Multiplexed Target Profiling with Integrated Chemical Genomics and Chemical Proteomics.

Target identification is crucial for elucidating the mechanisms of bioactive molecules in drug discovery. However, traditional methods assess compounds individually, making it challenging to efficiently examine multiple compounds in parallel, especially for structurally diverse compounds. This study reports a novel strategy called chemical genomics-facilitated chemical proteomics (CGCP) for multiplexing the target identification of bioactive small molecules. CGCP correlates compounds' perturbation of global transcription, or chemical genomic profiles, with their reactivity toward target proteins, enabling simultaneous identification of targets. We demonstrated the utility of CGCP by studying the targets of celastrol (Cel) and four other electrophilic compounds with varying levels of similarity to Cel based on their chemical genomic profiles. We identified multiple novel targets and binding sites shared by the compounds in a single experiment. CGCP enabled multiplexity and improved the efficiency of target identification for structurally distinct compounds, indicating its potential to accelerate drug discovery.

ACLY and ACSS2 link nutrient-dependent chromatin accessibility to CD8 T cell effector responses.

Coordination of cellular metabolism is essential for optimal T cell responses. Here, we identify cytosolic acetyl-CoA production as an essential metabolic node for CD8 T cell function in vivo. We show that CD8 T cell responses to infection depend on acetyl-CoA derived from citrate via the enzyme ATP citrate lyase (ACLY). However, ablation of ACLY triggers an alternative, acetate-dependent pathway for acetyl-CoA production mediated by acyl-CoA synthetase short-chain family member 2 (ACSS2). Mechanistically, acetate fuels both the TCA cycle and cytosolic acetyl-CoA production, impacting T cell effector responses, acetate-dependent histone acetylation, and chromatin accessibility at effector gene loci. When ACLY is functional, ACSS2 is not required, suggesting acetate is not an obligate metabolic substrate for CD8 T cell function. However, loss of ACLY renders CD8 T cells dependent on acetate (via ACSS2) to maintain acetyl-CoA production and effector function. Together, ACLY and ACSS2 coordinate cytosolic acetyl-CoA production in CD8 T cells to maintain chromatin accessibility and T cell effector function.

Transcriptional programming mediated by the histone demethylase KDM5C regulates dendritic cell population heterogeneity and function.

Functional and phenotypic heterogeneity of dendritic cells (DCs) play crucial roles in facilitating the development of diverse immune responses essential for host protection. Here, we report that KDM5C, a histone lysine demethylase, regulates conventional or classical DC (cDC) and plasmacytoid DC (pDC) population heterogeneity and function. Mice deficient in KDM5C in DCs have increased proportions of cDC2Bs and cDC1s, which is partly dependent on type I interferon (IFN) and pDCs. Loss of KDM5C results in an increase in Ly6C- pDCs, which, compared to Ly6C+ pDCs, have limited ability to produce type I IFN and more efficiently stimulate antigen-specific CD8 T cells. KDM5C-deficient DCs have increased expression of inflammatory genes, altered expression of lineage-specific genes, and decreased function. In response to Listeria infection, KDM5C-deficient mice mount reduced CD8 T cell responses due to decreased antigen presentation by cDC1s. Thus, KDM5C is a key regulator of DC heterogeneity and critical driver of the functional properties of DCs.

Homeobox and Polycomb target gene methylation in human solid tumors.

DNA methylation is an epigenetic mark that plays an important role in defining cancer phenotypes, with global hypomethylation and focal hypermethylation at CpG islands observed in tumors. These methylation marks can also be used to define tumor types and provide an avenue for biomarker identification. The homeobox gene class is one that has potential for this use, as well as other genes that are Polycomb Repressive Complex 2 targets. To begin to unravel this relationship, we performed a pan-cancer DNA methylation analysis using sixteen Illumina HM450k array datasets from TCGA, delving into cancer-specific qualities and commonalities between tumor types with a focus on homeobox genes. Our comparisons of tumor to normal samples suggest that homeobox genes commonly harbor significant hypermethylated differentially methylated regions. We identified two homeobox genes, HOXA3 and HOXD10, that are hypermethylated in all 16 cancer types. Furthermore, we identified several potential homeobox gene biomarkers from our analysis that are uniquely methylated in only one tumor type and that could be used as screening tools in the future. Overall, our study demonstrates unique patterns of DNA methylation in multiple tumor types and expands on the interplay between the homeobox gene class and oncogenesis.

