bluuebunny/crossref_metadata_2025 huggingface dataset:
Expanding Understanding of Electrocochleography in Cochlear Implantation: Auditory Neuropathy Spectrum Disorder With Normal Pure Tone Average
Authors: Buhle Anna C. , McCrary Hilary C. , Gordon Steven A. , Johnson Kathryn M. , Babajanian Eric E. , Patel Neil S.
Published: June 2023

Objective:

Describe the preoperative decision-making, intraoperative electrocochleographic (ECoG) findings, and outcome of cochlear implantation (CI) in a patient with auditory neuropathy spectrum disorder (ANSD) and normal pure-tone thresholds.

Patients:

A 19-year-old with a history of hypoxic ischemic encephalopathy and seizures was referred for hearing rehabilitation in the setting of typical hearing by pure tone audiometry but poor speech understanding. A diagnosis of ANSD was made based on acoustic brainstem response (ABR), distortion product otoacoustic emission, and acoustic reflex testing. Imaging revealed no central cause of hearing impairment.

Interventions:

Right-sided CI.

Main Outcome Measures:

Preoperative and postoperative audiometric data. Intraoperative ECoG.

Results:

Preoperatively the patient underwent comprehensive audiologic testing with behavioral audiometry, ABR testing, and CI candidacy evaluation. In the right ear, the pure tone average (PTA) was 15 dB and word recognition score was 36%. ABR confirmed ANSD. Preoperative CNC and AzBio in quiet were 8% and 0%, respectively. Intraoperative ECoG amplitudes and audiometry showed responses in the 100 uV range and estimated PTA of 42 dB HL. Postoperative testing at 1-month post-initial activation revealed PTA of 45 dB HL and unchanged word and sentence scores. However, the patient cites an improved ability to communicate and increased confidence and averages over 14 hours of device use daily.

Conclusions:

To our knowledge, this is the first reported case of CI in an ear with normal PTA. Given that nearly all presently available ECoG data comes from patients with greater degrees of hearing loss, this unique case adds to our understanding of hearing preservation in CI.
Anatomic Variations of the Lateral Branch of the Supraorbital Nerve Observed in Endoscopic Forehead Surgery
Authors: Kim Sung-Eun , Jung Jaemin
Published: June 2023

Surgeons dissect carefully in the medial third of the supraorbital rim to preserve the supraorbital nerve (SON) during surgical forehead rejuvenation. However, the anatomic variations of SON exit from the frontal bone have been researched in cadaver or imaging studies. In this study, we report a variation in the lateral branch of SON observed in an endoscopic view during forehead lifts. A retrospective review of 462 patients who underwent endoscopy-assisted forehead lifts between January 2013 and April 2020 was performed. Data, including the location, number, and form of the exit point and thickness of SON and its lateral branch variant, were recorded and reviewed intraoperatively, utilizing high-definition endoscopic assistance. Thirty-nine patients and 51 sides were included, and all patients were female, with a mean age of 44.53 (18–75) years. This nerve exited a foramen in the frontal bone ~8.82 ± 2.79 cm lateral to SON and ~1.89 ± 1.34 cm from the supraorbital margin vertically. Observed thickness variations of the lateral branch of SON included 20 small, 25 medium, and 6 large nerves. This study revealed various positional and morphologic variations of the lateral branch of SON in an endoscopic view. Thus, surgeons can be alerted of the anatomic variations of SON and establish careful dissection during procedures. In addition, the findings of this study will be useful in planning nerve blocks, filler injections, and migraine treatments in the supraorbital region.
Intraorbital Wooden Foreign Body in a Soldier
Authors: Hwang Kun , Park Chan Yong
Published: June 2023

The authors report a case of an intraorbital wooden foreign body that was misinterpreted as a radiolucent area of retained air on a computed tomography (CT) scan. A 20-year-old soldier presented to an outpatient clinic following an impingement with a bough while cutting down a tree. He had a 1-cm-deep laceration on the inner canthal area of his right eye. A military surgeon explored the wound and suspected a foreign body, but could not find or extract anything. Thereafter, the wound was sutured and the patient was transferred. An examination revealed an acutely ill-looking man with distressing pain in the medial canthal and supraorbital area associated with ipsilateral ptosis and periorbital edema. A CT scan showed a radiolucent area suspected to be retained air in the medial periorbital area. The wound was explored. Upon removal of the stitch, yellowish pus was drained. An intraorbital piece of wood measuring 1.5 cm×0.7 cm was extracted. The patient’s hospital course was uneventful. Pus culture revealed growth of Staphylococcus epidermidis. Wood has a density similar to air and fat and can be difficult to distinguish from soft tissue both on plain x-ray films and CT. In this case, the CT scan showed a radiolucent area resembling retained air. Magnetic resonance imaging is a better method of investigation in cases of a suspected organic intraorbital foreign body. Clinicians should be aware of the possibility of retention of an intraorbital foreign body in patients presenting with periorbital trauma, especially those with even a small open wound.
The Influence of Bolus of Methylprednisolone on Postorthognathic Surgery Symptoms: A Controlled Clinical Trial
Authors: Amodeo Giulia , Cerbelli Edoardo , Pisano Annalinda , Minieri Luciana , Scopelliti Domenico
Published: June 2023

Objective:

Despite improvements in maxillary and mandibular osteotomy, complications still result in around 20%. Post and intraoperative standard therapies, based on the use of betamethasone and tranexamic acid, could help to minimize the onset of side effects. The aim of the study was to compare the role of a supplementary bolus of methylprednisolone rather than the standard therapy in the onset of postoperative symptoms.

