Functional analysis and clinical classification of 462 germline BRCA2 missense variants affecting the DNA binding domain.

Variants of uncertain significance (VUSs) in BRCA2 are a common result of hereditary cancer genetic testing. While more than 4,000 unique VUSs, comprised of missense or intronic variants, have been identified in BRCA2, the few missense variants now classified clinically as pathogenic or likely pathogenic are predominantly located in the region encoding the C-terminal DNA binding domain (DBD). We report on functional evaluation of the influence of 462 BRCA2 missense variants affecting the DBD on DNA repair activity of BRCA2 using a homology-directed DNA double-strand break repair assay. Of these, 137 were functionally abnormal, 313 were functionally normal, and 12 demonstrated intermediate function. Comparisons with other functional studies of BRCA2 missense variants yielded strong correlations. Sequence-based in silico prediction models had high sensitivity, but limited specificity, relative to the homology-directed repair assay. Combining the functional results with clinical and genetic data in an American College of Medical Genetics (ACMG)/Association for Molecular Pathology (AMP)-like variant classification framework from a clinical testing laboratory, after excluding known splicing variants and functionally intermediate variants, classified 431 of 442 (97.5%) missense variants (129 as pathogenic/likely pathogenic and 302 as benign/likely benign). Functionally abnormal variants classified as pathogenic by ACMG/AMP rules were associated with a slightly lower risk of breast cancer (odds ratio [OR] 5.15, 95% confidence interval [CI] 3.43-7.83) than BRCA2 DBD protein truncating variants (OR 8.56, 95% CI 6.03-12.36). Overall, functional studies of BRCA2 variants using validated assays substantially improved the variant classification yield from ACMG/AMP models and are expected to improve clinical management of many individuals found to harbor germline BRCA2 missense VUS.

An atlas of combinatorial transcriptional regulation in mouse and man.

Combinatorial interactions among transcription factors are critical to directing tissue-specific gene expression. To build a global atlas of these combinations, we have screened for physical interactions among the majority of human and mouse DNA-binding transcription factors (TFs). The complete networks contain 762 human and 877 mouse interactions. Analysis of the networks reveals that highly connected TFs are broadly expressed across tissues, and that roughly half of the measured interactions are conserved between mouse and human. The data highlight the importance of TF combinations for determining cell fate, and they lead to the identification of a SMAD3/FLI1 complex expressed during development of immunity. The availability of large TF combinatorial networks in both human and mouse will provide many opportunities to study gene regulation, tissue differentiation, and mammalian evolution.

Biodiversity impacts and conservation implications of urban land expansion projected to 2050.

SignificanceUnderstanding the impacts of urbanization and the associated urban land expansion on species is vital for informed urban planning that minimizes biodiversity loss. Predicting habitat that will be lost to urban land expansion for over 30,000 species under three different future scenarios, we find that up to 855 species are directly threatened due to unmitigated urbanization. Our projections pinpoint rapidly urbanizing regions of sub-Saharan Africa, South America, Mesoamerica, and Southeast Asia where, without careful planning, urbanization is expected to cause particularly large biodiversity loss. Our findings highlight the urgent need for an increased focus on urban land in global conservation strategies and identify high-priority areas for this engagement.

Synthesis of indol-3-yl-benzofurans and carbazoles via Cu(OTf)2-catalyzed [3 + 2] and [4 + 2] cycloaddition.

An efficient Cu(OTf)2-catalyzed [3 + 2] cycloaddition of indole-3-acrylate with p-benzoquinone has been developed to construct two distinct indole-tethered benzofuran scaffolds, offering the first-ever selective access to these scaffolds. Moreover, the [4 + 2] cycloaddition reaction of indole-3-acrylate with vinyl ketone derivatives was used to synthesize carbazoles in a one-pot manner. The disclosed strategies provided a series of selective transformations under low-catalyst loading, with a broad substrate scope featuring diverse applicability and practical simplicity of the developed protocol with easily available substrates.

Structure of the membrane-assembled retromer coat determined by cryo-electron tomography.

