bluuebunny/crossref_metadata_2025 huggingface dataset:
Correlation Between Quantitative Cage Pressure Measurements and Surgeons’ Qualitative Tactile Assessments During Extraction in Lumbar Lateral Interbody Fusion
Authors: Sono Takashi , Shimizu Takayoshi , Murata Koichi , Yamamoto Koji , Matsuda Shuichi , Otsuki Bungo
Published: October 2024

Study Design:

A cadaveric study.

Objective:

Measuring the pressure exerted on lumbar lateral interbody fusion (LLIF) cages and examining its correlation with qualitative assessment of tactile feedback related to pullout strength during cage extraction to determine the optimal cage height.

Summary of Background Data:

No data exists on the relationship between the surgeon’s tactile feedback related to pullout strength during the LLIF cage extraction and the cage pressures measured during surgery.

Methods:

We used four cadavers to insert the original stress-measuring cages at the L2/3 to L4/5 levels (12 intervertebral spaces) using the oblique lumbar lateral approach. The intervertebral disc height (IDH) was measured before cage insertion. These stainless-steel stress-measuring cages were designed with the same shape as standard cages and included a built-in load cell to measure the stress applied. The cage heights were set at 8, 10, and 12 mm and they were inserted sequentially from 8mm, with stress measurements taken at each step. Four spine surgeons qualitatively evaluated the extraction strength using three rating categories (“loose,” “appropriate,” and “hard to extract”). After cage removal, endplate damage (ED) and anterior longitudinal ligament injury (ALLI) were checked. The anterior part of the vertebral body was dissected to expose the ALL and it is checked for obvious injuries. Additionally, a surgical probe is used to check for ED and ALLI.

Results:

The measured cage pressures were 45, 120, and 191 N for the “loose,” “appropriate,” and “hard to extract” ratings, respectively (P < 0.001). ED was observed in five intervertebral spaces, whereas no ALLI was noted. The average maximum pressure when ED occurred was 127 N. The primary risk factor for ED was identified as the difference between the height of the inserted cage and IDH, with a cut-off value of 4.5 mm.

Conclusion:

The appropriate extraction strength corresponded to a cage pressure of 120 N. A cage pressure ≥127 N posed a risk for ED. ED incidence was high when the difference between the IDH and the height of the inserted cage exceeded 4.5 mm.

Level of Evidence:

Level Three
Comparable Overall Risk of Neurologic Adverse Events Following Cervicothoracic Interlaminar and Transforaminal Epidural Injections
Authors: Seddio Anthony E. , McNamara Katelyn F. , Gouzoulis Michael J. , Jabbouri Sahir S. , Vasudevan Rajiv S. , Day Wesley , Ratnasamy Philip P. , Rubio Daniel R. , Grauer Jonathan N.
Published: October 2024

Study Design/Setting.

Retrospective cohort study

Objective.

To characterize the incidence and odds of neurologic adverse events following interlaminar (IL) and transforaminal (TF) cervicothoracic epidural spinal injections (CESI).

Summary of Background Data.

CESI may be considered in the management of various cervical pathology. Adverse events, although rare, can be devastating and have been reported following both IL and TF injections. The literature is mixed with regard to the risk-profile of these two types of CESI, but is largely limited to case reports, single centered studies, and literature reviews, which may incompletely characterize the relative risk of these injections at a national level.

Methods.

All adult patients undergoing IL and TF-CESI were identified from a large, national, multi-insurance database. The incidence of any post-injection neurologic complication was reported per 1,000 patients. The odds of specific neurologic adverse events occurring within 48-hours following TF-CESI, relative to IL-CESI, were compared by multivariable logistic regression controlling for age, sex, and Elixhauser comorbidity index (ECI).

Results.

A total of 1,073,215 IL-CESI patients and 220,597 TF-CESI patients were identified. The overall incidence of any neurologic complication following IL and TF-CESI occurred at a rate of 4.15 and 4.56 per 1,000 patients, respectively (P=0.889). TF-CESI was associated with higher odds ratio (OR) of nerve root injury (OR 1.69, P<0.001), but lower odds of epidural hematoma (OR 0.60, P=0.040), relative to IL-CESI. Conversely, no other neurologic adverse events were statistically different between approaches (P>0.05 for all).

Conclusions.

Following IL and TF-CESI, adverse events are relatively rare but not absent. Although the odds of the majority of individual neurologic adverse events were found to be similar, both approaches were independently associated with specific complications. Providers should therefore recognize that, at the national level, one CESI approach may not be universally associated with a lower risk of complications.
Effect of Nurse-Assisted Early Warning Intervention for Prevention of Venous Thromboembolism Following Cesarean Delivery
Authors: Wan Bichao , Fu Dongying , Chen Shijiang , Tao Fuying , Jiang Jianan , Tian Yingying
Published: October 2024

Objective

The aim of the study is to assess the role of a nurse-assisted early warning intervention in improving prophylaxis against obstetric venous thromboembolism (VTE) and preventing VTE following cesarean delivery (CD).

Methods

A prospective cohort study conducted between January 1, 2020, and December 30, 2022, enrolled pregnant women who underwent CD in the obstetric unit of Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital. The patients were assigned to a control group (routine nursing care) or the intervention group (nurse-assisted early warning intervention) depending on whether or not the nurse-assisted early warning intervention had been implemented. The χ
2 test and Student’s t test were used for statistical analysis. The primary outcome was the incidence of systemic VTE following CD, and secondary outcomes were the rates of mechanical or pharmacologic prophylaxis receipts for VTE and the frequency and severity of adverse events related to pharmacologic prophylaxis.

