bluuebunny/crossref_metadata_2025 huggingface dataset:
The Evolving Landscape of Immune Checkpoint Inhibitors and Antibody Drug Conjugates in the Treatment of Early-Stage Breast Cancer
Authors: Bhardwaj Prarthna V , Abdou Yara G
Published: August 2023

For decades, chemotherapy has been the mainstay of breast cancer treatment. Novel therapies are expanding the therapeutic options and altering the treatment algorithms to manage this disease. The use and approval of immune checkpoint inhibitors (ICIs) and antibody-drug conjugates (ADCs) represent a few areas of progress. These therapies initially gained attention in the metastatic setting but have subsequently found a role in early-stage breast cancer. Although human epidermal growth factor receptor 2 (HER2) is at the center of ADC development, other surface antigens with a differential expression between tumor and normal cells may be appropriate for ADC targeting. This has led to the discovery of new ADCs targeting other receptors, including TROP-2, HER-3, and LIV-1, to name a few. Similarly, the addition of pembrolizumab in treating early-stage triple-negative breast cancer has led to exploring other ICIs in this setting. However, it has also raised important scientific questions regarding optimal patient selection, biomarkers that predict the success of ICIs, ideal chemotherapy partners, and the financial implications of bringing newer therapies to the forefront. In this review, we discuss the evolving landscape of ICIs and ADCs in managing early-stage breast cancer and provide an overview of potential future advancement in the field.
Racial Disparities and Molecular Insights in Translocation Renal Cell Carcinoma: Advancing Understanding and Treatment Approaches
Authors: Campbell Patrick , Gebrael Georges , Agarwal Neeraj
Published: August 2023

This commentary remarks on the study conducted by Lu et al, which contributes to the existing knowledge on translocation renal cell carcinoma (tRCC) by examining how race may influence susceptibility to tRCC and how distinct transcriptomic profiles among different races may explain variations in tRCC prognosis.
An experimental study on how accents affect public perceptions of the police
Authors: He Mu , Yang Anting , Lu Jiahui , Shi Chen
Published: August 2023

Public perceptions of the police have profound impact on public–police relations and the effectiveness of policing practices. Previous research on public perceptions of the police has focussed on citizens’ socio-demographic profile (e.g. age, race) and police officers’ visual characteristics (e.g. attire), but scant attention has been paid to the impact of accent. The purpose of this research is to investigate the effect of accent on perceptions of the police. In a matched-guise experiment, 160 participants rated officers on their police professional and aesthetic traits after listening to their speeches performed in standard Chinese versus Chinese with a regional accent. The results showed that police officers were rated higher on all the traits when they spoke standard Chinese than accented Chinese, and gender may play a moderating role. The present study revealed that accent can be powerful in affecting the public image of the police.
Pathogen Profile of Klebsiella variicola, the Causative Agent of Banana Sheath Rot
Authors: Sun Yunhao , Zheng Chuanyuan , Zhou Jianuan , Zhen Meng , Wei Xingying , Yan Xun , Guo Xiaojian , Zheng Li , Shao Mingwei , Li Chunji , Qin Di , Zhang Jie , Xiong Lina , Xing Juejun , Huang Bingzhi , Dong Zhangyong , Cheng Ping , Yu Guohui
Published: August 2023

Banana (Musa spp.) is an important fruit and food crop worldwide. In recent years, banana sheath rot has become a major problem in banana cultivation, causing plant death and substantial economic losses. Nevertheless, the pathogen profile of this disease has not been fully characterized. Klebsiella variicola is a versatile bacterium capable of colonizing different hosts, such as plants, humans, insects, and animals, and is recognized as an emerging pathogen in various hosts. In this study, we obtained 12 bacterial isolates from 12 different banana samples showing banana sheath rot in Guangdong and Guangxi Provinces, China. Phylogenetic analysis based on 16S rRNA sequences confirmed that all 12 isolates were K. variicola strains. We sequenced the genomes of these strains, performed comparative genomic analysis with other sequenced K. variicola strains, and found a lack of consistency in accessory gene content among these K. variicola strains. However, prediction based on the pan-genome of K. variicola revealed 22 unique virulence factors carried by the 12 pathogenic K. variicola isolates. Microbiome and microbial interaction network analysis of endophytes between the healthy tissues of diseased plants and healthy plants of two cultivars showed that Methanobacterium negatively interacts with Klebsiella in banana plants and that Herbaspirillum might indirectly inhibit Methanobacterium to promote Klebsiella growth. These results suggest that banana sheath rot is caused by the imbalance of plant endophytes and opportunistic pathogenic bacteria, providing an important basis for research and control of this disease.

