bluuebunny/crossref_metadata_2025 huggingface dataset:
Outcome Assessment in Neurocritical Care Trials
Authors: Fitzgerald Emily , Donaldson Lachlan , Flower Oliver , Hammond Naomi , Leung Kwan Yee , McDonald Gabrielle , Rowcliff Kirsten , Vlok Ruan , Delaney Anthony
Published: March 2023

Introduction

The assessment of patient reported outcomes following neurological injury remains a challenging area of neurocritical care research. Mortality amongst the neurocritical patient population remains high with a significant proportion of survivors left suffering functional, cognitive and emotional deficits, often with a reduced health-related quality of life and leaving them dependent on caregivers. Numerous instruments have been developed to assess the level of impairment patients experience following a global neurological injury. Previous systematic reviews have reported significant heterogeneity in outcome assessment in neurocritical car trials, including the outcome measure used, method of ascertainment and the timing of outcome assessment. It has been suggested that this heterogeneity in outcome assessment has complicated the design of neurocritical care clinical trials, the pooling and meta-analysis of trial data and has led to conflicting and controversial trial results. It is unclear what impact the methods of performing outcome assessment has on loss follow up rates and the validity of outcome data in neurocritical care trials.

We aim to systematically review the methods of performing outcome assessment in neurocritical care trials to identify current trends in outcome assessment in this patient population and to examine loss to follow up rates and factors impacting cohort attrition. It is hoped that an understanding of the relationship between methods of outcome assessment and loss to follow up will inform future design of neurocritical care trials.

Methods and analysis

This systematic review will include randomized clinical trials and large prospective observational cohort studies where the included population is adults with a diagnosis of traumatic brain injury or a subarachnoid haemorrhage and reporting at least one patient reported outcome measure. Inclusion will not be limited based on intervention nor comparator. We will limit the searches to human studies, with reports published in the English language and published within the last 10 years. We will search the Medline, EMBASE, and The Cochrane Central registry of clinical trial (CENTRAL) for eligible trials. We will manually search the reference list of relevant primary review articles, clinical registries, and abstracts from recent relevant conferences

Conclusion

This systematic review and will provide clinicians with an understanding of the relationship between methods of outcome assessment and loss to follow up will inform future design of neurocritical care trials.
Spatially-resolved wastewater-based surveillance enables COVID-19 case localization across a university campus, and confirms lower SARS-CoV-2 RNA burden relative to the surrounding community
Authors: Lee Jangwoo , Acosta Nicole , Waddell Barbara J. , Du Kristine , Xiang Kevin , Van Doorn Jennifer , Low Kashtin , Bautista Maria A. , McCalder Janine , Dai Xiaotian , Lu Xuewen , Chekouo Thierry , Pradhan Puja , Sedaghat Navid , Papparis Chloe , Beaudet Alexander Buchner , Chen Jianwei , Chan Leslie , Vivas Laura , Westlund Paul , Bhatnagar Srijak , Stefani September , Visser Gail , Cabaj Jason , Achari Gopal , Clark Rhonda G. , Hrudey Steve E. , Lee Bonita E. , Pang Xiaoli , Webster Brandan , Ghali William Amin , Buret Andre Gerald , Williamson Tyler , Southern Danielle A. , Meddings Jon , Frankowski Kevin , Hubert Casey R.J. , Parkins Michael D.
Published: March 2023

Wastewater-based surveillance (WBS) has been established as a powerful tool that can guide health policy at multiple levels of government. However, this technology has not been well assessed at more granular scales, including large work sites such as University campuses. Between August 2021-April 2022, we explored the occurrence of SARS-CoV-2 RNA in wastewater from multiple complimentary sewer catchments and residential buildings spanning the University of Calgary’s campus and how this compared to levels from the municipal wastewater treatment plant servicing the campus. Concentrations of wastewater SARS-CoV-2 N1 and N2 RNA varied significantly across six sampling sites – regardless of several normalization strategies – with certain catchments consistently demonstrating values 1–2 orders higher than the others. Additionally, our comprehensive monitoring strategy enabled an estimation of the total burden of SARS-CoV-2 for the campus per capita, which was significantly lower than the surrounding community (p≤0.01). Real-time contact tracing data was used to confirm an association between wastewater SARS-CoV-2 burden and clinically confirmed cases proving the potential of WBS as a tool for disease monitoring across worksites. Allele-specific qPCR assays confirmed that variants across campus were representative of the community at large, and at no time did emerging variants first debut on campus. This study demonstrates how WBS can be efficiently applied to locate hotspots of disease activity at a very granular scale, and predict disease burden across large, complex worksites.

Synopsis

‘This study establishes that wastewater-based surveillance with a node-based sampling strategy can be used to passively monitor for disease, locate disease “hotspots” and approximate the burden of infected individuals’
Circulating white blood cell traits and colorectal cancer risk: A Mendelian randomization study
Authors: Constantinescu Andrei-Emil , Bull Caroline J , Jones Nicholas , Mitchell Ruth , Burrows Kimberley , Dimou Niki , Bézieau Stéphane , Brenner Hermann , Buchanan Daniel D , D’Amato Mauro , Jenkins Mark A , Moreno Victor , Pai Rish K , Um Caroline Y , White Emily , Murphy Neil , Gunter Marc , Timpson Nicholas J , Huyghe Jeroen R , Vincent Emma E
Published: March 2023

