bluuebunny/crossref_metadata_2025 huggingface dataset:
CAR T cells recognizing CD276 and Dual-CAR T cells against CD276/FGFR4 promote rhabdomyosarcoma clearance in orthotopic mouse models
Authors: Timpanaro Andrea , Piccand Caroline , Dzhumashev Dzhangar , Anton-Joseph Stenija , Robbi Andrea , Moser Janine , Rössler Jochen , Bernasconi Michele
Published: September 2023

Background

Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in childhood, whose prognosis is still poor especially for metastatic, high-grade, and relapsed RMS. New treatments are urgently needed, especially systemic therapies. Chimeric Antigen Receptor T cells (CAR Ts) are very effective against hematological malignancies, but their efficacy against solid tumors needs to be improved. CD276 is a target upregulated in RMS and detected at low levels in normal tissues. FGFR4 is a very specific target for RMS. Here, we optimized CAR Ts for these two targets, alone or in combination, and tested their anti-tumor activityin vitroandin vivo.

Methods

Four different single-domain antibodies were used to select the most specific FGFR4-CAR construct. RMS cell killing and cytokine production by CD276- and FGFR4-CAR Ts expressing CD8α or CD28 HD/TM domains in combination with 4-1BB and/or CD28 co-stimulatory domains were testedin vitro.The most effective CD276- and FGFR4-CAR Ts were used to generate Dual-CAR Ts. Tumor killing was evaluatedin vivoin three orthotopic RMS mouse models.

Results

CD276.V-CAR Ts (276.MG.CD28HD/TM.CD28CSD.3z) showed the strongest killing of RMS cells, and the highest release of IFN-γ and Granzyme Bin vitro. FGFR4.V-CAR Ts (F8-FR4.CD28HD/TM.CD28CSD.3z) showed the most specific killing. CD276-CAR Ts successfully eradicated RD- and Rh4-derived RMS tumorsin vivo, achieving complete remission in 3/5 and 5/5 mice, respectively. In CD276lowJR-tumors, however, they achieved complete remission in only 1/5 mice. FGFR4 CAR Ts instead delayed of Rh4 tumor growth. Dual-CAR Ts promoted Rh4-tumors clearance in 5/5 mice.

Conclusions

CD276- and CD276/FGFR4-directed CAR Ts showed effective RMS cell killingin vitroand eradication of CD276highRMS tumorsin vivo. CD276lowtumors escaped the therapy showing a correlation of antigen density and effectiveness. FGFR4-CAR Ts showed specific killingin vitrobut could only delay RMS growthin vivo. Our results show that combined expression of CD276-CAR with other CAR does not reduce its benefit. Introducing immunotherapy with CD276-CAR Ts in RMS seems to be feasible and promising, although CAR constructs design and target combinations have to be further improved to eradicate tumors with low target expression.
Bacterial Sphingolipids Exacerbate Colitis by Inhibiting ILC3-derived IL-22 Production
Authors: Bao Bin , Wang Youyuan , Boudreau Pavl , Song Xinyang , Wu Meng , Chen Xi , Patik Izabel , Tang Ying , Ouahed Jodie , Ringel Amit , Barends Jared , Wu Chuan , Balskus Emily , Thiagarajah Jay , Liu Jian , Wessels Michael R. , Lencer Wayne , Kasper Dennis L. , An Dingding , Horwitz Bruce , Snapper Scott B.
Published: September 2023

Commensal bacteria of the Bacteroidetes phylum are the primary producers of sphingolipids in the gut lumen. These lipids serve dual roles as bacterial virulence factors and regulators of the host mucosal immune system, including regulatory T cells and invariant natural killer T cells (iNKT). Sphingolipid composition is significantly altered in fecal samples of patients with inflammatory bowel disease (IBD). However, the specific mechanisms by which bacterial sphingolipids modulate mucosal homeostasis and regulate intestinal inflammation remain unclear. In this study, we investigated the impact of bacterial sphingolipids on intestinal inflammation by mono-colonizing mice withBacteroides fragilisstrains that either express or lack sphingolipids during DSS-induced colitis. We discovered thatB. fragilissphingolipids exacerbate intestinal inflammation. Mice mono-colonized withB. fragilislacking sphingolipids exhibited less severe DSS-induced colitis. This amelioration of colitis was associated with increased production of interleukin-22 (IL-22) by innate lymphoid cell type 3 (ILC3). Consistent with the inhibitory effect of sphingolipids on IL-22 production, mice colonized withB. fragilislacking sphingolipids showed enhanced epithelial STAT3 activity, intestinal cell proliferation, and antimicrobial peptide production following DSS treatment compared to those colonized withB. fragilisproducing sphingolipids. Additionally, colitis severity in mice colonized withB. fragilislacking sphingolipids was exacerbated upon IL-22 blockade. Furthermore, our study reveals that bacterial sphingolipids restrict epithelial IL-18 production following DSS treatment and interfere with IL-22 production by a subset of ILC3 cells expressing both the interleukin-18 receptor (IL-18R) and major histocompatibility complex class II (MHC II). These findings indicate thatB. fragilis-derived sphingolipids exacerbate mucosal inflammation by impeding epithelial IL-18 expression, resulting in compromised production of IL-22 by ILC3 cells.

Highlights

B. fragilis-derived sphingolipids exacerbate DSS-induced colitis in mono-colonized C57BL/6 mice.

B. fragilis-derived sphingolipids constrain ILC3-derived IL-22, leading to reduced colonic epithelial cell proliferation and compromised barrier function.

