• 

  The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models

  Rozowsky, Joel; Gao, Jiahao; Borsari, Beatrice; Yang, Yucheng T; Galeev, Timur; Gürsoy, Gamze; Epstein, Charles B; Xiong, Kun; Xu, Jinrui; Li, Tianxiao; et al. (2023-03-30)

  Understanding how genetic variants impact molecular phenotypes is a key goal of functional genomics, currently hindered by reliance on a single haploid reference genome. Here, we present the EN-TEx resource of 1,635 open-access datasets from four donors (∼30 tissues × ∼15 assays). The datasets are mapped to matched, diploid genomes with long-read phasing and structural variants, instantiating a catalog of >1 million allele-specific loci. These loci exhibit coordinated activity along haplotypes and are less conserved than corresponding, non-allele-specific ones. Surprisingly, a deep-learning transformer model can predict the allele-specific activity based only on local nucleotide-sequence context, highlighting the importance of transcription-factor-binding motifs particularly sensitive to variants. Furthermore, combining EN-TEx with existing genome annotations reveals strong associations between allele-specific and GWAS loci. It also enables models for transferring known eQTLs to difficult-to-profile tissues (e.g., from skin to heart). Overall, EN-TEx provides rich data and generalizable models for more accurate personal functional genomics.
• 

  Crystal Structures of Inhibitor-Bound Main Protease from Delta- and Gamma-Coronaviruses

  Zvornicanin, Sarah N; Shaqra, Ala M; Huang, Qiuyu J; Ornelas, Elizabeth; Moghe, Mallika; Knapp, Mark; Moquin, Stephanie; Dovala, Dustin; Schiffer, Celia A; Kurt Yilmaz, Nese (2023-03-18)

  With the spread of SARS-CoV-2 throughout the globe causing the COVID-19 pandemic, the threat of zoonotic transmissions of coronaviruses (CoV) has become even more evident. As human infections have been caused by alpha- and beta-CoVs, structural characterization and inhibitor design mostly focused on these two genera. However, viruses from the delta and gamma genera also infect mammals and pose a potential zoonotic transmission threat. Here, we determined the inhibitor-bound crystal structures of the main protease (Mpro) from the delta-CoV porcine HKU15 and gamma-CoV SW1 from the beluga whale. A comparison with the apo structure of SW1 Mpro, which is also presented here, enabled the identification of structural arrangements upon inhibitor binding at the active site. The cocrystal structures reveal binding modes and interactions of two covalent inhibitors, PF-00835231 (active form of lufotrelvir) bound to HKU15, and GC376 bound to SW1 Mpro. These structures may be leveraged to target diverse coronaviruses and toward the structure-based design of pan-CoV inhibitors.
• 

  Cryo-EM structure of the human Sirtuin 6-nucleosome complex [preprint]

  Chio, Un Seng; Rechiche, Othman; Bryll, Alysia R; Zhu, Jiang; Feldman, Jessica L; Peterson, Craig L; Tan, Song; Armache, Jean-Paul (2023-03-18)

  Sirtuin 6 (SIRT6) is a multifaceted protein deacetylase/deacylase and a major target for small-molecule modulators of longevity and cancer. In the context of chromatin, SIRT6 removes acetyl groups from histone H3 in nucleosomes, but the molecular basis for its nucleosomal substrate preference is unknown. Our cryo-electron microscopy structure of human SIRT6 in complex with the nucleosome shows that the catalytic domain of SIRT6 pries DNA from the nucleosomal entry-exit site and exposes the histone H3 N-terminal helix, while the SIRT6 zinc-binding domain binds to the histone acidic patch using an arginine anchor. In addition, SIRT6 forms an inhibitory interaction with the C-terminal tail of histone H2A. The structure provides insights into how SIRT6 can deacetylate both H3 K9 and H3 K56. Teaser: The structure of the SIRT6 deacetylase/nucleosome complex suggests how the enzyme acts on both histone H3 K9 and K56 residues.
• 

  Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease [preprint]

