Developmental estrogen exposure in mice disrupts uterine epithelial cell differentiation and causes adenocarcinoma via Wnt/ß-catenin and PI3K/AKT signaling.

Tissue development entails genetically programmed differentiation of immature cell types to mature, fully differentiated cells. Exposure during development to non-mutagenic environmental factors can contribute to cancer risk, but the underlying mechanisms are not understood. We used a mouse model of endometrial adenocarcinoma that results from brief developmental exposure to an estrogenic chemical, diethylstilbestrol (DES), to determine causative factors. Single-cell RNA sequencing (scRNAseq) and spatial transcriptomics of adult control uteri revealed novel markers of uterine epithelial stem cells (EpSCs), identified distinct luminal and glandular progenitor cell (PC) populations, and defined glandular and luminal epithelium (LE) cell differentiation trajectories. Neonatal DES exposure disrupted uterine epithelial cell differentiation, resulting in a failure to generate an EpSC population or distinguishable glandular and luminal progenitors or mature cells. Instead, the DES-exposed epithelial cells were characterized by a single proliferating PC population and widespread activation of Wnt/ß-catenin signaling. The underlying endometrial stromal cells had dramatic increases in inflammatory signaling pathways and oxidative stress. Together, these changes activated phosphoinositide 3-kinase/AKT serine-threonine kinase signaling and malignant transformation of cells that were marked by phospho-AKT and the cancer-associated protein olfactomedin 4. Here, we defined a mechanistic pathway from developmental exposure to an endocrine disrupting chemical to the development of adult-onset cancer. These findings provide an explanation for how human cancers, which are often associated with abnormal activation of PI3K/AKT signaling, could result from exposure to environmental insults during development.

Functional Pdgfra fibroblast heterogeneity in normal and fibrotic mouse lung.

Aberrant fibroblast function plays a key role in the pathogenesis of idiopathic pulmonary fibrosis, a devastating disease of unrelenting extracellular matrix deposition in response to lung injury. Platelet-derived growth factor α-positive (Pdgfra+) lipofibroblasts (LipoFBs) are essential for lung injury response and maintenance of a functional alveolar stem cell niche. Little is known about the effects of lung injury on LipoFB function. Here, we used single-cell RNA-Seq (scRNA-Seq) technology and PdgfraGFP lineage tracing to generate a transcriptomic profile of Pdgfra+ fibroblasts in normal and injured mouse lungs 14 days after bleomycin exposure, generating 11 unique transcriptomic clusters that segregated according to treatment. While normal and injured LipoFBs shared a common gene signature, injured LipoFBs acquired fibrogenic pathway activity with an attenuation of lipogenic pathways. In a 3D organoid model, injured Pdgfra+ fibroblast-supported organoids were morphologically distinct from those cultured with normal fibroblasts, and scRNA-Seq analysis suggested distinct transcriptomic changes in alveolar epithelia supported by injured Pdgfra+ fibroblasts. In summary, while LipoFBs in injured lung have not migrated from their niche and retain their lipogenic identity, they acquire a potentially reversible fibrogenic profile, which may alter the kinetics of epithelial regeneration and potentially contribute to dysregulated repair, leading to fibrosis.

Essential role of Mg2+ in mouse preimplantation embryo development revealed by TRPM7 chanzyme-deficient gametes.

TRPM7 (transient receptor potential cation channel subfamily M member 7) is a chanzyme with channel and kinase domains essential for embryo development. Using gamete-specific Trpm7-null lines, we report that TRPM7-mediated Mg2+ influx is indispensable for reaching the blastocyst stage. TRPM7 is expressed dynamically from gametes to blastocysts; displays stage-specific localization on the plasma membrane, cytoplasm, and nucleus; and undergoes cleavage that produces C-terminal kinase fragments. TRPM7 underpins Mg2+ homeostasis, and excess Mg2+ but not Zn2+ or Ca2+ overcomes the arrest of Trpm7-null embryos; expressing Trpm7 mRNA restores development, but mutant versions fail or are partially rescued. Transcriptomic analyses of Trpm7-null embryos reveal an abundance of oxidative stress-pathway genes, confirmed by mitochondrial dysfunction, and a reduction in transcription factor networks essential for proliferation; Mg2+ supplementation corrects these defects. Hence, TRPM7 underpins Mg2+ homeostasis in preimplantation embryos, prevents oxidative stress, and promotes gene expression patterns necessary for developmental progression and cell-lineage specification.