Methods:

The authors enrolled 10 patients, affected by class 2 and 3 Dentoskeletal, submitted to the institution for maxillomandibular repositioning osteotomy between October 2020 and April 2021. Patients were divided into 2 groups as follows: 5 patients (groupA) received standard therapy consisting of the administration of 4 mg of betamethasone, intraoperatively, and 1 g of tranexamic acid in 2 administrations. The remaining 5 patients (groupB) received a supplementary bolus of 20 mg methylprednisolone before the end of the surgery.

All patients received, in the postoperative period, 4 mg of betamethasone every 12 hours, for 3 days. Postoperative outcomes were evaluated with a questionnaire evaluating speaking discomfort, pain when swallowing, feeding discomfort, drinking discomfort, swelling, and ache. Each parameter was associated with a numeric rating scale ranging from 0 to 5.

Results:

The authors observed that patients treated with a supplementary bolus of methylprednisolone (groupB) had a statistically significant reduction of all postoperative symptoms as compared with patients of groupA(*P< 0.05, **P<0.01 Fig. 1).

Conclusion:

The study highlighted that the additional bolus of methylprednisolone improved all of the 6 parameters investigated by the questionnaire submitted to patients, resulting in a faster recovery and improvement of the patient’s compliance with surgery. Further studies with a larger population are needed to confirm preliminary results.
A Randomized Controlled Trial to Assess the Impact of Enhanced Recovery After Surgery on Patients Undergoing Elective Spine Surgery
Authors: Ali Zarina S. , Albayar Ahmed , Nguyen Jessica , Gallagher Ryan S. , Borja Austin J. , Kallan Michael J. , Maloney Eileen , Marcotte Paul J. , DeMatteo Ronald P. , Malhotra Neil R.
Published: June 2023

Objective:

To conduct a prospective, randomized controlled trial (RCT) of an enhanced recovery after surgery (ERAS) protocol in an elective spine surgery population.

Summary Background Data:

Surgical outcomes such as length of stay (LOS), discharge disposition, and opioid utilization greatly contribute to patient satisfaction and societal healthcare costs. ERAS protocols are multimodal, patient-centered care pathways shown to reduce postoperative opioid use, reduced LOS, and improved ambulation; however, prospective ERAS data is limited in spine surgery.

Methods :

This single-center, IRB-approved, prospective RCT enrolled adult patients undergoing elective spine surgery between March 2019 and October 2020. Primary outcomes were peri-operative and 1-month postoperative opioid use. Patients were randomized to ERAS (n=142) or standard of care (SOC; n=142) based on power analyses to detect a difference in postoperative opioid use.

Results:

Opioid use during hospitalization and the first postoperative month was not significantly different between groups (ERAS 112.2 vs. SOC 117.6 MME, P=0.76; ERAS 38.7% vs. SOC 39.4%, P=1.00 respectively). However, patients randomized to ERAS were less likely to use opioids at 6 months postoperatively (ERAS 11.4% vs. SOC 20.6%, P=0.046) and more likely to be discharged to home after surgery (ERAS 91.5% vs. SOC 81.0%, P=0.015).

Conclusion:

Here, we present a novel ERAS prospective RCT in the elective spine surgery population. While we do not detect a difference in the primary outcome of short-term opioid use, we observe significantly reduced opioid use at 6-month follow-up as well as an increased likelihood of home disposition after surgery in the ERAS group.
Body Mass Index is Associated with Pediatric Complicated Appendicitis and Postoperative Complications
Authors: Hebballi Nutan B. , DeSantis Stacia , Brown Eric L. , Markham Christine , Tsao KuoJen
Published: June 2023

Objective:

To investigate the association between body mass index (BMI) spectrum and complicated appendicitis and postoperative complications in pediatric patients.

Summary Background Data:

Despite the impact of being overweight and obese on complicated appendicitis and postoperative complications, the implications of underweight are unknown.

Methods:

A retrospective review of pediatric patients was conducted using NSQIP (2016–2020) data. Patient’s BMI percentiles were categorized into underweight, normal weight, overweight, and obese. The 30-day postoperative complications were grouped into minor, major, and any. Univariate and multivariable logistic regression models were performed.

Results:

Among 23,153 patients, the odds of complicated appendicitis were 66% higher in underweight patients (OR=1.66; 95% CI: 1.06-2.59) and 28% lower in overweight patients (OR=0.72; 95% CI: 0.54-0.95) than normal-weight patients. A statistically significant interaction between overweight and preoperative white blood cells (WBC) increased the odds of complicated appendicitis (OR=1.02; 95% CI: 1.00-1.03). Compared to normal-weight patients, obese patients had 52% higher odds of minor (OR=1.52; 95% CI: 1.18-1.96) and underweight patients had three times the odds of major (OR=2.77; 95% CI: 1.22-6.27) and any (OR=2.82; 95% CI: 1.31-6.10) complications. A statistically significant interaction between underweight and preoperative WBC lowered the odds of major (OR=0.94; 95% CI: 0.89-0.99) and any complications (OR=0.94; 95% CI: 0.89-0.98).

