systems such as causal inference and dynamical systems approaches. We hope to provide and encourage the use of a wide array of options for quantitative cell biologists to learn as much as possible from their observations at all stages of understanding of their system of interest. Finally, we provide our own recipe of how to empirically determine quantitative relationships and growth laws from live cell microscopy data, the resultant predictions of which can then be verified with perturbation experiments. We also include an extended supplement which describes further inference algorithms and theory for the interested reader.

PMID:39639772 | DOI:10.1016/j.bpj.2024.12.003

J Med Virol. 2024 Dec;96(12):e70099. doi: 10.1002/jmv.70099.

ABSTRACT

In the 2018 yellow fever (YF) outbreak in Brazil, we generated new transcriptomic data and combined it with clinical and immunological data to decode the pathogenesis of YF. Analyzing 79 patients, we found distinct gene expression patterns between acute YF, other viral infections, and the milder YF-17D vaccine infection. We identified a critical role for low-density, immature neutrophils in severe outcomes, marked by the downregulation of genes essential for neutrophil migration and maturation, such as PADI4, CSF3R, and ICAM1, in deceased patients. Our study also revealed complex interactions among inflammation-related genes, including increased CXCL10 and IL1R2 expression and decreased IL-1b expression in the acute phase. The diminished expression of HLA class II genes indicates impaired antigen presentation. These findings highlight the delicate balance of immune responses in YF pathogenesis and lay the groundwork for future therapeutic and diagnostic advancements.

PMID:39639628 | DOI:10.1002/jmv.70099

Cancer Commun (Lond). 2024 Dec 5. doi: 10.1002/cac2.12634. Online ahead of print.

NO ABSTRACT

PMID:39639599 | DOI:10.1002/cac2.12634

Adv Sci (Weinh). 2024 Dec 5:e2410360. doi: 10.1002/advs.202410360. Online ahead of print.

ABSTRACT

Secreted phosphosprotein 1 (SPP1)High tumor-associated macrophages (TAM) are abundant tumor myeloid cells that are immunosuppressive, pro-tumorigenic, and have a highly negative prognostic factor. Despite this, there is a lack of efficient TAM-specific therapeutics capable of reducing SPP1 expression. Here, on a phenotypic screen is reported to identify small molecule SPP1 modulators in macrophages. Several hits and incorporated them into a TAM-avid systemic nanoformulation are identified. It is shown that the lead compound (CANDI460) can down-regulate SPP1 in vitro and in vivo and lead to tumor remissions in different murine models. These findings are important as they offer a promising avenue for developing novel therapeutic strategies targeting TAM.

PMID:39639496 | DOI:10.1002/advs.202410360

Nat Methods. 2024 Dec 5. doi: 10.1038/s41592-024-02495-0. Online ahead of print.

ABSTRACT

Over a lifetime, hematopoietic stem cells (HSCs) adjust their lineage output to support age-aligned physiology. In model organisms, stereotypic waves of hematopoiesis have been observed corresponding to defined age-biased HSC hallmarks. However, how the properties of hematopoietic stem and progenitor cells change over the human lifespan remains unclear. To address this gap, we profiled individual transcriptome states of human hematopoietic stem and progenitor cells spanning gestation, maturation and aging. Here we define the gene expression networks dictating age-specific differentiation of HSCs and the dynamics of fate decisions and lineage priming throughout life. We additionally identifiy and functionally validate a fetal-specific HSC state with robust engraftment and multilineage capacity. Furthermore, we observe that classification of acute myeloid leukemia against defined transcriptional age states demonstrates that utilization of early life transcriptional programs associates with poor prognosis. Overall, we provide a disease-relevant framework for heterochronic orientation of stem cell ontogeny along the real time axis of the human lifespan.

PMID:39639169 | DOI:10.1038/s41592-024-02495-0

Sci Rep. 2024 Dec 6;14(1):30408. doi: 10.1038/s41598-024-81789-x.

