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Found 36604 matches. Displaying 51-60
Navrazhina K, Garcet S, Frew JW, Zheng XZ, Coats I, Guttman-Yassky E, Krueger JG
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The inflammatory proteome of hidradenitis suppurativa skin is more expansive than that of psoriasis vulgaris

Background: Although hidradenitis suppurativa (HS) shares some transcriptomic and cellular infiltrate features with psoriasis, their skin proteome remains unknown. Objective: To define and compare inflammatory protein biomarkers of HS and psoriasis skin. Methods: We assessed 92 inflammatory biomarkers in HS (n = 13), psoriasis (n = 11), and control skin (n = 11) using Olink high-throughput proteomics. We also correlated HS skin and blood biomarkers using proteomics and RNA sequencing. Results: We identified 57 differentially expressed proteins (DEPs) in lesional psoriasis and 64 DEPs in lesional HS skin, compared to healthy controls. Both HS and psoriasis lesional skin demonstrated a significant upregulation of T helper 1 and T helper 17 proteins. Healthy-appearing perilesional HS skin had 63 DEPs compared to healthy controls. Nonlesional HS and psoriasis skin had 24 and 7 DEPs, respectively, compared to healthy controls. Tumor necrosis factor and 8 other proteins were significantly correlated with clinical severity in perilesional HS skin (2 cm from a nodule). Limitations: Inclusion of only moderate-to-severe patients and the cohort size. Conclusion: HS has a greater inflammatory profile and is more diffusely distributed compared with psoriasis. Proteins correlated with disease severity are potential disease mediators. Perilesional skin is comparably inflamed to lesional skin, suggesting the need to treat beyond skin nodules. ( J Am Acad Dermatol 2022;86:322-30.)
McKerrow W, Wang XY, Mendez-Dorantes C, Mita P, Cao S, Grivainis M, Ding L, LaCava J, Burns KH, Boeke JD, Fenyo D
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LINE-1 expression in cancer correlates with p53 mutation, copy number alteration, and S phase checkpoint

Retrotransposons are genomic DNA sequences that copy them-selves to new genomic locations via RNA intermediates; LINE-1 is the only active and autonomous retrotransposon in the human genome. The mobility of LINE-1 is largely repressed in somatic tissues but is derepressed in many cancers, where LINE-1 retrotransposition is correlated with p53 mutation and copy number alteration (CNA). In cell lines, inducing LINE-1 expression can cause double-strand breaks (DSBs) and replication stress. Reanalyzing multiomic data from breast, ovarian, endometrial, and colon cancers, we confirmed correlations between LINE-1 expression, p53 mutation status, and CNA. We observed a consistent correlation between LINE-1 expression and the abundance of DNA replication complex components, indicating that LINE-1 may also induce replication stress in human tumors. In endometrial cancer, high-quality phosphoproteomic data allowed us to identify the DSB-induced ATM-MRN-SMC S phase checkpoint pathway as the primary DNA damage response (DDR) pathway associated with LINE-1 expres-sion. Induction of LINE-1 expression in an in vitro model led to increased phosphorylation of MRN complex member RAD50, suggesting that LINE-1 directly activates this pathway.
Wang ZQ, Forelli N, Hernandez Y, Ternei M, Brady SF
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Lapcin, a potent dual topoisomerase I/II inhibitor discovered by soil metagenome guided total chemical synthesis

NATURE COMMUNICATIONS 2022 FEB 11; 13(1):? Article 842
Chemical synthesis of secondary metabolites isolated from nature, and derivatives thereof, is still a paradigm of significance to drug development. Here the authors instead use bioinformatics to analyze a biosynthetic gene cluster found in the soil metagenome, and chemical synthesis of its predict product to produce lapcin, a dual topoisomerase I/II inhibitor with promising activity against cancer cell lines. In natural product discovery programs, the power of synthetic chemistry is often leveraged for the total synthesis and diversification of characterized metabolites. The synthesis of structures that are bioinformatically predicted to arise from uncharacterized biosynthetic gene clusters (BGCs) provides a means for synthetic chemistry to enter this process at an early stage. The recent identification of non-ribosomal peptides (NRPs) containing multiple rho-aminobenzoic acids (PABAs) led us to search soil metagenomes for BGCs that polymerize PABA. Here, we use PABA-specific adenylation-domain sequences to guide the cloning of the lap BGC directly from soil. This BGC was predicted to encode a unique N-acylated PABA and thiazole containing structure. Chemical synthesis of this structure gave lapcin, a dual topoisomerase I/II inhibitor with nM to pM IC50s against diverse cancer cell lines. The discovery of lapcin highlights the power of coupling metagenomics, bioinformatics and total chemical synthesis to unlock the biosynthetic potential contained in even complex uncharacterized BGCs.
Wang BL, Yang M, Li SJ
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Numb and Numblike regulate sarcomere assembly and maintenance

