Cancer-associated fibroblasts undergoing neoadjuvant chemotherapy suppress rectal cancer revealed by single-cell and spatial transcriptomics.

Neoadjuvant chemotherapy (NAC) for rectal cancer (RC) shows promising clinical response. The modulation of the tumor microenvironment (TME) by NAC and its association with therapeutic response remain unclear. Here, we use single-cell RNA sequencing and spatial transcriptome sequencing to examine the cell dynamics in 29 patients with RC, who are sampled pairwise before and after treatment. We construct a high-resolution cellular dynamic landscape remodeled by NAC and their associations with therapeutic response. NAC markedly reshapes the populations of cancer-associated fibroblasts (CAFs), which is strongly associated with therapeutic response. The remodeled CAF subsets regulate the TME through spatial recruitment and crosstalk to activate immunity and suppress tumor progression through multiple cytokines, including CXCL12, SLIT2, and DCN. In contrast, the epithelial-mesenchymal transition of malignant cells is upregulated by CAF_FAP through MIR4435-2HG induction, resulting in worse outcomes. Our study demonstrates that NAC inhibits tumor progression and modulates the TME by remodeling CAFs.

Development of a Robust Consensus Modeling Approach for Identifying Cellular and Media Metabolites Predictive of Mesenchymal Stromal Cell Potency.

Mesenchymal stromal cells (MSCs) have shown promise in regenerative medicine applications due in part to their ability to modulate immune cells. However, MSCs demonstrate significant functional heterogeneity in terms of their immunomodulatory function because of differences in MSC donor/tissue source, as well as non-standardized manufacturing approaches. As MSC metabolism plays a critical role in their ability to expand to therapeutic numbers ex vivo, we comprehensively profiled intracellular and extracellular metabolites throughout the expansion process to identify predictors of immunomodulatory function (T-cell modulation and indoleamine-2,3-dehydrogenase (IDO) activity). Here, we profiled media metabolites in a non-destructive manner through daily sampling and nuclear magnetic resonance (NMR), as well as MSC intracellular metabolites at the end of expansion using mass spectrometry (MS). Using a robust consensus machine learning approach, we were able to identify panels of metabolites predictive of MSC immunomodulatory function for 10 independent MSC lines. This approach consisted of identifying metabolites in 2 or more machine learning models and then building consensus models based on these consensus metabolite panels. Consensus intracellular metabolites with high predictive value included multiple lipid classes (such as phosphatidylcholines, phosphatidylethanolamines, and sphingomyelins) while consensus media metabolites included proline, phenylalanine, and pyruvate. Pathway enrichment identified metabolic pathways significantly associated with MSC function such as sphingolipid signaling and metabolism, arginine and proline metabolism, and autophagy. Overall, this work establishes a generalizable framework for identifying consensus predictive metabolites that predict MSC function, as well as guiding future MSC manufacturing efforts through identification of high-potency MSC lines and metabolic engineering.

Metabolomics and cytokine profiling of mesenchymal stromal cells identify markers predictive of T-cell suppression.

BACKGROUND AIMS: Mesenchymal stromal cells (MSCs) have shown great promise in the field of regenerative medicine, as many studies have shown that MSCs possess immunomodulatory function. Despite this promise, no MSC therapies have been licensed by the Food and Drug Administration. This lack of successful clinical translation is due in part to MSC heterogeneity and a lack of critical quality attributes. Although MSC indoleamine 2,3-dioxygnease (IDO) activity has been shown to correlate with MSC function, multiple predictive markers may be needed to better predict MSC function. METHODS: Three MSC lines (two bone marrow-derived, one induced pluripotent stem cell-derived) were expanded to three passages. At the time of harvest for each passage, cell pellets were collected for nuclear magnetic resonance (NMR) and ultra-performance liquid chromatography mass spectrometry (MS), and media were collected for cytokine profiling. Harvested cells were also cryopreserved for assessing function using T-cell proliferation and IDO activity assays. Linear regression was performed on functional data against NMR, MS and cytokines to reduce the number of important features, and partial least squares regression (PLSR) was used to obtain predictive markers of T-cell suppression based on variable importance in projection scores. RESULTS: Significant functional heterogeneity (in terms of T-cell suppression and IDO activity) was observed between the three MSC lines, as were donor-dependent differences based on passage. Omics characterization revealed distinct differences between cell lines using principal component analysis. Cell lines separated along principal component one based on tissue source (bone marrow-derived versus induced pluripotent stem cell-derived) for NMR, MS and cytokine profiles. PLSR modeling of important features predicted MSC functional capacity with NMR (R2 = 0.86), MS (R2 = 0.83), cytokines (R2 = 0.70) and a combination of all features (R2 = 0.88). CONCLUSIONS: The work described here provides a platform for identifying markers for predicting MSC functional capacity using PLSR modeling that could be used as release criteria and guide future manufacturing strategies for MSCs and other cell therapies.