  Sullivan, Patrick F; Meadows, Jennifer R S; Gazal, Steven; Phan, BaDoi N; Li, Xue; Genereux, Diane P; Dong, Michael X; Bianchi, Matteo; Andrews, Gregory; Sakthikumar, Sharadha; et al. (2023-03-10)

  Although thousands of genomic regions have been associated with heritable human diseases, attempts to elucidate biological mechanisms are impeded by a general inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function that is agnostic to cell type or disease mechanism. Here, single base phyloP scores from the whole genome alignment of 240 placental mammals identified 3.5% of the human genome as significantly constrained, and likely functional. We compared these scores to large-scale genome annotation, genome-wide association studies (GWAS), copy number variation, clinical genetics findings, and cancer data sets. Evolutionarily constrained positions are enriched for variants explaining common disease heritability (more than any other functional annotation). Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease.
• 

  Divalent siRNAs are bioavailable in the lung and efficiently block SARS-CoV-2 infection

  Hariharan, Vignesh N; Shin, Minwook; Chang, Ching-Wen; O'Reilly, Daniel; Biscans, Annabelle; Yamada, Ken; Guo, Zhiru; Somasundaran, Mohan; Tang, Qi; Monopoli, Kathryn; et al. (2023-03-09)

  The continuous evolution of SARS-CoV-2 variants complicates efforts to combat the ongoing pandemic, underscoring the need for a dynamic platform for the rapid development of pan-viral variant therapeutics. Oligonucleotide therapeutics are enhancing the treatment of numerous diseases with unprecedented potency, duration of effect, and safety. Through the systematic screening of hundreds of oligonucleotide sequences, we identified fully chemically stabilized siRNAs and ASOs that target regions of the SARS-CoV-2 genome conserved in all variants of concern, including delta and omicron. We successively evaluated candidates in cellular reporter assays, followed by viral inhibition in cell culture, with eventual testing of leads for in vivo antiviral activity in the lung. Previous attempts to deliver therapeutic oligonucleotides to the lung have met with only modest success. Here, we report the development of a platform for identifying and generating potent, chemically modified multimeric siRNAs bioavailable in the lung after local intranasal and intratracheal delivery. The optimized divalent siRNAs showed robust antiviral activity in human cells and mouse models of SARS-CoV-2 infection and represent a new paradigm for antiviral therapeutic development for current and future pandemics.
• 

  Provider perceptions of barriers and facilitators to care in eating disorder treatment for transgender and gender diverse patients: a qualitative study

  Ferrucci, Katarina A; McPhillips, Emily; Lapane, Kate L; Jesdale, Bill M; Dubé, Catherine E (2023-03-08)

  Background: The prevalence of eating disorders is higher in transgender and non-binary compared to cisgender people. Gender diverse people who seek eating disorder treatment often report struggling to find affirming and inclusive treatment from healthcare clinicians. We sought to understand eating disorder care clinicians' perceptions of facilitators of and barriers to effective eating disorder treatment for transgender and gender diverse patients. Methods: In 2022, nineteen US-based licensed mental health clinicians who specialized in eating disorder treatment participated in semi-structured interviews. We used inductive thematic analysis to identify themes around perceptions and knowledge of facilitators and barriers to care for transgender and gender diverse patients diagnosed with eating disorders. Results: Two broad themes were identified: (1) factors affecting access to care; and (2) factors affecting care while in treatment. Within the first theme, the following subthemes were found: stigmatization, family support, financial factors, gendered clinics, scarcity of gender-competent care, and religious communities. Within the second theme, prominent subthemes included discrimination and microaggressions, provider lived experience and education, other patients and parents, institutions of higher education, family-centered care, gendered-centered care, and traditional therapeutic techniques. Conclusion: Many barriers and facilitators have potential to be improved upon, especially those caused by clinicians' lack of knowledge or attitudes towards gender minority patients in treatment. Future research is needed to identify how provider-driven barriers manifest and how they can be improved upon to better patient care experiences.
• 