A unique poly(A) tail profile uncovers the stability and translational activation of TOP transcripts during neuronal differentiation.

Cell differentiation is associated with global changes in translational activity. Here, we characterize how mRNA poly(A) tail processing supports this dynamic. We observe that decreased translation during neuronal differentiation of P19 cells correlates with the downregulation of 5'-terminal oligopyrimidine (TOP) transcripts which encode the translational machinery. Despite their downregulation, TOP transcripts remain highly stable and show increased translation as cells differentiate. Changes in TOP mRNA metabolism are reflected by their accumulation with poly(A) tails ∼60-nucleotide (nt) long. The dynamic changes in poly(A) processing can be partially recapitulated by depleting LARP1 or activating the mTOR pathway in undifferentiated cells. Although mTOR-induced accumulation of TOP mRNAs with tails ∼60-nt long does not trigger differentiation, it is associated with reduced proliferation of neuronal progenitors. We propose that while TOP mRNAs are transcriptionally silenced, their post-transcriptional regulation mediated by a specific poly(A) processing ensures an adequate supply of ribosomes to complete differentiation.

TUT4/7-mediated uridylation of a coronavirus subgenomic RNAs delays viral replication.

Coronaviruses are positive-strand RNA viruses with 3' polyadenylated genomes and subgenomic transcripts. The lengths of the viral poly(A) tails change during infection by mechanisms that remain poorly understood. Here, we use a splint-ligation method to measure the poly(A) tail length and poly(A) terminal uridylation and guanylation of the mouse hepatitis virus (MHV) RNAs. Upon infection of 17-CL1 cells with MHV, a member of the Betacoronavirus genus, we observe two populations of terminally uridylated viral transcripts, one with poly(A) tails ~44 nucleotides long and the other with poly(A) tails shorter than ~22 nucleotides. The mammalian terminal uridylyl-transferase 4 (TUT4) and terminal uridylyl-transferase 7 (TUT7), referred to as TUT4/7, add non-templated uracils to the 3'-end of endogenous transcripts with poly(A) tails shorter than ~30 nucleotides to trigger transcript decay. Here we find that depletion of the host TUT4/7 results in an increased replication capacity of the MHV virus. At late stages of infection, the population of uridylated subgenomic RNAs with tails shorter than ~22 nucleotides is reduced in the absence of TUT4/7 while the viral RNA load increases. Our findings indicate that TUT4/7 uridylation marks the MHV subgenomic RNAs for decay and delays viral replication.

UV-exposure, endogenous DNA damage, and DNA replication errors shape the spectra of genome changes in human skin.

Human skin is continuously exposed to environmental DNA damage leading to the accumulation of somatic mutations over the lifetime of an individual. Mutagenesis in human skin cells can be also caused by endogenous DNA damage and by DNA replication errors. The contributions of these processes to the somatic mutation load in the skin of healthy humans has so far not been accurately assessed because the low numbers of mutations from current sequencing methodologies preclude the distinction between sequencing errors and true somatic genome changes. In this work, we sequenced genomes of single cell-derived clonal lineages obtained from primary skin cells of a large cohort of healthy individuals across a wide range of ages. We report here the range of mutation load and a comprehensive view of the various somatic genome changes that accumulate in skin cells. We demonstrate that UV-induced base substitutions, insertions and deletions are prominent even in sun-shielded skin. In addition, we detect accumulation of mutations due to spontaneous deamination of methylated cytosines as well as insertions and deletions characteristic of DNA replication errors in these cells. The endogenously induced somatic mutations and indels also demonstrate a linear increase with age, while UV-induced mutation load is age-independent. Finally, we show that DNA replication stalling at common fragile sites are potent sources of gross chromosomal rearrangements in human cells. Thus, somatic mutations in skin of healthy individuals reflect the interplay of environmental and endogenous factors in facilitating genome instability and carcinogenesis.