Logistic regression analysis of risk factors for post-operative morbidities in parotidectomy: a retrospective cohort study.

OBJECTIVE: In this study, we reviewed the post-operative complications in parotidectomy and its association with various patient, tumour and surgical factors. METHODS: All parotidectomies performed in our regional unit between 2013 to 2020 were identified. Electronic medical record and clinic letters were reviewed for any post-operative complications. A logistical regression model was applied on data collected on twelve patient factors, three tumour factors and four surgical factors. RESULTS: 379 cases of parotidectomy were identified in the eight-year study period. 55% (n = 210) were documented with nine types of post-operative complications. This study identified age >80 (odds ratio = 1.89, p = 0.018), active smoker (odds ratio = 0.94, p = 0.018), total parotidectomy approach (odds ratio = 1.77, p = 0.012), longer operation time (odds ratio = 0.006, p = 0.015) and hypertension (odds ratio = 1.23, p = 0.019) were associated with a higher risk of facial nerve palsy. Predictive factors were also identified for auricular nerve numbness and Frey syndrome. CONCLUSION: This study revealed the incidences and potential predictors of post-operative complications in parotidectomy. Notably, the grade of operator (consultants/ registrars) had no effect on the possibility of adverse outcome, reflecting patient safety was not compromised for training. These findings can be used in patient counselling and guide treatment options to minimise post-operative complications.

Coronavirus disease 2019 pandemic telephone two-week-wait referrals in head and neck cancer - how safe were they?

OBJECTIVE: During the coronavirus disease 2019 pandemic, ENT-UK recommended a move from face-to-face clinics to telephone appointments. This study reviewed the safety of telephone clinics for urgent two-week-wait cancer referrals. METHODS: Patients consulted in telephone clinics between April and November 2020 were identified from an electronic database. Study patients included those diagnosed with malignant disease at six months. The Head and Neck Cancer Risk Calculator version 2 score, outcome of the initial clinic and final diagnoses were reviewed. RESULTS: A total of 1062 patients were triaged in clinic; 9.2 per cent (n = 98) were diagnosed with cancer at 6 months. Of these 98 patients, 69 received an urgent face-to-face appointment, 26 underwent urgent scans and 3 had a delayed telephone review. Twenty patients (20.4 per cent) diagnosed with cancer had a low-risk Head and Neck Cancer Risk Calculator score. CONCLUSION: The late diagnosis rate of 0.28 per cent suggests a small proportion of cancer could have been missed. Telephone clinics, whilst a pragmatic means to maintain patient flow during the pandemic, could result in late diagnoses.

Association of MRI Volume Parameters in Predicting Patient Outcome at Time of Initial Diagnosis of Glioblastoma.