ABSTRACT

Dimethyl sulfoxide (DMSO) is a widely used solvent in drug research. However, recent studies indicate that even at low concentration DMSO might cause structural changes of proteins and RNA. The pyrazolopyrimidine antiviral OBR-5-340 dissolved in DMSO inhibits rhinovirus-B5 infection yet is inactive against RV-A89. This is consistent with our structural observation that OBR-5-340 is only visible at the pocket factor site in rhinovirus-B5 and not in RV-A89, where the hydrophobic pocket is collapsed. Here, we analyze the impact of DMSO in RV-A89 by high-resolution cryo-electron microscopy. Our 1.76 Å cryo-EM reconstruction of RV-A89 in plain buffer, without DMSO, reveals that the pocket-factor binding site is occupied by myristate and that the previously observed local heterogeneity at protein-RNA interfaces is absent. These findings suggest that DMSO elutes the pocket factor, leading to a collapse of the hydrophobic pocket of RV-A89. Consequently, the conformational heterogeneity observed at the RNA-protein interface in the presence of DMSO likely results from increased capsid flexibility due to the absence of the pocket factor and DMSO-induced affinity modifications. This local asymmetry may promote a directional release of the RNA genome during infection.

PMID:39639094 | DOI:10.1038/s41598-024-81789-x

NPJ Syst Biol Appl. 2024 Dec 5;10(1):145. doi: 10.1038/s41540-024-00469-8.

ABSTRACT

HSCs differentiation has been difficult to study experimentally due to the high number of components and interactions involved, as well as the impact of diverse physiological conditions. From a 200-node network, that was grounded on experimental data, we derived a 21-node regulatory network by collapsing linear pathways and retaining the functional feedback loops. This regulatory network core integrates key nodes and interactions underlying HSCs differentiation, including transcription factors, metabolic, and redox signaling pathways. We used Boolean, continuous, and stochastic dynamic models to simulate the hypoxic conditions of the HSCs niche, as well as the patterns and temporal sequences of HSCs transitions and differentiation. Our findings indicate that HSCs differentiation is a plastic process in which cell fates can transdifferentiate among themselves. Additionally, we found that cell heterogeneity is fundamental for HSCs differentiation. Lastly, we found that oxygen activates ROS production, inhibiting quiescence and promoting growth and differentiation pathways of HSCs.

PMID:39639033 | DOI:10.1038/s41540-024-00469-8

Cell Death Dis. 2024 Dec 5;15(12):880. doi: 10.1038/s41419-024-07273-6.

NO ABSTRACT

PMID:39639011 | DOI:10.1038/s41419-024-07273-6

PLoS One. 2024 Dec 5;19(12):e0314754. doi: 10.1371/journal.pone.0314754. eCollection 2024.

ABSTRACT

COVID-19 and other pandemic viruses continue being important for public health and the global economy. Therefore, it is essential to explore the pathogenesis of COVID-19 more deeply, particularly its association with inflammatory and antiviral processes. In this study, we used the RNA-seq technique to analyze mRNA and non-coding RNA profiles of human peripheral blood mononuclear cells (PBMCs) from healthy individuals after SARS-CoV-2 in vitro exposure, to identify pathways related to immune response and the regulatory post-transcriptional mechanisms triggered that can serve as possible complementary therapeutic targets. Our analyses show that SARS-CoV-2 induced a significant regulation in the expression of 790 genes in PBMCs, of which 733 correspond to mRNAs and 57 to non-coding RNAs (lncRNAs). The immune response, antiviral response, signaling, cell proliferation and metabolism are the main biological processes involved. Among these, the inflammatory response groups the majority of regulated genes with an increase in the expression of chemokines involved in the recruitment of monocytes, neutrophils and T-cells. Additionally, it was observed that exposure to SARS-CoV-2 induces the expression of genes related to the IL-27 pathway but not of IFN-I or IFN-III, indicating the induction of ISGs through this pathway rather than the IFN genes. Moreover, several lncRNA and RNA binding proteins that can act in the cis-regulation of genes of the IL-27 pathway were identified. Our results indicate that SARS-CoV-2 can regulate the expression of multiple genes in PBMCs, mainly related to the inflammatory and antiviral response. Among these, lncRNAs establish an important mechanism in regulating the immune response to the virus. They could contribute to developing severe forms of COVID-19, constituting a possible therapeutic target.

PMID:39637135 | DOI:10.1371/journal.pone.0314754

PLoS One. 2024 Dec 5;19(12):e0314875. doi: 10.1371/journal.pone.0314875. eCollection 2024.

ABSTRACT

The reproducibility of computational biology models can be greatly facilitated by widely adopted standards and public repositories. We examined 50 models from the BioModels Database and attempted to validate the original curation and correct some of them if necessary. For each model, we reproduced these published results using Tellurium. Once reproduced we manually created a new set of files, with the model information stored by the Systems Biology Markup Language (SBML), and simulation instructions stored by the Simulation Experiment Description Markup Language (SED-ML), and everything included in an Open Modeling EXchange (OMEX) file, which could be used with a variety of simulators to reproduce the same results. On the one hand, the reproducibility procedure of 50 models developed a manual workflow that we would use to build an automatic platform to help users more easily curate and verify models in the future. On the other hand, these exercises allowed us to find the limitations and possible enhancement of the current curation and tooling to verify and curate models.