Results

A total of 27,074 cases were enrolled. The incidence of symptomatic VTE following CD was significantly lower in the intervention group (0.29 per 1000 deliveries) than in the control group (2.4 per 1000 deliveries) (P < 0.001). Significantly more cases received mechanical and pharmacological VTE prophylaxis in the intervention group than in the control group (respectively, 19.8% vs. 12.6% receiving mechanical prophylaxis and 0.9% vs. 0.2% receiving pharmacological prophylaxis). No cases of life-threatening bleeding occurred in either group.

Conclusion

The application of nurse-assisted early warning intervention may be an effective method for preventing VTE following CD.
High-dose chemotherapy with autologous stem cell rescue in children and young adults with high-risk Ewing sarcoma
Authors: Lee Chih-Ying , Hou Ming-Hsin , Hung Giun-Yi , Ho Cheng-Yin , Yu Ting-Yen , Wu Po-Kuei , Chen Chao-Ming , Yen Chueh-Chuan , Shiau Cheng-Ying , Chen Paul Chih-Hsueh , Wu Hung-Ta Hondar , Wu Ching-Lan , Yen Hsiu-Ju , Chen Wei-Ming
Published: October 2024

Background:

A combination treatment of surgery, chemotherapy, and radiotherapy can improve the survivals of pediatric patients with Ewing sarcoma (ES). However, prognosis remains poor for patients with metastatic disease at diagnosis or recurrence. Other high-risk (HR) features include large tumor burden, tumors of the axial skeleton, and poor histologic response. Several studies have documented high-dose chemotherapy with autologous stem cell rescue (HDC-ASCR) to be effective in such patients. In this retrospective study, we present the results of HDC-ASCR for high-risk ES (HRES) in children and young adults in a single institute.

Methods:

From March 2004 to March 2021, patients with ES, Ewing-like sarcoma, or round cell sarcoma received HDC-ASCR as part of treatment were included. The patients’ characteristics, disease status, stem cell dose, engraftment status, post-transplant complications, and outcomes were analyzed.

Results:

Twenty patients receiving HDC-ASCR at complete response (n = 6), partial response (n = 13), and stable disease (n = 1) were enrolled. The male-to-female ratio was 11:9. Median age at diagnosis and transplant was 15.6 years old (range: 3.3-28.9) and 16.2 (range: 4.2-29.9), respectively. The conditioning regimens included ifosfamide-based in two and melphalan-based in 19. All patients achieved successful engraftment without transplant-related mortality. The 5-year progression-free and overall survival (OS) rate were 35% and 54.5%, respectively. The causes of death (n = 8) were all contributed to disease progression. Patients in the complete response group or with localized HRES exhibited a higher 5-year OS (p = 0.047 and 0.05, respectively). Compared with the historical cohort without HDC-ASCR as part of primary treatment, the current cohort had a significantly better 5-year OS (p = 0.018).

Conclusion:

HDC-ASCR seems promising as an alternative treatment for HRES in improving OS in this retrospective study with a limited case number.
Induction of the ISR by AB5 subtilase cytotoxin drives type-I IFN expression in pDCs via STING activation
Authors: Barros Daniela , Ferreira Beatriz H. , Garcia-Gonzalez Paulina , Carbone Francesco , Luka Marine , Leite-Pinheiro Fátima , Antas Paulo , Mendes Andreia , Machado Mariana D. , Zhang Lichen , Cresci Marina , Galliot Lou , Gigan Julien , Reverendo Marisa , Su Bing , Paton Adrienne W. , Paton James C. , Rocchi Stéphane , Rieux-Laucat Frédéric , Argüello Rafael J. , Nal Béatrice , Liang Yinming , Ménager Mickaël , Gatti Evelina , Almeida Catarina R. , Pierre Philippe
Published: October 2024

We demonstrate that exposure to the AB5 subtilase cytotoxin (SubAB) induces the unfolded protein response (UPR) in human peripheral blood mononuclear cells, concomitant with a pro-inflammatory response across distinct cell subsets. Notably, SubAB selectively induces type-I interferon (IFN) expression in plasmacytoid dendritic cells, acting synergistically with Toll-like receptor 7 stimulation. The induction of type-I IFN in response to SubAB relies on stimulator of interferon genes (STING) activation, coupled with protein synthesis inhibition mediated by protein kinase R-like endoplasmic reticulum kinase and phosphorylation of the eukaryotic translation initiation factor 2 subunit-alpha. By impeding mRNA translation through the integrated stress response, SubAB precipitates the downregulation of the negative innate signaling feedback regulator Tax1-binding protein 1. This downregulation is necessary to unleash TANK-binding kinase 1 signaling associated with STING activation. These findings shed new light on how UPR-inducing conditions may regulate the immune system during infection or pathogenesis.
Linking candidate causal autoimmune variants to T cell networks using genetic and epigenetic screens in primary human T cells
Authors: Ho Ching-Huang , Dippel Maxwell A. , McQuade Meghan S. , Mishra Arpit , Pribitzer Stephan , Nguyen LeAnn P. , Hardy Samantha , Chandok Harshpreet , Chardon Florence , McDiarmid Troy A. , DeBerg Hannah A. , Buckner Jane H. , Shendure Jay , de Boer Carl G. , Guo Michael H. , Tewhey Ryan , Ray John P.
Published: October 2024