PURPOSE: Patients with glioblastoma (GBM) may demonstrate varying patterns of infiltration and relapse. Improving the ability to predict these patterns may influence the management strategies at the time of initial diagnosis. This study aims to examine the impact of the ratio (T2/T1) of the non-enhancing volume in T2-weighted images (T2) to the enhancing volume in MRI T1-weighted gadolinium-enhanced images (T1gad) on patient outcome. METHODS AND MATERIALS: A retrospective audit was performed from established prospective databases in patients managed consecutively with radiation therapy (RT) for GBM between 2016 and 2019. Patient, tumour and treatment-related factors were assessed in relation to outcome. Volumetric data from the initial diagnostic MRI were obtained via the manual segmentation of the T1gd and T2 abnormalities. A T2/T1 ratio was calculated from these volumes. The initial relapse site was assessed on MRI in relation to the site of the original T1gad volume and surgical cavity. The major endpoints were median relapse-free survival (RFS) from the date of diagnosis and site of initial relapse (defined as either local at the initial surgical site or any distance more than 20 mm from initial T1gad abnormality). The analysis was performed for association between known prognostic factors as well as the radiological factors using log-rank tests for subgroup comparisons, with correction for multiple comparisons. RESULTS: One hundred and seventy-seven patients with GBM were managed consecutively with RT between 2016 and 2019 and were eligible for the analysis. The median age was 62 years. Seventy-four percent were managed under a 60Gy (Stupp) protocol, whilst 26% were on a 40Gy (Elderly) protocol. Major neuroanatomical subsites were Lateral Temporal (18%), Anterior Temporal (13%) and Medial Frontal (10%). Median volumes on T1gd and T2 were 20 cm3 (q1-3:8-43) and 37 cm3 (q1-3: 17-70), respectively. The median T2/T1 ratio was 2.1. For the whole cohort, the median OS was 16.0 months (95%CI:14.1-18.0). One hundred and forty-eight patients have relapsed with a median RFS of 11.4 months (95%CI:10.4-12.5). A component of distant relapse was evident in 43.9% of relapses, with 23.6% isolated relapse. Better ECOG performance Status (p = 0.007), greater extent of resection (p = 0.020), MGMT methylation (p < 0.001) and RT60Gy Dose (p = 0.050) were associated with improved RFS. Although the continuous variable of initial T1gd volume (p = 0.39) and T2 volume (p = 0.23) were not associated with RFS, the lowest T2/T1 quartile (reflecting a relatively lower T2 volume compared to T1gd volume) was significantly associated with improved RFS (p = 0.016) compared with the highest quartile. The lowest T2/T1 ratio quartile was also associated with a lower risk of distant relapse (p = 0.031). CONCLUSION: In patients diagnosed with GBM, the volumetric parameters of the diagnostic MRI with a ratio of T2 and T1gad abnormality may assist in the prediction of relapse-free survival and patterns of relapse. A further understanding of these relationships has the potential to impact the design of future radiation therapy target volume delineation protocols.

Single-embryo RNA sequencing for continuous and sex-specific gene expression analysis on Drosophila.

Exploring early embryonic gene expression is challenging due to the rate of development and the limited material available. Here, we present a protocol for ordering Drosophila embryos along a developmental pseudo-time trajectory and determining the sex of the embryos using RNA-seq data. We describe steps for sample collection, RNA isolation, RNA-seq, and RNA-seq data processing. We then detail the establishment of a continuous transcriptome dataset for assessing gene expression throughout early development and in a sex-specific manner. For complete details on the use and execution of this protocol, please refer to Pérez-Mojica et al.1.

Establishment of paternal methylation imprint at the H19/Igf2 imprinting control region.

The insulator model explains the workings of the H19 and Igf2 imprinted domain in the soma, where insulation of the Igf2 promoter from its enhancers occurs by CTCF in the maternally inherited unmethylated chromosome but not the paternally inherited methylated allele. The molecular mechanism that targets paternal methylation imprint establishment to the imprinting control region (ICR) in the male germline is unknown. We tested the function of prospermatogonia-specific broad low-level transcription in this process using mouse genetics. Paternal imprint establishment was abnormal when transcription was stopped at the entry point to the ICR. The germline epimutation persisted into the paternal allele of the soma, resulting in reduced Igf2 in fetal organs and reduced fetal growth, consistent with the insulator model and insulin-like growth factor 2 (IGF2)'s role as fetal growth factor. These results collectively support the role of broad low-level transcription through the H19/Igf2 ICR in the establishment of its paternal methylation imprint in the male germ line, with implications for Silver-Russell syndrome.

Differential effects of sugar and fat on adipose tissue inflammation.

