Light modulates glucose metabolism by a retina-hypothalamus-brown adipose tissue axis.

Public health studies indicate that artificial light is a high-risk factor for metabolic disorders. However, the neural mechanism underlying metabolic modulation by light remains elusive. Here, we found that light can acutely decrease glucose tolerance (GT) in mice by activation of intrinsically photosensitive retinal ganglion cells (ipRGCs) innervating the hypothalamic supraoptic nucleus (SON). Vasopressin neurons in the SON project to the paraventricular nucleus, then to the GABAergic neurons in the solitary tract nucleus, and eventually to brown adipose tissue (BAT). Light activation of this neural circuit directly blocks adaptive thermogenesis in BAT, thereby decreasing GT. In humans, light also modulates GT at the temperature where BAT is active. Thus, our work unveils a retina-SON-BAT axis that mediates the effect of light on glucose metabolism, which may explain the connection between artificial light and metabolic dysregulation, suggesting a potential prevention and treatment strategy for managing glucose metabolic disorders.

Melanopsin retinal ganglion cells mediate light-promoted brain development.

During development, melanopsin-expressing intrinsically photosensitive retinal ganglion cells (ipRGCs) become light sensitive much earlier than rods and cones. IpRGCs project to many subcortical areas, whereas physiological functions of these projections are yet to be fully elucidated. Here, we found that ipRGC-mediated light sensation promotes synaptogenesis of pyramidal neurons in various cortices and the hippocampus. This phenomenon depends on activation of ipRGCs and is mediated by the release of oxytocin from the supraoptic nucleus (SON) and the paraventricular nucleus (PVN) into cerebral-spinal fluid. We further characterized a direct connection between ipRGCs and oxytocin neurons in the SON and mutual projections between oxytocin neurons in the SON and PVN. Moreover, we showed that the lack of ipRGC-mediated, light-promoted early cortical synaptogenesis compromised learning ability in adult mice. Our results highlight the importance of light sensation early in life on the development of learning ability and therefore call attention to suitable light environment for infant care.

Mammalian Near-Infrared Image Vision through Injectable and Self-Powered Retinal Nanoantennae.

Mammals cannot see light over 700 nm in wavelength. This limitation is due to the physical thermodynamic properties of the photon-detecting opsins. However, the detection of naturally invisible near-infrared (NIR) light is a desirable ability. To break this limitation, we developed ocular injectable photoreceptor-binding upconversion nanoparticles (pbUCNPs). These nanoparticles anchored on retinal photoreceptors as miniature NIR light transducers to create NIR light image vision with negligible side effects. Based on single-photoreceptor recordings, electroretinograms, cortical recordings, and visual behavioral tests, we demonstrated that mice with these nanoantennae could not only perceive NIR light, but also see NIR light patterns. Excitingly, the injected mice were also able to differentiate sophisticated NIR shape patterns. Moreover, the NIR light pattern vision was ambient-daylight compatible and existed in parallel with native daylight vision. This new method will provide unmatched opportunities for a wide variety of emerging bio-integrated nanodevice designs and applications. VIDEO ABSTRACT.

Moderate UV Exposure Enhances Learning and Memory by Promoting a Novel Glutamate Biosynthetic Pathway in the Brain.

Sunlight exposure is known to affect mood, learning, and cognition. However, the molecular and cellular mechanisms remain elusive. Here, we show that moderate UV exposure elevated blood urocanic acid (UCA), which then crossed the blood-brain barrier. Single-cell mass spectrometry and isotopic labeling revealed a novel intra-neuronal metabolic pathway converting UCA to glutamate (GLU) after UV exposure. This UV-triggered GLU synthesis promoted its packaging into synaptic vesicles and its release at glutamatergic terminals in the motor cortex and hippocampus. Related behaviors, like rotarod learning and object recognition memory, were enhanced after UV exposure. All UV-induced metabolic, electrophysiological, and behavioral effects could be reproduced by the intravenous injection of UCA and diminished by the application of inhibitor or short hairpin RNA (shRNA) against urocanase, an enzyme critical for the conversion of UCA to GLU. These findings reveal a new GLU biosynthetic pathway, which could contribute to some of the sunlight-induced neurobehavioral changes.

Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution.

Spatial transcriptomics approaches have substantially advanced our capacity to detect the spatial distribution of RNA transcripts in tissues, yet it remains challenging to characterize whole-transcriptome-level data for single cells in space. Addressing this need, researchers have developed integration methods to combine spatial transcriptomic data with single-cell RNA-seq data to predict the spatial distribution of undetected transcripts and/or perform cell type deconvolution of spots in histological sections. However, to date, no independent studies have comparatively analyzed these integration methods to benchmark their performance. Here we present benchmarking of 16 integration methods using 45 paired datasets (comprising both spatial transcriptomics and scRNA-seq data) and 32 simulated datasets. We found that Tangram, gimVI, and SpaGE outperformed other integration methods for predicting the spatial distribution of RNA transcripts, whereas Cell2location, SpatialDWLS, and RCTD are the top-performing methods for the cell type deconvolution of spots. We provide a benchmark pipeline to help researchers select optimal integration methods to process their datasets.

Phylogenomic conflict analyses of the plastid and mitochondrial genomes via deep genome skimming highlight their independent evolutionary histories: A case study in the cinquefoil genus Potentilla sensu lato (Potentilleae, Rosaceae).

Phylogenomic conflicts are widespread among genomic data, with most previous studies primarily focusing on nuclear datasets instead of organellar genomes. In this study, we investigate phylogenetic conflict analyses within and between plastid and mitochondrial genomes using Potentilla as a case study. We generated three plastid datasets (coding, noncoding, and all-region) and one mitochondrial dataset (coding regions) to infer phylogenies based on concatenated and multispecies coalescent (MSC) methods. Conflict analyses were then performed using PhyParts and Quartet Sampling (QS). Both plastid and mitochondrial genomes divided the Potentilla into eight highly supported clades, two of which were newly identified in this study. While most organellar loci were uninformative for the majority of nodes (bootstrap value < 70%), PhyParts and QS detected conflicting signals within the two organellar genomes. Regression analyses revealed that conflict signals mainly occurred among shorter loci, whereas longer loci tended to be more concordant with the species tree. In addition, two significant disagreements between the two organellar genomes were detected, likely attributed to hybridization and/or incomplete lineage sorting. Our results demonstrate that mitochondrial genes can fully resolve the phylogenetic relationships among eight major clades of Potentilla and are not always linked with plastome in evolutionary history. Stochastic inferences appear to be the primary source of observed conflicts among the gene trees. We recommend that the loci with short sequence length or containing limited informative sites should be used cautiously in MSC analysis, and suggest the joint application of concatenated and MSC methods for phylogenetic inference using organellar genomes.

Relationship between subtype-specific minimal residual disease level and long-term prognosis in children with acute lymphoblastic leukemia.

Minimal residual disease (MRD) based risk stratification criteria for specific genetic subtypes remained unclear in childhood acute lymphoblastic leukemia (ALL). Among 723 children with newly diagnosed ALL treated with the Chinese Children Leukemia Group CCLG-2008 protocol, MRD was assessed at time point 1 (TP1, at the end of induction) and TP2 (before consolidation treatment) and the MRD levels significantly differed in patients with different fusion genes or immunophenotypes (P all < 0.001). Moreover, the prognostic impact of MRD varied by distinct molecular subtypes. We stratified patients in each molecular subtype into two MRD groups based on the results. For patients carrying BCR::ABL1 or KMT2A rearrangements, we classified patients with MRD < 10-2 at both TP1 and TP2 as the low MRD group and the others as the high MRD group. ETV6::RUNX1+ patients with TP1 MRD < 10-3 and TP2 MRD-negative were classified as the low MRD group and the others as the high MRD group. For T-ALL, We defined children with TP1 MRD ≥ 10-3 as the high MRD group and the others as the low MRD group. The 10-year relapse-free survival of low MRD group was significantly better than that of high MRD group. We verified the prognostic impact of the subtype-specific MRD-based stratification in patients treated with the BCH-ALL2003 protocol. In conclusion, the subtype-specific MRD risk stratification may contribute to the precise treatment of childhood ALL.