Patterns, Profiles, and Parsimony: Dissecting Transcriptional Signatures From Minimal Single-Cell RNA-Seq Output With SALSA.

Single-cell RNA sequencing (scRNA-seq) technologies have precipitated the development of bioinformatic tools to reconstruct cell lineage specification and differentiation processes with single-cell precision. However, current start-up costs and recommended data volumes for statistical analysis remain prohibitively expensive, preventing scRNA-seq technologies from becoming mainstream. Here, we introduce single-cell amalgamation by latent semantic analysis (SALSA), a versatile workflow that combines measurement reliability metrics with latent variable extraction to infer robust expression profiles from ultra-sparse sc-RNAseq data. SALSA uses a matrix focusing approach that starts by identifying facultative genes with expression levels greater than experimental measurement precision and ends with cell clustering based on a minimal set of Profiler genes, each one a putative biomarker of cluster-specific expression profiles. To benchmark how SALSA performs in experimental settings, we used the publicly available 10X Genomics PBMC 3K dataset, a pre-curated silver standard from human frozen peripheral blood comprising 2,700 single-cell barcodes, and identified 7 major cell groups matching transcriptional profiles of peripheral blood cell types and driven agnostically by < 500 Profiler genes. Finally, we demonstrate successful implementation of SALSA in a replicative scRNA-seq scenario by using previously published DropSeq data from a multi-batch mouse retina experimental design, thereby identifying 10 transcriptionally distinct cell types from > 64,000 single cells across 7 independent biological replicates based on < 630 Profiler genes. With these results, SALSA demonstrates that robust pattern detection from scRNA-seq expression matrices only requires a fraction of the accrued data, suggesting that single-cell sequencing technologies can become affordable and widespread if meant as hypothesis-generation tools to extract large-scale differential expression effects.

Developmentally Programmed Tankyrase Activity Upregulates ß-Catenin and Licenses Progression of Embryonic Genome Activation.

Embryonic genome activation (EGA) is orchestrated by an intrinsic developmental program initiated during oocyte maturation with translation of stored maternal mRNAs. Here, we show that tankyrase, a poly(ADP-ribosyl) polymerase that regulates ß-catenin levels, undergoes programmed translation during oocyte maturation and serves an essential role in mouse EGA. Newly translated TNKS triggers proteasomal degradation of axin, reducing targeted destruction of ß-catenin and promoting ß-catenin-mediated transcription of target genes, including Myc. MYC mediates ribosomal RNA transcription in 2-cell embryos, supporting global protein synthesis. Suppression of tankyrase activity using knockdown or chemical inhibition causes loss of nuclear ß-catenin and global reductions in transcription and histone H3 acetylation. Chromatin and transcriptional profiling indicate that development arrests prior to the mid-2-cell stage, mediated in part by reductions in ß-catenin and MYC. These findings indicate that post-transcriptional regulation of tankyrase serves as a ligand-independent developmental mechanism for post-translational ß-catenin activation and is required to complete EGA.

Single-cell RNA sequencing reveals a heterogeneous response to Glucocorticoids in breast cancer cells.

Steroid hormone receptors such as the Glucocorticoid Receptor (GR) mediate transcriptional responses to hormones and are frequently targeted in the treatment of human diseases. Experiments using bulk populations of cells have provided a detailed picture of the global transcriptional hormone response but are unable to interrogate cell-to-cell transcriptional heterogeneity. To examine the glucocorticoid response in individual cells, we performed single cell RNA sequencing (scRNAseq) in a human breast cancer cell line. The transcriptional response to hormone was robustly detected in individual cells and scRNAseq provided additional statistical power to identify over 100 GR-regulated genes that were not detected in bulk RNAseq. scRNAseq revealed striking cell-to-cell variability in the hormone response. On average, individual hormone-treated cells showed a response at only 30% of the total set of GR target genes. Understanding the basis of this heterogeneity will be critical for the development of more precise models of steroid hormone signaling.