Obese individuals experience low grade inflammation initiated within their adipose tissue. However, the early events that lead to the release of these inflammatory factors from adipose tissue are poorly characterized. To separate glucose effects from lipid effects on adipose tissue, we used an adipose-specific TXNIP knockout model where excess basal glucose influx into adipocytes led to modest increase in adiposity without using high fat diet. We found an uncoupling of two events that are generally presumed to be coregulated: (1) an increase of adipose tissue macrophage (ATM) number; and (2) pro-inflammatory activation of ATMs. These two events are associated with different triggering signals: elevated free fatty acids output and extracellular matrix remodeling with increased ATM number, whereas decreased adiponectin level with activated ATM. This separation reflects non-overlapping pathways regulated by glucose and lipids in adipocytes, and neither group alone is sufficient to elicit the full inflammatory response in adipose tissue.

Ketolysis drives CD8+ T cell effector function through effects on histone acetylation.

Environmental nutrient availability influences T cell metabolism, impacting T cell function and shaping immune outcomes. Here, we identified ketone bodies (KBs)-including ß-hydroxybutyrate (ßOHB) and acetoacetate (AcAc)-as essential fuels supporting CD8+ T cell metabolism and effector function. ßOHB directly increased CD8+ T effector (Teff) cell cytokine production and cytolytic activity, and KB oxidation (ketolysis) was required for Teff cell responses to bacterial infection and tumor challenge. CD8+ Teff cells preferentially used KBs over glucose to fuel the tricarboxylic acid (TCA) cycle in vitro and in vivo. KBs directly boosted the respiratory capacity and TCA cycle-dependent metabolic pathways that fuel CD8+ T cell function. Mechanistically, ßOHB was a major substrate for acetyl-CoA production in CD8+ T cells and regulated effector responses through effects on histone acetylation. Together, our results identify cell-intrinsic ketolysis as a metabolic and epigenetic driver of optimal CD8+ T cell effector responses.

Cysteine-rich intestinal protein 1 is a novel surface marker for human myometrial stem/progenitor cells.

Myometrial stem/progenitor cells (MyoSPCs) have been proposed as the cells of origin for uterine fibroids, but the identity of the MyoSPC has not been well established. We previously identified SUSD2 as a possible MyoSPC marker, but the relatively poor enrichment in stem cell characteristics of SUSD2+ over SUSD2- cells compelled us to find better markers. We combined bulk RNA-seq of SUSD2+/- cells with single cell RNA-seq to identify markers for MyoSPCs. We observed seven distinct cell clusters within the myometrium, with the vascular myocyte cluster most highly enriched for MyoSPC characteristics and markers. CRIP1 expression was found highly upregulated by both techniques and was used as a marker to sort CRIP1+/PECAM1- cells that were both enriched for colony forming potential and able to differentiate into mesenchymal lineages, suggesting that CRIP1+/PECAM1- cells could be used to better study the etiology of uterine fibroids.

Peritoneal Carcinomatosis From Metastatic Prostate Cancer Identified on 68 Ga-Prostate-Specific Membrane Antigen PET/CT.

ABSTRACT: A 69-year-old man with locally advanced prostate adenocarcinoma (Gleason score 9), who had completed hormone therapy and definitive radiotherapy, presented to hospital with abdominal pain and distension. A CT scan of the abdomen and pelvis revealed ascites and extensive peritoneal/omental nodules. Serum prostate-specific antigen was not raised (0.07 µg/L). 68 Ga-prostate-specific membrane antigen (PSMA) PET/CT demonstrated PSMA-avid disease in the prostate and widespread PSMA-avid peritoneal/omental and liver metastases but with no PSMA-avid bony metastases. Peritoneal nodule biopsy confirmed metastatic prostate cancer.

Deficiency of the Polycomb Protein RYBP and TET Methylcytosine Oxidases Promotes Extensive CpG Island Hypermethylation and Malignant Transformation.