Magnetism, half-metallicity, and topological signatures in Fe2-xVxPO5 (x = 0, 0.5, 1, 1.5, 2) materials: a potential class of advanced spintronic materials.

Novel spintronic materials combining both magnetism and nontrivial topological electronic structures have attracted increasing attention recently. Here, we systematically studied the doping effects, magnetism, half-metallicity, and topological properties in the family of Fe2-xVxPO5 (x = 0, 0.5, 1, 1.5, 2) compounds. Our results show that Fe2PO5 takes an antiferromagnetic (AFM) ordering with a zero total magnetic moment. Meanwhile, the material hosts a Dirac nodal line and a Weyl nodal line near the Fermi level. V2PO5 is a ferromagnetic (FM) nodal line half-metal with a 100% spin-polarized Weyl nodal line. After doping, we find that Fe1.5V0.5PO5, Fe1V1PO5 and Fe0.5V1.5PO5 all take ferrimagnetic (FiM) ordering, with the Fe and V atoms taking opposite spin directions. Both Fe1.5V0.5PO5 and Fe0.5V1.5PO5 are FiM half-metals. Meanwhile, they show several pairs of fully spin-polarized Weyl points near the Fermi level. Fe1V1PO5 is a FiM semiconductor with different sizes of band gaps in different spin channels. These Fe2-xVxPO5 materials not only provide a good research platform to study the novel properties combining magnetism and nontrivial band topology, but also have promising applications in spintronic applications.

Phosphorylation Modulates the Coregulatory Protein Exchange of the Nuclear Receptor Pregnane X Receptor.

The pregnane X receptor (PXR), or nuclear receptor (NR) 1I2, is a ligand-activated NR superfamily member that is enriched in liver and intestine in mammals. Activation of PXR regulates the expression of genes encoding key proteins involved in drug metabolism, drug efflux, and drug transport. Recent mechanistic investigations reveal that post-translational modifications (PTMs), such as phosphorylation, play a critical role in modulating the bimodal function of PXR-mediated transrepression and transactivation of target gene transcription. Upon ligand binding, PXR undergoes a conformational change that promotes dissociation of histone deacetylase-containing multiprotein corepressor protein complexes while simultaneously favoring recruitment histone acetyl transferase-containing complexes. Here we describe a novel adenoviral vector used to deliver and recover recombinant human PXR protein from primary cultures of hepatocytes. Using liquid chromatography and tandem mass spectrometry we report here that PXR is phosphorylated at amino acid residues threonine 135 (T135) and serine 221 (S221). Biochemical analysis reveals that these two residues play an important regulatory role in the cycling of corepressor and coactivator multiprotein complexes. These data further our foundational knowledge regarding the specific role of PTMs, namely phosphorylation, in regulating the biology of PXR. Future efforts are focused on using the novel tools described here to identify additional PTMs and protein partners of PXR in primary cultures of hepatocytes, an important experimental model system. SIGNIFICANCE STATEMENT: Pregnane X receptor (PXR), or nuclear receptor 1I2, is a key master regulator of drug-inducible CYP gene expression in liver and intestine in mammals. The novel biochemical tools described in this study demonstrate for the first time that in cultures of primary hepatocytes, human PXR is phosphorylated at amino acid residues threonine 135 (T135) and serine 221 (S221). Moreover, phosphorylation of PXR promotes the transrepression of its prototypical target gene CYP3A4 through modulating its interactions with coregulatory proteins.

