Open Access Publications

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Open access publications by faculty, postdocs, and graduate students in the Department of Biological Sciences

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Shared genetic risk between major orofacial cleft phenotypes in an African population
(Genetic Epidemiology, 2024-04-18) Alade, Azeez; Peter, Tabitha; Busch, Tamara; Awotoye, Waheed; Anand, Deepti; Abimbola, Oladayo; Aladenika, Emmanuel; Olujitan, Mojisola; Rysavy, Oscar; Nguyen, Phuong Fawng; Naicker, Thirona; Mossey, Peter A.; Gowans, Lord J. J.; Eshete, Mekonen A.; Adeyemo, Wasiu L.; Zeng, Erliang; Van Otterloo, Eric; O'Rorke, Michael; Adeyemo, Adebowale; Murray, Jeffrey C.; Lachke, Salil A.; Romitti, Paul A.; Butali, Azeez
Nonsyndromic orofacial clefts (NSOFCs) represent a large proportion (70%–80%) of all OFCs. They can be broadly categorized into nonsyndromic cleft lip with or without cleft palate (NSCL/P) and nonsyndromic cleft palate only (NSCPO). Although NSCL/P and NSCPO are considered etiologically distinct, recent evidence suggests the presence of shared genetic risks. Thus, we investigated the genetic overlap between NSCL/P and NSCPO using African genome-wide association study (GWAS) data on NSOFCs. These data consist of 814 NSCL/P, 205 NSCPO cases, and 2159 unrelated controls. We generated common single-nucleotide variants (SNVs) association summary statistics separately for each phenotype (NSCL/P and NSCPO) under an additive genetic model. Subsequently, we employed the pleiotropic analysis under the composite null (PLACO) method to test for genetic overlap. Our analysis identified two loci with genome-wide significance (rs181737795 [p = 2.58E−08] and rs2221169 [p = 4.5E−08]) and one locus with marginal significance (rs187523265 [p = 5.22E−08]). Using mouse transcriptomics data and information from genetic phenotype databases, we identified MDN1, MAP3k7, KMT2A, ARCN1, and VADC2 as top candidate genes for the associated SNVs. These findings enhance our understanding of genetic variants associated with NSOFCs and identify potential candidate genes for further exploration.
Modeling Cataract Surgery in Mice
(Journal of Visualized Experiments, 2023-12-01) O'Neill, Leah M.; Wang, Yan; Duncan, Melinda K.
Cataract surgery (CS) is an effective treatment for cataracts, a major cause of visual disability worldwide. However, CS leads to ocular inflammation, and in the long term, it can result in posterior capsular opacification (PCO) and/or lens dislocation driven by the post-surgical overgrowth of lens epithelial cells (LECs) and their conversion to myofibroblasts and/or aberrant fiber cells. However, the molecular mechanisms by which CS results in inflammation and PCO are still obscure because most in vitro models do not recapitulate the wound healing response of LECs seen in vivo, while traditional animal models of cataract surgery, such as rabbits, do not allow the genetic manipulation of gene expression to test mechanisms. Recently, our laboratory and others have successfully used genetically modified mice to study the molecular mechanisms that drive the induction of proinflammatory signaling and LEC epithelial to mesenchymal transition, leading to new insight into PCO pathogenesis. Here, we report the established protocol for modeling cataract surgery in mice, which allows for robust transcriptional profiling of the response of LECs to lens fiber cell removal via RNAseq, the evaluation of protein expression by semi-quantitative immunofluorescence, and the use of modern mouse genetics tools to test the function of genes that are hypothesized to participate in the pathogenesis of acute sequelae like inflammation as well as the later conversion of LECs to myofibroblasts and/or aberrant lens fiber cells.
Recessive TMOD1 mutation causes childhood cardiomyopathy
(Communications Biology, 2024-01-02) Vasilescu, Catalina; Colpan, Mert; Ojala, Tiina H.; Manninen, Tuula; Mutka, Aino; Ylänen, Kaisa; Rahkonen, Otto; Poutanen, Tuija; Martelius, Laura; Kumari, Reena; Hinterding, Helena; Brilhante, Virginia; Ojanen, Simo; Lappalainen, Pekka; Koskenvuo, Juha; Carroll, Christopher J.; Fowler, Velia M.; Gregorio, Carol C.; Suomalainen, Anu
Familial cardiomyopathy in pediatric stages is a poorly understood presentation of heart disease in children that is attributed to pathogenic mutations. Through exome sequencing, we report a homozygous variant in tropomodulin 1 (TMOD1; c.565C>T, p.R189W) in three individuals from two unrelated families with childhood-onset dilated and restrictive cardiomyopathy. To decipher the mechanism of pathogenicity of the R189W mutation in TMOD1, we utilized a wide array of methods, including protein analyses, biochemistry and cultured cardiomyocytes. Structural modeling revealed potential defects in the local folding of TMOD1R189W and its affinity for actin. Cardiomyocytes expressing GFP-TMOD1R189W demonstrated longer thin filaments than GFP-TMOD1wt-expressing cells, resulting in compromised filament length regulation. Furthermore, TMOD1R189W showed weakened activity in capping actin filament pointed ends, providing direct evidence for the variant’s effect on actin filament length regulation. Our data indicate that the p.R189W variant in TMOD1 has altered biochemical properties and reveals a unique mechanism for childhood-onset cardiomyopathy.