B. fragilis-derived sphingolipids restrict epithelial NLRC4 inflammasome activation and IL-18 secretion.

B. fragilis-derived sphingolipids modulate IL-22 production by IL18R+MHC II+ILC3s.
Rational design of a SOCS1-edited tumor infiltrating lymphocyte therapy for solid tumors using CRISPR/Cas9 screens
Authors: Schlabach Michael R. , Lin Sharon , Collester Zachary , Wrocklage Christopher , Shenker Sol , Calnan Conor , Xu Tianlei , Gannon Hugh , Williams Leila , Thompson Frank , Dunbar Paul , LaMothe Robert A. , Garrett Tracy E. , Colletti Nick , Hohmann Anja F. , Tubo Noah , Bullock Caroline , Le Mercier Isabelle , Sofjan Katri , Merkin Jason J. , Keegan Sean , Kryukov Gregory V. , Dugopolski Caroline , Stegmeier Frank , Wong Karrie , Sharp Fiona A. , Cadzow Louise , Benson Micah J.
Published: September 2023

Cell therapies such as Tumor Infiltrating Lymphocyte (TIL) therapy have shown promise in the treatment of patients with refractory solid tumors, with improvement in response rates and durability of responses nevertheless sought. To identify targets capable of enhancing the anti-tumor activity of T cell therapies, large-scale in vitro and in vivo CRISPR/Cas9 screens were performed, with the suppressor of cytokine signaling 1 (SOCS1) gene identified as a top T cell-enhancing target. In murine CD8 T cell therapy models, SOCS1 served as a critical checkpoint in restraining the accumulation of T central memory cells in lymphoid organs as well as intermediate (Texint) and effector (Texeff) exhausted T cell subsets derived from progenitor exhausted T cell (Texprog) cells in tumors. A comprehensive CRISPR tiling screen of theSOCS1coding region identified sgRNAs targeting the SH2 domain of SOCS1 as the most potent, with a sgRNA with minimal off-target cut sites used to manufacture KSQ-001, an engineered TIL therapy with SOCS1 inactivated by CRISPR/Cas9. KSQ-001 possessed increased responsiveness to cytokine signals and enhanced in vivo anti-tumor function in mouse models. These data demonstrate the use of CRISPR/Cas9 screens in the rational design of T cell therapies.
Investigating Task-Free Functional Connectivity Patterns in Newborns Using functional Near-Infrared Spectroscopy
Authors: Vahidi Homa , Kowalczyk Alexandra , Stubbs Kevin , Musabi Melab , Roychaudhuri Sriya , Kent Michaela , Bhattacharya Soume , de Ribaupierre Sandrine , Lawrence Keith St. , Mohsenzadeh Yalda , Duerden Emma
Published: September 2023

Significance

Resting-state networks (RSN), particularly the sensorimotor network, begin to develop in the third trimester of pregnancy and mature extensively by term age. The integrity and structure of these networks have been linked to neurological health outcomes in neonates, highlighting the significance of monitoring RSN development. To this end, functional near-infrared spectroscopy (fNIRS) has emerged as a neuroimaging technique that utilizes near-infrared light to indirectly measure neural activity by detecting changes in oxygenated (HbO) and deoxygenated (HbR) hemoglobin concentrations. Compared to other imaging methods, fNIRS is non-invasive and allows for naturalistic monitoring of neural activity at the bedside, particularly in awake infants.

Aim

Use fNIRS to expand on previous findings regarding the development of functional networks in awake neonates.

Approach

fNIRS was acquired in 41 term-born neonates (17 females, gestational age range=36+0 to 42+1 weeks) within the first 48 hours after birth.

Results

Group level analysis of functional connectivity showed strong positive connectivity in most channel-pairs over the sensorimotor network, especially the left hemisphere (q < 0.05). Next, we examined the relationship between functional connectivity, gestational age and postnatal age, while controlling for sex and subject effects. Both gestational and postnatal age were found to be positively associated with an increase in functional connectivity in the sensorimotor RSN, especially in channels covering the posterior portion.

Conclusions

Our findings emphasize the importance of considering developmental changes in functional networks in awake infants. Moreover, our study demonstrates the potential of fNIRS as a valuable tool for studying neural activity in naturalistic settings in neonates.
Trials and tribulations of Neotropical plant taxonomy: pace of tree species description
Authors: Luján Manuel , Lemos Rosalinda Medina , Lucas Eve , Michelangeli Fabián A. , Prance Ghillean , Pennington Terry D. , Rzedowski Jerzy , Santamaría-Aguilar Daniel , Serpell Ella , Sothers Cynthia , Zuntini Alexandre R.
Published: September 2023

One of the main aspects of taxonomic research is the description of new species. Identifying how to describe new species more efficiently is key to completing the inventory of the Neotropical flora in an era of massive biodiversity loss.

Here we calculate the interval between first specimen collection and new species publication for a group of 2126 Neotropical trees, and discuss the historical context surrounding specimen collection and new species publication events.

Our results reveal that on average, it takes almost 16 years from specimen collection to publication of a new Neotropical tree species, which is considerably shorter than previous estimates for other tropical groups. The central Andes is the region that had the longest average time lags, while the Choco had the shortest. Peru had the longest average time lags by country, while Haiti had the shortest. The average time lags increased until the early 1900s, when a decrease was observed, with the shortest lags between 1941 to 1960.

We found that the majority of the species described more rapidly are from plants collected and described by the same researcher. We demonstrate how political instability and conflict can delay or impede the completion of research initiatives in the region. We argue that enhancing international collaboration and training opportunities in Latin American countries, as well as ensuring safe plant collection campaigns, are critical to complete the inventory of the Neotropical flora.