Observational studies have suggested a protective role for eosinophils in colorectal cancer (CRC) development and implicated neutrophils, but the causal relationships remain unclear. Here, we aimed to estimate the causal effect of circulating white blood cell (WBC) counts (N = ∼550,000) for basophils, eosinophils, monocytes, lymphocytes and neutrophils on CRC risk (N = 52,775 cases and 45,940 controls) using Mendelian randomization (MR). For comparison, we also examined this relationship using individual-level data from UK Biobank (4,043 incident CRC cases and 332,773 controls) in a longitudinal cohort analysis. The inverse-variance weighted (IVW) MR analysis suggested a protective effect of increased basophil count and eosinophil count on CRC risk [OR per 1-SD increase: 0.88, CI(95%): 0.78-0.99,P=0.04; OR: 0.93, CI(95%): 0.88-0.98,P=0.01]. The protective effect of eosinophils remained [OR per 1-SD increase: 0.88, CI(95%): 0.80-0.97,P=0.01] following adjustments for all other WBC subtypes, to account for genetic correlation between the traits, using multivariable MR. A protective effect of increased lymphocyte count on CRC risk was also found [OR: 0.84, CI(95%): 0.76-0.93,P=6.70e-4] following adjustment. Consistent with MR results, a protective effect for eosinophils in the cohort analysis in the fully adjusted model [RR per 1-SD increase: 0.96, CI(95%): 0.93-0.99,P=0.02] and following adjustment for the other WBC subtypes [RR: 0.96, CI(95%): 0.93-0.99,P=0.001] was observed. Our study implicates peripheral blood immune cells, in particular eosinophils and lymphocytes, in CRC development, highlighting a need for mechanistic studies to interrogate these relationships.

What is already known of this topic

While previous observational studies have suggested a protective role for eosinophils in colorectal cancer development and implicated neutrophils, whether changes in the levels of circulating white blood cells causes colorectal cancer has not been explored.

What this study adds

Our study is the first to use Mendelian randomization (MR) to investigate this relationship. In parallel, for comparison, we also conduct the largest cohort study to date on the topic. We found evidence to suggest that elevated eosinophil and lymphocyte count may have a protective effect on CRC risk, adding new insights into the pathogenesis of CRC.

How this study might affect research, practice or policy

Our findings will encourage further mechanistic exploration to understand the biological mechanisms underpinning our findings, which may lead to new therapeutic approaches or risk reduction strategies.
Nanothermometry-enabled intelligent laser tissue soldering
Authors: Cipolato Oscar , Dosnon Lucas , Rosendorf Jachym , Sarcevic Sima , Bondi Alice , Liska Vaclav , Schlegel Andrea A. , Herrmann Inge K.
Published: March 2023

While often life-saving, surgical resectioning of diseased tissues puts patients at risk for post-operative complications. Sutures and staples are well-accepted and routinely used to reconnect tissues, however, their mechanical mismatch with biological soft tissue and invasiveness contribute to wound healing complications, infections, and post-operative fluid leakage. In principle, laser tissue soldering offers an attractive, minimally-invasive alternative for seamless soft tissue fusion. However, despite encouraging experimental observations, including accelerated healing and lowered infection risk, critical issues related to temperature monitoring and control during soldering and associated complications have prevented their clinical exploitation to date. Here, we introduce intelligent laser tissue soldering (iSoldering) with integrated nanothermometry as a promising yet unexplored approach to overcoming the critical shortcomings of laser tissue soldering. We demonstrate that adding thermoplasmonic and nanothermometry nanoparticles to proteinaceous solders enables heat confinement and non-invasive temperature monitoring and control, offering a route to high-performance, leak-tight tissue sealing even at deep tissue sites. The resulting tissue seals exhibit excellent mechanical properties and resistance to chemically-aggressive digestive fluids, including gastrointestinal juice. The iSolder can be readily cut and shaped by surgeons to optimally fit the tissue defect and can even be applied using infrared light from a medically approved light source, hence fulfilling key prerequisites for application in the operating theatre. Overall, iSoldering enables reproducible and well-controlled high-performance tissue sealing, offering new prospects for its clinical exploitation in diverse fields ranging from cardiovascular to visceral and plastic surgery.

Teaser

Intelligent solders containing nanothermometers and thermoplasmonics offer new route to high-performance tissue sealing.
Short-chain di-carboxylates as positive allosteric modulators of the pH-dependent pentameric ligand-gated ion channel GLIC: requirement of an intact vestibular pocket
Authors: Van Renterghem Catherine , Nemecz Ákos , Delarue-Cochin Sandrine , Joseph Delphine , Corringer Pierre-Jean
Published: March 2023

GLIC is a prokaryotic orthologue of brain pentameric neurotransmitter receptors. Using whole-cell patch-clamp electrophysiology in a host cell line, we show that short-chain di-carboxylate compounds are positive modulators of pHo 5-evoked GLIC activity, with a rank order of action fumarate > succinate > malonate > glutarate. Potentiation by fumarate depends on intracellular pH, mainly as a result of a strong decrease of the pHo 5-evoked current when intracellular pH decreases. The modulating effect of fumarate also depends on extracellular pH, as fumarate is a weak inhibitor at pHo 6 and shows no agonist action at neutral pHo. A mutational analysis of residue-dependency for succinate and fumarate effects, based on two carboxylate-binding pockets previously identified by crystallography (Fouratiet al. 2020), shows that positive modulation involves both the inter-subunit pocket, homologous to the neurotransmitter-binding orthotopic site, and the intra-subunit (also called vestibular) pocket. An almost similar pattern of mutational impact is observed for the effect of caffeate, a known negative modulator. We propose, for both di-carboxylate compounds and caffeate, a model where the inter-subunit pocket is the actual binding site, and the region corresponding to the vestibular pocket is required either for inter-subunit binding itself, or for binding-to-gating coupling during the allosteric transitions involved in pore gating modulation.