Eukaryotic cells traffic proteins and lipids between different compartments using protein-coated vesicles and tubules. The retromer complex is required to generate cargo-selective tubulovesicular carriers from endosomal membranes1-3. Conserved in eukaryotes, retromer controls the cellular localization and homeostasis of hundreds of transmembrane proteins, and its disruption is associated with major neurodegenerative disorders4-7. How retromer is assembled and how it is recruited to form coated tubules is not known. Here we describe the structure of the retromer complex (Vps26-Vps29-Vps35) assembled on membrane tubules with the bin/amphiphysin/rvs-domain-containing sorting nexin protein Vps5, using cryo-electron tomography and subtomogram averaging. This reveals a membrane-associated Vps5 array, from which arches of retromer extend away from the membrane surface. Vps35 forms the 'legs' of these arches, and Vps29 resides at the apex where it is free to interact with regulatory factors. The bases of the arches connect to each other and to Vps5 through Vps26, and the presence of the same arches on coated tubules within cells confirms their functional importance. Vps5 binds to Vps26 at a position analogous to the previously described cargo- and Snx3-binding site, which suggests the existence of distinct retromer-sorting nexin assemblies. The structure provides insight into the architecture of the coat and its mechanism of assembly, and suggests that retromer promotes tubule formation by directing the distribution of sorting nexin proteins on the membrane surface while providing a scaffold for regulatory-protein interactions.

Social Media Misinformation about Pregnancy and COVID-19 Vaccines: A Systematic Review.

OBJECTIVE: The objectives of this study were to identify common social media misconceptions about COVID-19 vaccination in pregnancy, explain the spread of misinformation, and identify solutions to guide clinical practice and policy. METHODOLOGY: A systematic review was conducted and the databases Embase and Medline were searched from December 2019 to February 8, 2023, using terms related to social media, pregnancy, COVID-19 vaccines and misinformation. The inclusion criteria were original research studies that discussed misinformation about COVID-19 vaccination during pregnancy on social media. The exclusion criteria were review articles, no full text, and not published in English. Two independent reviewers conducted screening, extraction, and quality assessment. RESULTS: Our search identified 76 articles, of which 3 fulfilled eligibility criteria. Included studies were of moderate and high quality. The social media platforms investigated included Facebook, Google Searches, Instagram, Reddit, TikTok, and Twitter. Misinformation was related to concerns regarding vaccine safety, and its association with infertility. Misinformation was increased due to lack of content monitoring on social media, exclusion of pregnant women from early vaccine trials, lack of information from reputable health sources on social media, and others. Suggested solutions were directed at pregnancy care providers (PCPs) and public health/government. Suggestions included: (i) integrating COVID-19 vaccination information into antenatal care, (ii) PCPs and public health should increase their social media presence to disseminate information, (iii) address population-specific vaccine concerns in a culturally relevant manner, and others. CONCLUSION: Increased availability of information from reputable health sources through multiple channels could increase COVID-19 vaccine uptake in the pregnant population and help combat misinformation.

Formation of retromer transport carriers is disrupted by the Parkinson disease-linked Vps35 D620N variant.

Retromer core complex is an endosomal scaffold that plays a critical role in orchestrating protein trafficking within the endosomal system. Here we characterized the effect of the Parkinson's disease-linked Vps35 D620N in the endo-lysosomal system using Vps35 D620N rescue cell models. Vps35 D620N fully rescues the lysosomal and autophagy defects caused by retromer knock-out. Analogous to Vps35 knock out cells, the endosome-to-trans-Golgi network transport of cation-independent mannose 6-phosphate receptor (CI-M6PR) is impaired in Vps35 D620N rescue cells because of a reduced capacity to form endosome transport carriers. Cells expressing the Vps35 D620N variant have altered endosomal morphology, resulting in smaller, rounder structures with less tubule-like branches. At the molecular level retromer incorporating Vps35 D620N variant has a decreased binding to retromer associated proteins wiskott-aldrich syndrome protein and SCAR homologue (WASH) and SNX3 which are known to associate with retromer to form the endosome transport carriers. Hence, the partial defects on retrograde protein trafficking carriers in the presence of Vps35 D620N represents an altered cellular state able to cause Parkinson's disease.

Design, Synthesis, and Applications of a Vanadium Complex: An Effective Catalyst for the Direct Conversion of Alcohols and Aldehydes to Esters.

A novel bench-stable V-catalyst [(L2)VIVO](ClO4) was synthesized and characterized by X-ray diffraction (XRD) analysis and FT-IR, UV-visible, and EPR spectroscopies, which confirmed its excellent catalytic activity. In application, aldehydes are rapidly converted into their corresponding esters without additives in a one-pot manner using a newly developed catalyst [(L2)VIVO](ClO4) and H2O2 as a green oxidant. The developed method is compatible with a broad range of densely substituted aldehydes and allows for the facile preparation of aliphatic, aromatic, and heterocyclic esters, including esters derived from CD3OD, methanol, ethanol, iso-propanol, n-butanol, sec-butyl alcohol, and propargylic alcohol. Gratifyingly, numerous alcohols also directly converted to their corresponding esters in a one-pot manner. We disclose herein the direct conversion of two different functionalities (alcohols and aldehydes) into esters (33 examples) with satisfactory yields, showing the potential of the developed catalyst toward varied oxidative organic transformations in a one-pot manner.

