Widespread somatic L1 retrotransposition in normal colorectal epithelium.

Throughout an individual's lifetime, genomic alterations accumulate in somatic cells1-11. However, the mutational landscape induced by retrotransposition of long interspersed nuclear element-1 (L1), a widespread mobile element in the human genome12-14, is poorly understood in normal cells. Here we explored the whole-genome sequences of 899 single-cell clones established from three different cell types collected from 28 individuals. We identified 1,708 somatic L1 retrotransposition events that were enriched in colorectal epithelium and showed a positive relationship with age. Fingerprinting of source elements showed 34 retrotransposition-competent L1s. Multidimensional analysis demonstrated that (1) somatic L1 retrotranspositions occur from early embryogenesis at a substantial rate, (2) epigenetic on/off of a source element is preferentially determined in the early organogenesis stage, (3) retrotransposition-competent L1s with a lower population allele frequency have higher retrotransposition activity and (4) only a small fraction of L1 transcripts in the cytoplasm are finally retrotransposed in somatic cells. Analysis of matched cancers further suggested that somatic L1 retrotransposition rate is substantially increased during colorectal tumourigenesis. In summary, this study illustrates L1 retrotransposition-induced somatic mosaicism in normal cells and provides insights into the genomic and epigenomic regulation of transposable elements over the human lifetime.

Clonal dynamics in early human embryogenesis inferred from somatic mutation.

Cellular dynamics and fate decision in early human embryogenesis remain largely unknown owing to the challenges of performing studies in human embryos1. Here, we explored whole-genomes of 334 single-cell colonies and targeted deep sequences of 379 bulk tissues obtained from various anatomical locations of seven recently deceased adult human donors. Using somatic mutations as an intrinsic barcode, we reconstructed early cellular phylogenies that demonstrate (1) an endogenous mutational rate that is higher in the first cell division but decreases to approximately one per cell per cell division later in life; (2) universal unequal contribution of early cells to embryo proper, resulting from early cellular bottlenecks that stochastically set aside epiblast cells within the embryo; (3) examples of varying degrees of early clonal imbalances between tissues on the left and right sides of the body, different germ layers and specific anatomical parts and organs; (4) emergence of a few ancestral cells that will substantially contribute to adult cell pools in blood and liver; and (5) presence of mitochondrial DNA heteroplasmy in the fertilized egg. Our approach also provides insights into the age-related mutational processes and loss of sex chromosomes in normal somatic cells. In sum, this study provides a foundation for future studies to complete cellular phylogenies in human embryogenesis.

Estimation of intrafamilial DNA contamination in family trio genome sequencing using deviation from Mendelian inheritance.

With the increasing number of sequencing projects involving families, quality control tools optimized for family genome sequencing are needed. However, accurately quantifying contamination in a DNA mixture is particularly difficult when genetically related family members are the sources. We developed TrioMix, a maximum likelihood estimation (MLE) framework based on Mendel's law of inheritance, to quantify DNA mixture between family members in genome sequencing data of parent-offspring trios. TrioMix can accurately deconvolute any intrafamilial DNA contamination, including parent-offspring, sibling-sibling, parent-parent, and even multiple familial sources. In addition, TrioMix can be applied to detect genomic abnormalities that deviate from Mendelian inheritance patterns, such as uniparental disomy (UPD) and chimerism. A genome-wide depth and variant allele frequency plot generated by TrioMix facilitates tracing the origin of Mendelian inheritance deviations. We showed that TrioMix could accurately deconvolute genomes in both simulated and real data sets.

Ultra-Low Level Somatic Mutations and Structural Variations in Focal Cortical Dysplasia Type II.