Structure-function analysis of the heme-binding WWD domain in the bacterial holocytochrome c synthase, CcmFH
(mBio, 2023-11-06) Grunow, Amber L.; Carroll, Susan C.; Kreiman, Alicia N.; Sutherland, Molly C.
Heme trafficking is a fundamental biological process, yet its direct study has been hampered due to heme’s tight intracellular regulation, heme cytotoxicity, and the transient nature of trafficking. The bacterial System I and System II cytochrome c biogenesis pathways are developing into models to interrogate heme trafficking mechanisms, as they function to transport heme from inside to outside the cell for attachment to apocytochrome c. Cytochromes c require heme for folding and to function in the context of electron transport chains for critical cellular functions, such as respiration. We focus on System I, comprised of eight membrane proteins, CcmABCDEFGH, proposed to function in two steps: CcmABCD mediates the transfer of heme and attachment to CcmE. HoloCcmE chaperones heme to CcmFH for attachment to apocytochrome c. While CcmFH is known to be the holocytochrome c synthase, the mechanism of heme interaction and positioning for attachment to apocytochrome c remains to be elucidated. A comprehensive structure-function analysis of the conserved WWD domain in CcmF was undertaken utilizing alanine-scanning and cysteine-scanning, revealing residues critical for CcmF’s synthase function and residues required for interaction with the 2- and 4-vinyls of heme. This analysis demonstrates for the first time that the CcmF WWD domain directly interacts with heme and that heme interactions within this domain are required for attachment to apocytochrome c. This in-depth interrogation of heme binding now allows for comparison across cytochrome c biogenesis proteins CcmF, CcmC, and CcsBA, revealing common mechanisms of heme interaction in these heme trafficking pathways. IMPORTANCE Heme is an essential co-factor for proteins involved with critical cellular functions, such as energy production and oxygen transport. Thus, understanding how heme interacts with proteins and is moved through cells is a fundamental biological question. This work studies the System I cytochrome c biogenesis pathway, which in some species (including Escherichia coli) is composed of eight integral membrane or membrane-associated proteins called CcmA-H that are proposed to function in two steps to transport and attach heme to apocytochrome c. Cytochrome c requires this heme attachment to function in electron transport chains to generate cellular energy. A conserved WWD heme-handling domain in CcmFH is analyzed and residues critical for heme interaction and holocytochrome c synthase activity are identified. CcmFH is the third member of the WWD domain-containing heme-handling protein family to undergo a comprehensive structure-function analysis, allowing for comparison of heme interaction across this protein family.
Fascination with Fluctuation: Luria and Delbrück’s Legacy
(Axioms, 2023-03-07) Robeva, Raina S.; Jungck, John R.
While Luria and Delbrück’s seminal work has found its way to some college biology textbooks, it is now largely absent from those in mathematics. This is a significant omission, and we consider it a missed opportunity to present a celebrated conceptual model that provides an authentic and, in many ways, intuitive example of the quantifiable nature of stochasticity. We argue that it is an important topic that could enrich the educational literature in mathematics, from the introductory to advanced levels, opening many doors to undergraduate research. The paper has two main parts. First, we present in detail the mathematical theory behind the Luria–Delbrück model and make suggestions for further readings from the literature. We also give ideas for inclusion in various mathematics courses and for projects that can be used in regular courses, independent projects, or as starting points for student research. Second, we briefly review available hands-on activities as pedagogical ways to facilitate problem posing, problem-based learning, and investigative case-based learning and to expose students to experiments leading to Poisson distributions. These help students with even limited mathematics backgrounds understand the significance of Luria–Delbrück’s work for determining mutation rates and its impact on many fields, including cancer chemotherapy, antibiotic resistance, radiation, and environmental screening for mutagens and teratogens.