[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
HIF‐1α inhibition in macrophages preserves acute liver failure by reducing IL‐1β production
Authors: Kong Xiangrong , Liu Wei , Zhang Xinwen , Zhou Chendong , Sun Xinyu , Cheng Long , Lin Jinxia , Xie Zhifu , Li Jingya
Published: August 2023

The development of acute liver failure (ALF) is dependent on its local inducer. Inflammation is a high‐frequency and critical factor that accelerates hepatocyte death and liver failure. In response to injury stress, the expression of the transcription factor hypoxia‐inducible factor‐1α (HIF‐1α) in macrophages is promoted by both oxygen‐dependent and oxygen‐independent mechanisms, thus promoting the expression and secretion of the cytokine interleukin‐1β (IL‐1β). IL‐1β further induces hepatocyte apoptosis or necrosis by signaling through the receptor (IL‐1R) on hepatocyte. HIF‐1α knockout in macrophages or IL‐1R knockout in hepatocytes protects against liver failure. However, whether HIF‐1α inhibition in macrophages has a protective role in ALF is unclear. In this study, we revealed that the small molecule HIF‐1α inhibitor PX‐478 inhibits the expression and secretion of IL‐1β, but not tumor necrosis factor α (TNFα), in bone marrow‐derived macrophages (BMDMs). PX‐478 pretreatment alleviates liver injury in LPS/D‐GalN‐induced ALF mice by decreasing the hepatic inflammatory response. In addition, preventive or therapeutic administration of PX‐478 combined with TNFα neutralizing antibody markedly improved LPS/D‐GalN‐induced ALF. Taken together, our data suggest that PX‐478 administration leads to HIF‐1α inhibition and decreased IL‐1β secretion in macrophages, which represents a promising therapeutic strategy for inflammation‐induced ALF.
Deoxyribonucleoside treatment rescues EtBr‐induced mtDNA depletion in iPSC‐derived neural stem cells with POLG mutations
Authors: Kristiansen Cecilie Katrin , Furriol Jessica , Chen Anbin , Sullivan Gareth John , Bindoff Laurence A. , Liang Kristina Xiao
Published: August 2023

Mutations in POLG, the gene encoding the catalytic subunit of the mitochondrial DNA (mtDNA) polymerase gamma (Pol‐γ), lead to diseases driven by defective mtDNA maintenance. Despite being the most prevalent cause of mitochondrial disease, treatments for POLG‐related disorders remain elusive. In this study, we used POLG patient‐induced pluripotent stem cell (iPSC)‐derived neural stem cells (iNSCs), one homozygous for the POLG mutation c.2243G>C and one compound heterozygous with c.2243G>C and c.1399G>A, and treated these iNSCs with ethidium bromide (EtBr) to study the rate of depletion and repopulation of mtDNA. In addition, we investigated the effect of deoxyribonucleoside (dNs) supplementation on mtDNA maintenance during EtBr treatment and post‐treatment repopulation in the same cells. EtBr‐induced mtDNA depletion occurred at a similar rate in both patient and control iNSCs, however, restoration of mtDNA levels was significantly delayed in iNSCs carrying the compound heterozygous POLG mutations. In contrast, iNSC with the homozygous POLG mutation recovered their mtDNA at a rate similar to controls. When we treated cells with dNs, we found that this reduced EtBr‐induced mtDNA depletion and significantly increased repopulation rates in both patient iNSCs. These observations are consistent with the hypothesis that mutations in POLG impair mtDNA repopulation also within intact neural lineage cells and suggest that those with compound heterozygous mutation have a more severe defect of mtDNA synthesis. Our findings further highlight the potential for dNs to improve mtDNA replication in the presence of POLG mutations, suggesting that this may offer a new therapeutic modality for mitochondrial diseases caused by disturbed mtDNA homeostasis.
miR‐125a‐3p regulates the expression of FSTL1, a pro‐inflammatory factor, during adipogenic differentiation, and inhibits adipogenesis in mice
Authors: Liu Haifeng , Wen Jie , Tian Xue , Li Tong , Zhao Ju , Cheng Jingjing , Huang Lishi , Zhao Ye , Cao Quanquan , Jiang Jun
Published: August 2023

Adipogenesis is tightly regulated by various factors, including genes and microRNAs. Excessive fat deposition is the key feature of obesity, which is a low‐grade chronic inflammatory disease. Follistatin‐like 1 (FSTL1) has been reported to be an important mediator involved in various inflammatory diseases. However, the underlying mechanism of FSTL1 in preadipocyte differentiation and inflammatory response is still unclear. The current study was designed to explore the biological function and potential mechanism of FSTL1 in mouse subcutaneous preadipocyte differentiation. We found that FSTL1 was highly expressed in the early stage of differentiation and subsequently decreased sharply, suggesting that FSTL1 played a possible role in adipogenesis. Meanwhile, the gain‐ and loss‐of‐function assays showed that FSTL1 was not only involved in the inflammatory response by inducing the expression of pro‐inflammatory factors IL‐1β and CCL2 but also significantly attenuated preadipocyte differentiation, as evidenced by the reduction of lipid accumulation and the levels of adipogenic genes, including PPARγ and FABP4. In addition, the target gene prediction and luciferase reporter assay validated that miR‐125a‐3p targeted the 3′ UTR region of FSTL1. These results demonstrated that miR‐125a‐3p negatively regulated the expression of FSTL1 at the mRNA and protein levels. Furthermore, overexpressing miR‐125a‐3p in preadipocytes dramatically accelerated adipogenic differentiation and downregulated the levels of IL‐1β and CCL2, which were in accordance with the knockdown of FSTL1. On the contrary, treatment with miR‐125a‐3p inhibitors attenuated adipogenesis but induced the expression of inflammatory genes. In summary, this study suggests a positive function of FSTL1 in adipocyte‐induced inflammation and negatively regulates preadipocyte differentiation. Further studies demonstrated that miR‐125a‐3p could reverse the effect by targeting FSTL1, which might provide a better understanding of treating obesity‐related inflammatory diseases.
Frizzled‐9 triggers actin polymerization and activates mechano‐transducer YAP to rescue simulated microgravity‐induced osteoblast dysfunction
Authors: Shi Qiusheng , Gui Jinpeng , Sun Lianwen , Song Yaxin , Na Jing , Zhang Jingyi , Fan Yubo , Zheng Lisha
Published: August 2023