Signatures of the Bromine Atom and Open-Shell Spin Coupling in the X-ray Spectrum of the Bromobenzene Cation.

Tabletop X-ray spectroscopy measurements at the carbon K-edge complemented by ab initio calculations are used to investigate the influence of the bromine atom on the carbon core-valence transitions in the bromobenzene cation (BrBz+). The electronic ground state of the cation is prepared by resonance-enhanced two-photon ionization of neutral bromobenzene (BrBz) and probed by X-rays produced by high-harmonic generation (HHG). Replacing one of the hydrogen atoms in benzene with a bromine atom shifts the transition from the 1sC* orbital of the carbon atom (C*) bonded to bromine by ∼1 eV to higher energy in the X-ray spectrum compared to the other carbon atoms (C). Moreover, in BrBz+, the X-ray spectrum is dominated by two relatively intense transitions, 1sC→π* and 1sC*→σ*(C*-Br), where the second transition is enhanced relative to the neutral BrBz. In addition, a doublet peak shape for these two transitions is observed in the experiment. The 1sC→π* doublet peak shape arises due to the spin coupling of the unpaired electron in the partially vacant π orbital (from ionization) with the two other unpaired electrons resulting from the transition from the 1sC core orbital to the fully vacant π* orbitals. The 1sC*→σ* doublet peak shape results from several transitions involving σ* and vibrational C*-Br mode activations following the UV ionization, which demonstrates the impact of the C*-Br bond length on the core-valence transition as well as on the relaxation geometry of BrBz+.

Clinical, biological, and outcome features of P2RY8-CRLF2 and CRLF2 over-expression in pediatric B-cell precursor acute lymphoblastic leukemia according to the CCLG-ALL 2008 and 2018 protocol.

OBJECTIVES: CRLF2 alterations are associated with B-cell precursor acute lymphoblastic leukemia (BCP-ALL). This study aimed to explore the clinical, biological, and outcome features of pediatric BCP-ALL with CRLF2 abnormalities. METHODS: This study enrolled 630 childhood BCP-ALLs treated on CCLG-ALL 2008 or 2018 protocol. P2RY8-CRLF2 was determined by Sanger sequencing and CRLF2 expression was evaluated by qRT-PCR. The correlation between clinical, biological features and outcomes with P2RY8-CRLF2 or CRLF2 over-expression were analyzed. RESULTS: P2RY8-CRLF2 and CRLF2 over-expression were found in 3.33% and 5.71% respectively. P2RY8-CRLF2 was associated with male, higher frequency of CD7 expression, high WBC and MRD before consolidation. CRLF2 over-expression showed ETV6-RUNX1- , higher frequency of CD22, CD34, CD66c, CD86 expression, hyperdiploidy and high MRD at early treatment. The lower overall survival (OS) was found in patients with P2RY8-CRLF2 and confined only in IR group. Furthermore, adverse event-free survival and OS of P2RY8-CRLF2 were discovered comparing to those without known fusions or treated on CCLG-ALL 2008 protocol. However, P2RY8-CRLF2 was not confirmed as independent prognostic factors and no prognostic impact of CRLF2 over-expression was found. CONCLUSIONS: These findings indicate P2RY8-CRLF2 identifies a subset of patients with specific features and adverse outcomes that could be improved by risk-directed treatment.