PMID:39636894 | DOI:10.1371/journal.pone.0314875

Clin Transplant. 2024 Dec;38(12):e70046. doi: 10.1111/ctr.70046.

ABSTRACT

BACKGROUND: Alemtuzumab can be an alternative to rabbit anti-thymocyte globulin (rATG) to treat severe or glucocorticoid-resistant acute T cell-mediated kidney transplant rejection (TCMR). Yet, there are few reports in which these two treatments are evaluated let alone, compared. This study describes the real-world clinical experience of both therapies and compares their efficacy and toxicity.

METHODS: Kidney transplant recipients of two Dutch transplant centers who received lymphocyte-depleting antibody therapy for severe or glucocorticoid-resistant TCMR were retrospectively evaluated. In the first, alemtuzumab was the standard treatment for this indication, in the second, it was rATG. Patient survival, graft survival and function, and the occurrence of infections and malignancies were reported and compared.

RESULTS: One hundred and forty-three patients treated with alemtuzumab and 57 patients with rATG were evaluated. Patient survival was not significantly different during follow-up (p = 0.55), and 5-year survival rates were 71.0% (95% confidence interval [CI]: 63.0-79.9) after alemtuzumab and 70.7% (95% CI: 58.3-85.7) after rATG. Graft survival was not significantly different during follow-up either (p = 0.24), and 5-year graft loss rates were 32.3% (95% CI: 24.2-40.5) after alemtuzumab and 29.2% (95% CI: 16.0-42.4) after rATG. The occurrence of infections and malignancies did not differ between groups.

CONCLUSION: Mostly, severe TCMRs have good long-term graft survival and function after either alemtuzumab or rATG therapy. No significant differences between the two therapies were found in this real-world clinical experience. Alemtuzumab is an effective alternative to rATG for the treatment of severe TCMR.

PMID:39636744 | DOI:10.1111/ctr.70046

STAR Protoc. 2024 Dec 4;5(4):103472. doi: 10.1016/j.xpro.2024.103472. Online ahead of print.

ABSTRACT

In a variety of biological contexts, characterizing genes associated with disease etiology and mediating global transcriptomic change is a key initial step. Here, we present a protocol to identify such key genes using our tool "PathExt," a tool that implements a network-based approach. We describe steps for installing libraries, preparing input data and detailed procedures for running PathExt, and characterizing differential pathways and key genes based on ripple centrality scores. For complete details on the use and execution of this protocol, please refer to Agrawal et al.1,2.

PMID:39636731 | DOI:10.1016/j.xpro.2024.103472

Elife. 2024 Dec 5;12:RP89851. doi: 10.7554/eLife.89851.

ABSTRACT

Entorhinal grid cells implement a spatial code with hexagonal periodicity, signaling the position of the animal within an environment. Grid maps of cells belonging to the same module share spacing and orientation, only differing in relative two-dimensional spatial phase, which could result from being part of a two-dimensional attractor guided by path integration. However, this architecture has the drawbacks of being complex to construct and rigid, path integration allowing for no deviations from the hexagonal pattern such as the ones observed under a variety of experimental manipulations. Here, we show that a simpler one-dimensional attractor is enough to align grid cells equally well. Using topological data analysis, we show that the resulting population activity is a sample of a torus, while the ensemble of maps preserves features of the network architecture. The flexibility of this low dimensional attractor allows it to negotiate the geometry of the representation manifold with the feedforward inputs, rather than imposing it. More generally, our results represent a proof of principle against the intuition that the architecture and the representation manifold of an attractor are topological objects of the same dimensionality, with implications to the study of attractor networks across the brain.

PMID:39636687 | DOI:10.7554/eLife.89851

Metabolomics. 2024 Dec 4;21(1):3. doi: 10.1007/s11306-024-02195-y.

ABSTRACT

INTRODUCTION: Coronavirus disease 2019 (COVID-19) has widely varying clinical severity. Currently, no single marker or panel of markers is considered standard of care for prediction of COVID-19 disease progression. The goal of this study is to gain mechanistic insights at the molecular level and to discover predictive biomarkers of severity of infection and outcomes among COVID-19 patients.