Dynamic elementomics of single-cell ICP–MS-derived signals in normal and calcium pump PMCA4-deficient mouse epididymal sperm during capacitation
(Metallomics, 2023-10-16) Zhang, Bao Li; Zhang, Ze Peng; Shi, Su Meng; Shi, Hui Juan; DeLeon, Patricia A.; Shum, Winnie
Currently, clinical analysis of male infertility mainly relies on parameters of semen and sperm cells. However, the high diagnostic failure rates indicate that the current assessment methods are not sufficient and a new approach to evaluating sperm function still needs to be developed. Here we explored the feasibility of single-cell inductively coupled plasma mass spectrometry (sc-ICP–MS)-derived profiles to determine the elemental characteristics in viable capacitated sperm under normal and deficient conditions. To validate the measurements, we used male sterile Pmca4-knockout (KO) mice with impaired calcium clearance, known to be dysregulated due to loss of calcium efflux capacity during sperm capacitation. Consistently, we observed significantly increased calcium intensities in Pmca4-KO sperm upon capacitation stimulation compared with control sperm from the caudaepididymides of wild-type control (WT) mice. More importantly, we explored that the characteristic signatures of calcium intensities in individual spikes derived from sc-ICP–MS was consistent with the dynamics of relative calcium levels in single sperm reported in the literature. Prominent alterations were also observed in the dynamic signatures of sc-ICP–MS-derived profiles of essential elements, particularly the redox-labile elements including copper, iron, manganese, selenium, and zinc in Pmca4-KO sperm compared to WT controls. Therefore, our study demonstrates that elementomics of sc-ICP–MS-derived signals can reveal ionic dysregulation in plasma membrane Ca2+-ATPase isoform 4 protein deficient sperm, and that sc-ICP–MS assay can be applied for functional analysis of viable sperm in functional activities, such as capacitation stimulation. We propose that cell elementomics can be used as an alternative approach to assessing sperm quality and male fertility at the single-cell level. Graphical Abstract available at: https://doi.org/10.1093/mtomcs/mfad059
Adseverin, an actin-binding protein, modulates hypertrophic chondrocyte differentiation and osteoarthritis progression
(Science Advances, 2023-08-04) Chan, Byron; Glogauer, Michael; Wang, Yongqiang; Wrana, Jeffrey; Chan, Kin; Beier, Frank; Bali, Supinder; Hinz, Boris; Parreno, Justin; Ashraf, Sajjad; Kandel, Rita
In osteoarthritis (OA), a disease characterized by progressive articular cartilage degradation and calcification, the articular chondrocyte phenotype changes and this correlates with actin cytoskeleton alterations suggesting that it regulates gene expression essential for proper phenotype. This study reports that OA is associated with the loss of adseverin, an actin capping and severing protein. Adseverin deletion (Adseverin−/−) in mice compromised articular chondrocyte function, by reducing F-actin and aggrecan expression and increasing apoptosis, Indian hedgehog, Runx2, MMP13, and collagen type X expression, and cell proliferation. This led to stiffer cartilage and decreased hyaline and increased calcified cartilage thickness. Together, these changes predisposed the articular cartilage to enhanced OA severity in Adseverin−/− mice who underwent surgical induction of OA. Adseverin−/− chondrocyte RNA sequencing and in vitro studies together suggests that adseverin modulates cell viability and prevents mineralization. Thus, adseverin maintains articular chondrocyte phenotype and cartilage tissue homeostasis by preventing progression to hypertrophic differentiation in vivo. Adseverin may be chondroprotective and a potential therapeutic target.