Key points summary

Using a bacterial orthologue of brain pentameric neurotransmitter receptors, we show that the orthotopic/orthosteric agonist site and the adjacent vestibular region are functionally inter-dependent in mediating compound-elicited modulation. We propose that the two sites in the extracellular domain are involved “in series”, a mechanism which may have relevance to Eukaryote receptors.

We show that short-chain di-carboxylate compounds are positive modulators of GLIC. The most potent compound identified is fumarate, known to occupy the orthotopic/orthosteric site in previously published crystal structures.

We show that intracellular pH modulates GLIC allosteric transitions, as previously known for extracellular pH.

We report a caesium to sodium permeabilityratio(PCs/PNa) of 0.54 for GLIC ion pore.
Transdermal Electrophysiological Recordings of Diabetic Small Fiber Peripheral Neuropathy Using a Needle Electrode Array in Mice and Men
Authors: Blaszkiewicz Magdalena , Caron Lydia , Villinski Brooke , Passarelli Joshua , Towne Julia M. , Story Naeemah M. , Merchant Erin , Khan Furrukh S. , Emanetoglu Nuri , Kass Leonard , Smith Rosemary L. , Townsend Kristy L.
Published: March 2023

Diabetic peripheral neuropathy (DPN) is a common complication of diabetes. Proactive treatment options remain limited, which is exacerbated by a lack of sensitive and convenient diagnostics, especially early in disease progression or specifically to assess small fiber neuropathy (SFN), the loss of distal small diameter axons that innervate tissues and organs. We designed, fabricated, tested, and validated a first-of-its-kind medical diagnostic device for the functional assessment of transdermal small fiber nerve activity. This device, the Detecting Early Neuropathy (DEN), is an electrically conductive needle array designed to record nerve electrical activity in the skin and subdermal tissues. DEN recordings were validated across a time course of diet-induced DPN in mice, using statistical and computational analyses compared to other SFN measures. Based on these preclinical mouse data, the device design was adapted to obtain recordings in human with a flexible printed circuit board to mold to the leg or other skin regions. The DEN successfully recorded various types of neural activity in mouse and human, with or without stimulation, including validated action potentials and electromyography signals. New functional diagnostic tools like DEN offer a promising outlook for patients needing an earlier or more sensitive diagnosis of SFN/DPN, to allow for earlier and more effective treatment options, especially as more become available in the clinic in future years.
Ultra-fast micro-CT of an unrestrained live insect
Authors: Davranoglou Leonidas-Romanos , Mortimer Beth , Schlepütz Christian Matthias , Taylor Graham K.
Published: March 2023

Micro-CT has revolutionized functional morphology by enabling volumetric reconstruction of biological specimens at micrometre scales, but its accuracy is compromised by fixation artefacts. State-of-the-artin vivoimaging avoids this, but still requires subjects to be tethered, anaesthetized, or stained. Here we use ultra-fast synchrotron-based micro-CT to produce the first 3D scan of an unrestrained living organism at micrometre resolution, demonstrating the potential of this method in physiology, behaviour, and biomechanics.
GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership
Authors: Carbonetto Peter , Luo Kaixuan , Sarkar Abhishek , Hung Anthony , Tayeb Karl , Pott Sebastian , Stephens Matthew
Published: March 2023

Parts-based representations, such as non-negative matrix factorization and topic modeling, have been used to identify structure from single-cell sequencing data sets, in particular structure that is not as well captured by clustering or other dimensionality reduction methods. However, interpreting the individual parts remains a challenge. To address this challenge, we extend methods for differential expression analysis by allowing cells to have partial membership to multiple groups. We call this grade of membership differential expression (GoM DE). We illustrate the benefits of GoM DE for annotating topics identified in several single-cell RNA-seq and ATAC-seq data sets.
Natural variation in expression of the mitochondrial flavoprotein WAH-1 alters response to cyanide inC. elegans
Authors: Mercado Maria P. , Tan June H. , Schertzberg Michael R. , Fraser Andrew G.
Published: March 2023

C. elegansis a free-living nematode that must adapt to a wide range of environments including both aerobic and anaerobic conditions. To survive in low oxygen,C. eleganscan use an unusual form of anaerobic respiration that relies on rhodoquinone (RQ) as an alternative electron carrier. Parasitic nematodes like hookworm and whipworm also require rhodoquinone-dependent metabolism (RQDM) to survive in the highly anaerobic conditions in the human gut. Understanding how RQDM is regulated inC. elegansmay thus identify new ways to combat these closely-related major human pathogens. We previously established a simple movement-based assay for RQDM inC. elegans. In this study, we tested a panel of wild-type isolates ofC. elegansin our RQDM assay and find substantial variation in their ability to use RQDM. We carried out a genome-wide association study (GWAS) to identify loci that affect RQDM — this identified a single major QTL on the right arm of Chromosome III. We used RNAi to test almost all genes within the QTL region for involvement in RQDM and found one gene,wah-1, that strongly modulates RQDM-dependent recovery inC. elegans. WAH-1 is a mitochondrial flavoprotein that affects the electron transport chain, consistent with a role in RQDM. We show thatwah-1expression varies between isolates due to major changes inwah-1transcript structures and this correlates tightly with variation in RQDM. Finally, we show that there is similar complexity towah-1transcription in parasitic nematodes and thatwah-1transcript structures change as parasites shift from aerobic to anaerobic, RQ- requiring metabolism. We thus conclude that reducedwah-1expression correlates with increased ability to survive in conditions where RQDM is essential.
An intracellular hydrophobic nexus is critical for slow deactivation in hERG channels
Authors: Stevens-Sostre Whitney A. , Flores-Aldama Lisandra , Bustos Daniel , Li Jin , Delemotte Lucie , Robertson Gail A.
Published: March 2023