A Catecholaldimine-Based NiII-Complex as an Effective Catalyst for the Direct Conversion of Alcohols to trans-Cinnamonitriles and Aldehydes.

A nickel(II) complex [Ni(HL)2] 1 was synthesized by treatment of a new catecholaldimine-based ligand with NiCl2·6H2O in methanol at room temperature. Complex 1 showed excellent catalytic activity where aromatic and heterocyclic alcohols were rapidly converted into trans-cinnamonitrile in a one-pot manner via oxidative olefination in the presence of KOH. The potential of the disclosed catalyst and the results obtained for the direct conversion of alcohols to two different functionalities (trans-cinnamonitrile and aldehydes) are well supported by DFT studies.

The rapid construction and biological evaluation of densely substituted pyrrolo[1,2-a]indoles via a BF3·OEt2-assisted cascade approach.

Lewis-acid cascade reactions promoted by BF3·OEt2 are reported for the synthesis of highly substituted pyrrolo[1,2-a]indoles and congeners of benzofuro[2,3-b]indoles. These reactions are highly regio- and diastereoselective towards generating up to five contiguous stereogenic centers, including two vicinal quaternary centers. Furthermore, an established cascade approach and the mechanism proposed herein are well supported by quantum chemistry calculations. In addition, a self-dimerization intermediate was trapped and isolated to establish a strategy for potential access to both pyrrolo and benzo indole derivatives, leaving sufficient freedom for broadening. Furthermore, in-silico molecular docking and all atomistic molecular dynamic (MD) simulation analysis suggests that the synthesized pyrrolo[1,2-a]indole derivatives stably bind at the active site of the mycobacterial secreted tyrosine phosphatase B (MptpB) enzyme, an emerging anti-mycobacterial drug target. Deep learning-based affinity predictions and MMPBGBSA-based energy calculations of the docked poses are presented herein.

Recent advances in cascade reactions and their mechanistic insights: a concise strategy to synthesize complex natural products and organic scaffolds.

The beauty of cascade reactions to bestow us with cumbersome organic scaffolds has made them a cutting-edge area of research. Although the planning of cascades may require intuition, their results can be highly impactful. The development of cascades to provide specific targeted molecules of an appropriate structural and stereochemical framework poses a significant challenge but can serve as one of the most impressive tools in organic synthesis. This review shares a broad interest in compiling cascade transformations towards the construction of polycyclic frameworks, induction of chirality/asymmetry in the protocol, etc. to solve diverse challenges in organic synthesis pursuits, as cascades enable the rapid and efficient construction of complex architectures from simple molecules. The studies highlighted herein manifest the utilization of a range of cascade reactions under various classifications for generating natural product skeletons such as palau'amine, benzosimuline, arcutinine, and others from simple building blocks, with emphasis on breakthroughs and potential for asymmetric synthesis. The exquisite synthetic designs of recently completed total synthesis of natural products with a focus on strategic concerns are also highlighted in this review.

Laying the groundwork for participatory research with a Rohingya refugee community.

Laying the groundwork in preparation for community-based participatory research (CBPR) is critical, particularly for academic-community partnerships with refugees and immigrants who have not yet engaged in CBPR. OBJECTIVE: In this article, we describe the process of developing and nurturing a CBPR partnership between university researchers and a newly arrived Rohingya refugee community, providing background on the community and our collaborative efforts to date. METHOD: Co-occurring, interdependent, and iterative processes related to relationship building, capacity building, and research and informal data gathering helped to develop and promote the partnership. RESULTS: Case study examples illustrate challenges and possible resolutions. CONCLUSIONS: Particularly for newly arrived refugee and immigrant communities, historical disenfranchisement and current stressors can impact how CBPR partnerships are developed and nurtured, thus, ongoing considerations of chronosystemic factors, attending to community-specific priorities while also connecting with other communities, and embracing multiple roles of academic researcher, advocate, and ally, can facilitate CBPR partnership development and future research projects. (PsycInfo Database Record (c) 2022 APA, all rights reserved).

Isotope-Coded Maleimide Affinity Tags for Proteomics Applications.