Interplay of permanent charge and hydrophobicity in the electrospray ionization of glycans.

The analysis of N-linked glycans by mass spectrometry (MS) has been characterized by low signal-to-noise ratios and high limits of detection due to their hydrophilicity and lack of basic sites able to be protonated. As a result, every step in glycan sample preparation must be thoroughly optimized in order to minimize sample loss, contamination, and analytical variability. Importantly, properties of glycans and their derivatized counterparts must be thoroughly studied in order to exploit certain characteristics for enhancing MS analysis. Herein, the effectiveness of the incorporation of a permanent charge is studied and determined to hamper glycan analysis. Also, a procedure for glycan hydrazone formation is optimized and outlined where a large number of variables were simultaneously analyzed using a fractional factorial design (FFD) in order to determine which conditions affected the reaction efficiency of the hydrazone formation reaction. Finally, the hydrophobic tagging of glycans is shown to be a viable opportunity to further increase the ion abundance of glycans in MS.

Barrier to linearity and anharmonic force field of the ketenyl radical.

The troublesome barrier to linearity of the ketenyl radical (HCCO) is precisely determined using state-of-the-art computations within the focal point approach, by combining complete basis set extrapolation, utilizing the aug-cc-pVXZ (X = D, T, Q, 5, 6) family of basis sets, with electron correlation treatments as extensive as coupled cluster theory with single, double, triple, and perturbative quadruple excitations [CCSDT(Q)]. Auxiliary terms such as diagonal Born-Oppenheimer corrections (DBOCs) and relativistic contributions are included. To gain a definitive theoretical treatment and to assess the effect of higher-order correlation on the structure of HCCO, we employ a composite approximation (c approximately ) to all-electron (AE) CCSDT(Q) theory at the complete basis set (CBS) limit for geometry optimizations. A final classical barrier to linearity of 630 +/- 30 cm(-1) is obtained for reaching the (2)Pi Renner-Teller configuration of HCCO from the (2)A'' ground state. Additionally, we compute fundamental vibrational frequencies and other spectroscopic constants by application of second-order vibrational perturbation theory (VPT2) to the full quartic force field at the AE-CCSD(T)/aug-cc-pCVQZ level. The resulting (nu(1), nu(2), nu(5)) fundamental frequencies of (3212, 2025, 483) cm(-1) agree satisfactorily with the experimental values (3232, 2023, 494) cm(-1).

The simulated photoelectron spectrum of 1-propynide.

The negative ion photoelectron spectrum of 1-propynide is computed by employing the multimode vibronic coupling approach. A three-state quasidiabatic Hamiltonian, H(d), is reported, which accurately represents the ab initio determined equilibrium geometries and harmonic frequencies of the ground X (2)A(1) state as well as the low-lying Jahn-Teller distorted components of the A (2)E excited state. It also reproduces both the minimum energy crossing point (MECP) on the symmetry-required (2)E(x)-(2)E(y) conical intersection seam and the MECP on the same symmetry (2)A(1)-(2)E(x) conical intersection seam. H(d) includes all terms through second order in internal coordinates for both the diagonal and off-diagonal blocks. It is centered at the (2)E(x)-(2)E(y) MECP and is determined using ab initio gradients and derivative couplings near both the (2)E(x)-(2)E(y) MECP and the X (2)A(1) equilibrium geometry. This construction is enabled by a recently reported normal equation based algorithm. The C(3v) symmetry of the system is used to significantly reduce the computational cost of the ab initio treatment. This H(d) is then expressed in a vibronic basis that is chosen for its ability to reduce the dimension of the vibronic expansion. The vibronic Hamiltonian matrix is diagonalized to obtain a negative ion photoelectron spectrum for 1-propynide-h(3). The determined spectrum compares favorably with previous spectroscopic results. In particular, the lines attributable to the (2)E state are found to be much weaker than those corresponding to the (2)A(1) state of 1-propynyl. This diminution of the (2)E state is attributable principally to the (2)E(x)-(2)A(1) conical intersection rather than an intrinsically small electronic transition moment for the production of the (2)E state.