Slow deactivation is a critical biophysical and physiological property of voltage-gated K+channels encoded by thehuman Ether-à-go-go-Related Gene(hERG). hERG channel deactivation is modulated by interactions between intracellular N-terminal Per-Arnt-Sim (PAS) and C-terminal cyclic nucleotide-binding homology (CNBh) domains. The PAS domain is multipartite, comprising a globular domain (residues 26-136) and an N-terminal PAS-cap that is further subdivided into an initial unstructured segment (residues 1-12) and an amphipathic α-helical region (residues 13-25). Disruption of interactions within the PAS-CNBhD complex accelerates deactivation kinetics and impairs the slow repolarization of the cardiac action potential. Similarly, deletion of the PAS-cap unstructured segment, modeled as a "foot-in-the-door,” accelerates channel closing. Here, we tested the hypothesis that a three-dimensional hydrophobic nexus, comprising residues in the PAS-cap α-helix, the globular PAS, and CNBh domains, plays a crucial role in slow deactivation. Utilizing structure-directed mutagenesis, electrophysiology, and molecular dynamics simulations, we provide evidence that altering hydrophobicity at this interface accelerates deactivation kinetics and causes a rearrangement in the network of residues comprising the hydrophobic nexus. Moreover, the PAS-cap unstructured segment disengages from the gating machinery. We propose that the nexus hydrophobicity positions the PAS-cap α-helix and promotes engagement of the upstream PAS-cap unstructured segment with the gating machinery, resulting in slow channel closing. Interestingly, several long QT syndrome disease mutations lie at this interface, underscoring the importance of the hydrophobic nexus and the novel role of the PAS-cap α-helix in hERG gating.
MerTK mediates the immunologically silent uptake of alpha-synuclein fibrils by human microglia
Authors: Dorion Marie-France , Senkevich Konstantin , Yaqubi Moein , Kieran Nicholas W. , Chen Carol X.-Q. , MacDonald Adam , Luo Wen , Wallis Amber , Shlaifer Irina , Hall Jeffery A. , Dudley Roy W. R. , Glass Ian A. ,   Birth Defects Research Laboratory, Stratton Jo Anne , Fon Edward , Bartels Tim , Antel Jack P. , Gan-or Ziv , Durcan Thomas M. , Healy Luke M.
Published: March 2023

MerTK is a receptor tyrosine kinase that mediates the immunologically silent phagocytic uptake of diverse types of cellular debris. Highly expressed on the surface of microglial cell, MerTK is of importance in brain development, homeostasis, plasticity, and disease. Yet, involvement of this receptor in the clearance of protein aggregates that accumulate with aging and in neurodegenerative diseases has yet to be defined. The current study explored the function of MerTK in the microglial uptake of alpha-synuclein fibrils which play a causative role in the pathobiology of synucleinopathies.

Using human primary and induced pluripotent stem cell-derived microglia, the MerTK- dependence of alpha-synuclein fibril internalization was investigatedin vitro. Relevance of this pathway to synucleinopathies was assessed by analyzing MerTK expression in patient-derived cells and tissues.

Pharmacological inhibition of MerTK and siRNA-mediatedMERTKknockdown both caused a decreased rate of alpha-synuclein fibril internalization by human microglia. Consistent with the immunologically silent nature of MerTK-mediated phagocytosis, alpha-synuclein fibril internalization did not induce secretion of pro-inflammatory cytokines from microglia. In addition, burden analysis in two independent patient cohorts revealed a significant association between rare functionally deleteriousMERTKvariants and Parkinson’s disease in one of the cohorts (p= 0.002). Accordingly,MERTKexpression was significantly upregulated in nigral microglia from Parkinson’s disease/Lewy body dementia patients compared to those from non-neurological control donors in a single-nuclei RNA-sequencing dataset (p= 5.08×10-21), and MerTK protein expression positively correlated with alpha-synuclein level in human cortex lysates (p= 0.0029).

Taken together, our findings define a novel role for MerTK in mediating the uptake of alpha-synuclein aggregates by human microglia, with possible involvement in limiting alpha-synuclein spread in synucleinopathies such as Parkinson’s disease.
Spatially-Resolved Transcriptomics Define Clinically Relevant Subsets of Macrophages in Diffuse Large B-cell Lymphoma
Authors: Liu Min , Bertolazzi Giorgio , Mulder Kevin , Sridhar Shruti , Lee Rui Xue , Jaynes Patrick , Hoppe Michal Marek , Fan Shuangyi , Peng Yanfen , Thng Jocelyn , Chua Reiya , De Mel Sanjay , Poon Limei , Chan Esther , Lee Joanne , Hue Susan Swee-Shan , Ng Siok-Bian , Chandy K George , Ginhoux Florent , Chee Yen Lin , Tripodo Claudio , Jeyasekharan Anand D.
Published: March 2023

Background

Macrophages are abundant immune cells in the microenvironment of diffuse large B-cell lymphoma (DLBCL). Conventional immunohistochemistry-based studies with varying prognostic significance precludes a comprehensive analysis of macrophage subtypes in DLBCL. We hypothesized that whole-transcriptomic analysis (WTA) of macrophage in-situ would identify new macrophage subsets of biological and clinical significances.