Societal Impact Statement

This study aims to answer the question of how long it takes to describe a new species of tree in the Neotropics by calculating the time elapsed from collection of the first specimen to the publication of a new species. Given the current unprecedented concerns for global biodiversity loss, it is critical to identify best practices for describing new species more efficiently so we can complete the inventory of the Neotropical flora and implement appropriate conservation strategies in a timely manner.
Salinity plays a limited role in determining rates of size evolution in fishes globally across multiple scales
Authors: Clarke John T. , Davis Robert B.
Published: September 2023

Substantial progress has been made to map biodiversity and its drivers across the planet at multiple scales, yet studies that quantify the evolutionary processes that underpin this biodiversity, and test their drivers at multiple scales, are comparatively rare. Studying most fish species, we quantify rates of body size evolution to test the role of fundamental salinity habitats in shaping rates of evolution at multiple scales. We also determine how four additional factors shape evolutionary rates.

In up to 1710 comparisons studying over 27,000 ray-finned fish species, we compare rates of body size evolution between five salinity habits using 12 metrics. The comparisons span a molecular tree, supertrees, and ten scales of observation to test for robust patterns and reveal how patterns change with scale. Then, three approaches assess the role of three non-salinity factors on rates, and an alternative habitat scheme tests if lakes influence evolutionary rates.

Rates of size evolution rarely differ consistently between salinity habitats; rate patterns are highly clade- and scale-dependent. One exception is freshwater-brackish fishes, which possess among the highest size rates of any salinity, and show higher rates than euryhaline fishes in most groupings studied at most scales, and verses marine, freshwater, and marine-brackish habitats at specific scales. Additionally, species richness had the greatest potential to predict phenotypic rates, followed by branch duration and absolute values of body size. Lacustrine environments were consistently associated with high rates of size evolution.

We reveal the rate patterns that underpin global body size diversity for fishes, identifying factors that play a limited role in shaping rates of size evolution, such as salinity, and those such as species richness, age, and lake environments that consistently shape evolutionary rates across half of vertebrate diversity.
Distinct adrenal gland macrophages regulate corticosteroid production
Authors: O’Brien Conan JO , Sidarta-Oliveira Davi , Stawiarski Aleksander , Ratti Giorgio , Loyher Pierre-Louis , Makhlouf Mélanie , AbouMoussa Eman H , Haberman Emma , Sweeney Charles , Mizuno Yusuke , Ishii Tomohiro , Hasegawa Tomonobu , Gomez-Sanchez Elise P , Gomez-Sanchez Celso E , Gordon Siamon , Greaves David R , Saraiva Luis R , Geissmann Frederic , Domingos Ana I
Published: September 2023

The adrenal glands are hormone secreting glands that sit on top of the kidneys. Adrenal glands produce glucocorticoids, mineralocorticoids, and catecholamines, and are therefore critical regulators of the stress response, the immune response, metabolism, and blood pressure. Despite being identified for more that 30 years, our understanding of adrenal macrophages remains incomplete. In numerous other tissues, macrophages carry out a plethora of physiological and homeostatic roles in addition to their classical immune functions. The aim of this study was to characterise the macrophage compartment of the adrenal gland and assess its contribution to adrenal function. Using anin vivoapproach, we herein describe two morphologically and spatially distinct subsets of adrenal macrophages – dendritic-like macrophages that are present throughout the gland in young and old mice, and “foamy” lipid-laden macrophages that accumulate in the murine adrenal cortex in an age and diet-dependent manner. Furthermore, we present data showing that these foamy-like macrophages accumulate cholesterol and thereby regulate adrenal hormonal output, at steady state and in the context of obesity. We hereby provide novel insights into the physiological roles of macrophages in the adrenal gland and the mechanisms by which adrenal hormone production is regulated.
Chromosome-level genome assembly for the angiospermSilene conica
Authors: Fields Peter D. , Weber Melody M. , Waneka Gus , Broz Amanda K. , Sloan Daniel B.
Published: September 2023

The angiosperm genusSilenehas been the subject of extensive study in the field of ecology and evolution, but the availability of high-quality reference genome sequences has been limited for this group. Here, we report a chromosome-level assembly for the genome ofSilene conicabased on PacBio HiFi, Hi-C and Bionano technologies. The assembly produced 10 scaffolds (one per chromosome) with a total length of 862 Mb and only ∼1% gap content. These results confirm previous observations thatS. conicaand its relatives have a reduced base chromosome number relative to the genus’s ancestral state of 12.Silene conicahas an exceptionally large mitochondrial genome (>11 Mb), predominantly consisting of sequence of unknown origins. Analysis of shared sequence content suggests that it is unlikely that transfer of nuclear DNA is the primary driver of this mitochondrial genome expansion. More generally, this assembly should provide a valuable resource for future genomic studies inSilene, including comparative analyses with related species that recently evolved sex chromosomes.