Hypermethylation of CpG islands (CGI) is a common feature of cancer cells and predominantly affects Polycomb-associated genomic regions. Elucidating the underlying mechanisms leading to DNA hypermethylation in human cancer could help identify chemoprevention strategies. Here, we evaluated the role of Polycomb complexes and 5-methylcytosine (5mC) oxidases in protecting CGIs from DNA methylation and observed that four genes coding for components of Polycomb repressive complex 1 (PRC1) are downregulated in tumors. Inactivation of RYBP, a key activator of variant PRC1 complexes, in combination with all three 5mC oxidases (TET proteins) in nontumorigenic bronchial epithelial cells led to widespread hypermethylation of Polycomb-marked CGIs affecting almost 4,000 target genes, which closely resembled the DNA hypermethylation landscape observed in human squamous cell lung tumors. The RYBP- and TET-deficient cells showed methylation-associated aberrant regulation of cancer-relevant pathways, including defects in the Hippo tumor suppressor network. Notably, the quadruple knockout cells acquired a transformed phenotype, including anchorage-independent growth and formation of squamous cell carcinomas in mice. This work provides a mechanism promoting hypermethylation of CGIs and shows that such hypermethylation can lead to cell transformation. The breakdown of a two-pronged protection mechanism can be a route towards genome-wide hypermethylation of CGIs in tumors. SIGNIFICANCE: Dysfunction of the Polycomb component RYBP in combination with loss of 5-methylcytosine oxidases promotes widespread hypermethylation of CpG islands in bronchial cells and induces tumorigenesis, resembling changes seen in human lung tumors.

Optimal HSF1 activation in response to acute cold stress in BAT requires nuclear TXNIP.

While TXNIP (thioredoxin interacting protein) in the plasma membrane and vesicular location is known to negatively regulate cellular glucose uptake by facilitating glucose transporter endocytosis, the function of TXNIP in the nucleus is far less understood. Herein, we sought to determine the function of nuclear TXNIP in vivo, using a new HA-tagged TXNIP knock-in mouse model. We observed that TXNIP can be found in the nucleus of a variety of cells from different tissues including hepatocytes (liver), enterocytes (small intestine), exocrine cells (pancreas), and brown adipocytes (BAT). Further investigations into the role of nuclear TXNIP in BAT revealed that cold stress rapidly and transiently activated HSF1 (heat shock factor 1). HSF1 interaction with TXNIP during its activation is required for optimal HSF1 directed cold shock response in BAT.

LKB1 controls inflammatory potential through CRTC2-dependent histone acetylation.

Deregulated inflammation is a critical feature driving the progression of tumors harboring mutations in the liver kinase B1 (LKB1), yet the mechanisms linking LKB1 mutations to deregulated inflammation remain undefined. Here, we identify deregulated signaling by CREB-regulated transcription coactivator 2 (CRTC2) as an epigenetic driver of inflammatory potential downstream of LKB1 loss. We demonstrate that LKB1 mutations sensitize both transformed and non-transformed cells to diverse inflammatory stimuli, promoting heightened cytokine and chemokine production. LKB1 loss triggers elevated CRTC2-CREB signaling downstream of the salt-inducible kinases (SIKs), increasing inflammatory gene expression in LKB1-deficient cells. Mechanistically, CRTC2 cooperates with the histone acetyltransferases CBP/p300 to deposit histone acetylation marks associated with active transcription (i.e., H3K27ac) at inflammatory gene loci, promoting cytokine expression. Together, our data reveal a previously undefined anti-inflammatory program, regulated by LKB1 and reinforced through CRTC2-dependent histone modification signaling, that links metabolic and epigenetic states to cell-intrinsic inflammatory potential.

Thymus antibody-secreting cells possess an interferon gene signature and are preferentially expanded in young female mice.