  Cross-ancestry, cell-type-informed atlas of gene, isoform, and splicing regulation in the developing human brain [preprint]

  Wen, Cindy; Margolis, Michael; Dai, Rujia; Zhang, Pan; Przytycki, Pawel F; Vo, Daniel D; Bhattacharya, Arujun; Kim, Minsoo; Matoba, Nana; Tsai, Ellen; et al. (2023-03-06)

  Genomic regulatory elements active in the developing human brain are notably enriched in genetic risk for neuropsychiatric disorders, including autism spectrum disorder (ASD), schizophrenia, and bipolar disorder. However, prioritizing the specific risk genes and candidate molecular mechanisms underlying these genetic enrichments has been hindered by the lack of a single unified large-scale gene regulatory atlas of human brain development. Here, we uniformly process and systematically characterize gene, isoform, and splicing quantitative trait loci (xQTLs) in 672 fetal brain samples from unique subjects across multiple ancestral populations. We identify 15,752 genes harboring a significant xQTL and map 3,739 eQTLs to a specific cellular context. We observe a striking drop in gene expression and splicing heritability as the human brain develops. Isoform-level regulation, particularly in the second trimester, mediates the greatest proportion of heritability across multiple psychiatric GWAS, compared with eQTLs. Via colocalization and TWAS, we prioritize biological mechanisms for ~60% of GWAS loci across five neuropsychiatric disorders, nearly two-fold that observed in the adult brain. Finally, we build a comprehensive set of developmentally regulated gene and isoform co-expression networks capturing unique genetic enrichments across disorders. Together, this work provides a comprehensive view of genetic regulation across human brain development as well as the stage- and cell type-informed mechanistic underpinnings of neuropsychiatric disorders.
• Performance of Rapid Antigen Tests Based on Symptom Onset and Close Contact Exposure: A secondary analysis from the Test Us At Home prospective cohort study [preprint]

  Herbert, Carly; Wang, Biqi; Lin, Honghuang; Hafer, Nathaniel; Pretz, Caitlin; Stamegna, Pamela; Tarrant, Seanan; Hartin, Paul; Ferranto, Julia; Behar, Stephanie; et al. (2023-02-24)

  Background: The performance of rapid antigen tests for SARS-CoV-2 (Ag-RDT) in temporal relation to symptom onset or exposure is unknown, as is the impact of vaccination on this relationship. Objective: To evaluate the performance of Ag-RDT compared with RT-PCR based on day after symptom onset or exposure in order to decide on 'when to test'. Design setting and participants: The Test Us at Home study was a longitudinal cohort study that enrolled participants over 2 years old across the United States between October 18, 2021 and February 4, 2022. All participants were asked to conduct Ag-RDT and RT-PCR testing every 48 hours over a 15-day period. Participants with one or more symptoms during the study period were included in the Day Post Symptom Onset (DPSO) analyses, while those who reported a COVID-19 exposure were included in the Day Post Exposure (DPE) analysis. Exposure: Participants were asked to self-report any symptoms or known exposures to SARS-CoV-2 every 48-hours, immediately prior to conducting Ag-RDT and RT-PCR testing. The first day a participant reported one or more symptoms was termed DPSO 0, and the day of exposure was DPE 0. Vaccination status was self-reported. Main outcome and measures: Results of Ag-RDT were self-reported (positive, negative, or invalid) and RT-PCR results were analyzed by a central laboratory. Percent positivity of SARS-CoV-2 and sensitivity of Ag-RDT and RT-PCR by DPSO and DPE were stratified by vaccination status and calculated with 95% confidence intervals. Results: A total of 7,361 participants enrolled in the study. Among them, 2,086 (28.3%) and 546 (7.4%) participants were eligible for the DPSO and DPE analyses, respectively. Unvaccinated participants were nearly twice as likely to test positive for SARS-CoV-2 than vaccinated participants in event of symptoms (PCR+: 27.6% vs 10.1%) or exposure (PCR+: 43.8% vs. 22.2%). The highest proportion of vaccinated and unvaccinated individuals tested positive on DPSO 2 and DPE 5-8. Performance of RT-PCR and Ag-RDT did not differ by vaccination status. Ag-RDT detected 78.0% (95% Confidence Interval: 72.56-82.61) of PCR-confirmed infections by DPSO 4. For exposed participants, Ag-RDT detected 84.9% (95% CI: 75.0-91.4) of PCR-confirmed infections by day five post-exposure (DPE 5). Conclusions and relevance: Performance of Ag-RDT and RT-PCR was highest on DPSO 0-2 and DPE 5 and did not differ by vaccination status. These data suggests that serial testing remains integral to enhancing the performance of Ag-RDT.
• The choroid plexus links innate immunity to CSF dysregulation in hydrocephalus