Robust Spin-Gapless Behavior in the Newly Discovered Half Heusler Compound MnPK.

Spin gapless semiconductors have aroused high research interest since their discovery and a lot of effort has been exerted on their exploration, in terms of both theoretical calculation and experimental verification. Among different spin gapless materials, Heusler compounds stand out thanks to their high Curie temperature and highly diverse compositions. Especially, both theoretical and experimental studies have reported the presence of spin gapless properties in this kind of material. Recently, a new class of d0 - d Dirac half Heusler compound was introduced by Davatolhagh et al. and Dirac, and spin gapless semiconductivity has been successfully predicted in MnPK. To further expand the research in this direction, we conducted a systematical investigation on the spin gapless behavior of MnPK with both generalized gradient approximation (GGA) and GGA + Hubbard U methods under both uniform and tetragonal strain conditions by first principles calculation. Results show the spin gapless behavior in this material as revealed previously. Different Hubbard U values have been considered and they mainly affect the band structure in the spin-down channel while the spin gapless feature in the spin-up direction is maintained. The obtained lattice constant is very well consistent with a previous study. More importantly, it is found that the spin gapless property of MnPK shows good resistance for both uniform and tetragonal strains, and this robustness is very rare in the reported studies and can be extremely interesting and practical for the final end application. This study elaborates the electronic and magnetic properties of the half Heusler compound MnPK under uniform and tetragonal strain conditions, and the obtained results can give a very valuable reference for related research works, or even further motivate the experimental synthesis of the relative material.

A SUMO-acetyl switch in PXR biology.

Post-translational modification (PTM) of nuclear receptor superfamily members regulates various aspects of their biology to include sub-cellular localization, the repertoire of protein-binding partners, as well as their stability and mode of degradation. The nuclear receptor pregnane X receptor (PXR, NR1I2) is a master-regulator of the drug-inducible gene expression in liver and intestine. The PXR-mediated gene activation program is primarily recognized to increase drug metabolism, drug transport, and drug efflux pathways in these tissues. The activation of PXR also has important implications in significant human diseases including inflammatory bowel disease and cancer. Our recent investigations reveal that PXR is modified by multiple PTMs to include phosphorylation, SUMOylation, and ubiquitination. Using both primary cultures of hepatocytes and cell-based assays, we show here that PXR is modified through acetylation on lysine residues. Further, we show that increased acetylation of PXR stimulates its increased SUMO-modification to support active transcriptional suppression. Pharmacologic inhibition of lysine de-acetylation using trichostatin A (TSA) alters the sub-cellular localization of PXR in cultured hepatocytes, and also has a profound impact upon PXR transactivation capacity. Both the acetylation and SUMOylation status of the PXR protein is affected by its ability to associate with the lysine de-acetylating enzyme histone de-acetylase (HDAC)3 in a complex with silencing mediator of retinoic acid and thyroid hormone receptor (SMRT). Taken together, our data support a model in which a SUMO-acetyl 'switch' occurs such that acetylation of PXR likely stimulates SUMO-modification of PXR to promote the active repression of PXR-target gene expression. This article is part of a Special Issue entitled: Xenobiotic nuclear receptors: New Tricks for An Old Dog, edited by Dr. Wen Xie.

Light scattering induced by opposite microdomains in LiNbO3:Fe:Hf crystals.

We report on the light scattering phenomenon in annealed multidomain LiNbO3:Fe:Hf crystals. The scattering sources are found to be some fog-like "defects", which cause the polarization-dependent scattering of the light, and can be removed completely by the illumination of visible light. Based on these results and the etch patterns, these "defects" are suggested to be refractive index fluctuations induced by the space charges accumulated at the boundary of opposite microdomains. The influence of quick heating-up on the "defects" is also studied and the results firmly support our suggestion about the nature of the "defects". At last, the temporal curves of the transmitted intensity during the light scattering are explained. The mechanism for the opposite microdomain formation is also explained from the view of crystal growth.