Conclusions:

Underweight, overweight, and interaction between overweight and preoperative WBC were associated with complicated appendicitis. Obesity, underweight and interaction between underweight and preoperative WBC were associated with minor, major, and any complications. Thus, personalized clinical pathways and parental education targeting at-risk patients can minimize postoperative complications.
Scalablein-vitroimmunostimulation of human blood for in-depth profiling of acute immune response effects
Authors: Reitzner Stefan Markus , Brodin Petter , Mikeš Jaromír
Published: June 2023

In-vitro immune stimulation of whole blood has great analytic potential for exploring the immune system function. However, logistical and biological constraints might limit the extent to which such investigations can be performed. Flexible and often even low-tech mobile applicability can increase the diversity of conditions that can be investigated. To this end, we developed and optimized a medium that enables prolongedin-vitrostimulation and enables highly functional immune responses within 24 hours of incubation. In addition, we also developed and optimized a low-tech water-based mobile incubator to enable logistical flexibility. Finally, we describe the implementation of both systems using a practical example of sample collection at a sampling site with no access to laboratory equipment outside of a research lab.
CRISPR-based gene drives generate super-Mendelian inheritance in the disease vectorCulex quinquefasciatus
Authors: Harvey-Samuel Tim , Feng Xuechun , Okamoto Emily M. , Purusothaman Deepak-Kumar , Leftwich Philip T. , Alphey Luke , Gantz Valentino M.
Published: June 2023

Culexmosquitoes pose a significant public health threat as vectors for a variety of diseases including West Nile virus and lymphatic filariasis, and transmit pathogens threatening livestock, companion animals, and endangered birds. Rampant insecticide resistance makes controlling these mosquitoes challenging and necessitates the development of new control strategies. Gene drive technologies have made significant progress in other mosquito species, although similar advances have been lagging inCulex. Here we test the first CRISPR-based homing gene drive forCulex quinquefasciatus, demonstrating the possibility of using this technology to controlCulexmosquitoes. Our results show that the inheritance of two split-gene-drive transgenes, targeting different loci, are biased in the presence of a Cas9-expressing transgene although with modest efficiencies. Our findings extend the list of disease vectors where engineered homing gene drives have been demonstrated to includeCulexalongsideAnophelesandAedes, and pave the way for future development of these technologies to controlCulexmosquitoes.
Neural Signatures of Emotion Regulation
Authors: Rieck Jared , Wrobel Julia , Porras Antonio R. , McRae Kateri , Gowin Joshua
Published: June 2023

Emotional experience is central to a fulfilling life. Although exposure to negative experiences is inevitable, an individual’s emotion regulation response may buffer against psychopathology. Identification of neural activation patterns associated with emotion regulation via an fMRI task is a promising and non-invasive means of furthering our understanding of the how the brain engages with negative experiences. Prior work has applied multivariate pattern analysis to identify signatures of response to negative emotion-inducing images; we adapt these techniques to establish novel neural signatures associated with conscious efforts to modulate emotional response. We model voxel-level activation via LASSO principal components regression and linear discriminant analysis to predict if a subject was engaged in emotion regulation and to identify brain regions which define this emotion regulation signature. We train our models using 82 participants and evaluate them on a holdout sample of 40 participants, demonstrating an accuracy up to 82.5% across three classes. Our results suggest that emotional regulation produces a unique signature that is differentiable from passive viewing of negative imagery.
Consideration of sex as a biological variable in diabetes research across twenty years
Authors: Cherian Celena , Reeves Hayley , De Silva Duneesha , Tsao Serena , Marshall Katie E. , Rideout Elizabeth J.
Published: June 2023

Sex differences exist in the risk of developing both type 1 and type 2 diabetes, and in the risk of developing diabetes-associated complications. Sex differences in glucose homeostasis, islet and β cell biology, and peripheral insulin sensitivity have also been reported in multiple animals. To determine the degree to which biological sex has been addressed in published literature related to diabetes and insulin biology, we developed a scoring system to assess the inclusion of biological sex in papers related to these topics. We scored manuscripts published inDiabetes, published by the American Diabetes Association, as this journal focuses on diabetes and diabetes-related research. We scored papers published across three years within a 20-year period (1999, 2009, 2019), a timeframe that spans the introduction of funding agency and journal policies to improve the consideration of biological sex as a variable. Our analysis shows fewer than 15% of papers used sex-based analysis in even one figure across all study years, a trend that was reproduced across journal-defined categories of diabetes research (e.g., islet studies, signal transduction). Single-sex studies accounted for approximately 40% of all manuscripts, of which >87% used male subjects only. While we observed a modest increase in the overall inclusion of sex as a biological variable during our study period, our results highlight significant opportunities to improve consideration of sex as a biological variable in diabetes research. In particular, we show that journal policies represent one way to promote better consideration of biological sex as a variable. In the long term, improved practices will reveal sex-specific mechanisms underlying diabetes risk and complications, generating insights to support the development of sex-informed prevention and treatment strategies.
Gut microbiota dysbiosis observed in tuberculosis patients resolves partially with anti-tuberculosis therapy
Authors: Sahu Sukanya , Kaushik Sandeep R. , Chaudhary Shweta , Mahapatra Amit kumar , Kappa Rukuwe , Kapfo Wetesho , Saha Sourav , Das Ranjit , Das Anjan , Khamo Vinotsole , Nanda Ranjan Kumar
Published: June 2023

Objective

Mycobacterium tuberculosis(Mtb) primarily affects the lungs with involvement of other organs causing tuberculosis (TB) in humans. Since the lung-gut axis is bidirectional, and the gut microbiota contributes to metabolic and immune homeostasis, we looked at the gut microbiota and metabolites of TB patients and controls, and whether the perturbations, if any, resolve with anti-tuberculosis treatment.