Genetic variants associated with autoimmune diseases are highly enriched within putativecis-regulatory regions of CD4+T cells, suggesting that they alter disease risk via changes in gene regulation. However, very few genetic variants have been shown to affect T cell gene expression or function. We tested >18,000 autoimmune disease-associated variants for allele-specific expression using massively parallel reporter assays in primary human CD4+T cells. The 545 expression-modulating variants (emVars) identified greatly enrich for likely causal variants. We provide evidence that many emVars are mediated by common upstream regulatory conduits, and that putative target genes of primary T cell emVars are highly enriched within a lymphocyte activation network. Using bulk and single-cell CRISPR-interference screens, we confirm that emVar-containing T cellcis-regulatory elements modulate both known and novel target genes that regulate T cell proliferation, providing plausible mechanisms by which these variants alter autoimmune disease risk.
Cerebral Small Vessel Disease genetic determinant TRIM47 controls brain homeostasisviathe NRF2 antioxidant system
Authors: Duplàa Cécile , Delobel Valentin , Boulestreau Romain , Rubin Sébastien , Vaurs Juliette , Jaspard-Vinassa Béatrice , Busson Muriel , Combrouze Cloé , Proust Carole , Morel Jean- Luc , Bontempi Bruno , Mishra Aniket , Debette Stéphanie , Couffinhal Thierry , Peghaire Claire
Published: October 2024

Cerebral small vessel disease (cSVD) is a leading cause of stroke, cognitive decline and dementia, for which no specific mechanism-based treatments are available to date. Genome-wide and whole-exome association studies previously identified robust associations of common variants at chr17q25 with cSVD features on magnetic resonance imaging, with converging bioinformatic and experimental data for a causal involvement ofTRIM47. Preliminary functional evaluation of TRIM47, an ubiquitin ligase enriched in brain endothelial cells (ECs), suggested its potential role in blood brain barrier (BBB) integrity. Here, we show that TRIM47 regulates brain EC resilience and adaptive responses to oxidative stress by binding to KEAP1, stabilizing NRF2 protein levels and promoting the NRF2 antioxidant signaling pathway.In vivo,Trim47-deficient mice exhibit downregulation of NRF2 target genes, BBB dysfunction, astrogliosis and cognitive impairments. Endothelial-specific deletion ofTrim47recapitulates these phenotypes. Treatment with the NRF2 activator tert- butylhydroquinone normalized BBB integrity and cognitive function inTrim47-deficient mice, highlighting the role of endothelial TRIM47 in driving brain homeostasis through NRF2 pathway activation. This work indicates that loss of the protective TRIM47/NRF2 axis may increase the susceptibility to developing human cSVD and that targeting the TRIM47/NRF2 axis could be a promising therapeutic approach for vascular cognitive impairment and dementia.
MEDOC: A fast, scalable and mathematically exact algorithm for the site-specific prediction of the protonation degree in large disordered proteins
Authors: Fossat Martin J.
Published: October 2024

Intrinsically disordered regions are found in most eukaryotic proteins and are enriched in positively and negatively charged residues. While it is often convenient to assume these residues follow their model-compound pKavalues, recent work has shown that local charge effects (charge regulation) can upshift or downshift sidechain pKavalues with major consequences for molecular function. Despite this, charge regulation is rarely considered when investigating disordered regions. The number of potential charge microstates that can be populated through acid/base regulation of a given number of ionizable residues in a sequence,N, scales as ∼2N. This exponential scaling makes the assessment of the full charge landscape of most proteins computationally intractable. To address this problem, we developed MEDOC (Multisite Extent of Deprotonation Originating from Context) to determine the degree of protonation of a protein based on the local sequence context of each ionizable residue. We show that we can drastically reduce the number of parameters necessary to determine the full, analytic, Boltzmann partition function of the charge landscape at both global and site-specific levels. Our algorithm applies the structure of theq-canonical ensemble, combined with novel strategies to rapidly obtain the minimal set of parameters, thereby circumventing the combinatorial explosion of the number of charge microstates even for proteins containing a large number of ionizable amino acids. We apply MEDOC to several sequences, including a global analysis of the distribution of pKavalues across the entire DisProt database. Our results show differences in the distribution of predicted pKavalues for different amino acids, in agreement with NMR-measured distributions in proteins.
vScreenML v2.0: Improved Machine Learning Classification for Reducing False Positives in Structure-Based Virtual Screening
Authors: Andrianov Grigorii V. , Haroldsen Emeline , Karanicolas John
Published: October 2024

Enthusiastic adoption of make-on-demand chemical libraries for virtual screening has highlighted the need for methods that deliver improved hit-finding discovery rates. Traditional virtual screening methods are often inaccurate, with most compounds nominated in a virtual screen not engaging the intended target protein to any detectable extent. Emerging machine learning approaches have made significant progress in this regard, including our previously-described tool vScreenML. Broad adoption of vScreenML was hindered by its challenging usability and dependencies on certain obsolete or proprietary software packages. Here, we introduce vScreenML 2.0 (https://github.com/gandrianov/vScreenML2) to address each of these limitations with a streamlined Python implementation. Through careful benchmarks, we show that vScreenML 2.0 outperforms other widely-used tools for virtual screening hit discovery.
DigestR an open-source software tool for visualizing LC-MS proteomics data resulting from natural protein catabolism
Authors: de Lamache Dimitri Desmonts , Aburashed Raied , Wacker Soren , Lewis Ian A.
Published: October 2024