Methods

Digital spatial profiling with WTA of CD68+ cells was performed in 47 DLBCL and 17 reactive lymphoid tissues (RLTs), to define macrophage signatures (termed “MacroSigs”) of distinct lymphoid spatial niches and clinical scenarios. Eight independent DLBCL datasets (4,594 patients) with transcriptomic and survival information were used for validation of MacroSigs.

Results

Digital spatial profiling revealed previously unrecognized transcriptomic differences between macrophages populating distinct spatial compartments in RLTs (light zone (LZ)/ dark zone (DZ), germinal center (GC)/ interfollicular (IF) regions), and in between disease states (RLTs and DLBCL with or without relapsed disease). This transcriptomic diversity of macrophages was categorized into eight MacroSigs. Spatial-MacroSigs associate with specific cell-of-origin (COO) subtypes of DLBCL, of particular interest being the IF-MacroSig enriched in the unclassified COO (P<0.005, 6/8 datasets). MacroSigs of relapsed-DLBCL and DZ were prognostic for shorter overall survival (P<0.05 in 5/8 datasets;P<0.05 in 8/8 datasets, respectively). Projection onto a macrophage single-cell RNA-sequencing atlas reveals the Non-relapse-DLBCL MacroSig to depict HES1/FOLR2-like macrophages, while relapse-DLBCL-MacroSig represents IL1B-like monocytes, with unique therapeutic vulnerabilities for each.

Conclusions

This study first provides spatially-resolved macrophage WTA in reactive and malignant lymphoid tissues. Gene expression signatures of macrophages in the DZ and relapsed-DLBCL samples are consistently prognostic in multiple datasets and offer insights into novel therapeutic strategies for DLBCL.
KSHV uses viral IL6 to expand infected immunosuppressive macrophages
Authors: Shimoda Michiko , Inagaki Tomoki , Davis Ryan R. , Merleev Alexander , Tepper Clifford G. , Maverakis Emanual , Izumiya Yoshihiro
Published: March 2023

Kaposi’s sarcoma-associated herpesvirus (KSHV) is an oncogenic double-stranded DNA virus and the etiologic agent of Kaposi’s sarcoma and hyperinflammatory lymphoproliferative disorders. Understanding the mechanism by which KSHV increases the infected cell population is crucial for curing KSHV-associated diseases. Here we demonstrate that KSHV preferentially infects CD14+monocytes and sustains viral replication through the viral interleukin-6 (vIL6)-mediated activation of STAT1 and 3. Using vIL6-sufficient and vIL6-deficient recombinant KSHV, we demonstrated that vIL6 plays a critical role in promoting the proliferation and differentiation of KSHV-infected monocytes into macrophages. The macrophages derived from vIL6-sufficient KSHV infection showed a distinct transcriptional profile of elevated IFN-pathway activation with immune suppression and were compromised in T-cell stimulation function compared to those from vIL6-deficient KSHV infection or uninfected control. These results highlight a clever strategy, in which KSHV utilizes vIL6 to secure its viral pool by expanding infected dysfunctional macrophages. This mechanism also facilitates KSHV to escape from host immune surveillance and to establish a lifelong infection. 160

KSHV causes multiple inflammatory diseases, however, the underlying mechanism is not clear. Shimoda et al. demonstrate that KSHV preferentially infects monocytes and utilizes virally encoded interleukin-6 to expand and deregulate infected monocytes. This helps the virus escape from host immune surveillance.
Circulating tumor DNA association with residual cancer burden after neoadjuvant chemotherapy in triple-negative breast cancer in TBCRC 030
Authors: Parsons Heather A. , Blewett Timothy , Chu Xiangying , Sridhar Sainetra , Santos Katheryn , Xiong Kan , Abramson Vandana G. , Patel Ashka , Cheng Ju , Brufsky Adam , Rhoades Justin , Force Jeremy , Liu Ruolin , Traina Tiffany A. , Carey Lisa A. , Rimawi Mothaffar F. , Miller Kathy D. , Stearns Vered , Specht Jennifer , Falkson Carla , Burstein Harold J. , Wolff Antonio C. , Winer Eric P. , Tayob Nabihah , Krop Ian E. , Makrigiorgos G. Mike , Golub Todd R. , Mayer Erica L. , Adalsteinsson Viktor A.
Published: March 2023

Purpose

To examine circulating tumor DNA (ctDNA) and its association with residual cancer burden (RCB) using an ultrasensitive assay in patients with triple-negative breast cancer (TNBC) receiving neoadjuvant chemotherapy (NAT).

Patients and Methods

We identified responders (RCB-0/1) and matched non-responders (RCB-2/3) from the phase II TBCRC 030 prospective study of neoadjuvant paclitaxel vs. cisplatin in TNBC. We collected plasma samples at baseline, three weeks, and twelve weeks (end of therapy). We created personalized ctDNA assays utilizing MAESTRO mutation enrichment sequencing. We explored associations between ctDNA and RCB status and disease recurrence.

Results

Of 139 patients, 68 had complete samples and no additional NAT. Twenty-two were responders and 19 of those had sufficient tissue for whole-genome sequencing. We identified an additional 19 non-responders for a matched case-control analysis of 38 patients using a MAESTRO ctDNA assay tracking 319-1000 variants (median 1000) to 114 plasma samples from 3 timepoints. Overall, ctDNA positivity was 100% at baseline, 79% at week 3, and 55% at week 12. Median tumor fraction (TFx) was 3.7 × 10−4(range: 7.9 × 10−7to 4.9 × 10−1). TFx decreased 285-fold from baseline to week 3 in responders and 24-fold in non-responders. Week 12 ctDNA clearance correlated with RCB: clearance was observed in 10/11 patients with RCB-0, 3/8 with RCB-1, 4/15 with RCB-2, and 0/4 with RCB-3. Among 6 patients with known recurrence five had persistent ctDNA at week 12.