OBJECTIVE: Brain somatic mutations in mTOR pathway genes are a major genetic etiology of focal cortical dysplasia type II (FCDII). Despite a greater ability to detect low-level somatic mutations in the brain by deep sequencing and analytics, about 40% of cases remain genetically unexplained. METHODS: We included 2 independent cohorts consisting of 21 patients with mutation-negative FCDII without apparent mutations on conventional deep sequencing of bulk brain. To find ultra-low level somatic variants or structural variants, we isolated cells exhibiting phosphorylation of the S6 ribosomal protein (p-S6) in frozen brain tissues using fluorescence-activated cell sorting (FACS). We then performed deep whole-genome sequencing (WGS; >90×) in p-S6+ cells in a cohort of 11 patients with mutation-negative. Then, we simplified the method to whole-genome amplification and target gene sequencing of p-S6+ cells in independent cohort of 10 patients with mutation-negative followed by low-read depth WGS (10×). RESULTS: We found that 28.6% (6 of 21) of mutation-negative FCDII carries ultra-low level somatic mutations (less than 0.2% of variant allele frequency [VAF]) in mTOR pathway genes. Our method showed ~34 times increase of the average mutational burden in FACS mediated enrichment of p-S6+ cells (average VAF = 5.84%) than in bulky brain tissues (average VAF = 0.17%). We found that 19% (4 of 21) carried germline structural variations in GATOR1 complex undetectable in whole exome or targeted gene sequencing. CONCLUSIONS: Our method facilitates the detection of ultra-low level somatic mutations, in specifically p-S6+ cells, and germline structural variations and increases the genetic diagnostic rate up to ~80% for the entire FCDII cohort. ANN NEUROL 2023;93:1082-1093.

Short tandem repeat expansions in cortical layer-specific genes implicate in phenotypic severity and adaptability of autism spectrum disorder.

AIM: Short tandem repeats (STRs) are repetitive DNA sequences and highly mutable in various human disorders. While the involvement of STRs in various genetic disorders has been extensively studied, their role in autism spectrum disorder (ASD) remains largely unexplored. In this study, we aimed to investigate genetic association of STR expansions with ASD using whole genome sequencing (WGS) and identify risk loci associated with ASD phenotypes. METHODS: We analyzed WGS data of 634 ASD families and performed genome-wide evaluation for 12,929 STR loci. We found rare STR expansions that exceeded normal repeat lengths in autism cases compared to unaffected controls. By integrating single cell RNA and ATAC sequencing datasets of human postmortem brains, we prioritized STR loci in genes specifically expressed in cortical development stages. A deep learning method was used to predict functionality of ASD-associated STR loci. RESULTS: In ASD cases, rare STR expansions predominantly occurred in early cortical layer-specific genes involved in neurodevelopment, highlighting the cellular specificity of STR-associated genes in ASD risk. Leveraging deep learning prediction models, we demonstrated that these STR expansions disrupted the regulatory activity of enhancers and promoters, suggesting a potential mechanism through which they contribute to ASD pathogenesis. We found that individuals with ASD-associated STR expansions exhibited more severe ASD phenotypes and diminished adaptability compared to non-carriers. CONCLUSION: Short tandem repeat expansions in cortical layer-specific genes are associated with ASD and could potentially be a risk genetic factor for ASD. Our study is the first to show evidence of STR expansion associated with ASD in an under-investigated population.

A Formal γ-C-H Functionalization of Carboxylic Acids Guided by Metal-Nitrenoids as an Unprecedented Mechanistic Motif.

Harnessing the key intermediates in metal-catalyzed reactions is one of the most essential strategies in the development of selective organic transformations. The nitrogen group transfer reactivity of metal-nitrenoids to ubiquitous C-H bonds allows for diverse C-N bond formation to furnish synthetically valuable aminated products. In this study, we present an unprecedented reactivity of iridium and ruthenium nitrenoids to generate remote carbocation intermediates, which subsequently undergo nucleophile incorporation, thus developing a formal γ-C-H functionalization of carboxylic acids. Mechanistic investigations elucidated a unique singlet metal-nitrenoid reactivity to initiate an abstraction of γ-hydride to form the carbocation intermediate that eventually reacts with a broad range of carbon, nitrogen, and oxygen nucleophiles, as well as biorelevant molecules. Alternatively, the same intermediate can lead to deprotonation to afford ß,γ-unsaturated amides in a less nucleophilic solvent.

Visible to near-infrared single pixel microspectrometer using electrothermal MEMS grating.

Compact spectrometers facilitate non-destructive and point-of-care spectral analysis. Here we report a single-pixel microspectrometer (SPM) for visible to near-infrared (VIS-NIR) spectroscopy using MEMS diffraction grating. The SPM consists of slits, electrothermally rotating diffraction grating, spherical mirror, and photodiode. The spherical mirror collimates an incident beam and focuses the beam on the exit slit. The photodiode detects spectral signals dispersed by electrothermally rotating diffraction grating. The SPM was fully packaged within 1.7 cm3 and provides a spectral response range of 405 nm to 810 nm with an average 2.2 nm spectral resolution. This optical module provides an opportunity for diverse mobile spectroscopic applications such as healthcare monitoring, product screening, or non-destructive inspection.