Association of Behavioral and Clinical Risk Factors With Cataract: A Two-Sample Mendelian Randomization Study
(Investigative Ophthalmology & Visual Science, 2023-07) Jiang, Chen; Melles, Ronald B.; Sangani, Poorab; Hoffmann, Thomas J.; Hysi, Pirro G.; Glymour, M. Maria; Jorgenson, Eric; Lachke, Salil A.; Choquet, Hélène
Purpose: To investigate the association of genetically determined primary open-angle glaucoma (POAG), myopic refractive error (RE), type 2 diabetes (T2D), blood pressure (BP), body mass index (BMI), cigarette smoking, and alcohol consumption with the risk of age-related cataract. Methods: To assess potential causal effects of clinical or behavioral factors on cataract risk, we conducted two-sample Mendelian randomization analyses. Genetic instruments, based on common genetic variants associated with risk factors at genome-wide significance (P < 5 × 10−8), were derived from published genome-wide association studies (GWAS). For age-related cataract, we used GWAS summary statistics from our previous GWAS conducted in the Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort (28,092 cataract cases and 50,487 controls; all non-Hispanic whites) or in the UK Biobank (31,852 cataract cases and 428,084 controls; all European-descent individuals). We used the inverse-variance weighted (IVW) method as our primary source of Mendelian randomization estimates and conducted common sensitivity analyses. Results: We found that genetically determined POAG and mean spherical equivalent RE were significantly associated with cataract risk (IVW model: odds ratio [OR] = 1.04; 95% confidence interval [CI], 1.01–1.08; P = 0.018; per diopter more hyperopic: OR = 0.92; 95% CI, 0.89–0.93; P = 6.51 × 10−13, respectively). In contrast, genetically determined T2D, BP, BMI, cigarette smoking, or alcohol consumption were not associated with cataract risk (P > 0.05). Conclusions: Our results provide evidence that genetic risks for POAG and myopia may be causal risk factors for age-related cataract. These results are consistent with previous observational studies reporting associations of myopia with cataract risk. This information may support population cataract risk stratification and screening strategies.
Matrix Degradability Contributes to the Development of Salivary Gland Progenitor Cells with Secretory Functions
(ACS Applied Materials and Interfaces, 2023-07-12) Metkari, Apoorva S.; Fowler, Eric W.; Witt, Robert L.; Jia, Xinqiao
Synthetic matrices that are cytocompatible, cell adhesive, and cell responsive are needed for the engineering of implantable, secretory salivary gland constructs to treat radiation induced xerostomia or dry mouth. Here, taking advantage of the bioorthogonality of the Michael-type addition reaction, hydrogels with comparable stiffness but varying degrees of degradability (100% degradable, 100DEG; 50% degradable, 50DEG; and nondegradable, 0DEG) by cell-secreted matrix metalloproteases (MMPs) were synthesized using thiolated HA (HA-SH), maleimide (MI)-conjugated integrin-binding peptide (RGD-MI), and MI-functionalized peptide cross-linkers that are protease degradable (GIW-bisMI) or nondegradable (GIQ-bisMI). Organized multicellular structures developed readily in all hydrogels from dispersed primary human salivary gland stem cells (hS/PCs). As the matrix became progressively degradable, cells proliferated more readily, and the multicellular structures became larger, less spherical, and more lobular. Immunocytochemical analysis showed positive staining for stem/progenitor cell markers CD44 and keratin 5 (K5) in all three types of cultures and positive staining for the acinar marker α-amylase under 50DEG and 100DEG conditions. Quantitatively at the mRNA level, the expression levels of key stem/progenitor markers KIT, KRT5, and ETV4/5 were significantly increased in the degradable gels as compared to the nondegradable counterparts. Western blot analyses revealed that imparting matrix degradation led to >3.8-fold increase in KIT expression by day 15. The MMP-degradable hydrogels also promoted the development of a secretary phenotype, as evidenced by the upregulation of acinar markers α-amylase (AMY), aquaporin-5 (AQP5), and sodium-potassium chloride cotransporter 1 (SLC12A2). Collectively, we show that cell-mediated matrix remodeling is necessary for the development of regenerative pro-acinar progenitor cells from hS/PCs.
A Review of IsomiRs in Colorectal Cancer
(Non-Coding RNA, 2023-06-07) Lausten, Molly A.; Boman, Bruce M.
As advancements in sequencing technology rapidly continue to develop, a new classification of microRNAs has occurred with the discovery of isomiRs, which are relatively common microRNAs with sequence variations compared to their established template microRNAs. This review article seeks to compile all known information about isomiRs in colorectal cancer (CRC), which has not, to our knowledge, been gathered previously to any great extent. A brief overview is given of the history of microRNAs, their implications in colon cancer, the canonical pathway of biogenesis and isomiR classification. This is followed by a comprehensive review of the literature that is available on microRNA isoforms in CRC. The information on isomiRs presented herein shows that isomiRs hold great promise for translation into new diagnostics and therapeutics in clinical medicine.