Significance

Whole-genome sequences have been largely lacking for species in the genusSileneeven though these flowering plants have been used for studying ecology, evolution, and genetics for over a century. Here, we address this gap by providing a high-quality nuclear genome assembly forS. conica, a species known to have greatly accelerated rates of sequence and structural divergence in its mitochondrial and plastid genomes. This resource will be valuable in understanding the coevolutionary interactions between nuclear and cytoplasmic genomes and in comparative analyses across this highly diverse genus.
Cross-tolerance evolution is driven by selection on heat tolerance inDrosophila subobscura
Authors: Castañeda Luis E.
Published: September 2023

The evolution of heat tolerance is a crucial mechanism for the adaptive response to global warming, but it depends on the genetic variance carried by populations and on the intensity of thermal stress in nature. Experimental selection studies have greatly benefited research into heat tolerance, providing valuable insights into its evolutionary process. However, the impact of varying levels of heat stress intensity on the associated changes in resistance traits has not yet been explored. Here, the correlated evolution of increasing knockdown temperature inDrosophila subobscurawas evaluated on the knockdown time at different stress temperatures (35, 36, 37, and 38 °C), thermal death time (TDT) curves, and desiccation and starvation resistance. The selection of heat tolerance was performed using different ramping temperatures to compare the impact of heat intensity selection on resistance traits. Correlated evolution was found for these four resistance traits inD. subobscura, indicating that the evolutionary response to tolerance of higher temperatures also confers the ability to tolerate other stresses such as desiccation and starvation. However, these correlated responses depended on the intensity of thermal selection and sex, which may limit our ability to generalize these results to natural scenarios. Nevertheless, this study confirms the value of the experimental evolutionary approach for exploring and understanding the adaptive responses of natural populations to global warming.
Regulatory Transposable Elements in the Encyclopedia of DNA Elements
Authors: Du Alan Y. , Chobirko Jason D. , Zhuo Xiaoyu , Feschotte Cédric , Wang Ting
Published: September 2023

Transposable elements (TEs) make up about half of the human genome and many have the biochemical hallmarks of tissue- or cell type-specificcis-regulatory elements. While some TEs have been rigorously documented to contribute directly to host gene regulation, we still have a very partial view of their regulatory landscape. Leveraging Phase 4 ENCODE data, we carried out the most comprehensive study to date of TE contributions to the regulatory genome. Here we investigated the sequence origins of candidatecis-regulatory elements (cCREs), showing that ∼25% of human cCREs comprising 236,181 elements are derived from TEs. Human-mouse comparisons indicate that over 90% of TE-derived cCREs are lineage-specific, accounting for 8-36% of lineage-specific cCREs across cCRE types. Next, we found that cCRE-associated transcription factor (TF) binding motifs in TEs originated from TE ancestral sequences significantly more than expected in all TE classes except for SINEs. Using both cCRE and TF binding data, we discovered that TEs providing cCREs and TF binding sites are closer in genomic distance to non-TE sites compared to other TEs, suggesting that TE integration site influences their later co-option as regulatory elements. We show that TEs have promoted TF binding site turnover events since human-mouse divergence, accounting for 3-56% of turnover events across 30 TFs examined. Finally, we demonstrate that TE-derived cCREs share similar features with non-TE cCREs, including massively parallel reporter assay activity and GWAS variant enrichment. Overall, our results substantiate the notion that TEs have played an important role in shaping the human regulatory genome.
miR-6883 downregulates HIF1α in colorectal and breast cancer cells
Authors: Jensen-Velez Nicole , Carlsen Lindsey , El-Deiry Wafik
Published: September 2023

Colorectal cancer (CRC) and breast cancer (BC) are deadly diseases that rank as the second and fourth leading causes of cancer-related deaths, respectively. We have previously shown that miR-6883 targets CDK4/6 and that palbociclib-mediated CDK4/6 inhibition destabilizes HIF1α. We hypothesize that miR-6883 downregulates HIF1α in CRC and BC cells. miR-6883 was transfected under normoxia or hypoxia and western blot analysis revealed that miR-6883 downregulates CDK4/6 and HIF1α in CRC and BC cells, pointing to miR-6883 as a promising therapeutic to target hypoxic cancers or HIF1α-deregulated tumor cells. Future studies will further investigate miR-6883 as a cancer biomarker, effects on HIF–related proteins and therapeutic usesin vivo.

Abstract Figure

Figure 1.

miR-6883 downregulates CDK4/6 and HIF1α in colorectal and breast cancer cells

A) Colorectal cancer cells were treated with doses of palbociclib ranging from 0-20 µM. Cell viability was measured by imaging the bioluminescent signal after addition of CellTiter-Glo reagent. B) Percent viability of colorectal cancer cells treated with palbociclib was calculated and nonlinear regression analysis was completed using GraphPad Prism software. C-H) CRC cells were transfected with miR-6883 under normoxia or hypoxia (<0.5% O2) and protein levels of CDK4/6, HIF1α, Glut1, and Ran were measured by Western blot.
Quantitative proteomics reveals tissue-specific, infection-induced and species-specific neutrophil protein signatures
Authors: Sollberger Gabriel , Brenes Alejandro J. , Warner Jordan , Arthur J. Simon C. , Howden Andrew J.M.
Published: September 2023

Neutrophils are one of the first responders to infection and are a key component of the innate immune system through their ability to phagocytose and kill invading pathogens, secrete antimicrobial molecules and produce extracellular traps. Neutrophils are produced in the bone marrow, circulate within the blood and upon immune challenge migrate to the site of infection. We wanted to understand whether this transition shapes the mouse neutrophil protein landscape, how the mouse neutrophil proteome is impacted by systemic infection and perform a comparative analysis of human and mouse neutrophils. Using quantitative mass spectrometry we reveal tissue-specific, infection-induced and species-specific neutrophil protein signatures. We show a high degree of proteomic conservation between mouse bone marrow, blood and peritoneal neutrophils, but also identify key differences in the molecules that these cells express for sensing and responding to their environment. Systemic infection triggers a change in the bone marrow neutrophil population with considerable impact on the core machinery for protein synthesis and DNA replication along with environmental sensors. We also reveal profound differences in mouse and human blood neutrophils, particularly their granule contents. Our proteomics data provides a valuable resource for understanding neutrophil function and phenotypes across species and model systems.
Genomic, Functional, and Metabolic Enhancements in Multidrug-ResistantEnterobacter bugandensisFacilitating its Persistence and Succession in the International Space Station
Authors: Sengupta Pratyay , Sivabalan Shobhan Karthick Muthamilselvi , Singh Nitin Kumar , Raman Karthik , Venkateswaran Kasthuri
Published: September 2023