Determining quasidiabatic coupled electronic state Hamiltonians using derivative couplings: A normal equations based method.

A self-consistent procedure for constructing a quasidiabatic Hamiltonian representing N(state) coupled electronic states in the vicinity of an arbitrary point in nuclear coordinate space is described. The matrix elements of the Hamiltonian are polynomials of arbitrary order. Employing a crude adiabatic basis, the coefficients of the linear terms are determined exactly using analytic gradient techniques. The remaining polynomial coefficients are determined from the normal form of a system of pseudolinear equations, which uses energy gradient and derivative coupling information obtained from reliable multireference configuration interaction wave functions. In a previous implementation energy gradient and derivative coupling information were employed to limit the number of nuclear configurations at which ab initio data were required to determine the unknown coefficients. Conversely, the key aspect of the current approach is the use of ab initio data over an extended range of nuclear configurations. The normal form of the system of pseudolinear equations is introduced here to obtain a least-squares fit to what would have been an (intractable) overcomplete set of data in the previous approach. This method provides a quasidiabatic representation that minimizes the residual derivative coupling in a least-squares sense, a means to extend the domain of accuracy of the diabatic Hamiltonian or refine its accuracy within a given domain, and a way to impose point group symmetry and hermiticity. These attributes are illustrated using the 1 (2)A(1) and 1 (2)E states of the 1-propynyl radical, CH(3)CC.

Homonuclear transition-metal trimers.

Density-functional theory has been used to determine the ground-state geometries and electronic states for homonuclear transition-metal trimers constrained to equilateral triangle geometries. This represents the first application of consistent theoretical methods to all of the ten 3d block transition-metal trimers, from scandium to zinc. A search of the potential surfaces yields the following electronic ground states and bond lengths: Sc3(2A1',2.83 A), Ti3(7E',2.32 A), V3(2E",2.06 A), Cr3(17E',2.92 A), Mn3(16A2',2.73 A), Fe3(11E",2.24 A), Co3(6E",2.18 A), Ni3(3A2",2.23 A), Cu3(2E',2.37 A), and Zn3(1A1',2.93 A). Vibrational frequencies, several low-lying electronic states, and trends in bond lengths and atomization energies are discussed. The predicted dissociation energies DeltaE(M3-->M2+M) are 49.4 kcal mol(-1)(Sc3), 64.3 kcal mol(-1)(Ti3), 60.7 kcal mol(-1)(V3), 11.5 kcal mol(-1)(Cr3), 32.4 kcal mol(-1)(Mn3), 61.5 kcal mol(-1)(Fe3), 78.0 kcal mol(-1)(Co3), 86.1 kcal mol(-1)(Ni3), 26.8 kcal mol(-1)(Cu3), and 4.5 kcal mol(-1)(Zn3).

The microwave and infrared spectroscopy of benzaldehyde: conflict between theory and experimental deductions.

Recently, it has been proposed that ab initio calculations cannot accurately treat molecules comprised of a benzene ring with a pi-conjugated substituent, for example, benzaldehyde. Theoretical predictions of the benzaldehyde barrier to internal rotation are typically a factor of 2 too high in comparison to the experimental values of 4.67 (infared) and 4.90 (microwave) kcal mol(-1). However, both experiments use Pitzer's 1946 model to compute the reduced moment of inertia and employ the experimentally observed torsional frequency to deduce benzaldehyde's rotational barrier. When Pitzer's model is applied to a system with a nonconjugated functional group, such as phenol, the model and theoretical values are in close agreement. Therefore, we conclude the model may not account for conjugation between the substituent and the pi-system of benzene. The experimental values of the benzaldehyde rotational barrier are therefore misleading. The true rotational barrier lies closer to the theoretically extrapolated limit of 7.7 kcal mol(-1), based on coupled cluster theory.