Isotope-coded affinity tags (ICATs) are valuable tools for mass spectrometry-based quantitative proteomics, in particular, for comparison of protein (cysteine-residue) thiol oxidation state in normal, stressed, and diseased tissue. However, the iodoacetamido electrophile used in most commercial ICATs suffers from poor thiol-selectivity and modest rates of adduct formation, which can lead to spurious results. Hence, we designed and synthesized three ICATs containing thiol-selective N-alkylmaleimide electrophiles (isotope-coded maleimide affinity tags = ICMATs) and assessed these as mass spectrometry probes for ratiometric analysis of lysozyme and muscle proteomes. Two ICMAT pairs containing butylene/D8-butylene linkers were effective MS probes, but not ideal for typical proteomics workflows, because peptides bearing these tags frequently did not coelute with HPLC. A switch to a phenylene/13C6-phenylene linker solved this issue without compromising the efficiency of adduct formation.

Design, Synthesis, and Biological Evaluation of Tubulysin Analogues, Linker-Drugs, and Antibody-Drug Conjugates, Insights into Structure-Activity Relationships, and Tubulysin-Tubulin Binding Derived from X-ray Crystallographic Analysis.

Molecular design, synthesis, and biological evaluation of tubulysin analogues, linker-drugs, and antibody-drug conjugates are described. Among the new discoveries reported is the identification of new potent analogues within the tubulysin family that carry a C11 alkyl ether substituent, rather than the usual ester structural motif at that position, a fact that endows the former with higher plasma stability than that of the latter. Also described herein are X-ray crystallographic analysis studies of two tubulin-tubulysin complexes formed within the α/ß interface between two tubulin heterodimers and two highly potent tubulysin analogues, one of which exhibited a different binding mode to the one previously reported for tubulysin M. The X-ray crystallographic analysis-derived new insights into the binding modes of these tubulysin analogues explain their potencies and provide inspiration for further design, synthesis, and biological investigations within this class of antitumor agents. A number of these analogues were conjugated as payloads with appropriate linkers at different sites allowing their attachment onto targeting antibodies for cancer therapies. A number of such antibody-drug conjugates were constructed and tested, both in vivo and in vitro, leading to the identification of at least one promising ADC (Herceptin-LD3), warranting further investigations.

A randomized group antenatal care pilot showed increased partner communication and partner HIV testing during pregnancy in Malawi and Tanzania.

BACKGROUND: HIV testing at antenatal care (ANC) is critical to achieving zero new infections in sub-Saharan Africa. Although most women are tested at ANC, they remain at risk for HIV exposure and transmission to their infant when their partners are not tested. This study evaluates how an HIV-enhanced and Centering-based group ANC model-Group ANC+ that uses interactive learning to practice partner communication is associated with improvements in partner HIV testing during pregnancy. METHODS: A randomized pilot study conducted in Malawi and Tanzania found multiple positive outcomes for pregnant women (n = 218) assigned to Group ANC+ versus individual ANC. This analysis adds previously unpublished results for two late pregnancy outcomes: communication with partner about three reproductive health topics (safer sex, HIV testing, and family planning) and partner HIV testing since the first antenatal care visit. Multivariate logistic regression models were used to assess the effect of type of ANC on partner communication and partner testing. We also conducted a mediation analysis to assess whether partner communication mediated the effect of type of care on partner HIV testing. RESULTS: Nearly 70% of women in Group ANC+ reported communicating about reproductive health with their partner, compared to 45% of women in individual ANC. After controlling for significant covariates, women in group ANC were twice as likely as those in individual ANC to report that their partner got an HIV test (OR 1.99; 95% CI: 1.08, 3.66). The positive effect of the Group ANC + model on partner HIV testing was fully mediated by increased partner communication. CONCLUSIONS: HIV prevention was included in group ANC health promotion without compromising services and coverage of standard ANC topics, demonstrating that local high-priority health promotion needs can be integrated into ANC using a Group ANC+. These findings provide evidence that greater partner communication can promote healthy reproductive behaviors, including HIV prevention. Additional research is needed to understand the processes by which group ANC allowed women to discuss sensitive topics with partners and how these communications led to partner HIV testing.

Sorting nexin 27 (SNX27) regulates the trafficking and activity of the glutamine transporter ASCT2.