Background

The International Space Station (ISS) stands as a testament to human achievement in space exploration. Despite its highly controlled environment, characterised by microgravity, increased CO2levels, and elevated solar radiation, microorganisms occupy a unique niche. These microbial inhabitants play a significant role in influencing the health and well-being of astronauts on board. One microorganism of particular interest in our study isEnterobacter bugandensis, primarily found in clinical specimens including the human gastrointestinal tract, and also reported to possess pathogenic traits, leading to a plethora of infections.

Results

Distinct from their Earth counterparts, ISSE. bugandensisstrains have exhibited resistance mechanisms that categorize them within the ESKAPE pathogen group, a collection of pathogens recognized for their formidable resistance to antimicrobial treatments. During the two-year Microbial Tracking 1 mission, 12 strains of multidrug resistantE. bugandensiswere isolated from various locations within the ISS. We have carried out a comprehensive study to understand the genomic intricacies of ISS-derivedE. bugandensisin comparison to terrestrial strains, with a keen focus on those associated with clinical infections. We unravel the evolutionary trajectories of pivotal genes, especially those contributing to functional adaptations and potential antimicrobial resistance. A hypothesis central to our study was that the singular nature of the stresses of the space environment, distinct from any on Earth, could be driving these genomic adaptations. Extending our investigation, we meticulously mapped the prevalence and distribution ofE. bugandensisacross the ISS over time. This temporal analysis provided insights into the persistence, succession, and potential patterns of colonization ofE. bugandensisin space. Furthermore, by leveraging advanced analytical techniques, including metabolic modelling, we delved into the coexisting microbial communities alongsideE. bugandensisin the ISS across multiple missions and spatial locations. This exploration revealed intricate microbial interactions, offering a window into the microbial ecosystem dynamics within the ISS.

Conclusions

Our comprehensive analysis illuminated not only the ways these interactions sculpt microbial diversity but also the factors that might contribute to the potential dominance and succession ofE. bugandensiswithin the ISS environment. The implications of these findings are two-fold. Firstly, they shed light on microbial behavior, adaptation, and evolution in extreme, isolated environments. Secondly, they underscore the need for robust preventive measures, ensuring the health and safety of astronauts by mitigating risks associated with potential pathogenic threats.
TheCandida albicansζ-crystallin homolog Zta1 promotes resistance to oxidative stress
Authors: Gandra Rafael M. , Johnson Chad J. , Nett Jeniel E. , Konopka James B.
Published: September 2023

The fungal pathogenCandida albicansis capable of causing lethal infections in humans. Its pathogenic potential is due in part to the ability to resist various stress conditions in the host, including oxidative stress. Recent studies showed that a family of four flavodoxin-like proteins (Pst1, Pst2, Pst3, Ycp4) that function as quinone reductases promotes resistance to oxidation and is needed for virulence. Therefore, in this study Zta1 was examined because it belongs to a structurally distinct family of quinone reductases that are highly conserved in eukaryotes and have been called the ζ-crystallins. The levels of Zta1 inC. albicansrapidly increased after exposure to oxidants, consistent with a role in resisting oxidative stress. Accumulation of reactive oxygen species was significantly higher in cells lackingZTA1upon exposure to quinones and other oxidants. Furthermore, deletion ofZTA1in a mutant lacking the four flavodoxin-like proteins, resulted in further increased susceptibility to quinones, indicating that these distinct quinone reductases work in combination. These results demonstrate that Zta1 contributes toC. albicanssurvival after exposure to oxidative conditions, which increases the understanding of howC. albicansresists stressful conditions in the host.

IMPORTANCE

Candida albicansis an important human pathogen that can cause lethal systemic infections. The ability ofC. albicansto colonize and establish infections is closely tied to its highly adaptable nature and capacity to resist various types of stress, including oxidative stress. Previous studies showed that fourC. albicansproteins belonging to the flavodoxin-like protein family of quinone reductases are needed for resistance to quinones and for virulence. Therefore, in this study we examined the role of a distinct type of quinone reductase, Zta1, and found that it acts in conjunction with the flavodoxin-like proteins to protect against oxidative stress.
Modelling Microtube Driven Invasion of Glioma
Authors: Hillen Thomas , Loy Nadia , Painter Kevin J. , Thiessen Ryan
Published: September 2023