  Robert, Stephanie M; Reeves, Benjamin C; Kiziltug, Emre; Duy, Phan Q; Karimy, Jason K; Mansuri, M Shahid; Marlier, Arnaud; Allington, Garrett; Greenberg, Ana B W; DeSpenza, Tyrone; et al. (2023-02-16)

  The choroid plexus (ChP) is the blood-cerebrospinal fluid (CSF) barrier and the primary source of CSF. Acquired hydrocephalus, caused by brain infection or hemorrhage, lacks drug treatments due to obscure pathobiology. Our integrated, multi-omic investigation of post-infectious hydrocephalus (PIH) and post-hemorrhagic hydrocephalus (PHH) models revealed that lipopolysaccharide and blood breakdown products trigger highly similar TLR4-dependent immune responses at the ChP-CSF interface. The resulting CSF "cytokine storm", elicited from peripherally derived and border-associated ChP macrophages, causes increased CSF production from ChP epithelial cells via phospho-activation of the TNF-receptor-associated kinase SPAK, which serves as a regulatory scaffold of a multi-ion transporter protein complex. Genetic or pharmacological immunomodulation prevents PIH and PHH by antagonizing SPAK-dependent CSF hypersecretion. These results reveal the ChP as a dynamic, cellularly heterogeneous tissue with highly regulated immune-secretory capacity, expand our understanding of ChP immune-epithelial cell cross talk, and reframe PIH and PHH as related neuroimmune disorders vulnerable to small molecule pharmacotherapy.
• 

  Non-canonical pattern recognition of a pathogen-derived metabolite by a nuclear hormone receptor identifies virulent bacteria in C. elegans

  Peterson, Nicholas D; Tse, Samantha Y; Huang, Qiuyu Judy; Wani, Khursheed A; Schiffer, Celia A; Pukkila-Worley, Read (2023-02-15)

  Distinguishing infectious pathogens from harmless microorganisms is essential for animal health. The mechanisms used to identify infectious microbes are not fully understood, particularly in metazoan hosts that eat bacteria as their food source. Here, we characterized a non-canonical pattern-recognition system in Caenorhabditis elegans (C. elegans) that assesses the relative threat of virulent Pseudomonas aeruginosa (P. Aeruginosa) to activate innate immunity. We discovered that the innate immune response in C. elegans was triggered by phenazine-1-carboxamide (PCN), a toxic metabolite produced by pathogenic strains of P. aeruginosa. We identified the nuclear hormone receptor NHR-86/HNF4 as the PCN sensor in C. elegans and validated that PCN bound to the ligand-binding domain of NHR-86/HNF4. Activation of NHR-86/HNF4 by PCN directly engaged a transcriptional program in intestinal epithelial cells that protected against P. aeruginosa. Thus, a bacterial metabolite is a pattern of pathogenesis surveilled by nematodes to identify a pathogen in its bacterial diet.
• 

  Modulation of neuronal excitability by binge alcohol drinking

  Gimenez-Gomez, Pablo; Le, Timmy; Martin, Gilles E (2023-02-14)