Protein catabolism is an essential biological function supported by every living organism. Although liquid chromatography mass spectrometry proteomics has advanced considerably over the past decade, protein catabolism in natural systems is still difficult to study. One reason for this is the lack of software tools designed specifically for decoding the complex mixtures of peptides that result fromin vivoprotein digestion. To address this, we developed DigestR, an open-source software tool designed specifically for the analysis of LC-MS proteomics data. DigestR allows users to visualize naturally occurring peptides and align them to a reference proteome at display them at either a proteome-wide and protein-specific level. These visualization tools allow users to track the patters of peptides occurring in natural systems and map naturally-occurring proteolytic cut sites. To demonstrate these functions, we used DigestR to analyze a mixture of peptides resulting from thein vitrodigestion of human hemoglobin and bovine albumin with a cocktail of well characterized proteases. As expected, DigestR correctly identified both the proteins involved and the proteolytic cut sites produced by our protease cocktail. We then used DigestR to analyze the complex semi-ordered hemoglobin digestion pathway used by the malaria parasitePlasmodium falciparum.We show that DigestR successfully identified the proteolytic cut sites linked to the Plasmepsins, a protease known to be involved in hemoglobin digestion by the parasite. Collectively, these findings show that DigestR can be used to help visualize and interpret the complex mixtures of peptides occurring throughin vivoprotein catabolism. DigestR can be downloaded fromwww.lewisresearchgroup.org/software.
Polymer Model Integrates Super-Resolution Imaging and Epigenomic Sequencing to Elucidate the Role of Epigenetic Reactions in Shaping 4D Chromatin Organization
Authors: Vinayak Vinayak , Basir Ramin , Golloshi Rosela , Toth Joshua , Sant’Anna Lucas , Lakadamyali Melike , McCord Rachel Patton , Shenoy Vivek B
Published: October 2024

Chromatin, with its complex spatial and temporal organization, plays a crucial role in regulating gene expression. Recent advancements in super-resolution microscopy have revealed that nanoscale domains of heterochromatin (repressed segments) embedded within a euchromatin (active segments) background are fundamental units of 3D chromatin organization. In tissue-resident cells, the size of these heterochromatin domains varies with the microenvironment, particularly its stiffness, and chromatin organization is also influenced by pharmacological and epigenetic drugs. However, the mechanisms governing heterochromatin domain size under various conditions and their impact on gene expression remain unclear. To address this knowledge gap, we have developed a dynamic, next-generation sequencing informed chromatin copolymer model. Our model simulates the spatiotemporal evolution of chromatin, driven by passive diffusion and active epigenetic reactions, which interconvert euchromatin and heterochromatin. By integrating chromatin-chromatin interaction energetics and diffusion-reaction dynamics, we predict the formation of nanoscale heterochromatin-rich domains and establish a scaling relationship between their size and the modulation of epigenetic reaction rates. Additionally, our model predicts that epigenetic and chromatin compaction changes in response to changes in global reaction rates occur predominantly at domain boundaries. We validated these predictions via Hi-C contact map analysis and super-resolution imaging of hyperacetylated melanoma cells. Subsequent RNA-seq analysis suggested a pivotal role of these epigenetic shifts in influencing the metastatic potential of these cells. We further validated our mesoscale findings against chromatin rearrangement in hMSCs, which exhibit sensitivity of epigenetic reaction rates to changes in microenvironmental stiffness. Finally, we evaluated the effects of cycling of epigenetic reaction rates in silico, mimicking the cellular transition to different extracellular conditions, and back again. This finding reveals a cell-type invariant mechanism driven by domain boundaries, whereby chromatin organization guides epigenetic memory formation. Our findings show that chromatin reorganization in response to changes in epigenetic reaction rates resulting from alterations in the microenvironment, drug exposure and disease progression impacts both immediate cellular responses and long-term epigenetic memory.
Identification and predictive machine learning models construction of gut microbiota associated with lymph node metastasis in colorectal cancer
Authors: Wu Yongzhi , Huang Xiaoliang , Huang Yongqi , Huang Zigui , Chen Chuanbin , Qin Mingjian , Wang Zhen , He Fuhai , Tang Binzhe , Long Chenyan , Mo Xianwei , Liu Jungang , Tang Weizhong
Published: October 2024

This study focuses on the significant role between gut microbiota and lymph node metastasis (LNM) in colorectal cancer (CRC). By conducting 16S rRNA sequencing on fecal samples from 147 CRC patients and combining it with the linear discriminant analysis effect size (LEfSe) algorithm, we successfully identified significant differences in the gut microbiota between patients with LNM and those with none lymph node metastasis (NLNM). Furthermore, using transcriptome data from 9 CRC patients, we constructed an immune cell infiltration matrix to deeply explore the biological functions associated with LNM. Eventually, using the characteristics of the gut microbiota associated with LNM, we developed random forest (RF) and multilayer perceptron (MLP) machine learning models to predict the lymph node metastasis status of CRC patients. We identified 21 differentially abundant gut microbes between the two groups, among whichBacteroides plebeius, significantly enriched in LNM group, is closely related to the upregulation of resting NK cells and chemokine CXCL8 expression, and this bacterial species is also positively correlated with the enhancement of fructose metabolism. The RF and MLP models constructed based on the LNM-associated gut microbiota showed good predictive efficacy in predicting LNM status in CRC. This study reveals thatBacteroides plebeiusmay play an important role in the progression of CRC, with its mechanism potentially involving changes in immune modulation and metabolic pathways. The classification model constructed based on gut microbiota characteristics can predict LNM status of CRC, providing a new perspective for personalized and precision treatment of CRC patients.