JOURNAL OF CLINICAL INVESTIGATION 2022 FEB 1; 132(3):? Article e139420
A sarcomere is the contractile unit of the myofibril in striated muscles such as cardiac and skeletal muscles. The assembly of sarcomeres depends on multiple molecules that serve as raw materials and participate in the assembly process. However, the mechanism of this critical assembly process remains largely unknown. Here, we found that the cell fate determinant Numb and its homolog Numblike regulated sarcomere assembly and maintenance in striated muscles. We discovered that Numb and Numblike are sarcomeric molecules that were gradually confined to the Z-disc during striated muscle development. Conditional knockout of Numb and Numblike severely compromised sarcomere assembly and its integrity and thus caused organelle dysfunction. Notably, we identified that Numb and Numblike served as sarcomeric alpha-Actin-binding proteins (ABPs) and shared a conserved domain that can bind to the barbed end of sarcomeric alpha-Actin. In vitro fluorometric alpha-Actin polymerization assay showed that Numb and Numblike also played a role in the sarcomeric alpha-Actin polymerization process. Last, we demonstrate that Numb and Numblike regulate sarcomeric alpha-Actinin-dependent (ACTN-dependent) Z-disc consolidation in the sarcomere assembly and maintenance. In summary, our studies show that Numb and its homolog Numblike regulate sarcomere assembly and maintenance in striated muscles, and demonstrate a molecular mechanism by which Numb/Numblike, sarcomeric alpha-Actin, and ACTN cooperate to control thin filament formation and Z-disc consolidation.
Saito Y, Hawley BR, Puno MR, Sarathy SN, Lima CD, Jaffrey SR, Darnell RB, Keeney S, Jain D
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YTHDC2 control of gametogenesis requires helicase activity but not m(6)A binding

GENES & DEVELOPMENT 2022 FEB 1; 36(3-4):180-194
In this study, Saito et al. sought to understand how the N-6-methyladenosine (m(6)A) reader and RNA helicase YTHDC2 switches cells from mitotic to meiotic gene expression programs. Their findings provide insight into YTHDC2's mechanism, and they propose a model in which YTHDC2 binds transcripts independent of m(6)A status and regulates gene expression during multiple stages of meiosis by distinct mechanisms. Mechanisms regulating meiotic progression in mammals are poorly understood. The N-6-methyladenosine (m(6)A) reader and 3 ' -> 5 ' RNA helicase YTHDC2 switches cells from mitotic to meiotic gene expression programs and is essential for meiotic entry, but how this critical cell fate change is accomplished is unknown. Here, we provide insight into its mechanism and implicate YTHDC2 in having a broad role in gene regulation during multiple meiotic stages. Unexpectedly, mutation of the m(6)A-binding pocket of YTHDC2 had no detectable effect on gametogenesis and mouse fertility, suggesting that YTHDC2 function is m(6)A-independent. Supporting this conclusion, CLIP data defined YTHDC2-binding sites on mRNA as U-rich and UG-rich motif-containing regions within 3 ' UTRs and coding sequences, distinct from the sites that contain m(6)A during spermatogenesis. Complete loss of YTHDC2 during meiotic entry did not substantially alter translation of its mRNA binding targets in whole-testis ribosome profiling assays but did modestly affect their steady-state levels. Mutation of the ATPase motif in the helicase domain of YTHDC2 did not affect meiotic entry, but it blocked meiotic prophase I progression, causing sterility. Our findings inform a model in which YTHDC2 binds transcripts independent of m(6)A status and regulates gene expression during multiple stages of meiosis by distinct mechanisms.
Radtke AJ, Chu CJ, Yaniv Z, Yao L, Marr J, Beuschel RT, Ichise H, Gola A, Kabat J, Lowekamp B, Speranza E, Croteau J, Thakur N, Jonigk D, Davis JL, Hernandez JM, Germain RN
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IBEX: an iterative immunolabeling and chemical bleaching method for high-content imaging of diverse tissues