  Drug use poses a serious threat to health systems throughout the world. The number of consumers rises every year being alcohol the drug of abuse most consumed causing 3 million deaths (5.3% of all deaths) worldwide and 132.6 million disability-adjusted life years. In this review, we present an up-to-date summary about what is known regarding the global impact of binge alcohol drinking on brains and how it affects the development of cognitive functions, as well as the various preclinical models used to probe its effects on the neurobiology of the brain. This will be followed by a detailed report on the state of our current knowledge of the molecular and cellular mechanisms underlying the effects of binge drinking on neuronal excitability and synaptic plasticity, with an emphasis on brain regions of the meso-cortico limbic neurocircuitry.
• 

  Large-scale organoid study suggests effects of trisomy 21 on early fetal neurodevelopment are more subtle than variability between isogenic lines and experiments

  Czerminski, Jan T; King, Oliver D; Lawrence, Jeanne B (2023-02-03)

  This study examines cortical organoids generated from a panel of isogenic trisomic and disomic iPSC lines (subclones) as a model of early fetal brain development in Down syndrome (DS). An initial experiment comparing organoids from one trisomic and one disomic line showed many genome-wide transcriptomic differences and modest differences in cell-type proportions, suggesting there may be a neurodevelopmental phenotype that is due to trisomy of chr21. To better control for multiple sources of variation, we undertook a highly robust study of ∼1,200 organoids using an expanded panel of six all-isogenic lines, three disomic, and three trisomic. The power of this experimental design was indicated by strong detection of the ∼1.5-fold difference in chr21 genes. However, the numerous expression differences in non-chr21 genes seen in the smaller experiment fell away, and the differences in cell-type representation between lines did not correlate with trisomy 21. Results suggest that the initial smaller experiment picked up differences between small organoid samples and individual isogenic lines, which "averaged out" in the larger panel of isogenic lines. Our results indicate that even when organoid and batch variability are better controlled for, variation between isogenic cell lines (even subclones) may obscure, or be conflated with, subtle neurodevelopmental phenotypes that may be present in ∼2nd trimester DS brain development. Interestingly, despite this variability between organoid batches and lines, and the "fetal stage" of these organoids, an increase in secreted Aβ40 peptide levels-an Alzheimer-related cellular phenotype-was more strongly associated with trisomy 21 status than were neurodevelopmental shifts in cell-type composition.
• 

  Neurexins in serotonergic neurons regulate neuronal survival, serotonin transmission, and complex mouse behaviors

  Cheung, Amy; Konno, Kotaro; Imamura, Yuka; Matsui, Aya; Abe, Manabu; Sakimura, Kenji; Sasaoka, Toshikuni; Uemura, Takeshi; Watanabe, Masahiko; Futai, Kensuke (2023-01-25)

  Extensive serotonin (5-hydroxytryptamine, 5-HT) innervation throughout the brain corroborates 5-HT's modulatory role in numerous cognitive activities. Volume transmission is the major mode for 5-HT transmission but mechanisms underlying 5-HT signaling are still largely unknown. Abnormal brain 5-HT levels and function have been implicated in autism spectrum disorder (ASD). Neurexin (Nrxn) genes encode presynaptic cell adhesion molecules important for the regulation of synaptic neurotransmitter release, notably glutamatergic and GABAergic transmission. Mutations in Nrxn genes are associated with neurodevelopmental disorders including ASD. However, the role of Nrxn genes in the 5-HT system is poorly understood. Here, we generated a mouse model with all three Nrxn genes disrupted specifically in 5-HT neurons to study how Nrxns affect 5-HT transmission. Loss of Nrxns in 5-HT neurons reduced the number of serotonin neurons in the early postnatal stage, impaired 5-HT release, and decreased 5-HT release sites and serotonin transporter expression. Furthermore, 5-HT neuron-specific Nrxn knockout reduced sociability and increased depressive-like behavior. Our results highlight functional roles for Nrxns in 5-HT neurotransmission, 5-HT neuron survival, and the execution of complex behaviors.
• Interactions between FUS and the C-terminal Domain of Nup62 are Sufficient for their Co-phase Separation into Amorphous Assemblies