Ultrafast X-ray Spectroscopy of Intersystem Crossing in Hexafluoroacetylacetone: Chromophore Photophysics and Spectral Changes in the Face of Electron-Withdrawing Groups.

Intersystem crossings between singlet and triplet states represent a crucial relaxation pathway in photochemical processes. Herein, we probe the intersystem crossing in hexafluoro-acetylacetone with ultrafast X-ray transient absorption spectroscopy at the carbon K-edge. We observe the excited state dynamics following excitation with 266 nm UV light to the 1ππ* (S2) state with element and site-specificity using a broadband soft X-ray pulse produced by high harmonic generation. These results are compared to X-ray spectra computed from orbital optimized density functional theory methods. It is found that the electron-withdrawing fluorine atoms decongest the X-ray absorption spectrum by enhancing separation between features originating from different carbon atoms. This facilitates the elucidation of structural and electronic dynamics at the chromophore. The evolution of the core-to-valence resonances at the carbon K-edge reveals an ultrafast population transfer between the 1nπ* (S1) and 3ππ* (T1) states on a 1.6 ± 0.4 ps time scale, which is similar to the 1.5 ps time scale earlier observed for acetylacetone [ J. Am. Chem. Soc. 2017, 139, 16576-16583, DOI: 10.1021/jacs.7b07532]. It therefore appears that terminal fluorination has little influence on the intersystem crossing rate of the acetylacetone chromophore. In addition, the significant role of hydrogen-bond opened and twisted rotational isomers is elucidated in the excited state dynamics by comparison of the experimental transient X-ray spectra with theory.

Protein structure prediction based on particle swarm optimization and tabu search strategy.

BACKGROUND: The stability of protein sequence structure plays an important role in the prevention and treatment of diseases. RESULTS: In this paper, particle swarm optimization and tabu search are combined to propose a new method for protein structure prediction. The experimental results show that: for four groups of artificial protein sequences with different lengths, this method obtains the lowest potential energy value and stable structure prediction results, and the effect is obviously better than the other two comparison methods. Taking the first group of protein sequences as an example, our method improves the prediction of minimum potential energy by 127% and 7% respectively. CONCLUSIONS: Therefore, the method proposed in this paper is more suitable for the prediction of protein structural stability.

Electrophysiological characterization of photoreceptor-like cells in human inducible pluripotent stem cell-derived retinal organoids during in vitro maturation.

Retinal organoids (ROs) derived from human inducible pluripotent stem cells (hiPSCs) exhibit considerable therapeutic potential. However, current quality control of ROs during in vitro differentiation is largely limited to the detection of molecular markers, often by immunostaining, polymerase chain reaction (PCR) assays and sequencing, often without proper functional assessments. As such, in the current study, we systemically characterized the physiological maturation of photoreceptor-like cells in hiPSC-derived ROs. By performing patch-clamp recordings from photoreceptor-like cells in ROs at distinct differentiation stages (ie, Differentiation Day [D]90, D150, and D200), we determined the electrophysiological properties of the plasma membrane and several characteristic ion channels closely associated with the physiological functions of the photoreceptors. Ionic hallmarks, such as hyperpolarization-activated cyclic nucleotide-gated (HCN) channels and cyclic nucleotide-gated (CNG) channels, matured progressively during differentiation. After D200 in culture, these characteristic currents closely resembled those in macaque or human native photoreceptors. Furthermore, we demonstrated that the hyperpolarization-activated inward current/depolarization-activated outward current ratio (I-120 /I+40 ), termed as the inward-outward current (IOC) ratio hereon, accurately represented the maturity of photoreceptors and could serve as a sensitive indicator of pathological state. Thus, this study provides a comprehensive dataset describing the electrophysiological maturation of photoreceptor-like cells in hiPSC-derived ROs for precise and sensitive quality control during RO differentiation.

Short- and long-term effects of 3.5-23.0 Tesla ultra-high magnetic fields on mice behaviour.