Methods

In this multicentric case-control study, a total of 107 fecal samples belonging to drug naïve active tuberculosis (ATB) patients and controls (non-tuberculosis: NTB and healthy), were collected from two clinical sites in India. A group of drug-naïve ATB patients (n=10) from one site was followed-up and monitored at 2, 4, 6, and 8 months of their anti-tuberculosis treatment. The fecal microbiome and metabolome of these study participants were characterized by 300 bp pair end sequencing of the V3-V4 region of 16S rRNA gene and gas chromatography-time of flight-mass spectrometry (GC-TOF-MS) respectively to identify disease and treatment-specific variations, if any.

Results

Drug naïveATB and NTB patients showed a significant reduction of gut microbial diversity with respect to age matched healthy controls in both the clinical sites. ATB patient’s had underrepresentation of gut commensals such asFaecalibacterium prausnitzii, Prevotella copriDSM 18205,Coprococcus catus,and overrepresentation ofClostridium difficileATCC 9689 = DSM 1296. Longitudinally followed-up ATB patients showed elimination ofAlkalihalobacilluswith treatment initiation, whereas harmful taxa such asStenotrophomonasandKlebsiella pneumoniaeappeared in treatment-completed subjects. Interestingly, the fecal metabolites also showed group-specific differences, clustering ATB patients away from the controls irrespective of the study sites. Consistently, fecal 2-piperidinone abundance was higher in ATB patients compared to healthy controls. The fecal metabolome of longitudinally followed-up ATB patients showed a gradual shift towards healthy during the course of treatment completion.

Conclusion

Gut microbial dysbiosis observed in tuberculosis patients at case presentation is partially resolved with 6 months of treatment completion and also reflected in their metabolite level. The observed microbial and metabolite imbalance in these ATB patients could explain disease pathology which needs further exploration to exploit their translational potential for therapeutics development.
High-fat diet-induced obesity increases susceptibility to endogenous and ethyl carbamate-induced somatic mutagenesis
Authors: Lichtler Rebecca , Wilson Mark J. , Wickliffe Jeffrey K.
Published: June 2023

Obesity and dietary fat consumption are associated with increased risk for certain cancers. We conducted a set of experiments designed to investigate both the inherent mutagenicity of high-fat diet (HFD) and the effect of HFD exposure on sensitivity to ethyl carbamate, a known mutagen. Greater body mass in females was associated with higher frequency of Pig-a mutant erythrocytes and HFD-induced obese female mice exhibited increased sensitivity to ethyl carbamate-induced mutagenesis compared to control mice. Together, these findings indicate that HFD exposure induces both endogenously generated changes related to mutagenesis and interacts with the mutagenic effects of ethyl carbamate.
Transgene-Free Ex Utero Derivation of A Human Post-Implantation Embryo Model Solely from Genetically Unmodified Naïve PSCs
Authors: Oldak Bernardo , Wildschutz Emilie , Bondarenko Vladyslav , Aguilera-Castrejon Alejandro , Zhao Cheng , Tarazi Shadi , Comar Mehmet-Yunus , Ashouokhi Shahd , Lokshtanov Dmitry , Roncato Francesco , Viukov Sergey , Ariel Eitan , Rose Max , Livnat Nir , Shani Tom , Joubran Carine , Cohen Roni , Addadi Yoseph , Kedmi Merav , Keren-Shaul Hadas , Petropoulos Sophie , Lanner Fredrik , Novershtern Noa , Hanna Jacob H.
Published: June 2023

Our ability to study early human post-implantation development remains highly limited due to the ethical and technical challenges associated with intrauterine development of the human embryo after implantation. Despite the great progress made on human gastruloids, axioloids and in vitro cultured blastoids, such elegant models do not constitute an integrated Stem cell-derived Embryo Models (SEMs) that includes all the key extra-embryonic tissues of the early post-implantation human conceptus (e.g., hypoblast, yolk-sac, trophoblasts, amnion, and extraembryonic mesoderm), and thus, do not recapitulate post-implantation epiblast development within the context of these extra-embryonic compartments. Mouse naïve pluripotent stem cells (PSCs) have recently been shown to give rise to embryonic and extra-embryonic stem cells capable of self-assembling into post-gastrulation mouse SEMs, while bypassing the blastocyst-like stage, and eventually initiating organogenesisex utero. Here, we implement critical adaptations to extend these finding to humans, while using only genetically unmodified human naïve PSCs, thus circumventing the need for ectopic expression of lineage promoting transgenes. Such integrated human SEMs recapitulate the organization of all known compartments of early post-implantation stage human embryos, including epiblast, hypoblast, extra-embryonic mesoderm, and trophoblast surrounding the latter layers. The organized human SEMs recapitulate key hallmarks of post-implantation stage embryogenesis up to 13-14 days post-fertilization (dpf, Carnegie stage 6a), such as bilaminar disk formation, epiblast lumenogenesis, amniogenesis, anterior-posterior symmetry breaking, PGC specification, primary and secondary yolk sac formation, and extra-embryonic mesoderm expansion that defines a chorionic cavity and a connective stalk. This new platform constitutes a tractable stem cell-based model for experimentally interrogating previously inaccessible windows of human peri- and early post-implantation development.
Cyclophosphamide induces the loss of taste bud innervation in mice
Authors: Wood Ryan M. , Vasquez Erin L. , Kuri Eduardo Gutierrez , Connelly Kevin , Humayun Saima , Macpherson Lindsey J.
Published: June 2023