  Kumar, Meenakshi Sundaram; Stallworth, Karly M; Murthy, Anastasia C; Lim, Su Min; Li, Nan; Jain, Aastha; Munro, James B; Fawzi, Nicolas L; Lagier-Tourenne, Clotilde; Bosco, Daryl A (2023-01-21)

  Deficient nucleocytoplasmic transport is emerging as a pathogenic feature of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), including in ALS caused by mutations in Fused in Sarcoma (FUS). Recently, both wild-type and ALS-linked mutant FUS were shown to directly interact with the phenylalanine-glycine (FG)-rich nucleoporin 62 (Nup62) protein, where FUS WT/ Nup62 interactions were enriched within the nucleus but ALS-linked mutant FUS/ Nup62 interactions were enriched within the cytoplasm of cells. Nup62 is a central channel Nup that has a prominent role in forming the selectivity filter within the nuclear pore complex and in regulating effective nucleocytoplasmic transport. Under conditions where FUS phase separates into liquid droplets in vitro, the addition of Nup62 caused the synergistic formation of amorphous assemblies containing both FUS and Nup62. Here, we examined the molecular determinants of this process using recombinant FUS and Nup62 proteins and biochemical approaches. We demonstrate that the structured C-terminal domain of Nup62 containing an alpha-helical coiled-coil region plays a dominant role in binding FUS and is sufficient for inducing the formation of FUS/Nup62 amorphous assemblies. In contrast, the natively unstructured, F/G repeat-rich N-terminal domain of Nup62 modestly contributed to FUS/Nup62 phase separation behavior. Expression of individual Nup62 domain constructs in human cells confirmed that the Nup62 C-terminal domain is essential for localization of the protein to the nuclear envelope. Our results raise the possibility that interactions between FUS and the C-terminal domain of Nup62 can influence the function of Nup62 under physiological and/or pathological conditions.
• 

  Presynaptic Gq-coupled receptors drive biphasic dopamine transporter trafficking that modulates dopamine clearance and motor function

  Kearney, Patrick J; Bolden, Nicholas C; Kahuno, Elizabeth; Conklin, Tucker L; Martin, Gilles E; Lubec, Gert; Melikian, Haley E (2023-01-12)

  Extracellular dopamine (DA) levels are constrained by the presynaptic DA transporter (DAT), a major psychostimulant target. Despite its necessity for DA neurotransmission, DAT regulation in situ is poorly understood, and it is unknown whether regulated DAT trafficking impacts dopaminergic signaling and/or behaviors. Leveraging chemogenetics and conditional gene silencing, we found that activating presynaptic Gq-coupled receptors, either hM3Dq or mGlu5, drove rapid biphasic DAT membrane trafficking in ex vivo striatal slices, with region-specific differences between ventral and dorsal striata. DAT insertion required D2 DA autoreceptors and intact retromer, whereas DAT retrieval required PKC activation and Rit2. Ex vivo voltammetric studies revealed that DAT trafficking impacts DA clearance. Furthermore, dopaminergic mGlu5 silencing elevated DAT surface expression and abolished motor learning, which was rescued by inhibiting DAT with a subthreshold CE-158 dose. We discovered that presynaptic DAT trafficking is complex, multimodal, and region specific, and for the first time, we identified cell autonomous mechanisms that govern presynaptic DAT tone. Importantly, the findings are consistent with a role for regulated DAT trafficking in DA clearance and motor function.
• 

  A comparative analysis of microglial inducible Cre lines [preprint]

  Faust, Travis E; Feinberg, Philip A; O'Connor, Ciara; Kawaguchi, Riki; Chan, Andrew; Strasburger, Haley; Masuda, Takahiro; Amann, Lukas; Knobeloch, Klaus-Peter; Prinz, Marco; et al. (2023-01-09)