Conclusion

NAT for TNBC reduced ctDNA TFx by 285-fold in responders and 24-fold in non-responders. In 58% (22/38) of patients, ctDNA TFx dropped below the detection level of a commercially available test, emphasizing the need for sensitive tests. Additional studies will determine if ctDNA-guided approaches can improve outcomes.
C-NODDI: a constrained NODDI model for axonal density and orientation determinations in cerebral white matter in normative aging
Authors: Alsameen Maryam H. , Gong Zhaoyuan , Qian Wenshu , Kiely Matthew , Triebswetter Curtis , Bergeron Christopher M. , Cortina Luis E. , Faulkner Mary E. , Laporte John P. , Bouhrara Mustapha
Published: March 2023

Purpose

Neurite orientation dispersion and density imaging (NODDI) provides measures of neurite density and dispersion through computation of the neurite density index (NDI) and the orientation dispersion index (ODI). However, NODDI overestimates the cerebrospinal fluid water fraction in white matter (WM) and provides physiologically unrealistic high NDI values. Furthermore, derived NDI values are echo time (TE)-dependent. In this work, we propose a modification of NODDI, named constrained NODDI (C-NODDI), for NDI and ODI mapping in WM.

Methods

Using NODDI and C-NODDI, we investigated age-related alterations in WM in a cohort of 58 cognitively unimpaired adults. Further, NDI values derived using NODDI or C-NODDI were correlated with the neurofilament light chain (NfL) concentration levels, a plasma biomarker of axonal degeneration.

Results

ODI derived values using both approaches were virtually identical. We confirm the previous finding that NDI estimation using NODDI is TE-dependent. In contrast, C-NODDI-NDI exhibit lower susceptibility to TE. Further, C-NODDI-NDI values were lower than NODDI-NDI. Further, our results indicate a quadratic relationship between NDI and age suggesting that axonal maturation continues until middle age followed by a decrease. This quadratic association was notably significant in several WM regions using C-NODDI, while limited to a few regions using NODDI. ODI exhibited overall constant trends with age. Finally, C-NODDI-NDI values exhibited a stronger correlation with NfL concentration levels as compared NODDI-NDI, with lower NDI values correspond to higher levels of NfL.

Conclusions

C-NODDI provides a complementary method to NODDI for determination of NDI in white matter in normative aging.
Tigerfish designs oligonucleotide-basedin situhybridization probes targeting intervals of highly repetitive DNA at the scale of genomes
Authors: Aguilar Robin , Camplisson Conor K. , Lin Qiaoyi , Miga Karen H. , Noble William S. , Beliveau Brian J.
Published: March 2023

Fluorescentin situhybridization (FISH) is a powerful method for the targeted visualization of nucleic acids in their native contexts. Recent technological advances have leveraged computationally designed oligonucleotide (oligo) probes to interrogate >100 distinct targets in the same sample, pushing the boundaries of FISH-based assays. However, even in the most highly multiplexed experiments, repetitive DNA regions are typically not included as targets, as the computational design of specific probes against such regions presents significant technical challenges. Consequently, many open questions remain about the organization and function of highly repetitive sequences. Here, we introduce Tigerfish, a software tool for the genome-scale design of oligo probes against repetitive DNA intervals. We showcase Tigerfish by designing a panel of 24 interval-specific repeat probes specific to each of the 24 human chromosomes and imaging this panel on metaphase spreads and in interphase nuclei. Tigerfish extends the powerful toolkit of oligo-based FISH to highly repetitive DNA.
ELITE: Expression deconvoLution using lInear optimizaTion in bulk transcriptomics mixturEs
Authors: Antoranz Asier , Mackintosh Carlos , Ortiz María , Pey Jon
Published: March 2023

Understanding the cellular composition of tissue samples is crucial for identifying the molecular mechanisms underlying diseases and developing cellular targets for therapeutic interventions. Digital cytometry methods have been developed to predict tissue composition from bulk transcriptomic data, avoiding the high cost associated with single-cell profiling. Here, we present ELITE, a new digital cytometry method that utilizes linear programming to solve the deconvolution problem. ELITE uses as inputs a mixture matrix representing bulk measurements, and a signature matrix representing molecular fingerprints of the cell types to be identified. The signature matrix can be obtained from single-cell datasets or the literature, making ELITE more flexible than other methods that rely solely on single-cell data. We evaluated ELITE on three publicly available single-cell datasets and compared it with five other deconvolution methods, showing superior performance, particularly when there were cell types with similar expression profiles. As a case study, we evaluated the prediction of tumor cellularity using purity estimates from 20 different TCGA carcinoma datasets.
Working memory-based and -free reward prediction in a dual dopamine system in the basal ganglia
Authors: Yoshizawa Tomohiko , Miyamura Yuuto , Ochi Yuta , Hira Riichiro , Funahashi Makoto , Sakai Yutaka , Cui Yilong , Isomura Yoshikazu
Published: March 2023