OBJECTIVES: Higher static magnetic field (SMF) enables higher imaging capability in magnetic resonance imaging (MRI), which encourages the development of ultra-high field MRIs above 20 T with a prerequisite for safety issues. However, animal tests of ≥ 20 T SMF exposure are very limited. The objective of the current study is to evaluate mice behaviour consequences of 3.5-23.0 T SMF exposure. METHODS: We systematically examined 112 mice for their short- and long-term behaviour responses to a 2-h exposure of 3.5-23.0 T SMFs. Locomotor activity and cognitive functions were measured by five behaviour tests, including balance beam, open field, elevated plus maze, three-chamber social recognition, and Morris water maze tests. RESULTS: Besides the transient short-term impairment of the sense of balance and locomotor activity, the 3.5-23.0 T SMFs did not have long-term negative effects on mice locomotion, anxiety level, social behaviour, or memory. In contrast, we observed anxiolytic effects and positive effects on social and spatial memory of SMFs, which is likely correlated with the significantly increased CaMKII level in the hippocampus region of high SMF-treated mice. CONCLUSIONS: Our study showed that the short exposures to high-field SMFs up to 23.0 T have negligible side effects on healthy mice and may even have beneficial outcomes in mice mood and memory, which is pertinent to the future medical application of ultra-high field SMFs in MRIs and beyond. KEY POINTS: • Short-term exposure to magnetic fields up to 23.0 T is safe for mice. • High-field static magnetic field exposure transiently reduced mice locomotion. • High-field static magnetic field enhances memory while reduces the anxiety level.

Integrating LASSO Feature Selection and Soft Voting Classifier to Identify Origins of Replication Sites.

Background: DNA replication plays an indispensable role in the transmission of genetic information. It is considered to be the basis of biological inheritance and the most fundamental process in all biological life. Considering that DNA replication initiates with a special location, namely the origin of replication, a better and accurate prediction of the origins of replication sites (ORIs) is essential to gain insight into the relationship with gene expression. Objective: In this study, we have developed an efficient predictor called iORI-LAVT for ORIs identification. Methods: This work focuses on extracting feature information from three aspects, including mono-nucleotide encoding, k-mer and ring-function-hydrogen-chemical properties. Subsequently, least absolute shrinkage and selection operator (LASSO) as a feature selection is applied to select the optimal features. Comparing the different combined soft voting classifiers results, the soft voting classifier based on GaussianNB and Logistic Regression is employed as the final classifier. Results: Based on 10-fold cross-validation test, the prediction accuracies of two benchmark datasets are 90.39% and 95.96%, respectively. As for the independent dataset, our method achieves high accuracy of 91.3%. Conclusion: Compared with previous predictors, iORI-LAVT outperforms the existing methods. It is believed that iORI-LAVT predictor is a promising alternative for further research on identifying ORIs.

Concordance of the 21-gene assay between core needle biopsy and resection specimens in early breast cancer patients.