  Cre/LoxP technology has revolutionized genetic studies and allowed for spatial and temporal control of gene expression in specific cell types. The field of microglial biology has particularly benefited from this technology as microglia have historically been difficult to transduce with virus or electroporation methods for gene delivery. Here, we interrogate four of the most widely available microglial inducible Cre lines. We demonstrate varying degrees of recombination efficiency and spontaneous recombination, depending on the Cre line and loxP distance. We also establish best practice guidelines and protocols to measure recombination efficiency in microglia, which could be extended to other cell types. There is increasing evidence that microglia are key regulators of neural circuit structure and function. Microglia are also major drivers of a broad range of neurological diseases. Thus, reliable manipulation of their function in vivo is of utmost importance. Identifying caveats and benefits of all tools and implementing the most rigorous protocols are crucial to the growth of the field of microglial biology and the development of microglia-based therapeutics.
• 

  The role of RNA-binding proteins in orchestrating germline development in Caenorhabditis elegans

  Albarqi, Mennatallah M Y; Ryder, Sean P (2023-01-04)

  RNA passed from parents to progeny controls several aspects of early development. The germline of the free-living nematode Caenorhabditis elegans contains many families of evolutionarily conserved RNA-binding proteins (RBPs) that target the untranslated regions of mRNA transcripts to regulate their translation and stability. In this review, we summarize what is known about the binding specificity of C. elegans germline RNA-binding proteins and the mechanisms of mRNA regulation that contribute to their function. We examine the emerging role of miRNAs in translational regulation of germline and embryo development. We also provide an overview of current technology that can be used to address the gaps in our understanding of RBP regulation of mRNAs. Finally, we present a hypothetical model wherein multiple 3'UTR-mediated regulatory processes contribute to pattern formation in the germline to ensure the proper and timely localization of germline proteins and thus a functional reproductive system.
• Association Between Patient and Facility Characteristics and Rehabilitation Outcomes After Joint Replacement Surgery in Different Rehabilitation Settings for Older Adults: A Systematic Review

  Osundolire, Seun; Mbrah, Attah; Liu, Shao-Hsien; Lapane, Kate L (2023-01-04)

  Background and purpose: In the United States, an exponential increase in total hip arthroplasty (THA) and total knee arthroplasty (TKA) demand has occurred over the last 2 decades. Evidence suggesting patients receiving inpatient rehabilitation following a TKA or THA experience similar outcomes as those with rehabilitation in other settings led to dramatic shifts in postsurgical care settings owing to Centers for Medicare & Medicaid Services (CMS) payment reforms. A contemporary synthesis of evidence about the association between patient and facility factors and outcomes from older adults undergoing THA or TKA in the United States is needed. Methods: To identify eligible studies, we searched PubMed, Scopus, and CINAHL. We followed PRISMA guidelines to identify articles evaluating either patient or facility factors associated with outcomes after THA or TKA for older adults who may have been cared for in inpatient settings (ie, inpatient rehabilitation or skilled nursing facility [SNF]). Eligible articles were conducted in the United States and were published between January 1, 2000, and December 31, 2021. Results: We included 8 articles focused on patient factors and 9 focused on facility factors. Most included older adults and the majority were White (in those reporting race/ethnicity). Most studies evaluated outcomes at discharge and showed that patients admitted to inpatient rehabilitation facilities had either similar or better functional outcomes (mobility, self-care, and functional independence measure (FIM) score) and lower length of stay compared with those in SNFs. Few studies focused on home health care. Conclusions: The systematic review focused on older adults showed that findings in these patients are consistent with previous research. Older adults undergoing THA/TKA had acceptable outcomes regardless of postsurgical, inpatient setting of care. Research conducted after CMS payment reforms, in home health care settings, and in more diverse samples is needed. Given the known racial/ethnic disparities in THA/TKA and the shifts to postsurgical home health care with little regulatory oversight of care quality, contemporary research on outcomes of postsurgical THA/TKA outcomes is warranted.
• 

  High bacillary burden and the ESX-1 type VII secretion system promote MHC class I presentation by Mycobacterium tuberculosis infected macrophages to CD8 T-cells [preprint]