Animals optimize their actions by predicting and verifying their outcomes (e.g., rewards). Reward prediction often requires working memory (WM)-based information. To elucidate the neural basis of WM-based reward prediction, we compared the activity of dopamine (DA) neurons in the ventral tegmental area (VTA) in an alternate reward condition (WM-based) with that in a random (WM-free) reward condition in rats and mice. Positron emission tomography revealed greater VTA activation in the WM-based than the WM-free condition. Lateral and medial VTA neurons displayed differential electrophysiological spike activities reflecting WM-based and WM-free reward prediction error, respectively. Furthermore, phasic DA release in the dorsal and ventral striatum changed as WM-based and WM-free classical conditioning progressed. Consistent with our WM-based model, reward acquisition caused a DA dip only in the dorsal striatum. Thus a dual DA system processes WM-based and WM-free reward prediction in parallel.
optimalTAD: annotation of topologically associating domains based on chromatin marks enrichment
Authors: Smirnov Dmitrii N. , Kononkova Anna D. , Toiber Debra , Gelfand Mikhail S. , Khrameeva Ekaterina E.
Published: March 2023

In many eukaryotes, chromosomes are organized as strings of spatially segregated Topologically Associating Domains (TADs), characterized by a substantially increased frequency of interactions within them. Boundaries of TADs are highly enriched in histone acetylation chromatin marks and occupied binding sites of architectural proteins, highlighting the functional role of TADs in the regulation of gene expression. While many computational approaches have been developed for TAD identification, it remains challenging because of their nested structure, resulting in weakly overlapping sets of TADs at different scales. Here, we propose a novel algorithmoptimalTADfor identifying the optimal set of TADs based on epigenetic marks enrichment. Assuming that the most dramatic enrichment corresponds to the best annotation of TAD boundaries, our algorithm optimizes TAD calling parameters by maximizing the difference in chromatin mark levels between TADs and their boundaries. Using this algorithm, we annotated TADs in multiple publicly available fruit fly and mammalian Hi-C datasets and identified a set of epigenetic marks that are best suited for TAD prediction. Through the analysis of diverse organisms and cell types with distinct underlying principles of TAD organization, we have shown thatoptimalTADis a universal tool suitable for studying TAD structure, functions, and properties unique to specific cell types and organisms.optimalTADis freely available at GitHub:https://github.com/cosmoskaluga/optimalTAD.

Key Points

We assume that the most dramatic enrichment of epigenetic marks corresponds to the best annotation of TAD boundaries.

Our algorithm optimizes TAD calling parameters by maximizing the difference in chromatin mark levels between TADs and their boundaries.

optimalTADis a universal tool that is applicable for studying TAD characteristics in diverse organisms and cell types.

optimalTADenables the identification of a specific set of epigenetic marks that are most suitable for annotating TADs.
Spontaneous Necker-Cube Reversals are not that Spontaneous
Authors: Wilson Mareike , Hecker Lukas , Joos Ellen , Aertsen Ad , Tebartz van Elst Ludger , Kornmeier Jürgen
Published: March 2023

During observation of the ambiguous Necker cube, our perception suddenly reverses between two about equally possible 3D interpretations. During passive observation, perceptual reversals seem to be sudden and spontaneous. A number of theoretical approaches postulate destabilization of neural representations as a precondition for spontaneous reversals of ambiguous figures. In the current study, we focused on possible EEG correlates of perceptual destabilization, that may allow to predict an upcoming perceptual reversal.

We presented ambiguous Necker cube stimuli in an onset-paradigm and investigated the neural processes underlying endogenous reversals as compared to perceptual stability across two consecutive stimulus presentations. In a separate experimental condition, disambiguated cube variants were alternated randomly, to exogenously induce perceptual reversals. We compared the EEG immediately before and during endogenous Necker cube reversals with corresponding time windows during exogenously induced perceptual reversals of disambiguated cube variants.

For the ambiguous Necker cube stimuli, we found the earliest differences in the EEG between reversal trials and stability trials already one second before a reversal occurred, at bilateral parietal electrodes. The traces remained similar until approximately 1100 ms before a perceived reversal, became maximally different at around 890 ms (p=7.59*10−6, Cohen’s d=1.35) and remained different until shortly before offset of the stimulus preceding the reversal. No such patterns were found in the case of disambiguated cube variants.

The identified EEG effects may reflect destabilized states of neural representations, related to destabilized perceptual states preceding a perceptual reversal. They further indicate that spontaneous Necker cube reversals are most probably not as spontaneous as generally thought. Rather, the destabilization may occur over a longer time scale, at least one second before a reversal event.
Analysis of multi-condition single-cell data with latent embedding multivariate regression
Authors: Ahlmann-Eltze Constantin , Huber Wolfgang
Published: March 2023

Identifying gene expression differences in heterogeneous tissues across experimental or observational conditions is a fundamental biological task, enabled by single-cell assays such as multi-condition sc-RNA-seq. Current data analysis approaches divide the constituent cells into clusters meant to represent cell types, and identify differentially expressed genes for each cluster. However, such discrete categorization tends to be an unsatisfactory model of the underlying biology. Use of more gradual representations of cell type or cell state promises higher statistical power, better usability and better interpretability. Here, we introduce Latent Embedding Multivariate Regression (LEMUR), a generative model that enables differential expression analysis using a continuous low-dimensional latent space parameterization of cell type and state diversity. It operates without, or before, commitment to discrete categorization. LEMUR (1) integrates data from the different conditions, (2) predicts how each cell’s gene expression would change as a function of the conditions and its position in latent space, and (3) for each gene, identifies compact neighborhoods of cells with consistent differential expression. Unlike statically defined clusters, these neighborhoods adapt to the underlying gene expression changes. We assess LEMUR’s performance on a compendium of single-cell datasets and show applications to the identification of tumor subpopulations with distinct drug responses, the interplay between cell state and developmental time in zebrafish embryos, and the discovery of cell state×environment interactions in a spatial single-cell study of plaques in Alzheimer’s disease. LEMUR is broadly applicable as a first-line analysis approach to multi-condition sc-RNA-seq data.