Long‐term spaceflight can result in bone loss and osteoblast dysfunction. Frizzled‐9 (Fzd9) is a Wnt receptor of the frizzled family that is vital for osteoblast differentiation and bone formation. In the present study, we elucidated whether Fzd9 plays a role in osteoblast dysfunction induced by simulated microgravity (SMG). After 1–7 days of SMG, osteogenic markers such as alkaline phosphatase (ALP), osteopontin (OPN), and Runt‐related transcription factor 2 (RUNX2) were decreased, accompanied by a decrease in Fzd9 expression. Furthermore, Fzd9 expression decreased in the rat femur after 3 weeks of hindlimb unloading. In contrast, Fzd9 overexpression counteracted the decrease in ALP, OPN, and RUNX2 induced by SMG in osteoblasts. Moreover, SMG regulated phosphorylated glycogen synthase kinase‐3β (pGSK3β) and β‐catenin expression or sublocalization. However, Fzd9 overexpression did not affect pGSK3β and β‐catenin expression or sublocalization induced by SMG. In addition, Fzd9 overexpression regulated protein kinase B also known as Akt and extracellular signal‐regulated kinase (ERK) phosphorylation and induced F‐actin polymerization to form the actin cap, press the nuclei, and increase nuclear pore size, thereby promoting the nuclear translocation of Yes‐associated protein (YAP). Our study findings provide mechanistic insights into the role of Fzd9 in triggering actin polymerization and activating YAP to rescue SMG‐induced osteoblast dysfunction and suggest that Fzd9 is a potential target to restore osteoblast function in individuals with bone diseases and after spaceflight.
Efficacy and safety of immune checkpoint inhibitors for advanced non-small cell lung cancer with or without PD-L1 selection: A systematic review and network meta-analysis
Authors: Li Yan , Liang Xueyan , Li Huijuan , Chen Xiaoyu
Published: August 2023

Background:

Immune checkpoint inhibitors (ICIs) are standard treatments for advanced non-small cell lung cancer (NSCLC); however, evidence regarding their relative efficacy and safety is lacking. This study compared the efficacy and safety of all currently available ICI treatments in patients with advanced NSCLC to identify optimal treatment regimens.

Methods:

PubMed, Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, and Embase databases were systematically searched for randomized controlled trials (RCTs) published up to August 8, 2022. The primary outcomes were overall survival (OS) and progression-free survival (PFS). Secondary outcomes included objective response rate (ORR) and adverse events (AEs).

Results:

Forty RCTs involving 22,526 patients were selected, and a total of 26 treatment regimens were identified. Treatment with anti-programmed cell death protein-1 (anti-PD-1) provided superior OS compared with anti-programmed death ligand 1 (anti-PD-L1) treatment. ICIs plus platinum-based chemotherapy (PBC) were superior to ICIs treatment alone, although the addition of PBC increased treatment toxicity. Cemiplimab ranked first for OS and lowest for any-grade AEs in advanced NSCLC patients without PD-L1 selection. Regarding grade ≥3 AEs, the toxicity of ICI monotherapy or ICI–ICI combination was consistently lower than that of the other treatments. For patients without PD-L1 selection, cemiplimab showed the best OS, pembrolizumab plus docetaxel (Pem-DXT) showed the best PFS, and atezolizumab plus bevacizumab and PBC (Atezo-Beva-PBC) showed the best ORR. Pembrolizumab plus PBC and Atezo-Beva-PBC were the most likely optimal treatments for OS and PFS in patients with PD-L1 expression <1%, respectively. In patients with PD-L1 expression ≥1%, treatment regimens containing anti-PD-1 provided superior OS benefits compared with those of anti-PD-L1 treatment, and sintilimab plus PBC (Sint-PBC) provided the best OS benefit; as for PFS, ICI plus PBC consistently showed greater PFS benefits than ICI or PBC alone. For patients with anti-PD-L1 expression of 1–49%, camrelizumab plus PBC provided the best benefit for OS and PFS among included treatment. Durvalumab-tremelimumab-PBC and Atezo-Beva-PBC respectively presented the highest OS and PFS for patients with PD-L1 expression ≥50%. Moreover, cemiplimab and Atezo-Beva-PBC yielded the best OS and PFS benefits as first-line treatments for patients with advanced NSCLC, respectively.

Conclusions:

Although ICI plus PBC likely resulted in superior survival outcomes compared to ICI treatment alone, it did increase toxicity. Cemiplimab presented a well-balanced efficacy and safety profile in advanced NSCLC treatment. Our findings with the current ICIs comparisons will aid future trials for cancer immunotherapy.