  Mott, Daniel; Yang, Jason; Baer, Christina; Papavinasasundaram, Kadamba; Sassetti, Christopher M.; Behar, Samuel M. (2023-01-02)

  Mycobacterium tuberculosis (Mtb) subverts host defenses to persist in macrophages despite immune pressure. CD4 T-cells can recognize macrophages infected with a single bacillus in vitro. Under identical conditions, CD8 T-cells inefficiently recognize infected macrophages and fail to restrict Mtb growth, although they can inhibit Mtb growth during high burden intracellular infection. We show that high intracellular Mtb numbers cause macrophage death, leading other macrophages to scavenge cellular debris and cross-present the TB10.4 antigen to CD8 T-cells. Presentation by infected macrophages requires Mtb to have a functional ESX-1 type VII secretion system. These data indicate that phagosomal membrane damage and cell death promote class I MHC presentation of the immunodominant antigen TB10.4 by macrophages. Although this mode of antigen-presentation stimulates cytokine production that we presume would be host beneficial; killing of uninfected cells could worsen immunopathology. We suggest that shifting the focus of CD8 T-cell recognition to uninfected macrophages would limit the interaction of CD8 T-cells with infected macrophages and impair CD8 T-cell mediated resolution of tuberculosis.
• 

  Comanagement with rheumatology and prescription biologics filled during pregnancy in women with rheumatic diseases: a retrospective analysis of US administrative claims data

  Shridharmurthy, Divya; Lapane, Kate L; Baek, Jonggyu; Nunes, Anthony; Kay, Jonathan; Liu, Shao-Hsien (2022-12-22)

  Objectives: To evaluate comanagement with rheumatology and biological prescriptions filled during pregnancy among women with axial spondyloarthritis (axSpA), rheumatoid arthritis (RA) or psoriatic arthritis (PsA) and to examine factors associated with receiving comanagement with rheumatology during pregnancy. Design: A retrospective analysis of US claims data. Setting: Commercially insured enrollees using data from the 2013-2018 IBM MarketScan Commercial Claims and Encounters Database. Participants: We identified 4131 pregnant women aged ≤55 years from the 2013-2018 IBM MarketScan Commercial Claims and Encounters Database with an International Classification of Disease, 9th Revision/10th Revision codes for RA, axSpA or PsA, with continuous enrolment at ≥3 months before the date of the last menstrual period (LMP) (index date) and throughout pregnancy. Primary outcomes: Filled biologics (prescriptions and infusions) claims were categorised by 90 days before the LMP and trimester, as were primary care, obstetrician and rheumatological claims. Results: The prevalence of axSpA, RA and PsA was 0.7%, 0.2% and 0.04% among reproductive age women. The average maternal age was 32.7 years (SD 5.7). During pregnancy, 9.1% of those with axSpA (n=2,410) and 56.4% of those with RA/PsA (n=1,721) had a rheumatological claim. Biologics claims were less common among those with axSpA (90 days before LMP: 1.6%, during pregnancy: 1.1%) than those with RA/PsA (90 days before LMP: 11.9%, during pregnancy: 6.9%). Medications during pregnancy included corticosteroids (axSpA: 0.3%, RA/PsA: 2.2%), non-biological disease-modifying antirheumatic drugs (axSpA: 0.2%, RA/PsA: 1.7%), non-steroidal anti-inflammatory drugs (axSpA: 0.2%, RA/PsA: 1.3%) and opioids (axSpA: 0.2%, RA/PsA: 0.6%). Established rheumatological care and biologics claims during the 90 days before LMP showed good prediction accuracy for receiving comanagement with rheumatology during pregnancy (axSpA: area under the receiver operator curve (AUC) 0.73, RA/PsA: AUC 0.70). Conclusion: Comanagement with rheumatology during pregnancy occurs infrequently, especially for women with axSpA. Biologics claims during pregnancy may not align with published guidelines. Future research is warranted to improve comanagement with rheumatology during pregnancy.

View more