NATURE PROTOCOLS 2022 FEB; 17(2):378-+
High-content imaging is needed to catalog the variety of cellular phenotypes and multicellular ecosystems present in metazoan tissues. We recently developed iterative bleaching extends multiplexity (IBEX), an iterative immunolabeling and chemical bleaching method that enables multiplexed imaging (>65 parameters) in diverse tissues, including human organs relevant for international consortia efforts. IBEX is compatible with >250 commercially available antibodies and 16 unique fluorophores, and can be easily adopted to different imaging platforms using slides and nonproprietary imaging chambers. The overall protocol consists of iterative cycles of antibody labeling, imaging and chemical bleaching that can be completed at relatively low cost in 2-5 d by biologists with basic laboratory skills. To support widespread adoption, we provide extensive details on tissue processing, curated lists of validated antibodies and tissue-specific panels for multiplex imaging. Furthermore, instructions are included on how to automate the method using competitively priced instruments and reagents. Finally, we present a software solution for image alignment that can be executed by individuals without programming experience using open-source software and freeware. In summary, IBEX is a noncommercial method that can be readily implemented by academic laboratories and scaled to achieve high-content mapping of diverse tissues in support of a Human Reference Atlas or other such applications. IBEX (iterative bleaching extends multiplexity) is an iterative immunolabeling and chemical bleaching method that enables highly multiplexed imaging in diverse tissues.
Tobari Y, Theofanopoulou C, Mori C, Sato Y, Marutani M, Fujioka S, Konno N, Suzuki K, Furutani A, Hakataya S, Yao CT, Yang EY, Tsai CR, Tang PC, Chen CF, Boeckx C, Jarvis ED, Okanoya K
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Oxytocin variation and brain region-specific gene expression in a domesticated avian species

GENES BRAIN AND BEHAVIOR 2022 FEB; 21(2):? Article e12780
The Bengalese finch was domesticated more than 250 years ago from the wild white-rumped munia (WRM). Similar to other domesticated species, Bengalese finches show a reduced fear response and have lower corticosterone levels, compared to WRMs. Bengalese finches and munias also have different song types. Since oxytocin (OT) has been found to be involved in stress coping and auditory processing, we tested whether the OT sequence and brain expression pattern and content differ in wild munias and domesticated Bengalese finches. We sequenced the OT from 10 wild munias and 11 Bengalese finches and identified intra-strain variability in both the untranslated and protein-coding regions of the sequence, with all the latter giving rise to synonymous mutations. Several of these changes fall in specific transcription factor-binding sites, and show either a conserved or a relaxed evolutionary trend in the avian lineage, and in vertebrates in general. Although in situ hybridization in several hypothalamic nuclei did not reveal significant differences in the number of cells expressing OT between the two strains, real-time quantitative PCR showed a significantly higher OT mRNA expression in the cerebrum of the Bengalese finches relative to munias, but a significantly lower expression in their diencephalon. Our study thus points to a brain region-specific pattern of neurochemical expression in domesticated and wild avian strains, which could be linked to domestication and the behavioral changes associated with it.
Fins JJ
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Consciousness, Conflations, and Disability Rights: Denials of Care for Children in the "Minimally Conscious State"

JOURNAL OF LAW MEDICINE & ETHICS 2022; 50(1):181-183 Article PII S1073110522000225
This essay critiques the fiercely utilitarian allocation scheme of Cameron et al. Children have no hope of recovery if their lives are cut short based on administrative protocols that misrepresent the nature of their conditions. Unilateral futility judgements - especially those based on a false predicate - are discriminatory. When considering the best interests of children, we should see possibility in disability and not advance ill-informed utilitarianism.
Sunkari YK, Siripuram VK, Nguyen TL, Flajolet M
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High-power screening (HPS) empowered by DNA-encoded libraries