Registration:

PROSPERO, https://www.crd.york.ac.uk/PROSPERO/, CRD42022323879.
Provision of chaplaincy services in U.S. hospitals
Authors: White Kelsey B. , Lee Shoou-Yih Daniel , Jennings J’Aime C. , Karimi Seyed , Johnson Christopher E. , Fitchett George
Published: August 2023

Background

Increasingly, hospitals are expected to provide patient-centered care that attends to patients’ health needs, including spiritual care needs. Chaplaincy services help to meet patients’ spiritual care needs, which have been shown to have a positive impact on health outcomes. Variation in the provision of chaplaincy services suggests hospitals do not uniformly conform to the expectation of making chaplaincy services available.

Purpose

The aim of this study was to examine the availability and factors that influence hospitals’ provision of chaplaincy services.

Methodology

Data were combined from the American Hospital Association annual surveys with the Area Health Resource File at the county level from 2010 to 2019. Observations on general, acute-care community hospitals were analyzed (45,384 hospital-year observations) using logistic regression that clustered standard errors at the hospital level.

Results

Hospitals with Joint Commission accreditation, more staffed beds, nonprofit and government ownership, teaching status, one or more intensive care units, a higher percentage of Medicare inpatient days, church affiliation, and system membership were more likely to provide chaplaincy services than their counterparts. Certification as a trauma hospital and market competition showed no influence on the provision of chaplaincy services.

Conclusion

The lack of chaplaincy services in many hospitals may be due to limited resources, workforce shortage, or a lack of consensus on scope and nature of chaplaincy services.

Practice Implications

Chaplaincy services are an underutilized resource that influences patient experience, clinician burnout and turnover, and the goal of ensuring care is patient-centered. Administrators should consider stronger partnerships where services are provided; researchers and policymakers should consider how the lack of these services in some hospitals may reinforce existing health disparities.
Extracellular vesicles stimulate smooth muscle cell migration by presenting collagen VI
Authors: Kapustin Alexander , Tsakali Sofia Serena , Whitehead Meredith , Chennell George , Wu Meng-Ying , Molenaar Chris , Kutikhin Anton , Bogdanov Leo , Sinitsky Maxim , Rubina Kseniya , Clayton Aled , Verweij Frederik J , Pegtel Dirk Michiel , Zingaro Simona , Lobov Arseniy , Zainullina Bozhana , Owen Dylan , Parsons Maddy , Cheney Richard E. , Warren Derek , Humphries Martin James , Iskratsch Thomas , Holt Mark , Shanahan Catherine M
Published: August 2023

The extracellular matrix (ECM) supports blood vessel architecture and functionality and undergoes active remodelling during vascular repair and atherogenesis. Vascular smooth muscle cells (VSMCs) are essential for vessel repair and, via their secretome, are able to invade from the vessel media into the intima to mediate ECM remodelling. Accumulation of fibronectin (FN) is a hallmark of early vascular repair and atherosclerosis and here we show that FN stimulates VSMCs to secrete small extracellular vesicles (sEVs) by activating the β1 integrin/FAK/Src pathway as well as Arp2/3-dependent branching of the actin cytoskeleton. Spatially, sEV were secreted via filopodia-like cellular protrusions at the leading edge of migrating cells. We found that sEVs are trapped by the ECMin vitroand colocalise with FN in symptomatic atherosclerotic plaquesin vivo. Functionally, ECM-trapped sEVs induced the formation of focal adhesions (FA) with enhanced pulling forces at the cellular periphery. Proteomic and GO pathway analysis revealed that VSMC-derived sEVs display a cell adhesion signature and are specifically enriched with collagen VI.In vitroassays identified collagen VI as playing the key role in cell adhesion and invasion. Taken together our data suggests that the accumulation of FN is a key early event in vessel repair acting to promote secretion of collage VI enriched sEVs by VSMCs. These sEVs stimulate migration and invasion by triggering peripheral focal adhesion formation and actomyosin contraction to exert sufficient traction forces to enable VSMC movement within the complex vascular ECM network.

Abstract Figure

Figure Abstract

Vascular smooth muscle cells sense fibronectin via β1 integrin and secrete small extracellular vesicles loaded with collagen VI via filopodia-like protrusions. These extracellular vesicles are entrapped in the extracellular matrix and induce formation of peripheral focal adhesions. Focal adhesions anchor extracellular matrix to the actin fibrils in the cell. Contraction of the actin fibrils generates the mechanical force for cell locomotion and invasion through the matrix. This figure was created with BioRender(https://biorender.com/).
On standardization of controls in lifespan studies
Authors: Spiridonova Olga , Kriukov Dmitrii , Nemirovich-Danchenko Nikolai , Peshkin Leonid
Published: August 2023

The search for interventions to slow down and even reverse aging is a burgeoning field. The literature cites hundreds of supposedly beneficial pharmacological and genetic interventions in model organisms: mice, rats, flies and worms, where research into physiology is routinely accompanied by lifespan data. Naturally the negative results are more frequent, yet scientifically quite valuable if analyzed systematically. Yet, there is a strong “discovery bias”, i.e. results of interventions which turn out not to be beneficial remain unpublished. Theoretically, all lifespan data is ripe for re-analysis: we could contrast the molecular targets and pathways across studies and help focus the further search for interventions. Alas, the results of most longevity studies are difficult to compare. This is in part because there are no clear, universally accepted standards for conducting such experiments or even for reporting such data. The situation is worsened by the fact that the authors often do not describe experimental conditions completely. As a result, works on longevity make up a set of precedents, each of which might be interesting in its own right, yet incoherent and incomparable. Here we point out specific issues and propose solutions for quality control by checking both inter- and intra-study consistency of lifespan data.
Tertiary lymphoid structures are associated with enhanced macrophage activation, immune checkpoint expression and predict outcome in cervical cancer
Authors: Gorvel Laurent , Panouillot Marylou , Rouvière Marie-Sarah , Billon Emilien , Fattori Stéphane , Sonongbua Jumaporn , Boucherit Nicolas , Ben Amara Amira , Quilichini Olivia , Granjeaud Samuel , Degos Clara , Nunes Jacques A. , Carcopino Xavier , Lambaudie Eric , Chretien Anne-Sophie , Sabatier Renaud , Dieu-Nosjean Marie-Caroline , Olive Daniel
Published: August 2023