Discovery of 3-((3-amino-1H-indazol-4-yl)ethynyl)-N-(4-((4-ethylpiperazin-1-yl)methyl)-3-(trifluoromethyl)phenyl)benzamide (AKE-72), a potent Pan-BCR-ABL inhibitor including the T315I gatekeeper resistant mutant.

BCR-ABL inhibition is an effective therapeutic approach for the treatment of chronic myeloid leukaemia (CML). Herein, we report the discovery of AKE-72 (5), a diarylamide 3-aminoindazole, as a potent pan-BCR-ABL inhibitor, including the imatinib-resistant mutant T315I. A focussed array of compounds 4a, 4b, and 5 has been designed based on our previously reported indazole I to improve its BCR-ABLT315I inhibitory activity. Replacing the morpholine moiety of I with the privileged tail (4-ethylpiperazin-1-yl)methyl afforded 5 (AKE-72) with IC50 values of < 0.5 nM, and 9 nM against BCR-ABLWT and BCR-ABLT315I, respectively. Moreover, AKE-72 potently inhibited a panel of other clinically important mutants in single-digit nanomolar IC50 values. AKE-72 elicited remarkable anti-leukemic activity against K-562 cell line (GI50 < 10 nM, TGI = 154 nM). In addition, AKE-72 strongly inhibited the proliferation of Ba/F3 cells expressing native BCR-ABL or its T315I mutant. Overall, AKE-72 may serve as a promising candidate for the treatment of CML, including those harbouring T315I mutation.

Overcoming the imatinib-resistant BCR-ABL mutants with new ureidobenzothiazole chemotypes endowed with potent and broad-spectrum anticancer activity.

The design of kinase inhibitors targeting the oncogenic kinase BCR-ABL constitutes a promising paradigm for treating chronic myeloid leukaemia (CML). Nevertheless, the efficacy of imatinib, the first FDA-approved targeted therapy for CML, is curbed by the emergence of resistance. Herein, we report the identification of the 2-methoxyphenyl ureidobenzothiazole AK-HW-90 (2b) as a potent pan-BCR-ABL inhibitor against imatinib-resistant mutants, particularly T315I. A concise array of six compounds 2a-f was designed based on our previously reported benzothiazole lead AKE-5l to improve its BCR-ABLT315I inhibitory activity. Replacing the 6-oxypicolinamide moiety of AKE-5l with o-methoxyphenyl and changing the propyl spacer with phenyl afforded 2a and AK-HW-90 (2b) with IC50 values of 2.0 and 0.65 nM against BCR-ABLT315I, respectively. AK-HW-90 showed superior anticancer potency to imatinib against multiple cancer cells (NCI), including leukaemia K-562. The obtained outcomes offer AK-HW-90 as a promising candidate for the treatment of CML and other types of cancer.

Discovery of New Quinolone-Based Diarylamides as Potent B-RAFV600E/C-RAF Kinase Inhibitors Endowed with Promising In Vitro Anticancer Activity.

The emergence of cancer resistance to targeted therapy represents a significant challenge in cancer treatment. Therefore, identifying new anticancer candidates, particularly those addressing oncogenic mutants, is an urgent medical demand. A campaign of structural modifications has been conducted to further optimize our previously reported 2-anilinoquinoline-diarylamides conjugate VII as a B-RAFV600E/C-RAF inhibitor. Considering the incorporation of a methylene bridge between the terminal phenyl and cyclic diamine, focused quinoline-based arylamides have been tailored, synthesized, and biologically evaluated. Among them, the 5/6-hydroxyquinolines 17b and 18a stood out as the most potent members, with IC50 values of 0.128 µM, 0.114 µM against B-RAFV600E, and 0.0653 µM, 0.0676 µM against C-RAF. Most importantly, 17b elicited remarkable inhibitory potency against the clinically resistant B-RAFV600K mutant with an IC50 value of 0.0616 µM. The putative binding mode of 17b and 18a were studied by molecular docking and molecular dynamics (MD). Moreover, the antiproliferative activity of all target compounds has been examined over a panel of NCI-60 human cancer cell lines. In agreement with cell-free assays, the designed compounds exerted superior anticancer impact over the lead quinoline VII against all cell lines at a 10 µM dose. Notably, both 17b and 18b showed highly potent antiproliferative activity against melanoma cell lines with growth percent under -90% (SK-MEL-29, SK-MEL-5, and UACC-62) at a single dose, while 17b maintained potency with GI50 values of 1.60-1.89 µM against melanoma cell lines. Taken together, 17b, a promising B-RAFV600E/V600K and C-RAF kinase inhibitor, may serve as a valuable candidate in the arsenal of anticancer chemotherapeutics.