BACKGROUND: Adjuvant therapy decisions may be partly based on the results of a multigene quantitative reverse transcription-polymerase chain reaction (RT-PCR)-based assay: the 21-gene recurrence score (RS) test of resection specimens. When necessary, core needle biopsy (CNB) may be considered as a surrogate. Here, we evaluated the concordance in gene expression according to results from RT-PCR-based RS testing between paired CNBs and resection specimens. METHODS: CNBs and resection specimens from 50 breast cancer (BC) patients were tested to calculate RSs. First, we examined the concordance of the ER, PR and HER-2 status of tissue samples indicated by immunohistochemical (IHC) and RT-PCR analyses. Then, we compared the IHC findings of ER, PR, HER-2 and Ki-67 staining across paired samples. Ultimately, the RS and single-gene results for ER, PR, HER-2 and Ki-67 were explored between paired samples. RESULTS: The concordance between IHC and RT-PCR was 100%, 80.0% and 100% for ER, PR and HER-2, respectively, in both resection specimens and CNBs. The concordance for IHC ER, PR, HER-2 and Ki-67 status was 100%, 94.0%, 52.0% and 82.0%, respectively, between paired samples. RS results from paired samples showed a strong correlation. The overall concordance in RS group classification between samples was 74%, 72% and 78% based on traditional cutoffs, TAILORx cutoffs and ASCO guidelines, respectively. ER, PR, HER-2 and Ki-67 were modestly- to- strongly correlated between paired samples according to the RT-PCR results. CONCLUSION: A modest- to- strong correlation of ER, PR, HER-2 and Ki-67 gene expression and RS between CNBs and resection specimens was observed in the present study. The 21-gene RS test could be reliably performed on CNBs. ER, PR and HER-2 status showed remarkable concordance between the IHC and RT-PCR analyses. The concordance between paired samples was high for the IHC ER, PR and Ki-67 results and low for HER-2.

Construction of Covalent Organic Frameworks via Three-Component One-Pot Strecker and Povarov Reactions.

Postsynthetic modification (PSM) has been demonstrated to be a powerful method for achieving new covalent organic frameworks (COFs) via single-step or multistep organic functional group transformations on established COF frameworks. PSM, however, might sometimes lead to collapse of the COF framework, decreases in crystallinity, or low postsynthetic yield due to the inherent limit of solid-state synthesis. Herein we report, for the first time, a new synthetic strategy that can generate new COFs via multicomponent one-pot in situ reactions. In total, 12 α-aminonitrile- and quinoline-linked COFs with high crystallinity and permanent porosity are successfully achieved by three-component one-pot in situ Strecker and Povarov reactions under solvothermal conditions in high yields. The obtained COFs feature the same structures as those obtained from the stepwise PSM approach on an established imine-linked COF. This in situ multicomponent assembly strategy, as a synthetic methodology parallel to PSM, might open a new route for constructing COFs that is not possible under PSM conditions.

Use Chou's 5-steps rule to identify DNase I hypersensitive sites via dinucleotide property matrix and extreme gradient boosting.

DNase I hypersensitive sites (DHSs) are highly sensitive active chromatin regions to DNase I enzymes, which provide the basis for the study of gene transcriptional regulation mechanism and play an important role in the analysis of gene expression regulatory elements. The identification of DHSs has contributed to biomedical research and genome analysis. There are already southern blotting technology and high-throughput sequencing technology to identify DHSs, but these experimental methods are often time-consuming and expensive, thus, novel and powerful computational methods are needed to predict DHSs. It is understood that researchers in related fields have proposed many feasible methods for the identification of DNase I hypersensitive sites. However, the accuracy of these methods is not satisfactory, so it is necessary to use more effective methods to predict DHSs. Therefore, on the basis of previous studies, we design a novel predictor called iDHS-DXG. First of all, we choose three sequence-derived feature representation methods to extract features, including kmer, mismatch and the dinucleotide property matrix based on Moran coefficient. Truncated singular value decomposition is selected for reducing the dimensionality of the benchmark dataset, and the optimal dimension is obtained through the test. Then, synthetic minority over-sampling technique is utilized to balance the positive and negative samples. After that, we introduce extreme gradient boosting ensemble classifier to predict DHSs. Compared with the previous research results, the main performance evaluation metrics of our method have been improved after five-fold cross-validation test. DHSs were identified on two human genome datasets with an accuracy of 90.84% and 91.27% respectively. This result shows that our method is a feasible, effective and competitive tool for the analysis of gene regulatory elements. Our research is helpful for biologists and geneticists to study genome analysis and gene regulation mechanism. Meanwhile, it is also of great significance to the development of human disease and drug design. Furthermore, the datasets and codes of iDHS-DXG can be obtained from the website: http://github.com/Xtian-696/iDHS-DXG/ .