NhaR, LeuO, and H-NS Are Part of an Expanded Regulatory Network for Ectoine Biosynthesis Expression
(Applied and Environmental Microbiology, 2023-06-06) Boas Lichty, Katherine E. Boas; Gregory, Gwendolyn J.; Boyd, E. Fidelma
Bacteria accumulate compatible solutes to maintain cellular turgor pressure when exposed to high salinity. In the marine halophile Vibrio parahaemolyticus, the compatible solute ectoine is biosynthesized de novo, which is energetically more costly than uptake; therefore, tight regulation is required. To uncover novel regulators of the ectoine biosynthesis ectABC-asp_ect operon, a DNA affinity pulldown of proteins interacting with the ectABC-asp_ect regulatory region was performed. Mass spectrometry analysis identified, among others, 3 regulators: LeuO, NhaR, and the nucleoid associated protein H-NS. In-frame non-polar deletions were made for each gene and PectA-gfp promoter reporter assays were performed in exponential and stationary phase cells. PectA-gfp expression was significantly repressed in the ΔleuO mutant and significantly induced in the ΔnhaR mutant compared to wild type, suggesting positive and negative regulation, respectively. In the Δhns mutant, PectA-gfp showed increased expression in exponential phase cells, but no change compared to wild type in stationary phase cells. To examine whether H-NS interacts with LeuO or NhaR at the ectoine regulatory region, double deletion mutants were created. In a ΔleuO/Δhns mutant, PectA-gfp showed reduced expression, but significantly more than ΔleuO, suggesting H-NS and LeuO interact to regulate ectoine expression. However, ΔnhaR/Δhns had no additional effect compared to ΔnhaR, suggesting NhaR regulation is independent of H-NS. To examine leuO regulation further, a PleuO-gfp reporter analysis was examined that showed significantly increased expression in the ΔleuO, Δhns, and ΔleuO/Δhns mutants compared to wild type, indicating both are repressors. Growth pattern analysis of the mutants in M9G 6%NaCl showed growth defects compared to wild type, indicating that these regulators play an important physiological role in salinity stress tolerance outside of regulating ectoine biosynthesis gene expression. IMPORTANCE Ectoine is a commercially used compatible solute that acts as a biomolecule stabilizer because of its additional role as a chemical chaperone. A better understanding of how the ectoine biosynthetic pathway is regulated in natural bacterial producers can be used to increase efficient industrial production. The de novo biosynthesis of ectoine is essential for bacteria to survive osmotic stress when exogenous compatible solutes are absent. This study identified LeuO as a positive regulator and NhaR as a negative regulator of ectoine biosynthesis and showed that, similar to enteric species, LeuO is an anti-silencer of H-NS. In addition, defects in growth in high salinity among all the mutants suggest that these regulators play a broader role in the osmotic stress response beyond ectoine biosynthesis regulation.
Nonmuscle Myosin IIA Regulates the Precise Alignment of Hexagonal Eye Lens Epithelial Cells During Fiber Cell Formation and Differentiation
(Investigative Ophthalmology & Visual Science, 2023-04-18) Islam, Sadia T.; Cheng, Catherine; Parreno, Justin; Fowler, Velia M.
Purpose: Epithelial cells in the equatorial region of the ocular lens undergo a remarkable transition from randomly packed cells into precisely aligned and hexagon-shaped cells organized into meridional rows. We investigated the function of nonmuscle myosin IIA (encoded by Myh9) in regulating equatorial epithelial cell alignment to form meridional rows during secondary fiber cell morphogenesis. Methods: We used genetic knock-in mice to study a common human Myh9 mutation, E1841K, in the rod domain. The E1841K mutation disrupts bipolar filament assembly. Lens shape, clarity, and stiffness were evaluated, and Western blots were used to determine the level of normal and mutant myosins. Cryosections and lens whole mounts were stained and imaged by confocal microscopy to investigate cell shape and organization. Results: We observed no obvious changes in lens size, shape, and biomechanical properties (stiffness and resilience) between the control and nonmuscle myosin IIA–E1841K mutant mice at 2 months of age. Surprisingly, we found misalignment and disorder of fiber cells in heterozygous and homozygous mutant lenses. Further analysis revealed misshapen equatorial epithelial cells that cause disorientation of the meridional rows before fiber cell differentiation in homozygous mutant lenses. Conclusions: Our data indicate that nonmuscle myosin IIA bipolar filament assembly is required for the precise alignment of the meridional rows at the lens equator and that the organization of lens fiber cells depends on the proper patterning of meridional row epithelial cells. These data also suggest that lens fiber cell organization and a hexagonal shape are not required for normal lens size, shape transparency, or biomechanical properties.