Background

Cervical tumors are usually treated using surgery, chemotherapy, and radiotherapy, and would benefit from immunotherapies. However, the immune microenvironment in cervical cancer remains poorly described. Tertiary lymphoid structures (TLS) were recently described as markers for better immunotherapy response and overall better prognosis in cancer patients.

Methods

We integratedly evaluated the cervical tumor immune microenvironment, and specifically TLS importance, using combined high-throughput phenotyping, soluble factor dosage, spatial interaction analyses, and statistical analyses.

Results

We demonstrate that TLS presence is associated with a more inflammatory soluble microenvironment, with the presence of B cells as well as more activated macrophages and dendritic cells (DCs). Furthermore, this myeloid cell activation is associated with expression of immune checkpoints, such as PD-L1 and CD40, and close proximity of activated conventional DC2 to CD8+T cells, therefore indicating better immune interactions and tumor control. Finally, we associate TLS presence, greater B cell density, and activated DC density to improved progression-free survival, and present it as an additional prognostic marker.

Conclusion

To conclude, our results provide an exhaustive depiction of the cervical tumor immune microenvironment where TLS presence marks cell activation and immunotherapy target expression. These findings provide predictive clues for patient response to targeted immunotherapies.

Significance

TLS maturation stratifies cervical cancer patients and associates with improved prognosis. TLS associate with the expression of immune checkpoints, notably in the macrophage compartment, which may represent a new therapeutic strategy.
Morphometry and mechanical instability at the onset of epithelial bladder cancer
Authors: Lampart Franziska L. , Vetter Roman , Wang Yifan , Yamauchi Kevin A. , Strohmeyer Nico , Meer Florian , Hussherr Marie-Didiée , Camenisch Gieri , Seifert Hans-Helge , Rentsch Cyrill A. , Magnen Clémentine Le , Müller Daniel J. , Bubendorf Lukas , Iber Dagmar
Published: August 2023

Malignancies of epithelial tissues, called carcinomas, account for the majority of cancer cases. Much cancer research has focused on genetic alterations and their relation to different carcinoma phenotypes. Besides a rewiring in the signalling networks, carcinoma progression is accompanied by mechanical changes in the epithelial cells and the extracellular matrix. Here, we reveal intricate morphologies in the basement membrane at the onset of bladder cancer, and propose that they emerge from a mechanical buckling instability upon epithelial overgrowth. Using a combination of microscopy imaging of the mouse and human bladder tissue, elasticity theory, and numerical simulations of differential growth in the bladder mucosa, we find that aberrant tissue morphologies can emerge through stiffness changes in the different mucosa layers. The resulting thickening, wrinkles and folds exhibit qualitative and quantitative similarity with imaged early papillary tumors and carcinomasin situ. Atomic force microscopy indeed reveals local stiffness changes in the pathological basement membrane. Our findings suggest a mechanical origin of the different carcinoma subtypes in the bladder, which have vastly different clinical prognosis. They might provide the basis for a new line of attack in medical carcinoma treatment and prophylaxis.
Chrysalis: decoding tissue compartments in spatial transcriptomics with archetypal analysis
Authors: Túrós Demeter , Vasiljevic Jelica , Hahn Kerstin , Rottenberg Sven , Valdeolivas Alberto
Published: August 2023

Dissecting tissue compartments in spatial transcriptomics (ST) remains challenging due to limited spatial resolution and dependence on single-cell reference data. We present Chrysalis, a novel method to rapidly detect tissue compartments through spatially variable gene (SVG) detection and archetypal analysis without external references. We applied Chrysalis on ST datasets originating from various species, tissues and technologies and demonstrated state-of-the-art performance in identifying cellular niches.
Comparative transcriptome in rhesus macaques and crab-eating macaques
Authors: Mao Yuxiang , Li Yamei , Yang Zikun , Xu Ning , Zhang Shilong , Wang Xuankai , Yang Xiangyu , Sun Qiang , Mao Yafei
Published: August 2023