Homochiral Covalent Organic Frameworks for Asymmetric Catalysis.

Owing to their permanent porosity, highly ordered and extended structure, good chemical stability, and tunability, covalent organic frameworks (COFs) have emerged as a new type of organic materials that can offer various applications in different fields. Benefiting from the huge database of organic reactions, the required functionality of COFs can be readily achieved by modification of the corresponding organic functional groups on either polymerizable monomers or established COF frameworks. This striking feature allows homochiral covalent organic frameworks (HCCOFs) to be reasonably designed and synthesized, as well as their use as a unique platform to fabricate asymmetric catalysts. This contribution provides an overview of new progress in HCCOF-based asymmetric catalysis, including design, synthesis, and their application in asymmetric organic synthesis. Moreover, major challenges and developing trends in this field are also discussed. It is anticipated that this review article will provide some new insights into HCCOFs for heterogeneous asymmetric catalysis and help to encourage further contributions in this young but promising field.

Prognostic significance of histologic grade and Ki-67 proliferation index in follicular lymphoma.

The prognostic value of histologic grading and the Ki-67 proliferation index in follicular lymphoma (FL) is controversial. This study investigated the clinical usefulness of these two factors in Asian FL patients. Four hundred and thirty-three patients diagnosed with FL were retrospectively reviewed with a median follow-up time of 47.0 months (range, 24.0-168.0). The 10-year overall survival (OS) rate and progression-free survival (PFS) rate were 91.0% and 47.1%, respectively. Grade 3B and grade 3B with diffuse large B cell lymphoma (DLBCL) showed a better PFS than grade 1-3A (P < 0.001), and similar findings were noted in patients who received rituximab-containing regimens (P = 0.002). In contrast, no significant differences in terms of OS or PFS were observed between grades 1-2 and 3A. In addition, patients with Ki-67 ≥ 30% had a significantly better PFS than patients with Ki-67 < 30% (P = 0.014), although the difference was eliminated in the multivariate analysis. Both grade and Ki-67 index had no impact on prognosis in patients who did not receive rituximab treatment. In conclusion, grade 3A is closely related to grade 1-2, as reflected by a similar indolent clinical course and a lower PFS rate than grade 3B/3B + DLBCL. In addition, a higher Ki-67 index seems to have a positive effect on PFS in FL patients.

Interplay of Open-Shell Spin-Coupling and Jahn-Teller Distortion in Benzene Radical Cation Probed by X-ray Spectroscopy.

We report a theoretical investigation and elucidation of the X-ray absorption spectra of neutral benzene and of the benzene cation. The generation of the cation by multiphoton ultraviolet (UV) ionization and the measurement of the carbon K-edge spectra of both species using a table-top high-harmonic generation source are described in the companion experimental paper [Epshtein, M.; et al. J. Phys. Chem. A http://dx.doi.org/10.1021/acs.jpca.0c08736]. We show that the 1sC → π transition serves as a sensitive signature of the transient cation formation, as it occurs outside of the spectral window of the parent neutral species. Moreover, the presence of the unpaired (spectator) electron in the π-subshell of the cation and the high symmetry of the system result in significant differences relative to neutral benzene in the spectral features associated with the 1sC → π* transitions. High-level calculations using equation-of-motion coupled-cluster theory provide the interpretation of the experimental spectra and insight into the electronic structure of benzene and its cation. The prominent split structure of the 1sC → π* band of the cation is attributed to the interplay between the coupling of the core → π* excitation with the unpaired electron in the π-subshell and the Jahn-Teller distortion. The calculations attribute most of the splitting (∼1-1.2 eV) to the spin coupling, which is visible already at the Franck-Condon structure, and we estimate the additional splitting due to structural relaxation to be around ∼0.1-0.2 eV. These results suggest that X-ray absorption with increased resolution might be able to disentangle electronic and structural aspects of the Jahn-Teller effect in the benzene cation.