Software availability

https://bioconductor.org/packages/lemur

Contact

constantin.ahlmann@embl.de
Morphine Re-arranges Chromatin Spatial Architecture of Primate Cortical Neurons
Authors: Wang Liang , Wang Xiaojie , Liu Chunqi , Xu Wei , Kuang Weihong , Bu Qian , Li Hongchun , Zhao Ying , Jiang Linhong , Chen Yaxing , Qin Feng , Li Shu , Wei Qinfan , Liu Xiaocong , Liu Bin , Chen Yuanyuan , Dai Yanping , Wang Hongbo , Tian Jingwei , Cao Gang , Zhao Yinglan , Cen Xiaobo
Published: March 2023

The expression of linear DNA sequences is precisely regulated by the three–dimensional (3D) architecture of chromatin. Morphine-induced aberrant gene networks of neurons have been extensively investigated; however, how morphine impacts the 3D genomic architecture of neuorns is still unknown. Here, we applied digestion-ligation-only high-throughput chromosome conformation capture (DLO Hi-C) technology to investigate the affection of morphine on 3D chromatin architecture of primate cortical neurons. After receiving continuous morphine administration for 90 days on rhesus monkeys, we discovered that morphine re-arranged chromosome territories, with a total of 391 segmented compartments being switched. Morphine altered over half of the detected topologically associated domains (TADs), most of which exhibited a variety of shifts, followed by separating and fusing types. Analysis of the looping events at kilobase-scale resolution revealed that morphine increased not only the number but also the length of differential loops. Moreover, all identified differentially expressed genes (DEGs) from the RNA sequencing (RNA-seq) were mapped to the specific TAD boundaries or differential loops, and were further validated to be significantly changed. Collectively, an altered 3D genomic architecture of cortical neurons may regulate the gene networks associated-morphine effects. Our finding provides critical hubs connecting chromosome spatial organization and gene networks associated with the morphine effects in humans.
BMP signaling to pharyngeal muscle in theC. elegansresponse to a bacterial pathogen regulates anti-microbial peptide expression and pharyngeal pumping
Authors: Ciccarelli Emma Jo , Bendelstein Moshe , Yamamoto Katerina K. , Reich Hannah , Savage-Dunn Cathy
Published: March 2023

Host response to pathogens recruits multiple tissues in part through conserved cell signaling pathways. InC. elegans, the bone morphogenetic protein (BMP) like DBL-1 signaling pathway has a role in the response to infection in addition to other roles in development and post-developmental functions. In the regulation of body size, the DBL-1 pathway acts through cell autonomous signal activation in the epidermis (hypodermis). We have now elucidated the tissues that respond to DBL-1 signaling upon exposure to two bacterial pathogens. The receptors and Smad signal transducers for DBL-1 are expressed in pharyngeal muscle, intestine, and epidermis. We demonstrate that expression of receptor-regulated Smad (R-Smad) genesma-3in the pharynx is sufficient to improve the impaired survival phenotype ofsma-3mutants and that expression ofsma-3in the intestine has no effect when exposing worms to bacterial infection of the intestine. We also show that two antimicrobial peptide genes –abf-2andcnc-2– are regulated by DBL-1 signaling through R-Smad SMA-3 activity in the pharynx. Finally, we show that pharyngeal pumping activity is reduced insma-3mutants and that other pharynx-defective mutants also have reduced survival on a bacterial pathogen. Our results identify the pharynx as a tissue that responds to BMP signaling to coordinate a systemic response to bacterial pathogens.

Significance Statement

Innate immunity is the first line of defense against pathogens. Conserved cell signaling pathways are known to be involved in host-pathogen response, but how they coordinate a systemic response is less well understood.

In the nematodeC. elegans,bone morphogenetic protein (BMP) signaling is required for survival on pathogenic bacteria. Using transgenic strains, the authors identify a major role for a specific organ, the pharynx, in BMP-dependent survival.

These findings demonstrate that an organ can serve as a pathogen sensor to trigger multiple modes of response to bacterial pathogens, include a barrier response and regulation of anti-microbial peptide expression.
Modelling capture efficiency of single cell RNA-sequencing data improves inference of transcriptome-wide burst kinetics
Authors: Tang Wenhao , Jørgensen Andreas Christ Sølvsten , Marguerat Samuel , Thomas Philipp , Shahrezaei Vahid
Published: March 2023

Gene expression is characterised by stochastic bursts of transcription that occur at brief and random periods of promoter activity. The kinetics of gene expression burstiness differs across the genome and is dependent on the promoter sequence, among other factors. Single-cell RNA sequencing (scRNA-seq) has made it possible to quantify the cell-to-cell variability in transcription at a global genome-wide level. However, scRNA-seq data is prone to technical variability, including low and variable capture efficiency of transcripts from individual cells. Here, we propose a novel mathematical theory for the observed variability in scRNA-seq data. Our method captures burst kinetics and variability in both cell size and capture efficiency, which allows us to propose several likelihood-based and simulation-based methods for the inference of burst kinetics from scRNA-seq data. Using both synthetic and real data, we show that the simulation-based methods provide an accurate, robust and flexible tool for inferring burst kinetics from scRNA-seq data. In particular, in supervised manner, a simulation-based inference method based on neural networks proves to be accurate and useful in application to both allele and non-allele specific scRNA-seq data.