Many common chemotherapeutics produce disruptions in the sense of taste which can lead to loss of appetite, nutritional imbalance, and reduced quality of life, especially if taste loss persists after treatment ends. Cyclophosphamide (CYP), an alkylating chemotherapeutic agent, affects taste sensitivity through its cytotoxic effects on mature taster receptor cells (TRCs) and on taste progenitor cell populations, retarding the capacity to replace TRCs. Mechanistic studies have focused primarily on taste cells, however, taste signaling requires communication between TRCs and the gustatory nerve fibers which innervate them. Here, we evaluate the effect of CYP on the peripheral gustatory nerve fibers that innervate the taste bud. Following histological analysis of tongue tissues, we find that CYP reduces innervation within the fungiform and circumvallate taste buds within 4-8 days after administration. To better understand the dynamics of the denervation process, we used 2-photon intravital imaging to observe the peripheral gustatory neuron arbors within individual fungiform taste buds before and after CYP treatment. We find that gustatory fibers retract from the taste bud proper but are maintained within the central papilla core. These data indicate that, in addition to TRCs, gustatory nerve fibers are also affected by CYP treatment. Because the connectivity between TRCs and gustatory neurons must be re-established for proper function, gustatory fibers should continue to be included in future studies to understand the mechanisms leading to chemotherapy-induced persistent taste loss.
Specific genomic targeting of the RNF12/RLIM E3 ubiquitin ligase selectively programmes developmental transcription
Authors: Espejo-Serrano Carmen , Aitken Catriona , Tan Beatrice F. , May Danielle G. , Chrisopulos Rachel J. , Roux Kyle J. , Mackintosh Samuel G. , Gribnau Joost , Bustos Francisco , Gontan Cristina , Findlay Greg M.
Published: June 2023

The E3 ubiquitin ligase RNF12/RLIM controls developmental gene expression and is mutated in the X-linked intellectual disability disorder Tonne-Kalscheuer syndrome (TOKAS). However, the mechanisms by which RNF12 E3 ubiquitin ligase activity controls specific gene expression signatures are not known. Here, we show that chromatin forms a regulatory platform for RNF12 substrate ubiquitylation and transcriptional patterning. RNF12 is recruited to specific genomic regions via a distinct consensus sequence motif, which enables targeting to key transcription factor substrate REX1. Mechanistically, RNF12 chromatin recruitment is largely REX1 independent, but is achieved via the conserved basic region (BR) adjacent to the RING domain. This region is critical for REX1 ubiquitylation on chromatin and downstream RNF12-dependent gene regulation. Furthermore, we find that RNF12 N-terminal sequences suppress chromatin recruitment and substrate ubiquitylation, uncovering a previously unappreciated autoinhibitory mechanism that governs genome targeting. Taken together, our results provide insight into mechanisms by which selective substrate targeting of an E3 ubiquitin ligase enables specific programming of gene expression.
Cell morphology best predicts tumorigenicity and metastasisin vivoacross multiple TNBC cell lines of different metastatic potential
Authors: Conner Sydney , Guarin Justinne R. , Le Thanh T. , Fatherree Jackson , Kelley Charlotte , Payne Samantha , Salhany Ken , McGinn Rachel , Henrich Emily , Yui Anna , Parker Savannah , Srinivasan Deepti , Bloomer Hanan , Borges Hannah , Oudin Madeleine J.
Published: June 2023

Background

Metastasis is the leading cause of death in breast cancer patients. For metastasis to occur, tumor cells must invade locally, intravasate, and colonize distant tissues and organs, all steps that require tumor cell migration. The majority of studies on invasion and metastasis rely on human breast cancer cell lines. While it is known that these cells have different properties and abilities for growth and metastasis, thein vitromorphological, proliferative, migratory, and invasive behavior of these cell lines and their correlation toin vivobehavior is poorly understood. Thus, we sought to classify each cell line as poorly or highly metastatic by characterizing tumor growth and metastasis in a murine model of six commonly used human triple-negative breast cancer xenografts, as well as determine which in vitro assays commonly used to study cell motility best predictin vivometastasis.

Methods

We evaluated the liver and lung metastasis of human TNBC cell lines MDA-MB-231, MDA-MB-468, BT549, Hs578T, BT20, and SUM159 in immunocompromised mice. We characterized each cell line’s cell morphology, proliferation, and motility in 2D and 3D to determine the variation in these parameters between cell lines.

Results

We identified MDA-MB-231, MDA-MB-468, and BT549 cells as highly tumorigenic and metastatic, Hs578T as poorly tumorigenic and metastatic, BT20 as intermediate tumorigenic with poor metastasis to the lungs but highly metastatic to the livers, and SUM159 as intermediate tumorigenic but poorly metastatic to the lungs and livers. We showed that metrics that characterize cell morphology are the most predictive of tumor growth and metastatic potential to the lungs and liver. Further, we found that no singlein vitromotility assay in 2D or 3D significantly correlated with metastasisin vivo.