Importance

This study highlights the pivotal role of gut microbiota in lymph node metastasis (LNM) of CRC, identifying key microbial differences between LNM and NLNM patients. Our findings implicateBacteroides plebeiusin CRC progression via immune modulation and metabolic alterations. Moreover, machine learning models based on gut microbiota predict LNM status accurately, offering a novel approach for personalized CRC treatment.
Metabolic reprogramming tips vaccinia virus infection outcomes by stabilizing interferon-γ induced IRF1
Authors: Chang Tyron , Alvarez Jessica , Chappidi Sruthi , Crockett Stacey , Sorouri Mahsa , Orchard Robert C. , Hancks Dustin C.
Published: October 2024

Interferon (IFN) induced activities are critical, early determinants of immune responses and infection outcomes. A key facet of IFN responses is the upregulation of hundreds of mRNAs termed interferon-stimulated genes (ISGs) that activate intrinsic and cell-mediated defenses. While primary interferon signaling is well-delineated, other layers of regulation are less explored but implied by aberrant ISG expression signatures in many diseases in the absence of infection. Consistently, our examination of tonic ISG levels across uninfected human tissues and individuals revealed three ISG subclasses. As tissue identity and many comorbidities with increased virus susceptibility are characterized by differences in metabolism, we characterized ISG responses in cells grown in media known to favor either aerobic glycolysis (glucose) or oxidative phosphorylation (galactose supplementation). While these conditions over time had a varying impact on the expression of ISG RNAs, the differences were typically greater between treatments than between glucose/galactose. Interestingly, extended interferon-priming led to divergent expression of two ISG proteins: upregulation of IRF1 in IFN-γ/glucose and increased IFITM3 in galactose by IFN-α and IFN-γ. In agreement with a hardwired response, glucose/galactose regulation of interferon-γ induced IRF1 is conserved in unrelated mouse and cat cell types. In galactose conditions, proteasome inhibition restored interferon-γ induced IRF1 levels to that of glucose/interferon-γ. Glucose/interferon-γ decreased replication of the model poxvirus vaccinia at low MOI and high MOIs. Vaccinia replication was restored byIRF1KO. In contrast, but consistent with differential regulation of IRF1 protein by glucose/galactose, WT andIRF1KO cells in galactose media supported similar levels of vaccinia replication regardless of IFN-γ priming. Also associated with glucose/galactose is a seemingly second block at a very late stage in viral replication which results in reductions in herpes- and poxvirus titers but not viral protein expression. Collectively, these data illustrate a novel layer of regulation for the key ISG protein, IRF1, mediated by glucose/galactose and imply unappreciated subprograms embedded in the interferon response. In principle, such cellular circuitry could rapidly adapt immune responses by sensing changing metabolite levels consumed during viral replication and cell proliferation.
Multimodal integration of single cell ATAC-seq data enables highly accurate delineation of clinically relevant tumor cell subpopulations
Authors: Xiong Kewei , Ding Ruofan , Qin Yangmei , Zou Xudong , Wang Jiguang , Yu Chen , Li Lei
Published: October 2024

Accurately deciphering tumor cellular heterogeneity is crucial for developing effective treatments. While single-cell epigenomics assays offer powerful insights into studying tumor heterogeneity beyond the transcriptional level, their application remains a significant challenge. To address this, we introduce Multimodal-based Analysis of scATAC-Seq data (MAAS), a method designed to identify functional tumor cell subpopulations and reconstruct their lineages from single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq). MAAS uniquely integrates multimodal information, encompassing chromatin accessibility, copy number variations (CNVs), and single-nucleotide variants, through self-expressive multimodal matrix factorization. MAAS outperforms existing methods in accuracy and robustness on both simulated and real datasets. When applied to multiple glioma scATAC-seq datasets, MAAS uncovered a previously hidden tumor cell subpopulation resistant to temozolomide treatment. Furthermore, MAAS effectively detected clinically relevant subpopulations with low CNVs, such as those found in pediatric ependymoma and B-cell lymphoma. Additionally, we developed a novel MAAS-derived clinical signature that provides superior prognostic prediction than traditional clinicopathologic features across multiple cancer types. In summary, MAAS significantly advances the identification of clinically relevant tumor cell subpopulations, thereby accelerating the discovery of potential therapeutic targets.
Functional Activity and Binding Specificity of small Ankyrin Repeat Proteins called Ankyrons against SARS-CoV-2 variants.
Authors: Park Yun-Jong , Jankowski Wojciech , Hurst Nicholas C , Fry Jeremy W , Schwabe Nikolai F , Tan Linda C C , Sauna Zuben E.
Published: October 2024