The world is totally dependent on medications. As science progresses, new, better, and cheaper drugs are needed more than ever. The pharmaceutical industry has been predominantly dependent on high-throughput screening (HTS) for the past three decades. Considering that the discovery rate has been relatively constant, can one hope for a much-needed sudden trend uptick? DNA-encoded libraries (DELs) and similar technologies, that have several orders of magnitude more screening power than HTS, and that we propose to group together under the umbrella term of high-power screening (HPS), are very well positioned to do exactly that. HPS also offers novel screening options such as parallel screening, ex vivo and in vivo screening, as well as a new path to druggable alternatives such as proteolysis targeting chimeras (PROTACs). Altogether, HPS unlocks novel powerful drug discovery avenues.
Sun QS, Burgren NM, Cheraghlou S, Paller AS, Larralde M, Bercovitch L, Levinsohn J, Ren I, Hu RH, Zhou J, Zaki T, Fan R, Tian C, Saraceni C, Nelson-Williams CJ, Loring E, Craiglow BG, Milstone LM, Lifton RP, Boyden LM, Choate KA
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The Genomic and Phenotypic Landscape of Ichthyosis An Analysis of 1000 Kindreds

JAMA DERMATOLOGY 2022 JAN; 158(1):16-25
IMPORTANCE Ichthyoses are clinically and genetically heterogeneous disorders characterized by scaly skin. Despite decades of investigation identifying pathogenic variants in more than 50 genes, clear genotype-phenotype associations have been difficult to establish. OBJECTIVE To expand the genotypic and phenotypic spectra of ichthyosis and delineate genotype-phenotype associations. DESIGN, SETTING, AND PARTICIPANTS This cohort study recruited an international group of individuals with ichthyosis and describes characteristic and distinguishing features of common genotypes, including genotype-phenotype associations, during a 10-year period from June 2011 to July 2021. Participants of all ages, races, and ethnicities were included and were enrolled worldwide from referral centers and patient advocacy groups. A questionnaire to assess clinical manifestations was completed by those with a genetic diagnosis. MAIN OUTCOMES AND MEASURES Genetic analysis of saliva or blood DNA, a phenotyping questionnaire, and standardized clinical photographs. Descriptive statistics, such as frequency counts, were used to describe the cases in the cohort. Fisher exact tests identified significant genotype-phenotype associations. RESULTS Results were reported for 1000 unrelated individuals enrolled from around the world (mean [SD] age, 50.0 [34.0] years; 524 [52.4%] were female, 427 [42.7%] were male, and 49 [4.9%] were not classified); 75% were from the US, 12% from Latin America, 4% from Canada, 3% from Europe, 3% from Asia, 2% from Africa, 1% from the Middle East, and 1% from Australia and New Zealand. A total of 266 novel disease-associated variants in 32 genes were identified among 869 kindreds. Of these, 241 (91%) pathogenic variants were found through multiplex amplicon sequencing and 25 (9%) through exome sequencing. Among the 869 participants with a genetic diagnosis, 304 participants (35%) completed the phenotyping questionnaire. Analysis of clinical manifestations in these 304 individuals revealed that pruritus, hypohydrosis, skin pain, eye problems, skin odor, and skin infections were the most prevalent self-reported features. Genotype-phenotype association analysis revealed that the presence of a collodion membrane at birth (odds ratio [OR], 6.7; 95% CI, 3.0-16.7; P<.001), skin odor (OR, 2.8; 95% CI, 1.1-6.8; P=.02), hearing problems (OR, 2.9; 95% CI, 1.6-5.5; P<.001), eye problems (OR, 3.0; 95% CI, 1.5-6.0; P<.001), and alopecia (OR, 4.6; 95% CI, 2.4-9.0; P<.001) were significantly associated with TGM1 variants compared with other ichthyosis genotypes studied. Skin pain (OR, 6.8; 95% CI, 1.6-61.2; P=.002), odor (OR, 5.7; 95% CI, 2.0-19.7; P<.001), and infections (OR, 3.1; 95% CI, 1.4-7.7; P=.03) were significantly associated with KRT10 pathogenic variants compared with disease-associated variants in other genes that cause ichthyosis. Pathogenic variants were identified in 869 (86.9%) participants. Most of the remaining individuals had unique phenotypes, enabling further genetic discovery. CONCLUSIONS AND RELEVANCE This cohort study expands the genotypic and phenotypic spectrum of ichthyosis, establishing associations between clinical manifestations and genotypes. Collectively, the findings may help improve clinical assessment, assist with developing customized management plans, and improve clinical course prognostication.