Conclusions

Our results provide an important resource for the TNBC research community, identifying the metastatic potential of 6 commonly used cell lines. Our findings also support the use of cell morphological analysis to investigate the metastatic potential and emphasize the need for multiplein vitromotility metrics using multiple cell lines to represent the heterogeneity of metastasisin vivo.
Structural modeling of cytokine-receptor-JAK2 signaling complexes using AlphaFold Multimer
Authors: Pogozheva Irina D. , Cherepanov Stanislav , Park Sang-Jun , Raghavan Malini , Im Wonpil , Lomize Andrei L.
Published: June 2023

Homodimeric class 1 cytokine receptors include the erythropoietin (EPOR), thrombopoietin (TPOR), granulocyte colony-stimulating factor 3 (CSF3R), growth hormone (GHR), and prolactin receptors (PRLR). They are cell-surface single-pass transmembrane (TM) glycoproteins that regulate cell growth, proliferation, and differentiation and induce oncogenesis. An active TM signaling complex consists of a receptor homodimer, one or two ligands bound to the receptor extracellular domains and two molecules of Janus Kinase 2 (JAK2) constitutively associated with the receptor intracellular domains. Although crystal structures of soluble extracellular domains with ligands have been obtained for all the receptors except TPOR, little is known about the structure and dynamics of the complete TM complexes that activate the downstream JAK-STAT signaling pathway. Three-dimensional models of five human receptor complexes with cytokines and JAK2 were generated using AlphaFold Multimer. Given the large size of the complexes (from 3220 to 4074 residues), the modeling required a stepwise assembly from smaller parts with selection and validation of the models through comparisons with published experimental data. The modeling of active and inactive complexes supports a general activation mechanism that involves ligand binding to a monomeric receptor followed by receptor dimerization and rotational movement of the receptor TM α-helices causing proximity, dimerization, and activation of associated JAK2 subunits. The binding mode of two eltrombopag molecules to TM α-helices of the active TPOR dimer was proposed. The models also help elucidating the molecular basis of oncogenic mutations that may involve non-canonical activation route. Models equilibrated in explicit lipids of the plasma membrane are publicly available.
Second-order effects of chemotherapy pharmacodynamics and pharmacokinetics on tumor regression and cachexia
Authors: Pierik Luke , McDonald Patricia , Anderson Alexander R. A. , West Jeffrey
Published: June 2023

Drug dose response curves are ubiquitous in cancer biology, but these curves are often used to measure differential response in first-order effects: the effectiveness of increasing the cumulative dose delivered. In contrast, second-order effects (the variance of drug dose) are often ignored. Knowledge of second-order effects may improve the design of chemotherapy scheduling protocols, leading to improvements in tumor response without changing the total dose delivered. By considering treatment schedules with identical cumulative dose delivered, we optimize treatment by comparing high variance schedules (e.g. high dose, low dose) with low variance schedules (constant dose). We extend a previous framework used to quantify second-order effects, known as antifragility theory, to investigate the role of drug pharmacokinetics. Using a simple one-compartment model, we find that high variance schedules are effective for a wide range of cumulative dose values. Next, using a mouse-parameterized two-compartment model of 5-fluorouracil, we show that the optimal schedule depends on initial tumor volume. Finally, we illustrate the trade-off between tumor response and lean mass preservation. Mathematical modeling indicates that high variance dose schedules provide a potential path forward in mitigating the risk of chemotherapy-associated cachexia by preserving lean mass without sacrificing tumor response.
Characterization of cotton virus A, a novel and distinct member of the genusCaulimoviruswith endogenous viral elements inGossypiumspp
Authors: West-Ortiz Michael , Stuehler Douglas , Pollock Emma , Wilson Jennifer R. , Preising Stephanie , Larrea-Sarmiento Adriana , Alabi Olufemi , Fuchs Marc , Heck Michelle , Olmedo-Velarde Alejandro
Published: June 2023

The complete genome sequence of cotton virus A, a new virus infecting cotton (Gossypiumspp.), was determined using high-throughput sequencing, PCR and rolling circle amplification. The 7,482-nt genome is a circular dsDNA molecule that codes for six open reading frames similar to other members of theCaulimovirusgenus (familyCaulimoviridae) but presenting key genome organization differences. P3, P5 and P6 are presumed movement, coat, and reverse transcriptase proteins, respectively. P1, P2 and P4 showed no homology to virus proteins. Endogenous viral elements were found inG. hirsutumandG. tomentosum, but not inG. barbadense, G. arboreum,orG. herbaceum.
Evidence of Disrupted-in Schizophrenia 1 (DISC1) as an arsenic binding protein and implications regarding its role as a translational activator
Authors: Watanabe Muneaki , Khu Tung Mei , Warren Grant , Shin Juyoung , Stewart Charles E. , Roche Julien
Published: June 2023

Disrupted-in-schizophrenia-1 (DISC1) is a scaffold protein that plays a pivotal role in orchestrating signaling pathways involved in neurodevelopment, neural migration, and synaptogenesis. Among those, it has recently been reported that the role DISC1 in the Akt/mTOR pathway can shift from a global translational repressor to a translational activator in response to oxidative stress induced by arsenic. In this study we are providing evidence that DISC1 can directly bind arsenic via a C-terminal cysteine motif (C-X-C-X-C). A series of fluorescence-based binding assays were conducted with a truncated C-terminal domain construct of DISC1 and a of series of single, double, and triple cysteine mutants. We found that arsenous acid, a trivalent arsenic derivative, specifically binds to the C-terminal cysteine motif of DISC1 with low micromolar affinity. All three cysteines of the motif are required for high-affinity binding. Electron microscopy experiments combined with in silico structural predictions revealed that that the C-terminal of DISC1 forms an elongated tetrameric complex. The cysteine motif is consistently predicted to be located within a loop, fully exposed to solvent, providing a simple molecular framework to explain the high-affinity of DISC1 toward arsenous acid. This study sheds light on a novel functional facet of DISC1 as an arsenic binding protein and highlights its potential role as both a sensor and translational modulator within the Akt/mTOR pathway.
Cryo2StructData: A Large Labeled Cryo-EM Density Map Dataset for AI-based Modeling of Protein Structures
Authors: Giri Nabin , Wang Liguo , Cheng Jianlin
Published: June 2023