Effective management of COVID-19 requires clinical tools to treat the disease in addition to preventive vaccines. Several recombinant mAbs and their cocktails have been developed to treat COVID-19 but these have limitations. Here, we evaluate small ankyrin repeat proteins called Ankyrons that were generated to bind with high affinity to the SARS-CoV-2 virus. Ankyrons are ankyrin repeat proteins comprised of repetitions a structural module. Each module consists of a beta-turn followed by two antiparallel alpha-helices. The Ankyrons are directly selected in vitro from a highly diverse library of around a trillion clones in ribosome display and like antibodies can bind with high affinity to almost any target. We assessed Ankyrons that were generated against the wild-type SARS-CoV-2 and the Delta and Omicron variants in a binding assay. We determined that all Ankyrons were specific in that they did not bind to MERS, a related coronavirus. While all Ankyrons bound with high affinity to the variant they were generated against, some also showed cross-reactivity to all three SARS-CoV-2 variants. Binding assays are useful for screening analytes but do not provide information about clinical effectiveness. Therefore, we used a pseudovirus-based neutralization assay to show that five of the Ankyrons evaluated neutralized all three strains of SARS-CoV-2. We have provided a workflow for the evaluation of novel Ankyrons against a viral target. This suggests that Ankyrons could be useful for rapidly developing new research tools for studying other emerging infectious diseases rapidly with the optional further potential for developing Ankyrons into diagnostic and even therapeutic applications.
Arctic Ocean virus communities: seasonality, bipolarity, and prokaryotic interactions
Authors: Calayag Alyzza , Priest Taylor , Oldenburg Ellen , Muschiol Jan , Popa Ovidiu , Wietz Matthias , Needham David M.
Published: October 2024

Viruses play important roles in ocean environments as agents of mortality and genetic transfer, influencing ecology, evolution and biogeochemical processes. However, we know little about the diversity, seasonality, and host interactions of viruses in polar waters. To address this, we studied dsDNA viruses in the Arctic Fram Strait across four years via 47 long-read metagenomes of the cellular size-fraction. Among 5,662 vOTUs, 69%, 30% and 1.4% were bacteriophages (Myoviridae, Podoviridae, and Siphoviridae), Unassigned, and Phycodnaviridae, respectively. Viral coverage was, on average, 5-fold higher than prokaryotic coverage, and 8-fold higher in summer. Viral community composition showed annual peaks in similarity and was strongly correlated with prokaryotic community composition. Using a Convergent Cross Mapping network, we identified putative virus-host interactions and six ecological modules, each associated with distinct environmental conditions. The network also revealed putative novel cyanophages with time-lagged correlations to their hosts (late summer) as well as diverse viruses correlated with Nitrososphaerales (winter). By comparison with global metagenomes, we found that 42% of Fram Strait vOTUs peaked in abundance in high latitude regions of both hemispheres (average 61°N and 51°S), and encoded proteins with biochemical signatures of cold adaptation. Our study reveals a rich diversity of polar viruses with pronounced seasonality, providing a foundation for understanding how they regulate and impact ecosystem functionality in changing polar oceans.
Defacing biases visual quality assessments of structural MRI
Authors: Provins Céline , Savary Élodie , Sanchez Thomas , Mullier Emeline , Barranco Jaime , Fischi-Gómez Elda , Alemán-Gómez Yasser , Richiardi Jonas , Poldrack Russell A. , Hagmann Patric , Esteban Oscar
Published: October 2024

A critical requirement before data-sharing of human neuroimaging is removing facial features to protect individuals’ privacy. However, not only does this process redact identifiable information about individuals, but it also removes non-identifiable information. This introduces undesired variability into downstream analysis and interpretation. This registered report investigated the degree to which the so-calleddefacingaltered the quality assessment of T1-weighted images of the human brain from the openly available “IXI dataset”. The effect of defacing on manual quality assessment was investigated on a single-site subset of the dataset (N=185). By comparing two linear mixed-effects models, we determined that four trained human raters’ perception of quality was significantly influenced by defacing by comparing their ratings on the same set of images in two conditions: “nondefaced” (that is, preserving facial features) and “defaced”. In addition, we investigated these biases on automated quality assessments by applying repeated-measures multivariate ANOVA (rm-MANOVA) on the image quality metrics extracted withMRIQCon the full IXI dataset (N=581; three acquisition sites). This study found that defacing altered the quality assessments by humans and showed thatMRIQC’s quality metrics were mostly insensitive to defacing.
Isolated human Fos promoter in plasmid DNA is overactive
Authors: Andrei Gorbunov , Dmitrii Fedorov , Olga Kvitko , Olga Lopina , Elizaveta Klimanova
Published: October 2024

Changes in intracellular concentrations of Na+and K+are shown to alterFosgene expression. Here, we obtained a genetic construct encodingTurboGFP-dest1gene under control of the humanFospromoter (−549; +155) and studied its expression in HEK293T. Amplification of theFospromoter sequence from genomic DNA was only efficient in the presence of Li+ions. Ouabain and medium with replacement of Na+with Li+ions resulted in the accumulation of Na+and Li+in cells, respectively. These stimuli increased the mRNA level of endogenousFosand the average fluorescence intensity of TurboGFP-dest1 in transfected cells. The mRNA level ofTurboGFP-dest1was extremely higher than the mRNA level of endogenousFosand was little affected by the stimuli.
Provirus deletion fromHaloferax volcaniiaffects motility, stress resistance and CRISPR RNA expression
Authors: Di Cianni Nadia , Bolsinger Simon , Brendel Jutta , Raabe Monika , König Sabine , Mitchell Laura , Bischler Thorsten , Gräfenhan Tom , Read Clarissa , Erdmann Susanne , Allers Thorsten , Walther Paul , Urlaub Henning , Dyall-Smith Mike , Pfeiffer Friedhelm , Marchfelder Anita
Published: October 2024

Haloferax volcaniiharbours four putative proviruses: Halfvol1, Halfvol2, Halfvol3 and Halfvol4. In this study we successfully deleted all four provirus genomes, demonstrating, that they are not essential. Transcriptome comparison between this strain (ΔHalfvol1-4) and a wild type strain reveals an increase in archaella and chemotaxis gene expression, resulting in higher swarming motility in ΔHalfvol1-4. Furthermore, ΔHalfvol1-4 cells show an elongated cell shape and a higher resistance to H2O2stress compared to the wild type. RNA-seq also revealed down-regulation of CRISPR arrays in the provirus-free strain.