Malignant gliomas are notoriously invasive, a major impediment against their successful treatment. This invasive growth has motivated the use of predictive partial differential equation models, formulated at varying levels of detail, and including (i) “proliferation-infiltration” models, (ii) “go-or-grow” models, and (iii) anisotropic diffusion models. Often, these models use macroscopic observations of a diffuse tumour interface to motivate a phenomenological description of invasion, rather than performing a detailed and mechanistic modelling of glioma cell invasion processes. Here we close this gap. Based on experiments that support an important role played by long cellular protrusions, termed tumour microtubes, we formulate a new model for microtube-driven glioma invasion. In particular, we model a population of tumour cells that extend tissue-infiltrating microtubes. Mitosis leads to new nuclei that migrate along the microtubes and settle elsewhere. A combination of steady state analysis and numerical simulation is employed to show that the model can predict an expanding tumour, with travelling wave solutions led by microtube dynamics. A sequence of scaling arguments allows us reduce the detailed model into simpler formulations, including models falling into each of the general classes (i), (ii), and (iii) above. This analysis allows us to clearly identify the assumptions under which these various models can bea posteriorijustified in the context of microtube-driven glioma invasion. Numerical simulations are used to compare the various model classes and we discuss their advantages and disadvantages.
TGF-β blockade drives a transitional effector phenotype in T cells reversing SIV latency and decreasing SIV reservoirsin vivo
Authors: Kim Jinhee , Bose Deepanwita , Araínga Mariluz , Haque Muhammad R. , Fennessey Christine M , Caddell Rachel A , Thomas Yanique , Ferrell Douglas E , Ali Syed , Grody Emanuelle , Goyal Yogesh , Cicala Claudia , Arthos James , Keele Brandon F , Vaccari Monica , Lorenzo-Redondo Ramon , Hope Thomas J , Villinger Francois , Martinelli Elena
Published: September 2023

HIV-1 persistence during ART is due to the establishment of long-lived viral reservoirs in resting immune cells. Using an NHP model of barcoded SIVmac239 intravenous infection and therapeutic dosing of the anti-TGFBR1 inhibitor galunisertib (LY2157299), we confirmed the latency reversal properties ofin vivoTGF-β blockade, decreased viral reservoirs and stimulated immune responses. Eight SIV-infected macaques on ART were treated with four 2-week cycles of galunisertib. ART was discontinued 3 weeks after the last dose, and macaques euthanized 6 weeks after ART-interruption (ATI). 7 out of 8 macaques rebounded between week 2 and 6 post-ATI. Galunisertib led to viral reactivation as indicated by plasma viral load and immunoPET/CT with64Cu-DOTA-F(ab’)2-p7D3-probe. A decrease in cell-associated (CA-)SIV DNA was detected in lymph nodes, gut and PBMC, while intact pro-virus in PBMC decreased by 3-fold. No systemic increase in inflammatory cytokines was observed. High-dimensions cytometry, bulk, and single-cell (sc)RNAseq revealed a shift toward an effector phenotype in T and NK cells characterized by a progressive downregulation in TCF1.

In summary, we demonstrated that galunisertib, a clinical stage TGF-β inhibitor, reverses SIV latency and decreases SIV reservoirs by driving T cells toward an effector phenotype, enhancing immune responsesin vivoin absence of toxicity.

One-sentence summary

TGF-β blockade drives an effector phenotype in immune cells leading to SIV latency reversal and enhanced immune responses in vivo.
In Vivo Biorthogonal Antibody Click for Dual Targeting and Augmented Efficacy in Cancer Treatment
Authors: Panikar Sandeep Surendra , Berry Na-Keysha , Shmuel Shayla , Keltee Nai , Pereira Patrícia M.R.
Published: September 2023

Antibody-drug conjugates (ADCs) have emerged as promising therapeutics for cancer treatment; however, their effectiveness has been limited by single antigen targeting, potentially leading to resistance mechanisms triggered by tumor compensatory pathways or reduced expression of the target protein. Here, we present antibody-ADC click, an approach that harnesses bioorthogonal click chemistry forin vivodual receptor targeting, irrespective of the levels of the tumor’s expression of the ADC-targeting antigen. Antibody-ADC click enables targeting heterogeneity and enhances antibody internalization and drug delivery inside cancer cells, resulting in potent toxicity. We conjugated antibodies and ADCs to the bioorthogonal click moieties tetrazine (Tz) and trans-cyclooctene (TCO). Through sequential antibody administration in living biological systems, we achieved dual receptor targeting byin vivoclicking of antibody-TCO with antibody-Tz. We show that the clicked antibody therapy outperformed conventional ADC monotherapy or antibody combinations in preclinical models mimicking ADC-eligible, ADC-resistant, and ADC-ineligible tumors. Antibody-ADC click enablesin vivodual-antigen targeting without extensive antibody bioengineering, sustains tumor treatment, and enhances antibody-mediated cytotoxicity.
Hydroxychloroquine and Zinc ameliorate interleukin-6 associated hepato-renal toxicity induced byAspergillus fumigatusin experimental models
Authors: Okoye Jude Ogechukwu , Basil Anslem Tochukwu , Okoli Onyedikachi , Achebe Precious Onyemaechi
Published: September 2023

In Nigeria, immunocompromised persons, particularly those living with HIV, are at an increased risk of developing invasive pulmonary aspergillosis caused byAspergillus fumigatus. Interestingly, this condition produces symptoms that can be easily mistaken for those of COVID-19. To better understand the pathophysiology of Aspergillosis and determine the therapeutic and toxic effects of Zinc and HCQ, this study examined liver and renal functions in experimental models. This experimental study included 28 Albino rats, assigned into 7 Groups (n= 4 each); designated A to G. Group A received the standardized rat chow and distilled water only. Group B received a moderate dose of HCQ only. Group C receivedA. fumigatussuspension (AFS) without any treatments. Group D simultaneously received AFS and a low dose of HCQ. Group E simultaneously received AFS and a moderate dose of HCQ. Group F simultaneously received AFS and a high dose of HCQ. Group G simultaneously received AFS and a moderate dose of HCQ and Zinc. Serum levels of interleukins (IL)-6 and 10, liver enzymes, and renal parameters were measured accordingly. The lungs, liver, and kidneys were excited and weighed. Significance was set at p< 0.05. Higher levels of serum alanine transaminase, creatinine, and urea and lower relative lung weight were observed in group C compared with other groups (p< 0.001). Higher IL-6 levels and IL-6/IL-10 ratio were also observed in group C compared with other groups (p> 0.05). In conclusion, this study revealed that HCQ and Zinc ameliorate oxidative stress and damage induced byA. fumigatus.
Macroevolutionary inference of complex modes of chromosomal speciation in a cosmopolitan plant lineage
Authors: Tribble Carrie M. , Márquez-Corro José Ignacio , May Michael R. , Hipp Andrew L. , Escudero Marcial , Zenil-Ferguson Rosana
Published: September 2023