Alanine-, serine-, cysteine-preferring transporter 2 (ASCT2, SLC1A5) is responsible for the uptake of glutamine into cells, a major source of cellular energy and a key regulator of mammalian target of rapamycin (mTOR) activation. Furthermore, ASCT2 expression has been reported in several human cancers, making it a potential target for both diagnostic and therapeutic purposes. Here we identify ASCT2 as a membrane-trafficked cargo molecule, sorted through a direct interaction with the PDZ domain of sorting nexin 27 (SNX27). Using both membrane fractionation and subcellular localization approaches, we demonstrate that the majority of ASCT2 resides at the plasma membrane. This is significantly reduced within CrispR-mediated SNX27 knockout (KO) cell lines, as it is missorted into the lysosomal degradation pathway. The reduction of ASCT2 levels in SNX27 KO cells leads to decreased glutamine uptake, which, in turn, inhibits cellular proliferation. SNX27 KO cells also present impaired activation of the mTOR complex 1 (mTORC1) pathway and enhanced autophagy. Taken together, our data reveal a role for SNX27 in glutamine uptake and amino acid-stimulated mTORC1 activation via modulation of ASCT2 intracellular trafficking.

A role of GCC88 in the retrograde transport of CI-M6PR and the maintenance of lysosomal activity.

GCC88 is a golgin coiled-coil protein at the trans-Golgi (TGN) that functions as a tethering factor for the endosome-derived retrograde transport vesicles. Here, we demonstrate that GCC88 is required for the endosome-to-TGN retrograde transport of the cation-independent mannose 6-phosphate receptor (CI-M6PR). The knockout of GCC88 perturbs the retrieval of CI-M6PR and decreases its cellular level at the steady state, which causes the improper processing of newly synthesized cathepsin-D, a lysosomal hydrolase dependent on CI-M6PR for its delivery to lysosomes. At the whole cell level, the knockout of GCC88 reduces the lysosomal proteolytic capacity but does not impair of the efficiency of autophagy within these cells.

Improved Total Synthesis of Tubulysins and Design, Synthesis, and Biological Evaluation of New Tubulysins with Highly Potent Cytotoxicities against Cancer Cells as Potential Payloads for Antibody-Drug Conjugates.

Improved, streamlined total syntheses of natural tubulysins such as V (Tb45) and U (Tb46) and pretubulysin D (PTb-D43), and their application to the synthesis of designed tubulysin analogues (Tb44, PTb-D42, PTb-D47-PTb-D49, and Tb50-Tb120), are described. Cytotoxicity evaluation of the synthesized compounds against certain cancer cell lines revealed a number of novel analogues with exceptional potencies [e.g., Tb111: IC50 = 40 pM against MES SA (uterine sarcoma) cell line; IC50 = 6 pM against HEK 293T (human embryonic kidney cancer) cell line; and IC50 = 1.54 nM against MES SA DX (MES SA with marked multidrug resistance) cell line]. These studies led to a set of valuable structure-activity relationships that provide guidance to further molecular design, synthesis, and biological evaluation studies. The extremely potent cytotoxic compounds discovered in these investigations are highly desirable as potential payloads for antibody-drug conjugates and other drug delivery systems for personalized targeted cancer chemotherapies.

Parkinson Disease-linked Vps35 R524W Mutation Impairs the Endosomal Association of Retromer and Induces α-Synuclein Aggregation.

Endosomal sorting is a highly orchestrated cellular process. Retromer is a heterotrimeric complex that associates with endosomal membranes and facilitates the retrograde sorting of multiple receptors, including the cation-independent mannose 6-phosphate receptor for lysosomal enzymes. The cycling of retromer on and off the endosomal membrane is regulated by a network of retromer-interacting proteins. Here, we find that Parkinson disease-associated Vps35 variant, R524W, but not P316S, is a loss-of-function mutation as marked by a reduced association with this regulatory network and dysregulation of endosomal receptor sorting. Expression of Vps35 R524W-containing retromer results in the accumulation of intracellular α-synuclein-positive aggregates, a hallmark of Parkinson disease. Overall, the Vps35 R524W-containing retromer has a decreased endosomal association, which can be partially rescued by R55, a small molecule previously shown to stabilize the retromer complex, supporting the potential for future targeting of the retromer complex in the treatment of Parkinson disease.

Streamlined Total Synthesis of Trioxacarcins and Its Application to the Design, Synthesis, and Biological Evaluation of Analogues Thereof. Discovery of Simpler Designed and Potent Trioxacarcin Analogues.

A streamlined total synthesis of the naturally occurring antitumor agents trioxacarcins is described, along with its application to the construction of a series of designed analogues of these complex natural products. Biological evaluation of the synthesized compounds revealed a number of highly potent, and yet structurally simpler, compounds that are effective against certain cancer cell lines, including a drug-resistant line. A novel one-step synthesis of anthraquinones and chloro anthraquinones from simple ketone precursors and phenylselenyl chloride is also described. The reported work, featuring novel chemistry and cascade reactions, has potential applications in cancer therapy, including targeted approaches as in antibody-drug conjugates.