Alternative splicing in mesenchymal stem cell differentiation.

The differentiation and maturation of mesenchymal stem cells (MSCs) to mesodermal and other lineages are known to be controlled by various extrinsic and intrinsic signals. The dysregulation of the MSC differentiation balance has been linked to several pathophysiological conditions, including obesity and osteoporosis. Previous research of the molecular mechanisms governing MSC differentiation has mostly focused on transcriptional regulation. However, recent findings are revealing the underrated role of alternative splicing (AS) in MSC differentiation and functions. In this review, we discuss recent progress in elucidating the regulatory roles of AS in MSC differentiation. We catalogue and highlight the key AS events that modulate MSC differentiation to major osteocytes, chondrocytes, and adipocytes, and discuss the regulatory mechanisms by which AS is regulated.

Modular Tuning of Electrophilic Reactivity of Iridium Nitrenoids for the Intermolecular Selective α-Amidation of ß-Keto Esters.

We report herein an Ir-catalyzed intermolecular amino group transfer to ß-keto esters (amides) to access α-aminocarbonyl products with excellent chemoselectivity. The key strategy was to engineer electrophilicity of the putative Ir-nitrenoids by tuning electronic property of the κ2-N,O chelating ligands, thus facilitating nucleophilic addition of enol π-bonds of 1,3-dicarbonyl substrates.

Mariana serpentinite mud volcanism exhumes subducted seamount materials: implications for the origin of life.

The subduction of seamounts and ridge features at convergent plate boundaries plays an important role in the deformation of the overriding plate and influences geochemical cycling and associated biological processes. Active serpentinization of forearc mantle and serpentinite mud volcanism on the Mariana forearc (between the trench and active volcanic arc) provides windows on subduction processes.  Here, we present (1) the first observation of an extensive exposure of an undeformed Cretaceous seamount currently being subducted at the Mariana Trench inner slope; (2) vertical deformation of the forearc region related to subduction of Pacific Plate seamounts and thickened crust; (3) recovered Ocean Drilling Program and International Ocean Discovery Program cores of serpentinite mudflows that confirm exhumation of various Pacific Plate lithologies, including subducted reef limestone; (4) petrologic, geochemical and paleontological data from the cores that show that Pacific Plate seamount exhumation covers greater spatial and temporal extents; (5) the inference that microbial communities associated with serpentinite mud volcanism may also be exhumed from the subducted plate seafloor and/or seamounts; and (6) the implications for effects of these processes with regard to evolution of life. This article is part of a discussion meeting issue 'Serpentine in the Earth system'.

Comparison of vaginal hysterectomy and laparoscopic hysterectomy: a systematic review and meta-analysis.

BACKGROUND: There are various surgical approaches of hysterectomy for benign indications. This study aimed to compare vaginal hysterectomy (VH) and laparoscopic hysterectomy (LH) with respect to their complications and operative outcomes. METHODS: We selected randomised controlled trials that compared VH with LH for benign gynaecological indications. We included studies published after January 2000 in the following databases: Medline, EMBASE, and CENTRAL (The Cochrane Library). The primary outcome was comparison of the complication rate. The secondary outcomes were comparisons of operating time, blood loss, intraoperative conversion, postoperative pain, length of hospital stay and duration of recuperation. We used Review Manager 5.3 software to perform the meta-analysis. RESULTS: Eighteen studies of 1618 patients met the inclusion criteria. The meta-analysis showed no differences in overall complications, intraoperative conversion, postoperative pain on the day of surgery and at 48 h, length of hospital stay and recuperation time between VH and LH. VH was associated with a shorter operating time and lower postoperative pain at 24 h than LH. CONCLUSIONS: When both surgical approaches are feasible, VH should remain the surgery of choice for benign hysterectomy.