Understanding the variations in gene expression between species is pivotal for deciphering the evolutionary diversity in phenotypes. Rhesus macaques and crab-eating macaques serve as crucial nonhuman primate biomedical models with different phenotypes, but the large-scale of comparative transcriptome research between these two species has yet to be fully elucidated. Here, we conduct systematic comparisons utilizing newly sequenced RNA-seq data from 84 samples encompassing 14 common tissues. Our findings reveal that a small fraction of genes (∼3.7%) show differential expression between the two macaque species, while ∼36.5% of genes show tissue-specific expression in both macaques. We also compare gene expression between macaques and humans and ∼22.6 % of the orthologous genes show differential expression in at least 2 tissues. Moreover, ∼19.41% of genes overlapped with macaque-specific structural variants are more likely to show differential expression between humans and macaques. Of these,FAM220Ashows elevated gene expression in humans compared to macaques because of lineage-specific duplication. In summary, our study presents a large-scale analysis of the transcriptomes within macaque species and between macaques and humans. These insights into gene expression variations will enhance the biomedical utility of macaque models and contributing to the broader realm of primate genomic studies.
The effects of skin tone on photoacoustic imaging and oximetry
Authors: Else Thomas R. , Hacker Lina , Gröhl Janek , Bunce Ellie V. , Tao Ran , Bohndiek Sarah E.
Published: August 2023

Significance

Photoacoustic imaging (PAI) provides contrast based on the concentration of optical absorbers in tissue, enabling the assessment of functional physiological parameters such as blood oxygen saturation (sO2). Recent evidence suggests that variation in melanin levels in the epidermis leads to measurement biases in optical technologies, which could potentially limit the application of these biomarkers in diverse populations.

Aim

To examine the effects of skin melanin pigmentation on photoacoustic imaging and oximetry.

Approach

We evaluated the effects of skin tone in PAI using a computational skin model, two-layer melanin-containing tissue-mimicking phantoms, and mice of a consistent genetic background with varying pigmentations. The computational skin model was validated by simulating the diffuse reflectance spectrum using the adding-doubling method, allowing us to assign our simulation parameters to approximate Fitzpatrick skin types. Monte Carlo simulations and acoustic simulations were run to obtain idealised photoacoustic images of our skin model. Photoacoustic images of the phantoms and mice were acquired using a commercial instrument. Reconstructed images were processed with linear spectral unmixing to estimate blood oxygenation. Linear unmixing results were compared with a learned unmixing approach based on gradient-boosted regression.

Results

Our computational skin model was consistent with representative literature forin vivoskin reflectance measurements. We observed consistent spectral colouring effects across all model systems, with an overestimation of sO2and more image artefacts observed with increasing melanin concentration. The learned unmixing approach reduced the measurement bias, but predictions made at lower blood sO2still suffered from a skin tone-dependent effect.

Conclusion

PAI demonstrates measurement bias, including an overestimation of blood sO2, in higher Fitzpatrick skin types. Future research should aim to characterise this effect in humans to ensure equitable application of the technology.
Purification, crystallization, and preliminary structural analysis of multivalent immunogenic effector protein-anchored SARS-CoV-2 RBD
Authors: Kwon Taek Hun , Kim Tae Gyun
Published: August 2023

The continuous spread of highly transmissible variants of concern and the potential diminished effectiveness of existing vaccines necessitate ongoing research and development of new vaccines. Immunogenic molecule-anchored antigen has demonstrated superior efficacy in subunit vaccination, primarily due to enhanced cellular uptake facilitated by the affinity between the surface of Immunogenic molecule and the cell membrane. Based on the Immunogenic recombinaseB. malayiRecA (BmRecA), we have overexpressed the construct ofBmRecA with SARS-CoV-2 RBD (BmRecA-RBD) that exists as a stable helical filament formation; it was purified and crystallized to obtain X-ray diffraction data at 2.7 Å, belonged to the hexagonal symmetry groupP65in the unit-cell parameters of a=b=122.12, c=75.55 and α=β=90°, γ=120°. The Matthews coefficient was estimated to be 3.12 Å3Da-1, corresponding to solvent contents of 52.65.
Investigating the Effect of GLU283 Protonation State on the Conformational Heterogeneity of CCR5 by Molecular Dynamics Simulations
Authors: Dogan Berna , Durdagi Serdar
Published: August 2023

CCR5 is one of the co-receptors for HIV-1 entry into host cells and is class A GPCR. This receptor has vital roles in the immune system and is involved in the pathogenesis of different diseases. Various studies were conducted to understand its activation mechanism including structural studies in which inactive and active states of the receptor were determined in complex with various binding partners. These determined structures provided opportunities to perform molecular dynamics simulations (MD) and analyze conformational changes observed in protein structures. The atomic level dynamical studies allow us to explore the effects of ionizable residues in the receptor. Here, our aim was to investigate the changes observed in the conformation of CCR5 when it is in complex with inhibitor maraviroc (MRV), an approved anti-HIV drug or HIV-1 envelope protein GP120 in comparison to when the receptor was inapoform. In our simulations, we considered both ionized and protonated states of ionizable binding site residue GLU2837.39in CCR5 as the protonation state of this residue was considered ambiguously in previous studies. Our simulation results suggested that in fact, the change in the protonation state of GLU2837.39caused interaction profiles to be different between CCR5 and its binding partners, GP120 or MRV. We observed that when the protonated state of GLU2837.39was considered in complex with envelope protein GP120, there were substantial structural changes in CCR5 indicating it adopts more of an active-like conformation. On the other hand, CCR5 when it was in complex with MRV always adopted inactive conformation regardless of the protonation state. Hence, CCR5 coreceptor displays conformational heterogeneity not only based on its binding partner but also on the state of the protonation state of a binding site residue GLU2837.39. This outcome is also in accordance with some studies showing that GP120 binding could activate signaling pathways. Additionally, this outcome could also have critical implications for the discovery of novel CCR5 inhibitors to be used as anti-HIV drugs by in silico methods such as molecular docking since consideration of the protonated state of GLU2837.39could be required.
Effect of analytical variability in estimating EEG-based functional connectivity
Authors: Allouch Sahar , Kabbara Aya , Duprez Joan , Paban Véronique , Khalil Mohamad , Modolo Julien , Hassan Mahmoud
Published: August 2023