Innate immune pathway modulator screen identifies STING pathway activation as a strategy to inhibit multiple families of arbo and respiratory viruses
(Cell Reports Medicine, 2023-05-16) Garcia, Gustavo Jr.; Irudayam, Joseph Ignatius; Jeyachandran, Arjit Vijey; Dubey, Swati; Chang, Christina; Castillo Cario, Sebastian; Price, Nate; Arumugam, Sathya; Marquez, Angelica L.; Shah, Aayushi; Fanaei, Amir; Chakravarty, Nikhil; Joshi, Shantanu; Sinha, Sanjeev; French, Samuel W.; Parcells, Mark S.; Ramaiah, Arunachalam; Arumugaswami, Vaithilingaraja
Highlights: • Screen identifies innate immune agonists blocking multiple families of RNA viruses • Dectin-1 and cGAS-STING pathway agonists exhibit broader antiviral activity • STING activator cAIMP blocks ZIKV, WNV, CHIKV, EV-D68, and SARS-CoV-2 infections • cAIMP provides protection against CHIKV-mediated chronic arthritis in mouse model Summary: RNA viruses continue to remain a threat for potential pandemics due to their rapid evolution. Potentiating host antiviral pathways to prevent or limit viral infections is a promising strategy. Thus, by testing a library of innate immune agonists targeting pathogen recognition receptors, we observe that Toll-like receptor 3 (TLR3), stimulator of interferon genes (STING), TLR8, and Dectin-1 ligands inhibit arboviruses, Chikungunya virus (CHIKV), West Nile virus, and Zika virus to varying degrees. STING agonists (cAIMP, diABZI, and 2′,3′-cGAMP) and Dectin-1 agonist scleroglucan demonstrate the most potent, broad-spectrum antiviral function. Furthermore, STING agonists inhibit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and enterovirus-D68 (EV-D68) infection in cardiomyocytes. Transcriptome analysis reveals that cAIMP treatment rescue cells from CHIKV-induced dysregulation of cell repair, immune, and metabolic pathways. In addition, cAIMP provides protection against CHIKV in a chronic CHIKV-arthritis mouse model. Our study describes innate immune signaling circuits crucial for RNA virus replication and identifies broad-spectrum antivirals effective against multiple families of pandemic potential RNA viruses. Graphical abstract available at: https://doi.org/10.1016/j.xcrm.2023.101024
Clinicians’ Perspectives on Proactive Patient Safety Behaviors in the Perioperative Environment
(Jama Network Open, 2023-04-11) Duffy, Caoimhe; Menon, Neil; Horak, David; Bass, Geoffrey D.; Talwar, Ruchika; Lorenzi, Cara; Vo, Christina Taing; Chiang, Chienhui; Ziemba, Justin B.
Importance The perioperative environment is hazardous, but patients remain safe with a successful outcome during their care due to staff adaptability and resiliency. The behaviors that support this adaptability and resilience have yet to be defined or analyzed. One Safe Act (OSA), a tool and activity developed to capture self-reported proactive safety behaviors that staff use in their daily practice to promote individual and team-based safe patient care, may allow for improved definition and analysis of these behaviors. Objective To thematically analyze staff behaviors using OSA to understand what may serve as the basis for proactive safety in the perioperative environment. Design, Setting, and Participants This qualitative thematic analysis included a convenience sample of perioperative staff at a single-center, tertiary care academic medical center who participated in an OSA activity during a 6-month period in 2021. All perioperative staff were eligible for inclusion. A combined deductive approach, based on a human factor analysis and classification framework, as well as an inductive approach was used to develop themes and analyze the self-reported staff safety behaviors. Exposures Those selected to participate were asked to join an OSA activity, which was conducted in-person by a facilitator. Participants were to self-reflect about their OSA (proactive safety behavior) and record their experience as free text in an online survey tool. Main Outcome and Measures The primary outcome was the development and application of a set of themes to describe proactive safety behaviors in the perioperative environment. Results A total of 140 participants (33 nurses [23.6%] and 18 trainee physicians [12.9%]), which represented 21.3% of the 657 total perioperative department full-time staff, described 147 behaviors. A total of 8 non–mutually exclusive themes emerged with the following categories and frequency of behaviors: (1) routine-based adaptations (46 responses [31%]); (2) resource availability and assessment adaptations (31 responses [21%]); (3) communication and coordination adaptation (23 responses [16%]); (4) environmental ergonomics adaptation (17 responses [12%]); (5) situational awareness adaptation (12 responses [8%]); (6) personal or team readiness adaptation (8 responses [5%]); (7) education adaptation (5 responses [3%]); and (8) social awareness adaptation (5 responses [3%]). Conclusions and Relevance The OSA activity elicited and captured proactive safety behaviors performed by staff. A set of behavioral themes were identified that may serve as the basis for individual practices of resilience and adaptability that promote patient safety.
The actin bundling protein Fascin is important for proper early development in Strongylocentrotus purpuratus embryos
(microPublication Biology, 2023-03-21) Testa, Michael D.; Remsburg, Carolyn M.; Song, Jia L.