METHOD: This cohort study (n = 76) included participants aged 16-78 years who tested positive for SARS-CoV-2 and enrolled in Memphis, TN between August 2020 to July 2022. Clinical outcomes were classified as Non-severe (n = 39) or Severe (n = 37). LC/HRMS-based untargeted metabolomics/lipidomics was conducted to examine the difference in plasma metabolome and lipidome between the two groups.

RESULTS: Metabolomics data indicated that the kynurenine pathway was activated in Severe participants. Significant increases in short chain acylcarnitines, and short and medium chain acylcarnitines containing OH-FA chain in Severe vs. Non-severe group, which indicates that (1) the energy pathway switched to FA β-oxidation to maintain the host energy homeostasis and to provide energy for virus proliferation; (2) ROS status was aggravated in Severe vs. Non-severe group. Based on PLS-DA and correlation analysis to severity score, IL-6, and creatine, a biomarker panel containing glucose (pro-inflammation), ceramide and S1P (inflammation related), 4-hydroxybutyric acid (oxidative stress related), testosterone sulfate (immune related), and creatine (kidney function), was discovered. This novel biomarker panel plus IL-6 with an AUC of 0.945 provides a better indication of COVID-19 clinical outcomes than that of IL-6 alone or the three clinical biomarker panel (IL-6, glucose and creatine) with AUCs of 0.875 or 0.892.

PMID:39636373 | DOI:10.1007/s11306-024-02195-y

Elife. 2024 Dec 5;12:RP92499. doi: 10.7554/eLife.92499.

ABSTRACT

The environmental challenges the human malaria parasite, Plasmodium falciparum, faces during its progression into its various lifecycle stages warrant the use of effective and highly regulated access to chromatin for transcriptional regulation. Microrchidia (MORC) proteins have been implicated in DNA compaction and gene silencing across plant and animal kingdoms. Accumulating evidence has shed light on the role MORC protein plays as a transcriptional switch in apicomplexan parasites. In this study, using the CRISPR/Cas9 genome editing tool along with complementary molecular and genomics approaches, we demonstrate that PfMORC not only modulates chromatin structure and heterochromatin formation throughout the parasite erythrocytic cycle, but is also essential to the parasite survival. Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) experiments suggests that PfMORC binds to not only sub-telomeric regions and genes involved in antigenic variation but may also play a role in modulating stage transition. Protein knockdown experiments followed by chromatin conformation capture (Hi-C) studies indicate that downregulation of PfMORC impairs key histone marks and induces the collapse of the parasite heterochromatin structure leading to its death. All together these findings confirm that PfMORC plays a crucial role in chromatin structure and gene regulation, validating this factor as a strong candidate for novel antimalarial strategies.

PMID:39636094 | DOI:10.7554/eLife.92499

Int J Cancer. 2024 Dec 5. doi: 10.1002/ijc.35274. Online ahead of print.

ABSTRACT

Triple-negative breast cancer (TNBC) is the most aggressive breast cancer subtype with substantial disease heterogeneity, limited treatment options, and dismal clinical outcomes. Some TNBCs display homologous recombination deficiency (HRD), a phenotype with elevated genomic burden and worse prognosis if left untreated but chemotherapeutic sensitivity. While the molecular landscape of TNBC is distinct from other breast cancer subtypes, the TNBC-specific link between HRD and epigenome-wide methylation has not been established. This study reports two independent cohorts of TNBC tumors (n = 32 and n = 58) with HRD and epigenomic landscapes measured by the Multiplex Ligation-dependent Probe Amplification assay and the Illumina MethylationEPIC arrays, respectively. Genome-wide copy number and methylation alterations were significantly higher in HRD (all p <.05). Methylation of genome-wide repeat element Alu and transcriptional regulatory regions were significantly lower in HRD (all p <.05). An age-adjusted epigenome-wide association study of the continuous HRD probability scores revealed significant loci (all FDR <0.05) that were depleted from the CpG-rich "island" regions often seen in gene promoters but enriched in the CpG-poor "open sea" regions localized to gene enhancers. The significant loci implicated well-known candidate genes involved in the epithelial-to-mesenchymal transition, Wnt signaling, and DNA damage response. Supervised machine learning of HRD with nucleotide-specific methylation as the input enabled clinically relevant tumor stratification. Taken together, this study provides novel biological and translational insights into HRD in TNBCs.