The effects of single chromosome number change—dysploidy—mediating diversification remain poorly understood. Dysploidy modifies recombination rates, linkage, or reproductive isolation, especially for one-fifth of all eukaryote lineages with holocentric chromosomes. Dysploidy effects on diversification have not been estimated because modeling chromosome numbers linked to diversification with heterogeneity along phylogenies is quantitatively challenging.

We propose a new state-dependent diversification model of chromosome evolution that links diversification rates to dysploidy rates considering heterogeneity and differentiates between anagenetic and cladogenetic changes. We apply this model toCarex(Cyperaceae), a cosmopolitan flowering plant clade with holocentric chromosomes.

We recover two distinct modes of chromosomal evolution and speciation inCarex. In one diversification mode, dysploidy occurs frequently and drives faster diversification rates. In the other mode, dysploidy is rare and diversification is driven by hidden, unmeasured factors. When we use a model that excludes hidden states, we mistakenly infer a strong, uniform positive effect of dysploidy on diversification, showing that standard models may lead to confident but incorrect conclusions about diversification.

This study demonstrates that dysploidy can have a significant role in large plant clade speciation despite the presence of other unmeasured factors that simultaneously affect diversification.
A potential space making role for a lytic transglycosylase in cell wall biogenesis revealed by a beta-lactamase induction phenotype inPseudomonas aeruginosa
Authors: Fumeaux Coralie , Bernhardt Thomas G.
Published: September 2023

Pseudomonas aeruginosaencodes the beta-lactamase AmpC, which promotes resistance to beta-lactam antibiotics. Expression ofampCis induced by fragments of the peptidoglycan (PG) cell wall released upon beta-lactam treatment. These drugs target transpeptidase enzymes that form cell wall crosslinks. However, they do not block the activity of the transglycosylases that polymerize the glycan chains. Thus, drug-treated cells produce uncrosslinked PG polymers that have been shown to be rapidly degraded in the related gram-negative bacteriumEscherichia coli. This degradation is performed by enzymes called lytic transglycosylases (LTs), which generate the anhydro-muropeptide (AMP) products sensed by the AmpR regulator that activatesampCexpression. To identify factors required for proper PG biogenesis inP. aeruginosa, we used a reporter gene fusion to theampCpromoter to screen for mutants induced forampCexpression in the absence of drug. To our surprise, we found that inactivation of SltB1, an LT enzyme expected to produce the AMP products required forampCinduction, counterintuitively led to elevatedampCexpression. This induction required another LT enzyme called MltG, suggesting that inactivation of SltB1 reduces the efficiency of PG crosslinking, causing the degradation of a subset of nascent PG strands by MltG to generate the inducing signal. Our results therefore support a model in which SltB1 uses its LT activity to open space in the PG matrix for the efficient insertion of new material, a function commonly thought to be restricted to endopeptidases that cut cell wall crosslinks.

IMPORTANCE

Inducible beta-lactamases like theampCsystem ofPseudomonas aeruginosaare a common determinant of beta-lactam resistance among gram-negative bacteria. The regulation ofampCis elegantly tuned to detect defects in cell wall synthesis caused by beta-lactam drugs. Studies of mutations causingampCinduction in the absence of drug therefore promise to reveal new insights into the process of cell wall biogenesis in addition to aiding our understanding of how resistance to beta-lactam antibiotics arises in the clinic. In this study, anampCinduction phenotype for a mutant lacking an enzyme that cleaves cell wall glycans was used to uncover a potential role for glycan cleavage in making space in the wall matrix for the insertion of new material during cell growth.
Loss of Wdr23 drives neuronal mitochondrial biogenesis
Authors: Irwin Ronald , Liu Jiahui , Duangjan Chatrawee , Curran Sean P.
Published: September 2023

Mitochondrial adaptation is important for stress resistance throughout life. Here we show that WDR23 loss results in an enrichment for genes regulated by nuclear respiratory factor 1 (NRF1), which coordinates mitochondrial biogenesis and respiratory functions, and an increased steady state level of nuclear coded mitochondrial resident proteins in the brain.Wdr23KOalso increases the endogenous levels of insulin degrading enzyme (IDE) and the relaxin-3 peptide (RLN3), both of which mediate mitochondrial metabolic and oxidative stress responses. Taken together, these studies reveal an important role for WDR23 as a component of the mitochondrial homeostat in the murine brain.

HIGHLIGHTS

Loss of Wdr23 increases nuclear-coded mitochondrial resident proteins.

Promoters of transcripts dysregulated in the hippocampus ofWdr23KOmice are enriched for NRF1 regulatory sequences.

Insulin degrading enzyme (IDE) expression, which can localize to the mitochondria, is increased in the brain tissues lacking WDR23.