Autologous Fat Injection for the Correction of Facial Depression Resulting From Silent Sinus Syndrome.

The case of a 59-year-old woman who underwent endoscopic sinus surgery for right maxillary sinusitis 5 years before visiting our otorhinolaryngologic department complaining of right-sided facial depression was described in this study. Computed tomography (CT) scans revealed right facial depression and retraction of the orbital floor due to a hypoplastic right maxillary sinus. Symptoms and CT findings corresponded with silent sinus syndrome. Facial depression is a rare symptom in silent sinus syndrome and is well corrected by autologous fat transfer.

Catalytic Alkyne Arylation Using Traceless Directing Groups.

By using Pd0 /Mandyphos, we achieved a three-component aminoarylation of alkynes to generate enamines, which are then hydrolyzed to either α-arylphenones or α,α-diarylketones. This Pd-catalyzed method overcomes established known pathways to enable the use of amines as traceless directing groups for C-C bond formation.

Internal jugular vein thrombosis with OHSS.

Ovarian hyperstimulation syndrome (OHSS) includes ovarian enlargement and ascites. It is usually mild but can be, rarely, fatal. Deep vein thrombosis (DVT) is among the potentially fatal complications of OHSS. During pregnancy, DVT is more common in the lower extremities than in the upper part of the body, but OHSS-related DVT occurs more frequently in the upper part. Internal jugular vein thrombosis is considered rare, and duplex ultrasound is the appropriate examination for its diagnosis. We present a rare case of internal jugular vein thrombosis following OHSS. © 2016 Wiley Periodicals, Inc. J Clin Ultrasound 45:450-452, 2017.

Rhodium-Catalyzed Enantioselective Cycloisomerization to Cyclohexenes Bearing Quaternary Carbon Centers.

We report a Rh-catalyzed enantioselective cycloisomerization of α,ω-heptadienes to afford cyclohexenes bearing quaternary carbon centers. Rhodium(I) and a new SDP ligand promote chemoselective formation of a cyclohex-3-enecarbaldehyde motif that is inaccessible by the Diels-Alder cycloaddition. Various α,α-bisallylaldehydes rearrange to generate six-membered rings by a mechanism triggered by aldehyde C-H bond activation. Mechanistic studies suggest a pathway involving regioselective carbometalation and endocyclic ß-hydride elimination.

Quencher-free molecular aptamer beacons (QF-MABs) for detection of ATP.

We have constructed a simple and efficient system-based on quencher-free molecular aptamer beacons (QF-MABs)-for probing ATP. In the absence of ATP, the fluorescence of a pyrene fluorophore on the loop position (15 nucleotides from the 5' end) of the optimal QF-MAB was quenched by the neighboring nucleobases; in its presence, fluorescence was recovered, due to a conformational change in the secondary structure of the QF-MAB.

Metal-organic cooperative catalysis in C-C bond activation.

This review describes recent advances that have been made in studies of transition metal-promoted metal-organic cooperative C-C single bond activation reactions of unstrained organic substances, which use 2-aminopicoline as a temporal chelating ligand. In addition, metal-organic cooperative C-C double bond and C-C triple bond cleavage processes are discussed in association with transition metal-catalyzed C-H bond activation. Recent progress made in these areas has opened up the new paradigms in synthetic organic chemistry for the construction of organic frameworks by structural reorganization of organic backbones. Among the many strategies devised, chelation-assisted C-C bond cleavage reactions, which operate through cooperation between metal complexes and organic substances, have attracted perhaps the greatest attention. Utilizing this approach, efficient C-C single bond activation reactions have been developed for a variety of substrates, including linear alkyl ketones, secondary alcohols, primary amines, and cycloalkanones. In addition, reactions that lead to cleavage of C-C double and triple bonds can be facilitated by using the metal-organic cooperation strategy. C-C double bonds in α,ß-enones can be cleaved by addition of cyclohexylamine, which facilitates Michael addition and retro-Mannich type fragmentation cascades proceeding via ß-aminoketimine intermediates. Aldehydes, which serve as one of the fragmentation products of these processes, can be trapped by chelation-assisted hydroacylation reactions to produce ketones. Finally, C-C triple bond cleavage of alkynes can be achieved through hydroacylation reactions with aldehydes and subsequent C-C double bond cleavage of the resulting α,ß-enones.