PMID:39635770 | DOI:10.1002/ijc.35274

iScience. 2024 Sep 10;27(10):110918. doi: 10.1016/j.isci.2024.110918. eCollection 2024 Oct 18.

ABSTRACT

Telomere maintenance in neuroblastoma is linked to poor outcome and caused by either telomerase reverse transcriptase (TERT) activation or through alternative lengthening of telomeres (ALT). In contrast to TERT activation, commonly caused by genomic rearrangements or MYCN amplification, ALT is less well understood. Alterations at the ATRX locus are key drivers of ALT but only present in ∼50% of ALT tumors. To identify potential new pathways to telomere maintenance, we investigate allele-specific gene dosage effects from whole genomes and transcriptomes in 115 primary neuroblastomas. We show that copy-number dosage deregulates telomere maintenance, genomic stability, and neuronal pathways and identify upregulation of variants of histone H3 and H2A as a potential alternative pathway to ALT. We investigate the interplay between TERT activation, overexpression and copy-number dosage and reveal loss of imprinting at the RTL1 gene associated with poor clinical outcome. These results highlight the importance of gene dosage in key oncogenic mechanisms in neuroblastoma.

PMID:39635126 | PMC:PMC11615189 | DOI:10.1016/j.isci.2024.110918

iScience. 2024 Sep 18;27(10):110974. doi: 10.1016/j.isci.2024.110974. eCollection 2024 Oct 18.

ABSTRACT

To identify environmental factors that accelerate hair loss, we focused on modern artificial and aberrant light environments which cause circadian dysfunction. We examined the effect of aberrant light environments on hair growth by exposing mice to repetitive light-dark reversal at three-day intervals, inducing chronic circadian misalignment. Dorsal hair-sheared male mice showed impaired hair growth under this light condition. In addition, synchronization of hair growth cycling by dorsal depilation in male and female mice revealed that this light condition caused a decrease in hair growth rate during anagen. Furthermore, a decrease in hair growth rate was confirmed in male mice by ex vivo culture of whisker hair follicles classified as in anagen. These lines of evidence indicate that artificial and aberrant light environments or chronic circadian misalignment cause impaired hair growth due to a decrease in hair growth rate during anagen and are therefore a potential risk factor for hair loss.

PMID:39635123 | PMC:PMC11615142 | DOI:10.1016/j.isci.2024.110974

Front Cell Infect Microbiol. 2024 Nov 20;14:1471469. doi: 10.3389/fcimb.2024.1471469. eCollection 2024.

ABSTRACT

Tigecycline, hailed as a pivotal agent in combating multidrug-resistant bacterial infections, confronts obstacles posed by the emergence of resistance mechanisms in Gram-negative bacilli. This study explores the complex mechanisms of tigecycline resistance in Gram-negative bacilli, with a particular focus on the role of efflux pumps and drug modification in resistance. By summarizing these mechanisms, our objective is to provide a comprehensive understanding of tigecycline resistance in Gram-negative bacilli, thereby illuminating the evolving landscape of antimicrobial resistance. This review contributes to the elucidation of current existing tigecycline resistance mechanisms and provides insights into the development of effective strategies to manage the control of antimicrobial resistance in the clinical setting, as well as potential new targets for the treatment of tigecycline-resistant bacterial infections.

PMID:39635040 | PMC:PMC11615727 | DOI:10.3389/fcimb.2024.1471469

J Pharm Anal. 2024 Nov;14(11):101064. doi: 10.1016/j.jpha.2024.101064. Epub 2024 Aug 5.

ABSTRACT

Recently, small nucleolar RNAs (snoRNAs) have transcended the genomic "noise" to emerge as pivotal molecular markers due to their essential roles in tumor progression. Substantial evidence indicates a strong association between snoRNAs and critical clinical features such as tumor pathology and drug resistance. Historically, snoRNA research has concentrated on two classical mechanisms: 2'-O-ribose methylation and pseudouridylation. This review specifically summarizes the novel regulatory mechanisms and functional patterns of snoRNAs in tumors, encompassing transcriptional, post-transcriptional, and post-translational regulation. We further discuss the synergistic effect between snoRNA host genes (SNHGs) and snoRNAs in tumor progression. More importantly, snoRNAs extensively contribute to the development of tumor cell resistance as oncogenes or tumor suppressor genes. Accordingly, we provide a comprehensive review of the clinical diagnosis and treatment associated with snoRNAs and explore their significant potential as novel drug targets.

PMID:39634568 | PMC:PMC11613181 | DOI:10.1016/j.jpha.2024.101064