Antibody-secreting cells (ASCs) are key contributors to humoral immunity through immunoglobulin production and the potential to be long-lived. ASC persistence has been recognized in the autoimmune thymus (THY); however, only recently has this population been appreciated in healthy THY tissue. We showed that the young female THY was skewed toward higher production of ASCs relative to males. However, these differences disappeared with age. In both sexes, THY ASCs included Ki-67+ plasmablasts which required CD154(CD40L) signals for their propagation. Single cell RNA-sequencing revealed that THY ASCs were enriched for an interferon responsive transcriptional signature relative to those from bone marrow and spleen. Flow cytometry confirmed that THY ASCs had increased levels of Toll-like receptor 7 as well as CD69 and major histocompatibility complex class II. Overall, we identified fundamental aspects of THY ASC biology which may be leveraged for future in depth studies of this population in both health and disease.

Continuous transcriptome analysis reveals novel patterns of early gene expression in Drosophila embryos.

The transformative events during early organismal development lay the foundation for body formation and long-term phenotype. The rapid progression of events and the limited material available present major barriers to studying these earliest stages of development. Herein, we report an operationally simple RNA sequencing approach for high-resolution, time-sensitive transcriptome analysis in early (≤3 h) Drosophila embryos. This method does not require embryo staging but relies on single-embryo RNA sequencing and transcriptome ordering along a developmental trajectory (pseudo-time). The resulting high-resolution, time-sensitive mRNA expression profiles reveal the exact onset of transcription and degradation for thousands of transcripts. Further, using sex-specific transcription signatures, embryos can be sexed directly, eliminating the need for Y chromosome genotyping and revealing patterns of sex-biased transcription from the beginning of zygotic transcription. Our data provide an unparalleled resolution of gene expression during early development and enhance the current understanding of early transcriptional processes.

Cysteine-Rich Intestinal Protein 1 is a Novel Surface Marker for Myometrial Stem/Progenitor Cells.

Myometrial stem/progenitor cells (MyoSPCs) have been proposed as the cells of origin for uterine fibroids, which are benign tumors that develop in the myometrium of most reproductive age women, but the identity of the MyoSPC has not been well established. We previously identified SUSD2 as a possible MyoSPC marker, but the relatively poor enrichment in stem cell characteristics of SUSD2+ over SUSD2- cells compelled us to find better discerning markers for more rigorous downstream analyses. We combined bulk RNA-seq of SUSD2+/- cells with single cell RNA-seq to identify markers capable of further enriching for MyoSPCs. We observed seven distinct cell clusters within the myometrium, with the vascular myocyte cluster most highly enriched for MyoSPC characteristics and markers, including SUSD2. CRIP1 expression was found highly upregulated in both techniques and was used as a marker to sort CRIP1+/PECAM1- cells that were both enriched for colony forming potential and able to differentiate into mesenchymal lineages, suggesting that CRIP1+/PECAM1- cells could be used to better study the etiology of uterine fibroids.

Uncovering a miltiradiene biosynthetic gene cluster in the Lamiaceae reveals a dynamic evolutionary trajectory.

The spatial organization of genes within plant genomes can drive evolution of specialized metabolic pathways. Terpenoids are important specialized metabolites in plants with diverse adaptive functions that enable environmental interactions. Here, we report the genome assemblies of Prunella vulgaris, Plectranthus barbatus, and Leonotis leonurus. We investigate the origin and subsequent evolution of a diterpenoid biosynthetic gene cluster (BGC) together with other seven species within the Lamiaceae (mint) family. Based on core genes found in the BGCs of all species examined across the Lamiaceae, we predict a simplified version of this cluster evolved in an early Lamiaceae ancestor. The current composition of the extant BGCs highlights the dynamic nature of its evolution. We elucidate the terpene backbones generated by the Callicarpa americana BGC enzymes, including miltiradiene and the terpene (+)-kaurene, and show oxidization activities of BGC cytochrome P450s. Our work reveals the fluid nature of BGC assembly and the importance of genome structure in contributing to the origin of metabolites.