The significant degree of variability and flexibility in neuroimaging analysis approaches has recently raised concerns. When running any neuroimaging study, the researcher is faced with a large number of methodological choices, often made arbitrarily. This can produce substantial variability in the results, ultimately hindering research replicability, and thus, robust conclusions. Here, we addressed the analytical variability in the EEG source connectivity pipeline and its effects on outcomes consistency. Like most neuroimaging analyses, the EEG source connectivity analysis involves the processing of high-dimensional data and is characterized by a complex workflow that leads to high analytical variability. In this study, we focused on source functional connectivity variability induced by three key factors along the analysis pipeline: 1) number of EEG electrodes, 2) inverse solution algorithms, and 3) functional connectivity metrics. Outcomes variability was assessed in terms of group-level consistency, inter-, and intra-subjects similarity, using resting-state EEG data (n = 88). As expected, our results showed that different choices related to the number of electrodes, source reconstruction algorithm, and functional connectivity measure substantially affect group-level consistency, between-, and within-subjects similarity. We believe that the significant impact of such methodological variability represents a critical issue for neuroimaging studies that should be prioritized.

Highlights

The significant impact of methodological variability is a recognized critical priority issue for neuroimaging studies.

Analytical variability related to the number of electrodes, source reconstruction algorithm, and functional connectivity measure is a prominent issue in the EEG source connectivity analysis.

Group-level consistency, between-, and within-subjects similarity are substantially affected by analytical variability in the EEG source connectivity analysis.
A fluorescence-based sensor screen identifies MED12 as a potential microsatellite instability regulator in colon cancer
Authors: Neto João M. Fernandes , Venkatesan Subramanian , Dias Matheus , Lieftink Cor , Morris Ben , Bresser Kaspar , Vecchione Loredana , Evers Bastiaan , Scheeren Ferenc , Schumacher Ton , Beijersbergen Roderick L. , Bernards René
Published: August 2023

Inactivation of the DNA mismatch repair (MMR) system, due to (epi)genetic alterations of MMR genes, increases the frequency of mutations across the genome, creating a phenotype known as microsatellite instability (MSI). Cancers with this phenotype have been associated with a better prognosis for some time, but only since recently it has been recognised as a predictive biomarker of response to immunotherapy. Because MSI tumours accumulate more insertions and/or deletions in coding regions of the genome containing microsatellites, there is an increase in neoantigens resulting from reading frame shifts, which promotes immunogenicity. To investigate if additional genes exist that can cause an MSI phenotype, we developed a fluorescence-based sensor to identify genes whose inactivation increases the rate of frameshift mutations on microsatellite sequences in cancer cells. Using genome-scale CRISPR/Cas9 screens, we identifiedMED12as a potential new regulator of microsatellite instability. Consistent with this, we found thatMED12mutant colon cancers that lack mutations in the known MMR genes are more likely to be of the MSI phenotype.
“Important enough to show the world”: Using Authentic Research Opportunities and Micropublications to Build Students’ Science Identities
Authors: Rubenstein Lisa DaVia , Woodruff Kelsey A. , Taylor April M. , Olesen James B. , Smaldino Philip J. , Rubenstein Eric M.
Published: August 2023

Primarily undergraduate institutions (PUIs) often struggle to provide authentic research opportunities that culminate in peer-reviewed publications due to “recipe-driven” lab courses and the comprehensive body of work necessary for traditional scientific publication. However, the advent of short-form, single-figure “micropublications” has created novel opportunities for early-career scientists to make and publish authentic scientific contributions on a scale and in a timespan compatible with their training periods. The purpose of this qualitative case study is to explore the benefits accrued by eight undergraduate and master’s students who participated in authentic, small-scale research projects and disseminated their work as coauthors of peer-reviewed micropublications at a PUI. In these interviews, students reported that through the process of conducting and publishing their research, they developed specific competencies: reading scientific literature, proposing experiments, and collecting/interpreting publication-worthy data. Further, they reported this process enabled them to identify as contributing members of the greater scientific community.
“Identifying and characterizing scene representations relevant for categorization behavior”
Authors: Singer Johannes J.D. , Karapetian Agnessa , Hebart Martin N. , Cichy Radoslaw M.
Published: August 2023

1.