Wdr23KOanimals have increased expression of relaxin-3 (RLN3) peptide, but not RLFP3 receptor.
DETERMINATION OF THE ROUTINE SELF-CARE PRACTICES AMONG PATIENTS WITH DMTII IN KITUI COUNTY
Authors: Musembi Mary , Mwenda Catherine Syombua , Ramani M Ramaligham
Published: September 2023

Worldwide, an estimated increase of 642 million patients will have been diagnosed with diabetes mellitus by the year 2035, out of this figure more than 90% will have type 2 diabetes mellitus. In Kenya the burden for the disease is equally on rise, consequently there is huge gap in knowledge deficient among the sick individuals and their families on diabetes management making most patients to present with poor self-care practices especially in rural settings where Resources are scarce. The study aims at developing a family-based intervention model to improve family participation in the management of patients with diabetes mellitus type II at Kitui County. A sample of 68 participants was required to participate in the study. Creating informative resources that highlight the importance of family involvement and provide guidance on DMTII self-care practices. A significant proportion of DMTII patients Out of the total sample size, 28 participants (representing 49.1% of the sample) reported that they monitor their blood sugars on a daily basis. On the other hand, 29 participants (50.9% of the sample) indicated that they do not engage in this practice. These monitoring overall health, reviewing medication plans, adjusting treatment as necessary, and receiving education on diabetes management. These findings emphasize the importance of targeted interventions and education to improve self-care practices among individuals with DMTII and address areas where adherence is lacking. While many individuals exhibit positive self-care behaviors, there are areas that require attention and improvement. Healthcare providers can utilize these findings to develop targeted interventions, patient education programs, and support systems to enhance self-care practices among DMTII patients. By promoting and facilitating optimal self-care activities, healthcare providers can help improve health outcomes and reduce the risk of complications for individuals living with DMTII.
Associations of Water Quality with Cholera in Case-Control Studies: A Systematic Review and Meta-Analysis
Authors: Nguyen Thuy Tien , Kim Chaelin , Goucher Gerard , Kim Jong-Hoon
Published: September 2023

Cholera is a significant health risk for low- and middle-income countries (LMIC), and the threat of outbreaks is likely to increase due to climate change. To keep up to date with the link between water quality and cholera, we conducted a systematic review and meta-analysis to update a previous review. We searched Embase, Web of Science and PubMed for literature published between 2016 and 2022. Search terms were consistent with the previous review. Study quality was assessed using Risk Of Bias In Non-randomized Studies - of Exposures (ROBINS-E). Exposures of water were categorized according to the WHO/UNICEF Joint Monitoring Program for Water Supply, Sanitation and Hygiene (JMP) and further divided by the service ladder. Odds ratios were extracted and pooled by performing random-effects meta-analysis. We identified 22 new eligible studies and analysed them together with the 45 studies included in the previous review. Analyses revealed higher odds of cholera when consuming sachet water (OR=1.69, 95% CI: 1.13 to 2.52), unimproved water (OR=2.91, 95% CI: 1.21 to 7.02), surface water (OR=3.40, 95% CI: 2.52 to 4.58), and untreated water (OR=2.51, 95% CI: 2.03 to 3.10). Meanwhile, treating water (OR=0.42, 95% CI: 0.27 to 0.65), by boiling (OR=0.38, 95% CI: 0.17 to 0.84) or chlorination (OR=0.37, 95% CI: 0.17 to 0.83), and drinking basic water (OR=0.44, 95% CI: 0.27 to 0.69) showed protection. Pooled estimates changed with updated evidence while qualitative insights on the protective or risk factors remain valid. Relatively low-cost methods like boiling or chlorinating water provide good protection comparable to providing basic water to the public.

Systematic review registration: PROSPERO 2021 CRD42021271881
Prediction of peak oxygen consumption using cardiorespiratory parameters from warm-up and submaximal stage of treadmill cardiopulmonary exercise test
Authors: Rosoł Maciej , Petelczyc Monika , Gąsior Jakub S. , Młyńczak Marcel
Published: September 2023

This study investigates the quality of peak oxygen consumption (VO2peak) prediction based on cardiac and respiratory parameters calculated from warmup and submaximal stages of treadmill cardiopulmonary exercise test (CPET) using machine learning (ML) techniques and assesses the importance of respiratory parameters for the prediction outcome. The database consists of the following parameters: heart rate (HR), respiratory rate (RespRate), pulmonary ventilation (VE), oxygen consumption (VO2) and carbon dioxide production (VCO2) obtained from 369 treadmill CPETs. Combinations of features calculated based on the HR, VE and RespRate time-series from different stages of CPET were used to create 11 datasets for VO2peakprediction. Thirteen ML algorithms were employed, and model performances were evaluated using cross-validation with mean absolute percentage error (MAPE), R2score, mean absolute error (MAE), and root mean squared error (RMSE) calculated after each iteration of the validation. The results demonstrated that incorporating respiratory-based features improves the prediction of VO2peak. The best results in terms of R2score (0.47) and RMSE (5.78) were obtained for the dataset which included both cardiac- and respiratory-based features from CPET up to 85% of age-predicted HRmax, while the best results in terms of MAPE (10.5%) and MAE (4.63) were obtained for the dataset containing cardiorespiratory features from the last 30 seconds of warmup. The study showed the potential of using ML models based on cardiorespiratory features from submaximal tests for prediction of VO2peakand highlights the importance of the monitoring of respiratory signals, enabling to include respiratory parameters into the analysis. Presented approach offers a feasible alternative to direct VO2peakmeasurement, especially when specialized equipment is limited or unavailable.