Circularised genomes of Halfvol1, Halfvol2 and Halfvol3 were found in the culture supernatant. This confirms excision of the proviruses from the chromosome, which seems to happen more efficiently at low temperature (30°C). Electron microscopy revealed potential viral particles in the supernatant, and mass spectrometry analysis confirmed the presence of structural viral proteins of Halfvol1 and Halfvol3 in the isolated virus sample. These observations suggest that these proviruses are active and cause a chronic infection inHfx. volcanii.
TGFβ1-TNFα regulated secretion of neutrophil chemokines is independent of epithelial-mesenchymal transitions in breast tumor cells
Authors: SenGupta Shuvasree , Cohen Erez , Serrenho Joseph , Ott Kaleb , Coulombe Pierre A. , Parent Carole A.
Published: October 2024

Neutrophils have tumor-promoting roles in breast cancer and are detected in higher numbers in aggressive breast tumors. How aggressive breast tumors recruit neutrophils remains undefined. Here, we investigated the roles of TGF-β1 and TNF-α in the regulation of neutrophil recruitment by breast cancer cells. TGF-β1 and TNF-α are pro-inflammatory factors upregulated in breast tumors and induce epithelial to mesenchymal transitions (EMT), a process linked to cancer cell aggressiveness. We report that, as expected, dual treatment with TGF-β1 and TNF-α induces EMT signatures in premalignant M2 cells, which are part of the MCF10A breast cancer progression model. Conditioned media (CM) harvested from M2 cells treated with TGF-β1/TNF-α gives rise to amplified neutrophil chemotaxis compared to CM from control M2 cells. This response correlates with higher levels of the neutrophil chemokines CXCL1, CXCL2, and CXCL8 and is significantly attenuated in the presence of a CXCL8-neutralizing antibody. Furthermore, we found that secretion of CXCL1 and CXCL8 from treated M2 cells depends on p38MAPK activity. By combining gene editing, immunological and biochemical approaches, we show that the regulation of neutrophil recruitment and EMT signatures are not mechanistically linked in treated M2 cells. Finally, analysis of publicly available cancer cell line transcriptomic databases revealed a significant correlation between CXCL8 and TGF-β1/TNF-α-regulated or effector genes in breast cancer. Together, our findings establish a novel role for the TGF-β1/TNF-α/p38 MAPK signaling axis in regulating neutrophil recruitment in breast cancer, independent of TGF-β1/TNF-α regulated EMT.
Novel Transgenic Humanized Alpha-1 Antitrypsin Deficiency Mouse Model on MurineSERPINA1Null Background
Authors: Oshins Regina , Aranyos Alek M. , Grey Skylar , Mohammad Naweed , Lu Yuanqing , Lascano Jorge E. , Flagg Tammy , Serban Karina , Brantly Mark , Khodayari Nazli
Published: October 2024

Alpha-1 antitrypsin deficiency (AATD) is a rare genetic disorder caused by accumulation of misfolded α-1 antitrypsin within hepatocytes. AATD patients are prone to develop liver disease that remains undiagnosed until the late stages of the disease. Due to challenges in manipulating the α-1 antitrypsin genes in mice, determining a true loss of function of α-1 antitrypsin in previous AATD mouse models has been challenging. Here, we report generation and liver characterization of a new humanized transgenic mouse model for AATD with a background of a CRISPR-Cas9 generatedSERPINA1-null mouse. Male and female transgenic mice for normal (Pi*M) and mutant (Pi*Z) variants of human α-1 antitrypsin at 4-6 months of age were subjected to this study. The accumulation of human α-1 antitrypsin in the hepatocytes and fibrotic features of the liver were monitored by performing an in vivo study. We demonstrate a strong liver phenotype satisfying clinically relevant manifestations of liver pathology associated with AATD, including hepatic accumulation of human α-1 antitrypsin globules, liver deposition of extracellular matrix proteins, hepatic ER stress, and liver fibrosis in Pi*Z mice, in addition to mild systemic inflammation. In addition to major phenotypic criteria of AATD-associated liver fibrosis, accompanying single-nucleus RNA-seq data demonstrate activation of pathways associated with liver metabolic changes, inflammation, and regeneration. Data from this study suggest our humanized transgenic AATD mouse model could provide a suitable model to study α-1 antitrypsin loss of function, replicate the pathophysiology of AATD associated liver disease, and evaluate therapeutic reagents against this disease.