The advent of single-particle cryo-electron microscopy (cryo-EM) has brought forth a new era of structural biology, enabling the routine determination of large biological molecules and their complexes at atomic resolution. The high-resolution structures of biological macromolecules and their complexes significantly expedite biomedical research and drug discovery. However, automatically and accurately building atomic models from high-resolution cryo-EM density maps is still time-consuming and challenging when template-based models are unavailable. Artificial intelligence (AI) methods such as deep learning trained on limited amount of labeled cryo-EM density maps generate inaccurate atomic models. To address this issue, we created a dataset called Cryo2StructData consisting of 7,600 preprocessed cryo-EM density maps whose voxels are labelled according to their corresponding known atomic structures for training and testing AI methods to build atomic models from cryo-EM density maps. It is larger and of higher quality than any existing, publicly available dataset. We trained and tested deep learning models on Cryo2StructData to make sure it is ready for the large-scale development of AI methods for building atomic models from cryo-EM density maps.
Pan-genome analysis highlights the role of structural variation in the evolution and environmental adaptation ofAsian honeybees
Authors: Li Yancan , Yao Jun , Sang Huiling , Wang Quangui , Su Long , Zhao Xiaomeng , Xia Zhenyu , Wang Feiran , Wang Kai , Lou Delong , Wang Guizhi , Waterhouse Robert M. , Wang Huihua , Luo Shudong , Sun Cheng
Published: June 2023

The Asian honeybee,Apis cerana, is an ecologically and economically important pollinator. Mapping its genetic variation is key to understanding population-level health, histories, and potential capacities to respond to environmental changes. However, most efforts to date were focused on single nucleotide polymorphisms (SNPs) based on a single reference genome, thereby ignoring larger-scale genomic variation. We employed long-read sequencing technologies to generate a chromosome-scale reference genome for the ancestral group ofA. cerana. Integrating this with 525 resequencing datasets, we constructed the first pan-genome ofA. cerana, encompassing almost the entire gene content. We found that 31.32% of genes in the pan-genome were variably present across populations, providing a broad gene pool for environmental adaptation. We identified and characterized structural variations (SVs) and found that they were not closely linked with SNP distributions, however, the formation of SVs was closely associated with transposable elements. Furthermore, phylogenetic analysis using SVs revealed a novelA. ceranaecological group not recoverable from the SNP data. Performing environmental association analysis identified a total of 44 SVs likely to be associated with environmental adaptation. Verification and analysis of one of these, a 330 bp deletion in theAtpalphagene, indicated that this SV may promote the cold adaptation ofA. ceranaby altering gene expression. Taken together, our study demonstrates the feasibility and utility of applying pan-genome approaches to map and explore genetic feature variations of honeybee populations, and in particular to examine the role of SVs in the evolution and environmental adaptation ofA. cerana.
Remodeling of lipid-foam prototissues by network-wide tension fluctuations induced by active particles
Authors: Gu Andre A. , Uçar Mehmet Can , Tran Peter , Prindle Arthur , Kamat Neha P. , Steinkühler Jan
Published: June 2023

Recent advances in the field of bottom-up synthetic biology have led to the development of synthetic cells that mimic some features of real cells, such as division, protein synthesis, or DNA replication. Larger assemblies of synthetic cells may be used to form prototissues. However, existing prototissues are limited by their relatively small lateral dimensions or their lack of remodeling ability. In this study, we introduce a lipid-based tissue mimetic that can be easily prepared and functionalized, consisting of a millimeter-sized “lipid-foam” with individual micrometer-sized compartments bound by lipid bilayers. We characterize the structural and mechanical properties of the lipid-foam tissue mimetic. We demonstrate self-healing capabilities enabled by the fluidity of the lipid bilayers. Upon inclusion of bacteria in the tissue compartments, we observe that the tissue mimetic exhibits network-wide tension fluctuations driven by membrane tension generation by the swimming bacteria. Active tension fluctuations facilitate the fluidization and reorganization of the lipid-foam tissue mimetic, providing a versatile platform for understanding and mimicking biological tissues.
HCCDB v2.0: Decompose the Expression Variations by Single-cell RNA-seq and Spatial Transcriptomics in HCC
Authors: Jiang Ziming , Wu Yanhong , Miao Yuxin , Deng Kaige , Yang Fan , Xu Shuhuan , Wang Yupeng , You Renke , Zhang Lei , Fan Yuhan , Guo Wenbo , Lian Qiuyu , Chen Lei , Zhang Xuegong , Zheng Yongchang , Gu Jin
Published: June 2023