Fascin is a conserved protein that has been shown to modulate the cytoskeleton. Its role in early development remains unclear. After fertilization, embryos undergo rapid cell divisions, requiring the precise regulation of cytoskeleton to segregate chromosomes. Results indicate that Fascin is in the cell cortex, enriched in the perinuclear region of non-dividing blastomeres and on the mitotic spindle of dividing blastomeres of the early embryo. Loss-of-function of Fascin leads to a significant developmental delay or arrest, indicating that Fascin is important for proper early embryonic development.
The v8-10 variant isoform of CD44 is selectively expressed in the normal human colonic stem cell niche and frequently is overexpressed in colon carcinomas during tumor development
(Cancer Biology & Therapy, 2023-04-02) Boman, Bruce M.; Viswanathan, Vignesh; Faceya, Caroline O. B.; Fields, Jeremy Z.; Stave, James W.
CD44 protein and its variant isoforms are expressed in cancer stem cells (CSCs), and various CD44 isoforms can have different functional roles in cells. Our goal was to investigate how different CD44 isoforms contribute to the emergence of stem cell (SC) overpopulation that drives colorectal cancer (CRC) development. Specific CD44 variant isoforms are selectively expressed in normal colonic SCs and become overexpressed in CRCs during tumor development. We created a unique panel of anti-CD44 rabbit genomic antibodies to 16 specific epitopes that span the entire length of the CD44 molecule. Our panel was used to comprehensively investigate the expression of different CD44 isoforms in matched pairs (n = 10) of malignant colonic tissue and adjacent normal mucosa, using two (IHC & IF) immunostaining approaches. We found that: i) CD44v8–10 is selectively expressed in the normal human colonic SC niche; ii) CD44v8–10 is co-expressed with the SC markers ALDH1 and LGR5 in normal and malignant colon tissues; iii) colon carcinoma tissues frequently (80%) stain for CD44v8–10 while staining for CD44v6 was less frequent (40%). Given that CD44v8–10 expression is restricted to cells in the normal human colonic SC niche and CD44v8–10 expression progressively increases during CRC development, CD44v8–10 expression likely contributes to the SC overpopulation that drives the development and growth of colon cancers. Since the CD44 variant v8–10 epitope is located on CD44’s extracellular region, it offers great promise for targeted anti-CSC treatment approaches.
Dynamic bioinspired coculture model for probing ER+ breast cancer dormancy in the bone marrow niche
(Science Advances, 2023-03-08) Pradhan, Lina; Moore, DeVonte; Ovadia, Elisa M.; Swedzinski, Samantha L.; Cossette, Travis; Sikes, Robert A.; van Golen, Kenneth; Kloxin, April M.
Late recurrences of breast cancer are hypothesized to arise from disseminated tumor cells (DTCs) that reactivate after dormancy and occur most frequently with estrogen receptor–positive (ER+) breast cancer cells (BCCs) in bone marrow (BM). Interactions between the BM niche and BCCs are thought to play a pivotal role in recurrence, and relevant model systems are needed for mechanistic insights and improved treatments. We examined dormant DTCs in vivo and observed DTCs near bone lining cells and exhibiting autophagy. To study underlying cell-cell interactions, we established a well-defined, bioinspired dynamic indirect coculture model of ER+ BCCs with BM niche cells, human mesenchymal stem cells (hMSCs) and fetal osteoblasts (hFOBs). hMSCs promoted BCC growth, whereas hFOBs promoted dormancy and autophagy, regulated in part by tumor necrosis factor–α and monocyte chemoattractant protein 1 receptor signaling. This dormancy was reversible by dynamically changing the microenvironment or inhibiting autophagy, presenting further opportunities for mechanistic and targeting studies to prevent late recurrence.