NEW & NOTEWORTHY

We have characterized a new humanized transgenic mouse model of α-1 antitrypsin deficiency with aSERPINA1-null background that shows strong manifestations of liver disease. Our data explores the altered phenotype of α-1 antitrypsin deficient hepatocytes and suggests a relationship between liver cell types during disease progression. This model may become a useful tool for investigating α-1 antitrypsin loss of function, pathogenic mechanisms, and for drug discovery aimed at both prevention and treatment of the disease.
Comparative analysis of rhesus macaque and human placental organoids highlights evolutionary differences in placentation
Authors: Caldwell Allyson , Yang Liheng , Scheef Elizabeth A. , Kaur Amitinder , Coyne Carolyn B.
Published: October 2024

Throughout evolution, the placenta has diversified in both structure and cellular composition while maintaining its fundamental function. Trophoblasts are fetal-derived cells responsible for nourishing and protecting the developing fetus and are a universal component of all placentas. While primate placentas exhibit many shared morphological features, species-specific differences in gene expression remain largely unexplored, primarily due to the lack of suitablein vitromodels. To address this gap, we developed organoids from rhesus macaque placentas, including trophoblast and maternal-derived decidua types, and compared them with organoids derived from human placentas. We performed comparative single-cell RNA sequencing to delineate shared and distinct transcriptional signatures between rhesus macaque and human trophoblasts. We further defined the differentiation trajectories leading to the multinucleated syncytiotrophoblast, highlighting both shared and unique transcriptional signatures between rhesus macaque and human placentas. This work establishes novelin vitromodels of the non-human primate placenta and characterizes distinct trophoblast gene profiles in rhesus macaques and humans, providing insights into interspecies variations in placental biology.
Reconstructing signaling history of single cells with imaging-based molecular recording
Authors: Hao Kai , Barrett Mykel , Samadi Zainalabedin , Zarezadeh Amirhossein , McGrath Yuka , Askary Amjad
Published: October 2024

The intensity and duration of biological signals encode information that allows a few pathways to regulate a wide array of cellular behaviors. Despite the central importance of signaling in biomedical research, our ability to quantify it in individual cells over time remains limited. Here, we introduce INSCRIBE, an approach for reconstructing signaling history in single cells using endpoint fluorescence images. By regulating a CRISPR base editor, INSCRIBE generates mutations in genomic target sequences, at a rate proportional to signaling activity. The number of edits is then recovered through a novel ratiometric readout strategy, from images of two fluorescence channels. We engineered human cell lines for recording WNT and BMP pathway activity, and demonstrated that INSCRIBE faithfully recovers both the intensity and duration of signaling. Further, we used INSCRIBE to study the variability of cellular response to WNT and BMP stimulation, and test whether the magnitude of response is a stable, heritable trait. We found a persistent memory in the BMP pathway. Progeny of cells with higher BMP response levels are likely to respond more strongly to a second BMP stimulation, up to 3 weeks later. Together, our results establish a scalable platform for genetic recording andin situreadout of signaling history in single cells, advancing quantitative analysis of cell-cell communication during development and disease.
Design of a biomolecular adaptive controller to restore sustained periodic behavior
Authors: Bisso Frank Britto , Dey Subham , Stan Guy-Bart , Cuba Samaniego Christian
Published: October 2024

Periodic behavior is a widespread biological phenomenon occurring across various spatiotemporal scales, where upstream stimuli are encoded into dynamic intracellular signals such as oscillations, varying in duration, amplitude, and frequency. Disruptions to this periodicity can lead to a range of pathologies, for which we propose an adaptive feedback controller with an Incoherent Feedforward Loop (IFFL)-like topology, based on chemical reactions, designed to restore sustained oscillations in systems that have lost their periodicity. By approximating the controller’s dynamics, we defined the design requirements for the first implementation of a biomolecular adaptive controller and tested its applicability for destabilizing the steady–state behavior of a self-inhibiting gene. Numerical simulations illustrate the adaptive behavior of the controller and its ability to tune both the amplitude and the period of the resulting oscillations.
How could you think that? Supervisor misattribution leads to reduced subsequent employee organizational citizenship behavior
Authors: Mcilveene Timothy R. , Davis Maggie , White Sonia
Published: October 2024

Purpose

From a social cognitive perspective, the current study examines how the relationship between the employee and the organization changes following supervisor motive misattribution of organizational citizenship behavior (OCB).

Design/methodology/approach

The current study utilizes an experimental vignette methodology (EVM), linear regression and Hayes' (2017) Process Version 4 macro in SPSS to examine the relationships between supervisor misattribution of employee OCB, personality and individual differences and future organizational citizenship behavior intentions.

Findings

Results indicate that supervisor misattribution of employee OCB, specifically when the act is attributed to impression management, will reduce the intention to engage in future OCBs. Results also indicate that this negative relationship is enhanced when subordinates are high in openness.

Research limitations/implications

This study extends social exchange theory by demonstrating how the misattribution of motivation to perform OCBs creates a negative social exchange and discourages future organizational citizenship behavior from the employee. The current research demonstrates the importance of supervisors understanding employees' motivations for engaging in (OCB). If an employee engages in OCB based on intrinsic motivation, such as a desire to help others, and their motivation is attributed to external motivation, such as impression management, the employee may feel misunderstood and believe their values and motivations are incorrectly perceived, leading to reduced OCB.

Originality/value

The current research is examined using EVM. By immersing participants in realistic hypothetical scenarios, experimental vignette methodology allows researchers to explore the intricacies of decision-making across unique scenarios, unraveling both the “why” and the “what next” behind decision-making.