Large-scale transcriptomic data are crucial for understanding the molecular features of hepatocellular carcinoma (HCC). By integrating 15 transcriptomic datasets of HCC clinical samples, the first version of HCCDB was released in 2018. The meta-analysis of differentially expressed genes and prognosis-related genes across multiple datasets provides a systematic view of the altered biological processes and the inter-patient heterogeneities of HCC with high reproducibility and robustness. After four years, the database needs to integrate recently published datasets. Furthermore, the latest single-cell and spatial transcriptomics provided a great opportunity to decipher the complex gene expression variations at the cellular level with spatial architecture. Here, we present HCCDB v2.0, an updated version that combines bulk, single-cell, and spatial transcriptomic data of HCC clinical samples. It dramatically expands the bulk sample size, adding 1656 new samples of 11 datasets to the existing 3917 samples, thereby enhancing the reliability of transcriptomic meta-analysis. A total of 182,832 cells and 69,352 spatial spots are added to the single-cell and spatial transcriptomics sections, respectively. A novel single-cell level and 2-dimension (sc-2D) metric was proposed to summarize the cell type-specific and dysregulated gene expression patterns. Results are all graphically visualized in our online portal, allowing users to easily retrieve data through a user-friendly interface and navigate between different views. With extensive clinical phenotypes and transcriptomic data in the database, we show two applications for identifying prognosis-associated cells and tumor microenvironment. HCCDB v2.0 is available athttp://lifeome.net/database/hccdb2.
Global transcriptome analysis revealsSalmonellaTyphimurium employs the nitrate-dependent anaerobic pathway to combat bile stress
Authors: Singh Madhulika , Chandra Deepti , Jagdish Sirisha , Nandi Dipankar
Published: June 2023

SalmonellaTyphimurium is an enteric pathogen that is highly tolerant to bile. Next-generation mRNA sequencing was performed to analyse the stress and adaptive responses ofS. Typhimurium to bile. We identified the cellular pathways affected during bile stress in wild type (WT) and a mutant lackingcspE (ΔcspE), which plays an essential role in protection from bile stress. We observed transcriptional upregulation of several genes involved in nitrate metabolism, in response to bile stress. These genes were also differentially expressed between the bile-resilient WT and the bile-sensitive ΔcspE strain. To understand the role of nitrate metabolism in bile stress response, we generated a strain lackingfnr(Δfnr), which is the global regulator of nitrate metabolism inS. Typhimurium.fnrwas highly induced in the bile treated WT strain but not in the ΔcspE strain. Notably, the Δfnrstrain was susceptible to bile-mediated killing. Our studies revealed a new role forfnrin mediating the bile stress response. In addition, a strain lackingarcA (ΔarcA), a two-component system response regulator involved in anaerobic metabolism, also showed a marked reduction in growth in presence of bile. This corroborated the significance of anaerobic metabolism inS. Typhimurium bile tolerance. Importantly, overexpression offnrandarcA lowered reactive oxygen species and significantly enhanced the survival of the bile-sensitive ΔcspE strain. We also observed thatS. Typhimurium pre-treated with nitrate displayed better growth in the presence of bile. Together, these results demonstrate that nitrate-dependent anaerobic metabolism promotes adaptation ofS. Typhimurium to bile.

Importance

SalmonellaTyphimurium, as an enteric pathogen, manifests an extreme example of bile tolerance. This study describes the diverse metabolic changes at the level of transcriptome inS. Typhimurium exposed to bile. We identified the differential expression of several genes involved in anaerobic metabolism between bile-tolerant WT and bile-sensitive ΔcspE strains. Two major regulators of anaerobic metabolism,fnrandarcA, support the growth ofS. Typhimurium in bile. Our results highlight that, in presence of bile,S. Typhimurium activates genes involved in anaerobic metabolism, specifically nitrate metabolism, that improves survival of bacteria during bile stress.
Targeting BTN2A1 enhances Vγ9Vδ2 T cell effector functions and triggers tumor cells pyroptosis
Authors: le Floch Anne Charlotte , Imbert Caroline , Boucherit Nicolas , Gorvel Laurent , Fattori Stéphane , Orlanducci Florence , Le Roy Aude , Archetti Lorenzo , Crescence Lydie , Panicot-Dubois Laurence , Dubois Christophe , Vey Norbert , Briantais Antoine , Anastasio Amandine , Cano Carla E. , Guittard Geoffrey , Frechin Mathieu , Olive Daniel
Published: June 2023

Vγ9Vδ2 T cells are potent but elusive cytotoxic effectors. Means to stimulate their function could lead to powerful new cancer immunotherapies. BTN2A1, a surface protein has recently been shown to bind the Vγ9 chain of the γδ TCR but its precise role in modulating Vγ9Vδ2 T cells functions remains unknown.

Here we show that 107G3B5, a monoclonal anti-BTN2A1 agonist antibody, significantly enhances Vγ9Vδ2 T cell functions against hematological or solid cell lines and against primary cells from adult acute lymphoblastic leukemia patients. New computer vision strategies applied to holotomographic microscopy videos show that 107G3B5 enhances the interaction between Vγ9Vδ2 T cells and target cells in a quantitative and qualitative manner. In addition, we provide evidence that Vγ9Vδ2 T cells activated by 107G3B5 induce caspase 3/7 activation in tumor cells, thereby triggering their death by pyroptosis.

We thus demonstrate that targeting BTN2A1 with 107G3B5 enhances the Vγ9Vδ2 T cell antitumor response by triggering the pyroptosis-induced immunogenic cell death.