Limiting Mrs2-dependent mitochondrial Mg2+ uptake induces metabolic programming in prolonged dietary stress
(Cell Reports, 2023-03-28) Madaris, Travis R.; Venkatesan, Manigandan; Maity, Soumya; Stein, Miriam C.; Vishnu, Neelanjan; Venkateswaran, Mridula K.; Davis, James G.; Ramachandran, Karthik; Uthayabalan, Sukanthathulse; Allen, Cristel; Osidele, Ayodeji; Stanley, Kristen; Bigham, Nicholas P.; Bakewell, Terry M.; Narkunan, Melanie; Le, Amy; Karanam, Varsha; Li, Kang; Mhapankar, Aum; Norton, Luke; Ross, Jean; Aslam, M. Imran; Reeves, W. Brian; Singh, Brij B.; Caplan, Jeffrey; Wilson, Justin J.; Stathopulos, Peter B.; Baur, Joseph A.; Madesh, Muniswamy
Highlights: • Mitochondrial Mg2+ channel Mrs2 rheostats MCU Ca2+ signals to maintain bioenergetic circuit • DNL precursor and cellular Mg2+ chelator citrate curbs HIF1α signal and oxidative metabolism • Lowering mMg2+ mitigates prolonged dietary-stress-induced obesity and metabolic syndrome • Mrs2 channel blocker CPACC reduces lipid accumulation and promotes browning and weight loss Summary The most abundant cellular divalent cations, Mg2+ (mM) and Ca2+ (nM-μM), antagonistically regulate divergent metabolic pathways with several orders of magnitude affinity preference, but the physiological significance of this competition remains elusive. In mice consuming a Western diet, genetic ablation of the mitochondrial Mg2+ channel Mrs2 prevents weight gain, enhances mitochondrial activity, decreases fat accumulation in the liver, and causes prominent browning of white adipose. Mrs2 deficiency restrains citrate efflux from the mitochondria, making it unavailable to support de novo lipogenesis. As citrate is an endogenous Mg2+ chelator, this may represent an adaptive response to a perceived deficit of the cation. Transcriptional profiling of liver and white adipose reveals higher expression of genes involved in glycolysis, β-oxidation, thermogenesis, and HIF-1α-targets, in Mrs2−/− mice that are further enhanced under Western-diet-associated metabolic stress. Thus, lowering mMg2+ promotes metabolism and dampens diet-induced obesity and metabolic syndrome. Graphical abstract Available at: https://doi.org/10.1016/j.celrep.2023.112155
RNA localization to the mitotic spindle is essential for early development and is regulated by kinesin-1 and dynein
(Journal of Cell Science, 2023-03-06) Remsburg, Carolyn M.; Konrad, Kalin D.; Song, Jia L.
Mitosis is a fundamental and highly regulated process that acts to faithfully segregate chromosomes into two identical daughter cells. Localization of gene transcripts involved in mitosis to the mitotic spindle might be an evolutionarily conserved mechanism to ensure that mitosis occurs in a timely manner. We identified many RNA transcripts that encode proteins involved in mitosis localized at the mitotic spindles in dividing sea urchin embryos and mammalian cells. Disruption of microtubule polymerization, kinesin-1 or dynein results in lack of spindle localization of these transcripts in the sea urchin embryo. Furthermore, results indicate that the cytoplasmic polyadenylation element (CPE) within the 3′UTR of the Aurora B transcript, a recognition sequence for CPEB, is essential for RNA localization to the mitotic spindle in the sea urchin embryo. Blocking this sequence results in arrested development during early cleavage stages, suggesting that RNA localization to the mitotic spindle might be a regulatory mechanism of cell division that is important for early development.
Lens Epithelial Explants Treated with Vitreous Humor Undergo Alterations in Chromatin Landscape with Concurrent Activation of Genes Associated with Fiber Cell Differentiation and Innate Immune Response
(Cells, 2023-02-03) Upreti, Anil; Padula, Stephanie L.; Tangeman, Jared A.; Wagner, Brad D.; O’Connell, Michael J.; Jaquish, Tycho J.; Palko, Raye K.; Mantz, Courtney J.; Anand, Deepti; Lovicu, Frank J.; Lachke, Salil A.; Robinson, Michael L.
Lens epithelial explants are comprised of lens epithelial cells cultured in vitro on their native basement membrane, the lens capsule. Biologists have used lens epithelial explants to study many different cellular processes including lens fiber cell differentiation. In these studies, fiber differentiation is typically measured by cellular elongation and the expression of a few proteins characteristically expressed by lens fiber cells in situ. Chromatin and RNA was collected from lens epithelial explants cultured in either un-supplemented media or media containing 50% bovine vitreous humor for one or five days. Chromatin for ATAC-sequencing and RNA for RNA-sequencing was prepared from explants to assess regions of accessible chromatin and to quantitatively measure gene expression, respectively. Vitreous humor increased chromatin accessibility in promoter regions of genes associated with fiber differentiation and, surprisingly, an immune response, and this was associated with increased transcript levels for these genes. In contrast, vitreous had little effect on the accessibility of the genes highly expressed in the lens epithelium despite dramatic reductions in their mRNA transcripts. An unbiased analysis of differentially accessible regions revealed an enrichment of cis-regulatory motifs for RUNX, SOX and TEAD transcription factors that may drive differential gene expression in response to vitreous.

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