Scene recognition is a core sensory capacity that enables humans to adaptively interact with their environment. Despite substantial progress in the understanding of the neural representations underlying scene recognition, the relevance of these representations for behavior given varying task demands remains unknown. To address this, we aimed to identify behaviorally relevant scene representations, to characterize them in terms of their underlying visual features, and to reveal how they vary across different tasks. We recorded fMRI data while human participants viewed scenes and linked brain responses to behavior in three tasks acquired in separate sessions: manmade/natural categorization, basic-level categorization, and fixation color discrimination. We found correlations between categorization response times and scene-specific brain responses, quantified as the distance to a hyperplane derived from a multivariate classifier. Across tasks, these effects were found in largely distinct parts of the ventral visual stream. This suggests that different scene representations are relevant for behavior depending on the task. Next, using deep neural networks as a proxy for visual feature representations, we found that early/intermediate layers mediated the relationship between scene representations and behavior for both categorization tasks, indicating a contribution of low-/mid-level visual features to these representations. Finally, we observed opposite patterns of brain-behavior correlations in the manmade/natural and the fixation task, indicating interference of representations with behavior for task demands that do not align with the content of representations. Together, these results reveal the spatial extent, content, and task-dependence of the visual representations that mediate behavior in complex scenes.
Massively Parallel Reporter Assay Confirms Regulatory Potential of hQTLs and Reveals Important Variants in Lupus and Other Autoimmune Diseases
Authors: Fu Yao , Kelly Jennifer A. , Gopalakrishnan Jaanam , Pelikan Richard C. , Tessneer Kandice L. , Pasula Satish , Grundahl Kiely , Murphy David A. , Gaffney Patrick M.
Published: August 2023

Objective

To systematically characterize the potential for histone post-translational modifications, i.e., histone quantitative trait loci (hQTLs), expression QTLs (eQTLs), and variants on systemic lupus erythematosus (SLE) and autoimmune (AI) disease risk haplotypes to modulate gene expression in an allele dependent manner.

Methods

We designed a massively parallel reporter assay (MPRA) containing ∼32K variants and transfected it into an Epstein-Barr virus transformed B cell line generated from an SLE case.

Results

Our study expands our understanding of hQTLs, illustrating that epigenetic QTLs are more likely to contribute to functional mechanisms than eQTLs and other variant types, and a large proportion of hQTLs overlap transcription start sites (TSS) of noncoding RNAs. In addition, we nominate 17 variants (including 11 novel) as putative causal variants for SLE and another 14 for various other AI diseases, prioritizing these variants for future functional studies primary and immortalized B cells.

Conclusion

We uncover important insights into the mechanistic relationships between genotype, epigenetics, gene expression, and SLE and AI disease phenotypes.
Identification andin vitrocharacterization of UDP-GlcNAc-RNA cap-modifying and decapping enzymes
Authors: Weber Frederik , Motzkus Nikolas Alexander , Brandl Leona , Möhler Marvin , Jäschke Andres
Published: August 2023

In recent years, several noncanonical RNA caps derived from cofactors and metabolites have been identified. Purine-containing RNA caps have been extensively studied, with multiple decapping enzymes identified and efficient capture and sequencing protocols developed for nicotinamide adenine dinucleotide (NAD)-RNA, which allowed for a stepwise elucidation of capping functions. Despite being identified as an abundant noncanonical RNA-cap, UDP-sugar-capped RNA remains poorly understood, which is partly due to its complexin vitropreparation. Here, we describe a scalable synthesis of sugar-capped uridine-guanosine dinucleotides from readily available protected building blocks and their enzymatic conversion into several cell wall precursor-capped dinucleotides. We employed these capped dinucleotides in T7 RNA polymerase-catalyzedin vitrotranscription reactions to efficiently generate RNAs capped with uridine diphosphateN-acetylglucosamine (UDP-GlcNAc), itsN-azidoacetyl derivative UDP-GlcNAz, and various cell wall precursors. We furthermore identified four enzymes capable of processing UDP-GlcNAc-capped RNAin vitro: MurA, MurB and MurC fromEscherichia colican sequentially modify the sugar-cap structure and were used to introduce a bioorthogonal, clickable moiety, and the human Nudix hydrolase Nudt5 was shown to efficiently decap UDP-GlcNAc-RNA. Our findings underscore the importance of efficient synthetic methods for capped model RNAs and provide useful enzymatic tools for the potential use in and development of UDP-GlcNAc capture and sequencing protocols.
Chromatin-associated cohesin turns over extensively and forms new cohesive linkages during meiotic prophase
Authors: Haseeb Muhammad A. , Weng Katherine A. , Bickel Sharon E.
Published: August 2023

In dividing cells, accurate chromosome segregation depends on sister chromatid cohesion, protein linkages that are established during DNA replication. Faithful chromosome segregation in oocytes requires that cohesion, first established in S phase, remain intact for days to decades, depending on the organism. Premature loss of meiotic cohesion in oocytes leads to the production of aneuploid gametes and contributes to the increased incidence of meiotic segregation errors as women age (maternal age effect). The prevailing model is that cohesive linkages do not turn over in mammalian oocytes. However, we have previously reported that cohesion-related defects arise in Drosophila oocytes when individual cohesin subunits or cohesin regulators are knocked down after meiotic S phase. Here we use two strategies to express a tagged cohesin subunit exclusively during mid-prophase in Drosophila oocytes and demonstrate that newly expressed cohesin is used to formde novolinkages after meiotic S phase. Moreover, nearly complete turnover of chromosome-associated cohesin occurs during meiotic prophase, with faster replacement on the arms than at the centromeres. Unlike S-phase cohesion establishment, the formation of new cohesive linkages during meiotic prophase does not require acetylation of conserved lysines within the Smc3 head. Our findings indicate that maintenance of cohesion between S phase and chromosome segregation in Drosophila oocytes requires an active cohesion rejuvenation program that generates new cohesive linkages during meiotic prophase.